ISAPP panel concludes that more evidence is needed to determine whether probiotics help restore an antibiotic-disrupted microbiota

/in ISAPP Science Blog /by KC

By Dr. Mary Ellen Sanders PhD, Mary Ellen Sanders LLC, Colorado, USA, Dr. Hania Szajewska MD, Medical University of Warsaw, Poland, Prof. Karen Scott PhD, Rowett Institute, University of Aberdeen, Scotland, UK

From the time scientists began to understand how antibiotics disrupt the gut microbiota, questions have been raised about whether probiotics could help recovery from this disruption by providing bacteria beneficial to the gut environment or disrupting the bloom of harmful ones. The topic was brought to popular attention after a prominent 2018 scientific paper, widely covered in the media, demonstrated that a certain 11-strain probiotic formulation impaired gut microbiota recovery after antibiotic treatment, sparking debate about possible harms of probiotics.

A microbiota that supports health should be both resilient – meaning it can return to its original state after disruption – and adaptive, but can probiotics facilitate these important features of the microbiota? Under the auspices of International Scientific Association for Probiotics and Prebiotics, we met as part of a group of 8 experts in clinical medicine, biostatistics, basic microbiome science and probiotic microbiology to consider whether probiotics could help restore an antibiotic-perturbed gut microbiota in humans.

Different antibiotics vary in the extent to which they disrupt the microbiota, but in general antibiotics can reduce microbial diversity and alter how the microbiome functions. The therapeutic value of antibiotics is undisputed; however, their clinical use is associated with some harms, including an increase of antibiotic-resistant pathogens, Clostridioides difficile infection, and antibiotic-associated diarrhea. Although specific probiotics have been shown to mitigate some of these clinical harms associated with antibiotic use, how they accomplish this is not clear.

At the outset, we recognized that the human response to both antibiotics and probiotics was multi-factorial. Factors such as microbiota composition and host genetics can vary substantially among individuals. Variation is also observed among the different probiotic strains and doses used in intervention trials. Further, the studies that have been conducted to assess microbiota composition and recovery employed different methods and are therefore difficult to compare.

After conducting a systematic review of human studies within the scope of this topic, and reviewing available clinical and microbiome data (composition and function of the microbiota), we concluded that current evidence does not support the conclusion that probiotics studied so far help restore the gut microbiota to its pre-antibiotic-challenged state. Studies adequately designed to directly address this question are rare. We found that only a few probiotic strains, such as Bifidobacterium lactis subsp. animalis BB-12, have been tested in randomized, controlled trials for their ability to mitigate the impact of antibiotics on gut microbiota.

Given that nature of the interaction of probiotics with the microbiota may be specific at the strain level, strain-specific research is essential to uncover targeted benefits, rather than making broad claims about probiotics as a whole. It is unlikely that a conclusion on the effect of probiotics in general on an antibiotic-perturbed microbiota composition or function can be reached. Instead, future conclusions should be strain-specific, based on research on particular probiotic preparations using meaningful microbiome measures.

Multiple microbiota readouts, including strain abundance possibly adjusted for host-related parameters, should be used to assess microbiota recovery. We also recognized that higher microbiota diversity, although frequently assessed, has not been causally linked to good health in humans and may be insufficient as a measure of a more ideal microbiota.

Our conclusions do not detract from evidence that some probiotics can improve certain clinical outcomes related to antibiotic use, such as reducing the risk of antibiotic-associated diarrhea or C. difficile infections. However, these clinical effects have not been shown to be causally linked to a probiotic-mediated impact on the function or composition of the microbiota. An important avenue for future research is study of the mechanism(s) through which probiotic bacteria can provide these clinical benefits.

 

The panel was composed of Prof. Hania Szajewska MD, Prof. Karen P. Scott PhD, Prof. Tim de Meij MD, Dr. Sofia K. Forslund-Startceva PhD, Prof. Rob Knight PhD, Prof. Omry Koren PhD, Prof. Paul Little MD, Prof. Bradley C. Johnston PhD, Dr. Jan Łukasik MD, Dr. Jotham Suez PhD, Prof. Daniel J. Tancredi PhD, and Dr. Mary Ellen Sanders PhD. This review was published in Nature Reviews Gastroenterology and Hepatology.

Travel costs of experts to London UK and local meeting expenses were paid by the International Scientific Association for Probiotics and Prebiotics.

See here for ISAPP’s clinical resource on probiotic use alongside antibiotics

Planning a Biotics Study? New Publication Recommends Adding Diet as a Variable

/in ISAPP Science Blog /by KC

By Prof. Maria Marco PhD and Prof. Kevin Whelan PhD

In studies on probiotics, prebiotics, and other biotics, the demonstrated health effect may depend on the personal characteristics and habits of the study participants. Take the following scenario: Person A and Person B consume the same prebiotic supplement. Person A typically eats a Mediterranean-style diet, meeting daily fiber requirements by consuming various fruits, leafy greens, nuts, and seeds daily. Person B eats mostly convenience foods that are low in fiber – pastries, fried foods, and frozen dinners. Is the prebiotic likely to have the same effect in both individuals?

The possibility that a prebiotic may have different effects in these two individuals seems intuitive. A plausible scenario is that the gut microbiome of Person A is enriched for bacterial species that feed well on the the prebiotic substrate and therefore is “primed” for more robust responses to prebiotic intake; Person B, on the other hand, doesn’t have the target bacterial species and therefore receives limited benefit from the prebiotic.

Both dietary patterns and specific foods are known to affect the digestive tract environment, either directly or indirectly (for example, by shaping the gut microbiome), and are therefore of interest as potential factors in the response of an individual to a biotic intervention. Surprisingly in the scientific literature, however, diet has been almost completely overlooked as a potential contributor to the effectiveness of probiotics and prebiotics.

In 2022 we gathered an international group of experts to discuss whether diet is potentially an important factor contributing to the efficacy of biotics. The result of our discussions was recently published as a Perspective in Nature Microbiology.

Evidence for how diet affects biotic efficacy

When our group reviewed the literature, we found surprisingly few examples of biotic clinical trials in which the researchers had gathered data on the background diet of the participants. Yet from the studies we did find, dietary influences on biotic efficacy are promising for future study. In one trial of a probiotic in participants with metabolic syndrome, dietary characteristics differentiated responders and non-responders. And in a prebiotic trial, participants who consumed more fiber at baseline had a more marked gut microbiota response and reported feeling fuller than those with lower fiber intake.

Our group members pointed out that, although the gut microbiome itself has increasingly been measured in biotics studies, microbiome features don’t capture the full picture of why someone responds to a biotic intervention. Diet may affect the efficacy of a biotic intervention through microbiome-mediated mechanisms or via other effects on the host, such as alterations in digestive function.

Recommendations for biotics trials

Our group agreed that including dietary data as a matter of course in biotics trials is a crucial way to move the field forward and continue to understand how biotics work in different individuals. From our extensive discussions and follow-up, we came up with ten recommendations for future studies on biotics to account for the effects of diet on biotic efficacy:

  • Consider whether and how to harmonize the diet of your study population before intervention.
  • Ideally, participants should not be involved in a biotic trial over religious festivals or holidays during which dietary intake can be dramatically altered.
  • The composition of the prebiotic (structure, degree of polymerization, source and purity) or probiotic (for example, strain), as well as the structure and composition of the delivery matrix, should be reported.
  • Details of prebiotic or probiotic intake (number of doses, timing, whether taken with or between meals and consumed with which foods) should be reported.
  • Appropriate microbiome analyses should be performed to disentangle the specific effect of the intervention versus background diet.
  • Dietary assessment should be performed during screening (if it is a requirement of inclusion), at baseline and at the end of an intervention.
  • Dietary assessment should record intakes of microbiome-relevant dietary exposures where possible and feasible.
  • Dietary assessment should be relevant to the hierarchical ontology of the dietary exposure of interest (for example, nutrient, food, food group or dietary pattern).
  • The method and duration of dietary assessment should depend on the research question and the exposure of interest.
  • A dietitian or nutritionist with expertise in microbiome research and dietary assessment should be included in the research team.

We acknowledge that in some cases implementing these recommendations will result in additional costs for a biotic trial, but we think these costs will be well justified given the potential to show stronger effect sizes, reduce unnecessary trials, and zero in on the populations that will benefit from a given biotic intervention.

The future of biotics

At this stage in the field of biotics, the literature indicates that demonstrating the efficacy of a biotic intervention through a clinical trial must take into account the complexity of individual participants – not just demographic factors, but also lifestyle factors such as diet. We believe that background diet may be a critical factor in determining biotic effectiveness, and thus should be included in as many future biotic studies as possible. By accounting for the influence of diet, scientists studying biotics may be able to show stronger and more targeted health benefits, allowing more personalized and effective interventions.

How do we know if a microbe is dead?

/in ISAPP Science Blog /by KC

By Prof. Maria Marco PhD, University of California, Davis

“Kills 99.9% of bacteria and viruses.” This percentage and others like it are frequently found on disinfectant labels.

Ideally, the microbicidal effect of the product is sufficient to kill more than the numbers of the target pathogen or pathogens expected to be in the environment where the disinfectant is used. However, if more of the target pathogen is present, 99.9% can be misleading or even result in illness. For example, for a surface with one million pathogenic E. coli cells, a 99.9% reduction would mean that 1000 living and infectious E. coli cells remain. That amount of E. coli could be sufficient to cause life threatening illness.

Declaring a microbe dead

The issue of quantity is only one of the conundrums when relaying information about microbial death. Another issue is how do we even know if a microbe is really dead? For viruses, they are not cells and so the terms “live” and “dead” do not apply. Viral inactivation is inferred by a loss in the ability to infect and multiply in host cells. For bacteria, the answer is not so simple. Bacteria can form dormant states, whereby their metabolic activity is minimal, but then, when conditions are right, they grow and divide again. Endospores formed by some bacteria are a great example of dormancy. But even bacteria that do not form endospores can be viable (alive) but dormant for long periods of time and may be inferred to be “dead”. Sometimes these dormant states are desirable, such as when drying bacterial strains for use as probiotics and retaining their capacity to reactivate when the conditions are right. 

Measuring dead microbes

Another problem with microbial death is how we measure it. Colony forming unit (CFU) enumeration on laboratory culture media is the gold-standard for quantifying viable bacterial cell numbers. However, it is now well known that only a very small fraction of all bacteria on Earth have been grown or “cultured” in the laboratory. Many microbes are “unculturable” mainly because the nutrients and environmental conditions needed for their enrichment in the laboratory have yet to be found. So, it is not possible to quantify viability of “unculturable” microorganisms using the gold standard approach.

Even for microbes that grow well in the laboratory (for example E. coli), they too may not always be culturable. After exposure to certain conditions, such as nutrient limitations, some bacteria can form Viable But Non Culturable (VBNC) states. Those VBNC microbes will not grow using routine culture methods, but they are viable and may return to a metabolically active, reproductive state later, such as when nutrients or environmental conditions change. Testing via CFU therefore may underestimate levels of viable bacteria – with important implications for measuring and monitoring both beneficial and pathogenic organisms.

Dead bacterial cells can best be described as having different states. Completely lysed bacterial cells, wherein the cell membrane is destroyed, and intracellular contents are released, are obviously dead. Yet, this state may constitute only a minor fraction of dead bacteria in a population. Bacteria can also be dead, but still have an intact cell membrane. Several methods have been developed to assess viability of cells in that state, including measurements of cellular enzymatic activity (MTT conversion assay) and uptake of fluorescent dyes impenetrable to intact cell membranes (SYTO9-propidium iodide staining).  While this question of evaluating cell viability is far from resolved, an intriguing recent recommendation was to use multiple tests, assessing both metabolic activity and reproductive capacity (1).

Implications for biotics

How does all this relate to biotics? Probiotics should be alive (viable) at the time of administration. Postbiotics are preparations of dead (inanimate) microbes. Both must deliver a health benefit. Decisions on how viable and dead microbes are enumerated in biotic preparations should address the fact that there are different bacterial viability states. The use of a single method such as CFU enumeration can lead to underestimating numbers of viable cells and will not be helpful for quantifying dead cells. Although we may never be able to say that a microbial population is either absolutely 100% alive or dead, such viability states may affect how well either a probiotic or a postbiotic performs for its intended purpose of conferring a health benefit.

Can Probiotics Prevent Respiratory Tract Infections in Infants and Children?

/in ISAPP Science Blog /by KC

By Prof. Hania Szajewska MD PhD, Medical University of Warsaw, Poland

Imagine you are a primary care pediatrician practicing in an area where respiratory tract infections (RTIs) are particularly common during the winter months. Due to the seasonal surge in viral infections, you might find yourself seeing 20-30 children per day with upper respiratory tract infections (URTIs) at the peak of cold and flu season.

Children who attend daycare centers and kindergartens are especially vulnerable, experiencing up to four times more RTIs compared to those cared for at home (1). This is largely due to close contact and shared environments, making it easy for viruses to spread. About 95% of these infections are caused by five main viruses: rhinovirus, influenza virus, respiratory syncytial virus, coronavirus, and adenovirus. These viruses are primarily spread through airborne aerosols but surface contamination also plays a role. (1, 2)

Frequent RTIs in young children lead to missed daycare or school days, placing strain on families and increasing the need for healthcare visits. They may also lead to prescriptions for antibiotics, which can disrupt the gut microbiota and are associated with other health problems later in development. Severe cases of RTI may result in complications such as ear infections, pneumonia, or worsened asthma symptoms.

Preventing RTIs is essential for maintaining children’s health and reducing the burden on families and healthcare systems. This raises the question: Can probiotics help reduce RTIs in generally healthy young children attending daycare (3)?

The role of probiotics in preventing RTIs

Probiotics have gained attention for their potential to reduce RTIs, especially in children who are frequently exposed to infections in group settings like daycare and kindergartens. Initially the idea of ingesting probiotics into the digestive tract to prevent infections of the respiratory tract may seem counterintuitive. However, research has shown several potential mechanisms by which probiotics in the gut may help prevent RTIs:

  • Enhancing the immune system
  • strengthening the epithelial barrier
  • producing antimicrobial compounds
  • competing with harmful pathogens

While some mechanisms are strain-specific, others are observed across different types of probiotics.

Evidence from clinical trials

Comprehensive reviews and meta-analyses, such as a 2022 Cochrane review (4) have highlighted how various probiotics can lower the risk of RTIs. In children, 10 clinical trials showed that probiotics were more effective than placebo or no treatment in reducing acute URTIs. Key findings for the groups receiving probiotics include:

  • 28% reduction in the risk of at least one URTI event (relative risk 0.72, 95% CI 0.58 to 0.89; P = 0.003; 2512 participants)
  • 21% lower incidence rate of acute URTIs (rate ratio 0.79, 95% CI 0.65 to 0.96; 1868 participants)
  • 41% reduction in antibiotic use for treating URTIs (relative risk 0.59, 95% CI 0.43 to 0.83; 1315 participants)

Most trials involved administering probiotics through milk-based foods, such as yogurt, over a period of three months or longer, with consistent benefits seen across various age groups (4).

Acting on the evidence

While further research is needed to make definitive recommendations, there are several steps you can take, based on the current evidence, to reduce the risk of respiratory infections:

  • Use evidence-based probiotics: Although uncertainty remains about which strains are most effective, strains such as Lacticaseibacillus rhamnosus GG (formerly Lactobacillus rhamnosus) have been shown to reduce RTIs (5).
  • Support immune health with a fiber-rich diet: A diet rich in fiber and fermented foods, such as kefir, sauerkraut, and fermented dairy products, can promote gut health and immunity.
  • Focus on hygiene: Teach children proper hygiene practices, including frequent handwashing, proper sneezing and coughing etiquette, and regular sanitization of shared toys and surfaces, especially in group care settings.
  • Responsible antibiotic use: Limit the use of antibiotics to when they are absolutely necessary, because overuse can disrupt the gut microbiota and weaken the body’s immune system.

Conclusion

While we await more conclusive research, probiotics offer a promising, low-risk approach to supporting immune health and reducing the frequency and severity of respiratory infections in children. Incorporating evidence-based probiotics, maintaining a healthy diet, and practicing good hygiene can help minimize the risk of RTIs, particularly in communal environments such as daycare centers and kindergartens.

 

Discovering novel bioactive peptides in fermented foods

/in ISAPP Science Blog /by KC

By Dr. Rounak Chourasia PhD, National Agri-food Biotechnology Institute, Mohali, Punjab, India

Food not only serves as a primary source of essential nutrients but also contains a wealth of potential bioactive compounds. Among these, peptides have garnered significant attention for their ability to impact health beyond basic nutrition. These short protein fragments, ranging from 2 to 20 amino acids, play critical roles in physiological functions and exhibit diverse health benefits, making them increasingly interesting to researchers and consumers. Food-derived bioactive peptides are especially promising due to their environmentally friendly production, lack of accumulation in the body, low toxicity, and biodegradability, making them appealing for safe and sustainable therapeutic alternative to synthetic compounds.

Fermented foods have recently gained renewed interest for their potential health benefits. One proposed way that fermented foods may confer health benefits is through bioactive compounds released by the catalytic action of fermenting microbes on the food substrate. Protein-rich food substrates are especially valuable for the release of bioactive peptides through fermentation. Microbial strains associated with food fermentation have diverse proteolytic capacities, leading to a unique peptidome for each fermented food produced using different microbial starter cultures. For example, Ile-Pro-Pro and Val-Pro-Pro are well-known milk-derived bioactive peptides with diverse health benefits (1). These tripeptides are available in several health supplements and functional foods, marketed for their ability to improve cardiovascular function by inhibiting angiotensin-I converting enzyme (ACE). Additionally, these tripeptides exert antioxidant and immunomodulatory properties. Discovering novel multifunctional peptides from fermented foods is a desirable goal for research aimed at maintaining a healthy lifestyle and preventing metabolic diseases.

In our research, we have identified both previously reported and novel bioactive peptides with diverse functional attributes from alkaline and acidic fermented foods of the Indian Himalayan regions, such as Chhurpi cheese and Kinema (fermented soybeans) (2, 3). These traditionally fermented foods are rich sources of bioactive peptides with potential health benefits. Chhurpi cheese, a fermented dairy product, and Kinema, a fermented soybean product, both exhibit a unique array of bioactive peptides due to the specific microbial strains involved in their fermentation. The identification of these peptides may enhance the functional value of these traditional foods and provides opportunities to explore the resident fermentation microorganisms for the development of novel functional foods.

Conventional methods for identifying novel peptides in fermented foods and validating their biological activity involve expensive and labor-intensive processes. These include the purification of bioactive fractions followed by LC-MS/MS-based identification and the synthesis of each individual peptide for bioactivity validation. However, the advent of in silico tools and machine learning models has made it faster and more affordable to predict the bioactivity of peptides identified by untargeted LC-MS/MS analysis (4). Qualitative and quantitative in silico tools, such as molecular docking, dynamics simulation, and structure-activity relationship models, help select specific peptides identified in fermented foods for validation of their bioactivity after synthesis. Nevertheless, these machine learning models require refinement and further improvement to achieve accurate predictions. Additionally, in silico tools such as Peptigram help us understand the proteolytic specificity of food-fermenting microorganisms, enabling the development of specific microbial starters for the production of fermented foods enriched with peptides for the prevention of targeted diseases.

One significant concern in the application of bioactive peptides is their bioavailability. Once ingested, these peptides are subject to hydrolysis in the gastrointestinal tract, which can lead to the loss of their bioactivity. The stability of these peptides in the bloodstream is also crucial, as they must remain intact to exert their beneficial effects. Thus, it is necessary to find solutions to accurately predict the susceptibility of peptides to gut hydrolysis and their pharmacokinetics in the blood. Advanced techniques and models are required to better understand and enhance the bioavailability of these peptides, ensuring that their health benefits are preserved from ingestion to absorption and systemic circulation.

The discovery of novel bioactive peptides from fermented foods has the potential to contribute to the development of functional foods with enhanced health benefits. As research advances, the integration of traditional fermentation processes with modern biotechnological tools promises to unlock new potential for supporting health through nutrition.

ISAPP elaborates criteria for prebiotics

/in ISAPP Science Blog /by KC

By Mary Ellen Sanders, PhD, Mary Ellen Sanders LLC, Probiotics Consulting, Prof. Bob Hutkins, PhD, University of Nebraska and Karen Scott PhD, Rowett Institute, University of Aberdeen.

Nearly one in four Americans say digestive health is the most important aspect of their overall health, according to a 2022 International Food Information Council survey. Prebiotics – a 30-year old concept – are growing in popularity among consumers interested in digestive health, although knowledge of what they are and what they do varies. For example, 18% of American consumers have never heard of prebiotics, while 22% state they are familiar with and actively try to consume them. Those consumers who say they are ‘familiar’ with prebiotics look for them in yogurt or kefir, where they are typically not found, but also in fruits and vegetables or dietary supplements, where they may be present.

Although clearly there is a need for scientifically sound information for consumers, experts recognize that a gap in understanding exists even for scientists. To help bring some clarity to the scientific principles involved in prebiotics, a group of scientists collaborated on an Expert Recommendation published October 2, 2024 in Nature Reviews Gastroenterology and Hepatology. This paper, titled “Classifying compounds as prebiotics—scientific perspectives and recommendations”, delineated what prebiotics are and what lines of research are needed to establish their status.

This paper reinforces the 2017 definition of prebiotic, “a substrate that is selectively utilized by host microorganisms conferring a health benefit”. It further breaks down the individual criteria that are explicitly and implicitly derived from this definition, summarized in the table below. Neither ISAPP nor the authors of this paper claim to be the arbiters of whether or not a given substance satisfies the prebiotic definition.  Rather, the primary motivation for this effort was to provide researchers clearly stated criteria that aid the development of the scientific rationale for concluding that a newly proposed substance can be legitimately termed a ‘prebiotic’. In transitioning ’candidate prebiotics’ to accepted prebiotics, it is important that proposed compounds meet all aspects of the prebiotic definition. In parallel, ISAPP developed a companion prebiotic checklist.

Perhaps the most challenging issue the authors addressed was defining selectivity. Although the idea that distinct components of the microbiota respond to a prebiotic is fundamental to the prebiotic concept, the complexity of the microbiota makes such a response difficult to quantify. Selective utilization is measured by tracking prebiotic-induced changes in composition or function of the microbiota. Many different possible approaches to measuring microbial function and composition, which will continue to expand with methodological advances, inform these research efforts. The extent of the modulation could be narrow or broad, but it should be reproducible and specific. Importantly, a sound hypothesis for why any such microbiome changes would underpin the observed health effect should be advanced. The authors of this paper agreed with the importance of allowing innovation in the prebiotic field, and as such, were not prescriptive by specifying which specific analyses are required.

Unlike probiotics – where no mechanism of action leading to the health benefit is specified by the definition – the prebiotic definition stipulates one. A prebiotic-induced health benefit should derive from the modulation of the microbiome (composition or function) that is a result of selective utilization. To date, most studies on prebiotics have shown an association of microbiome modulation and the health benefit by tracking both in the same efficacy trial in the target host. Such a study shows that the health benefit and microbiome modulation are correlated, but it does not prove that the microbiome modulation causes the health benefit. Such proof is difficult to obtain, and therefore is not required for prebiotic status, a position consistent with the 2017 consensus paper. But this new paper reemphasizes the value of research to address causality, which remains a challenging issue in the microbiome field, and discusses statistical approaches that can increase confidence that the relationship is causal.  Causality studies can be informed by a variety of methods, including mining relevant microbiome databases, in silico screening, in vitro and in vivo tracking of expression of microbiota-dependent metabolic pathways, machine learning, artificial intelligence, and animal models.

The authors anticipate that this paper will encourage scientists to coalesce their understanding of prebiotics around these concepts. As pointed out in the paper, “Adherence by all stakeholders to these criteria would benefit the prebiotic field by providing cohesion in prebiotic research, principles to underpin regulatory actions, and clarity to alleviate confusion for consumers.”

Table 1: Key criteria of a prebiotic derived from the ISAPP prebiotic definitiona (From Hutkins et al. 2024)

Prebiotic criteria Comments
Substrate A prebiotic is a substance administered to a host and utilized by autochthonous microorganisms. It might be an ingredient in a diet, but ‘prebiotic’ refers to a specific substance rather than a complete diet.
Identity and characterization Prebiotic must be sufficiently described to enable robust data comparisons and reproducible manufacture of the ingredient.
Selectively utilized by host microbiota Selective utilization can be shown by one microbial change or a change in many taxa or by specific functional readouts.
Demonstrated health benefit Type of health benefit endpoint assessed depends on intended regulatory category and must be demonstrated by well controlled studies (typically RCTs) in the target population.
Hypothesis for mechanism of how microbiome modulation might lead to the health benefit A sound rationale should be developed explaining how the pattern of selective utilization by host microorganisms observed for the prebiotic could lead to the health benefit.
Health benefit in the target host must be demonstrated in the same study that demonstrates selective utilization by the microbiota It is not essential to demonstrate a causal link between the selective utilization of the prebiotic and health benefit(s), as such evidence can be very difficult to obtain experimentally. However, research aimed at this goal is encouraged, aided by causal mediation design and analysis strategies. With regard to demonstrating the health benefit, animal studies in non-target hosts as well as in vitro studies might be useful to address mechanistic questions and to plan trials in the target host but cannot in isolation provide sufficient evidence to establish claimed health benefits in the target host.
Safe for intended use Adverse events must be tracked in studies conducted in target host. Safety requirements differ for different regulatory categories and target populations.
Confirmatory evidence, beyond minimum requirements Multiple studies demonstrating reproducibility of health effects and selective utilization increase confidence in outcomes.
Administered in dose or serving size shown to elicit health benefit and selective utilization by the host microbiota in controlled studies Advice on serving size should be provided so that sufficient dose for health benefit is achieved without eliciting adverse effects, such as toxicity, gastrointestinal symptoms, or choking, among others.

aBased on the ISAPP definition of prebiotic: a substrate that is selectively utilized by host microorganisms conferring a health benefit. Not all criteria are specifically stated in the definition, but are implicit in text in the accompanying paper.

The criteria within the paper are summarized in a downloadable prebiotic evidence checklist from ISAPP.

Join ISAPP’s upcoming webinar on this topic, with the date to be announced shortly. Sign up for the ISAPP newsletter or follow our social media platforms here to be notified of the date.

REFERENCE:

Hutkins R, Walter J, Gibson GR, Bedu-Ferrari C, Scott K, Tancredi DJ, Wijeyesekera A, Sanders ME. Classifying compounds as prebiotics – scientific perspectives and recommendations. Nat Rev Gastroenterol Hepatol. 2024. doi: 10.1038/s41575-024-00981-6.

Prebiotics: Does Delivery Format Matter?

/in ISAPP Science Blog /by KC

By Kelly S. Swanson, PhD, University of Illinois Urbana-Champaign, USA

Prebiotics (1) have long been appreciated for their benefits to digestive function, immunity, energy balance, and metabolism. From a nutritionist’s perspective, the best way to consume dietary fibers and prebiotics is by eating a healthy diet comprising adequate amounts of whole grains, fruits, and vegetables. Prebiotic substances are naturally present in the food supply, with onions, garlic, Jerusalem artichoke, and bananas serving as rich sources. Prebiotic intake can also be boosted in other ways – in recent years, food companies have developed prebiotic-containing breakfast cereals and bars, muffin mixes, breads, and other food products. A variety of prebiotic dietary supplements are also available and may be used to complement dietary sources.

Most prebiotic substances are water soluble and have a slightly sweet flavor. These properties not only make it easy to incorporate prebiotics into food products, but beverages as well. In addition to dairy-based beverages, fruit juices, fruit and vegetable smoothies, iced teas, and others, prebiotics have been added to carbonated soft drinks. While a growing consumer interest in gut health products and expansion of the prebiotic food and beverage market is good to see, a recent class-action lawsuit against a producer of prebiotic soda has stirred up the field and prompted a few important questions.

What prebiotic dose is needed for a product to deliver a health benefit?

The ongoing lawsuit provides an interesting example in applying prebiotic science to a commercial product. To carry the prebiotic term, the prebiotic ingredient in a product must be provided at a dosage to deliver health benefits in the target host. When it comes to evaluating prebiotic-containing foods and beverages, the dosage per serving, effects of processing, format and stability of the final product, and presence of other nutrients and bioactive substances must all be considered.

The suit is based on the prebiotic dosage (2 grams of agave inulin/12-oz can) and high sugar content (4-5 grams/12-oz can) of the sodas in question, but the effects of processing and format/stability of the final product are also relevant. Based on the dosage and published scientific evidence (2, 3), consumers would need to drink 4 cans of soda to notice inulin’s benefits. Is the 2 gram dosage per can sufficient to carry the gut health claim?

How does delivery format shape the benefits of a prebiotic?

Another key variable is the delivery matrix of the prebiotic. In this case, what is the stability of the agave inulin during the processing and storage of the carbonated soda? Is it similar to that of a dry powder, a capsule, or the format tested in a previous study (i.e., chocolate candy chews) (2, 3) or is there degradation over time? Prebiotic functionality and efficacy is known to differ based on degree of polymerization, sugar composition, degree of branching, and the type of glycosidic bonds present (4). Because inulin-based prebiotics are known to be susceptible to structural degradation when exposed to high temperatures, high pressure, and/or low pH (5, 6, 7), ensuring integrity of the active prebiotic ingredient over shelf life is an important consideration with regards to product efficacy.

What other substances are present in the final product?

A final consideration is the presence of other nutrients and/or bioactive substances in the final product. The presence of essential nutrients and other substances may influence if and how prebiotics are modified during processing and impact the overall health implications of the final product. In regard to processing, prebiotics may participate in Maillard reactions during heat treatment, forming prebiotic-protein conjugates (8). These structures may increase stability and prebiotic functionality and be a benefit to a product as long as Maillard reaction products are not excessive. Other prebiotic-nutrient interactions may occur during food and beverage processing, but the area has not been well studied.

The nutrient content of the final product also has implications on health beyond that of the prebiotic effect. Prebiotic foods and beverages that contain essential nutrients, antioxidants, healthy fats, or functional fibers would be viewed as being beneficial. On the other hand, products low in essential nutrients but high in added sugar, unhealthy fats, salt, or caffeine may be viewed as being detrimental and could offset the benefits of the prebiotic.

Ensuring effective products to support gut health

In the case of the soda lawsuit, time will tell how the courts weigh the dosage and potential positives of the prebiotic vs. the negatives of the added sugar content of soda. Regardless of the outcome, it serves as a reminder to food and beverage producers interested in the biotic area. Products carrying biotic terms and/or structure-function claims pertaining to gut health must be carefully formulated and processed, with daily serving sizes providing sufficient dosages and functional activity in their final form throughout shelf life.

Further reading: Applying probiotics and prebiotics in new delivery formats – is the clinical evidence transferable?

Postbiotics: A global perspective on regulatory progress

/in ISAPP Science Blog /by KC

By Dr. Gabriel Vinderola PhD, CONICET, National University of Litoral, Argentina

While the conceptualisation of postbiotics varies among scientists, some recent actions may suggest that regulatory agencies around the world are starting to align with the ISAPP definition (Salminen et al. 2021), understanding postbiotics as preparations of inanimate microorganisms able to confer a health benefit.

Before the May 2021 publication of the postbiotic consensus definition by an expert panel convened by ISAPP, a search in www.pubmed.com using the term postbiotics rendered around 320 entries in the period 1975-2021. Three years after the ISAPP publication, by August 2024, almost 1200 entries could be found. However, it is still to be examined how many of these entries use the term postbiotics to refer to (1) administered metabolites, (2) metabolites produced by the gut microbiota or (3) inanimate microbial preparations, the three most prevalent conceptualizations of the term. A future bibliometric analysis of the literature could be performed to shed light on this. Meanwhile outside academia, the discrepancy in postbiotic definitions continues: some companies market specific metabolites as postbiotics whereas other companies use the term postbiotics to refer to heat-inactivated lactobacilli.

The first movement I noticed towards potential regulatory adoption of the term was made by Health Canada, as suggested in a presentation by an officer at Probiota 2023 in Chicago last year. The presentation shared the ISAPP definition, stating that postbiotics would fall under the Natural and Non-Prescription Health Products Directorate (NNHPD), that some probiotic specifications may apply (strain specification, antibiotic resistance, etc,), and that quantification, in principle would be based on milligrams, expecting that more sophisticated and accurate methodologies would arise over time. This issue was addressed further in a Discussion Group in the recent ISAPP meeting at Cork (Ireland) – see the annual meeting report here. Presently, there is only one entry for the word postbiotics in the Health Canada webpage, where it is stated that “gut modifiers as livestock feed are products that, once fed, have a mode of action in the gastrointestinal tract of an animal. The gut modifier category can encompass a variety of feed ingredients, these ingredient types may include, but are not limited to viable microbial strains, prebiotics, postbiotics, enzymes, organic acids and essential oils”. However, no further indications of the meaning of the term postbiotic are stated on the website.

In January 2024, the trade journal Nutraingredients announced that the China Nutrition and Health Food Association (CNHFA) had decided to draft industry standards for quantifying postbiotics or inactivated cells and were rallying industry players and the public to take part in the draft process through a public consultation. The National Institutes for Food and Drug Control (NIFDC) was leading the process and it had drafted flow cytometry standards to measure postbiotics composed of inactivated cells of lactic acid bacteria. In addition, a fluorescent quantitative PCR detection method had been drafted for inactivated Bifidobacterium lactis cultures. In correspondence with the NIFDC, it was discussed that a direct counting method using a standard microscope for single culture postbiotics was being explored.

The TGA (Therapeutic Goods Administration) is the Australian body that regulates medicines, medical devices and biologicals. The TGA recently published a guidance to provide information for applications relating to microorganisms as active ingredients for use as new substances in listed medicines (the category which includes the majority of dietary supplements marketed in Australia), or as active ingredients in registered complementary medicines (RCM). Listed medicines and RCM containing microorganisms as active ingredients are generally referred to as probiotics or postbiotics. For the purpose of this guidance, microorganisms are whole and intact cells of bacteria and fungi (including yeasts) that are live or non-viable. This guidance is intended for the premarket assessment of new live and whole/intact non-viable microorganisms potentially used as probiotics and postbiotics. Interestingly, the guidance does not include cell fragments, which have different pharmacokinetics within the gut. It is worth noting that Australia is part of the ACCESS Consortium, consisting of Australia’s TGA, Health Canada, the UK’s MHRA, Swissmedic from Switzerland and Singapore’s Health Sciences Authority. However, it’s not yet known whether the ACCESS Consortium will take inspiration from the Australian guidance.

Which scientific publications may be influencing these regulatory directions? At the beginning of this blog I discussed the possibility of conducting a bibliometric analysis of the literature in order to find out how the term postbiotic has been used so far in relation to the different conceptualizations it may have. Surprisingly to me, a bibliometric analysis was published as a preprint last February at www.preprint.org and entitled “Who is qualified to write a review on postbiotics? A bibliometric analysis”. Authors indicated that between November 2021 and December 2023, 76 review articles were published on postbiotics, with a mean of almost 3 reviews per month. Authors concluded that a portion of this collection of work was written by first authors with no previous engagement with related research and lacking colleagues or mentors involved with microbiome/probiotics research to support them as senior authors. Our article “The Concept of Postbiotics”, in collaboration with Dr. Mary Ellen Sanders PhD and Prof. Seppo Salminen PhD ranks in third place among the top 10 publications according to the number of citations received.

While the academic and scientific sphere still debate the proper meaning of the term postbiotics, it seems the regulatory landscape for postbiotics is progressing to consider them to be preparations of inanimate microorganisms able to confer a health benefit, as proposed by ISAPP.

I come to praise ISAPP, not to bury it: Reflections on 15 years as a board member

/in ISAPP Science Blog /by KC

By Prof. Colin Hill PhD, University College Cork

I have been a Board member of ISAPP since 2009, serving as President from 2012 to 2015. This year, following our successful annual meeting in my home city of Cork, I have decided to step down and make way for new blood.

It is normal when a period like this comes to an end to reflect on all the advances in the field in that time and to highlight some of the great strides that have been made. But I don’t want to do that – the health of the field is obvious from the scientific literature and the extraordinary level of the research presented at the annual meeting. Maybe one could even argue that the field is now at a point of maturity where ISAPP has fulfilled its purpose in helping to establish the credibility of biotic research. So, what is the role of ISAPP in 2024 and beyond?  This of course is something for the board and ISAPP member companies to decide, but I will give some of my thoughts on what makes ISAPP special and why I think it is more important than ever to have such a strong scientific champion representing the field.

The ISAPP agora

The literal meaning of the word agora is “gathering place” or “assembly”, and I think that providing this function has been and continues to be one of the main benefits of ISAPP. The ISAPP agora is physically manifested in the annual meetings and other gatherings, but also goes on throughout the year at the monthly board meetings, which involve all of the academic board members plus the designated industry representatives. The ISAPP agora can be used to reach consensus, to debate topics, to identify new trends, to challenge accepted dogma and to defend rigorous science against unfounded claims. The biotic field can sometimes be a victim of individual researchers or companies making claims that are not supported by rigorous research. ISAPP is entirely focused on scientific excellence and its member companies accept that there are no shortcuts for biotics research in terms of rigour. We realise that the days of saying that it would be too difficult to ‘prove’ a health benefit are over. We still have many more associations than direct evidence of mechanism, but I for one think that is reason for excitement rather than a point of criticism.

Uniting industry and academia

While it is of course important that the board is composed of independent academic scientists, I have always thought that ISAPP benefits by placing scientists from industry and academia on an equal footing, and that everyone recognises the basic truth that it is rare that any discovery in an academic research lab will make a difference to a patient or a consumer without industry being involved. The degree of openness of the scientists from industry partners, the genuine enthusiasm for the field and the sense of common purpose is always obvious. Perhaps people in other industry-academic partnerships experience the same phenomenon, but whether or not they do, the field of biotic research has benefited enormously from this sense of togetherness that I think owes a lot to the existence of ISAPP.

A common language

Scientists, industry, regulators and others can only communicate effectively if we share a common language, and ISAPP has been a leader in providing and updating the definitions of the foundational terms of our scientific discourse; probiotics, prebiotics, synbiotics, postbiotics and fermented foods. This function should not be underestimated and although definitions always require ongoing debate and revision, ISAPP hopefully will continue to codify existing and new ‘biotics’ into the future.

A vibrant and talented board

I want to finish by commending the existing and previous board members for their dedication to promoting scientific excellence, the extraordinary amounts of time they volunteer to this cause, and their enormous patience in putting up with me for 15 years. The new leadership team (Executive Director Marla Cunningham, President Maria Marco and vice-President Sarah Lebeer) is outstanding, with the board members representing a who’s who of biotic science and so I leave with the association in the best of hands.

In my time on the board I was lucky to work with many of the giants in our field. If I start naming people I will inevitably omit someone who deserves mention, but I hope no-one will mind if I single out the two individuals who had the most profound influence on me, Todd Klaenhammer and Mary Ellen Sanders. It would take far too long to list the many ways that they have shaped my thinking and so I will simply express my gratitude toward them, and to all my other friends and colleagues among board members past and present. It has been a pleasure, and I look forward with interest to the next 15 years of ISAPP.

Audience observing panel on probiotics for preterm infants

Expert Panel at ISAPP Annual Meeting Addresses Probiotic Use for Premature Infants

/in ISAPP Science Blog /by KC

By Marla Cunningham, ISAPP Executive Director

The use of probiotics in premature infants has been highly topical in recent months. Probiotic use for the prevention of necrotising enterocolitis (NEC) in preterm infants has been studied in over 65 randomised clinical trials, with systematic reviews showing significant reductions in NEC as well as all cause mortality. However, the application of probiotics is not without risk – in vulnerable populations such as preterm infants, the translocation of probiotic bacteria into the bloodstream is a rare but documented occurrence. While probiotic bacteraemia is usually highly treatable with antibiotics, some isolated case reports of fatalities over the years have created significant concern. One such recent incident resulted in an FDA warning letter in September 2023 to all US healthcare practitioners, amongst other warning letters issued to companies for marketing breaches. The healthcare provider letter warned about the risk of probiotic products in premature infants and reminded clinicians that the recommendation of any non-approved products for disease prevention, such as NEC, must be conducted under an investigational new drug (IND) application. The prohibitive nature of IND applications in conjunction with the liability risk inherent in prescribing under the shadow of an FDA warning letter has severely limited the prescribing of probiotics in US neonatal intensive care units (NICUs). 

While recent US events have brought this issue to the forefront, evidence gaps and disparate clinical implementation rates are challenges that exist across the globe. To further explore this issue, ISAPP held a panel discussion at the 2024 ISAPP Annual Scientific meeting in Cork, Ireland. The panel featured seven experts sharing their unique perspectives on this complex issue, covering scientific, clinical, regulatory, industry, and patient family viewpoints.

Evaluating evidence for risk versus benefit

Dr. Geoffrey Preidis, MD PHD, paediatric and neonatal gastroenterologist at Baylor College of Medicine, set the scene with an overview of the current evidence base on probiotics for prevention of NEC in preterm infants. Covering recent meta analyses and systematic reviews (AGA 2020, Cochrane 2023), he explored the strength and quality of evidence for risk and benefit, and highlighted recommendations and concerns raised by clinical societies. While the American Gastroenterological Association (AGA) made a positive conditional recommendation for probiotic use for the prevention of NEC in premature infants supported by moderate/high quality evidence, the American Academy of Pediatrics (AAP), while acknowledging discretionary use in certain units, recommended against universal use in NICUs due to safety concerns. Exploring the specific safety concerns, Dr Preidis highlighted that sepsis risk due to contamination of probiotics with pathogenic organisms was a matter requiring ongoing attention and could approach zero with continued efforts, as outlined in a paper he co-authored in JAMA Pediatrics about optimising product standards. While probiotic organism-induced sepsis remains a risk with the administration of live microbes, Dr Preidis’ assessment of risk:benefit calculations remained strongly in favour of benefit. Reported number needed to treat with prophylactic probiotic administration is 50 infants to prevent 1 death, and while probiotic sepsis-induced mortality is difficult to accurately estimate, conservative calculations (likely overestimating risk) suggest 1:8000. 

Continuing data collection

Dr. Mark Underwood MDDr. Mark Underwood MD, neonatologist at Providence Sacred Heart Medical Center in Washington state, described two large ongoing trials of probiotics for NEC prevention, as well as the efforts to track preterm infant outcomes in the US before and after the FDA warning letter. He also outlined the current litigation environment in the US, with a surge in lawsuits addressing infant formula administration and NEC risk further intensifying the already litigious environment in the NICU. This situation contributes to why US hospitals are unwilling to allow probiotic administration in the NICU after the FDA warning. He highlighted key research priorities for the field, and explored the benefits of a cluster-randomized (per NICU) crossover trial with early gestational age (<32 weeks) infants, to overcome multiple NICU-specific confounders. Dr. Underwood also raised the question of clinical equipoise for ethical study design – with data on over 15,000 infants and significant effect sizes, does equipoise exist to conduct further placebo-controlled trials with infants?

Hearing European and UK perspectives 

Prof Hania Szajewska MD PhD, chair of Paediatrics at the Medical University of Warsaw, explored key points of the 2023 European Society for Paediatric Gastroenterology Hepatology and Nutrition (ESPGHAN) statement, produced following the FDA warning. The point was made that while a move to pharmaceutical grade products could reduce contamination risk, probiotic-induced sepsis rates were unlikely to be mitigated by such a strategy, and noted the risk for lives lost of abandoning currently available treatments in the short term. The statement also emphasised the crucial role of parents in decision making about infant care.

While rates of probiotic usage in US NICUs have plummeted to an estimated <3% since the FDA warning, usage rates across NICUs in the UK were estimated at around 40% of NICUs in 2022, and are not known to have been reduced.  Discussing UK implementation data and frameworks for use, Dr Janet Berrington MD, neonatal consultant in Newcastle, UK, also highlighted further research priorities for the field, including the limited data on probiotic use in <28 week/<1000g infants. She called for a focus on improved data collection on probiotic use and standardised diagnostic and outcome reporting for clinical studies as well as within national registries. Sharing work from her own studies, Dr Berrington highlighted the utility of pre-trial understanding of the gut microbiome impact of probiotics, where improved maturation of the microbiome in response to a given probiotic was predictive of benefits in clinical studies.

Prioritising shared decision making

Sharing perspectives from patient families of NEC sufferers, Marie Spruce, chair of the charity organisation NEC UK, highlighted parent concerns about lack of information about probiotic treatment options, possible risks and benefits, and the level of parent consultation in decision-making during NICU care of infants. Ultimately, she highlighted, parents live with the consequences of decisions made in hospital, and she emphasised the importance of ensuring parent views are sought within critical decision making windows.

Understanding the US legal environment

Understanding the legal, regulatory and practical barriers to improved utilisation in NICUs, across the US and globally, was deemed critical to moving forward.  Prof Diane Hoffmann of the University of Maryland explored current regulatory and legal constraints within the US environment, as well as potential paths forward for probiotic use, including medical food, drug and biologic pathways, and accelerated/expanded access for probiotic products undergoing IND approval. Questions were raised about the scope of regulatory influence over clinician autonomy in the practice of medicine – an area where different perspectives exist and where litigation remains a risk. 

Incorporating solutions from industry

Providing an industry perspective, Dr Greg Leyer PhD conveyed the capabilities of industry to support better infant health within manufacturing and regulatory constraints. Dr Leyer presented on the possibilities for improved product quality through manufacturing and testing standard initiatives, transparency and third party verification, as well as post-market surveillance initiatives. He noted that companies are at a crossroads in decision-making around infant-focused product development, considering the risks and markets in the US and globally.

Identifying priorities for the future

Engaging with the panel during Q+A time, a number of audience members questioned where legal liability lies for a failure to treat, given the level of evidence in support of probiotic administration. Prof Hoffmann noted that in the current US context and given the FDA warning, a lawsuit claiming fault from a lack of probiotic administration would most likely not be successful. Other audience members commented on treatment rights for parents with children in NICUs without established probiotic use protocols. While panelists noted a lack of clarity in this area, a strategy sometimes employed by mothers expressing milk for their hospitalised infants was maternal consumption of probiotics. Some audience members questioned whether the lack of alignment on recommendations from professional medical societies may have influenced regulatory decision-making and whether better alignment on clinical guidelines should be a priority moving forward. Closing recommendations included ensuring that appropriate consideration of the large body of scientific evidence is paramount in regulatory and clinical decision making as well as prioritising parent education and consultation for truly informed decisions.

 

See here for the ISAPP statement on probiotic administration in premature infants, published after the FDA warning to healthcare professionals.

 

Should everyone take a probiotic? Assessment of evidence of probiotics for healthy people

/in ISAPP Science Blog /by KC

By Prof. Daniel Merenstein MD and Dr. Mary Ellen Sanders PhD

During the ISAPP 2024 meeting, an article titled, “Is there evidence to support probiotic use for healthy people?” was published. The authors concluded, “…we did not find a high level of evidence to support recommendations for other endpoints we reviewed for healthy people. Although evidence for some indications is suggestive of preventive benefits of probiotics, additional research is needed.”

Those in the probiotic field are used to headlines critical of probiotics meant to sensationalize rather than accurately reflect the evidence. But this article takes a careful look at if probiotics should be used by everyone regardless of indication. 

Scientific grounding for the paper

This article is an ISAPP output derived from an ISAPP 2023 discussion group that included academic and industry scientists, including the nine authors. The discussion group aimed to examine the evidence that probiotics are beneficial to healthy people at a population recommendation level.

We assembled probiotic and evidence-based medicine experts to review the literature. We chose preventative indications that we felt had some compelling evidence that healthy people would benefit from probiotics. Thus, we examined the evidence that probiotics could reduce urinary, vaginal, gastrointestinal, and respiratory infections, reduce antibiotic use, and improve risk factors associated with cardiovascular health. Populations included certain groups of individuals, including generally healthy people, those at risk for recurrent urinary and vaginal infections, and children taking antibiotics. We considered that the evidence was too nascent for this exercise for endpoints such as cognitive function, athletic performance, and dental health, and therefore did not review these endpoints. 

The challenges of studying prevention

We undertook this effort to address the common question, “Should everyone take a probiotic?” In fact, there are few recommendations for any intervention for people free of underlying disease. Such interventions must have sufficient evidence of benefit and of relatively little to no risk of harm.

In raising this question for probiotics, we took inspiration from the approach of an organization tasked with evaluating preventive evidence: the United States Preventive Services Task Force (USPSTF). Since an important component of a USPSTF review is potential for harm, it is important to note here that experts considering the safety of probiotics recently concluded that commonly used probiotic strains are safe for use in the general population.

The USPSTF recognizes that preventive measures are difficult and expensive to study. Healthy populations are difficult to define and not uniformly defined across studies. The physiology of healthy people recruited into a study is generally unlikely to change, especially over the short term. So efficacy studies must either be long-term or must identify more accessible endpoints, such as validated biomarkers of disease or reduction of infectious disease, as targets for prevention. Further, the threshold of evidence for recommending any intervention to a healthy population has to be very high, partially due to the potential risk of harm. In a patient with an illness, a risk of harm may be tolerable if the benefit outweighs the risk. But in an asymptomatic individual this threshold is more difficult to determine. 

It is noteworthy that some preventive measures are widely believed by the general public to be effective, but upon scrutiny of the data have been found to lack supporting evidence. For example, for healthy adults younger than 75 years of age, the Endocrine Society recently recommended against Vitamin D supplementation above the current RDA. The USPSTF has concluded that there is insufficient evidence to recommend a daily multivitamin for the prevention of cancer or cardiovascular disease, to screen for skin cancer,  or to screen for speech and language delay disorders in children 5 years or younger or eating disorders in adolescents. Even diet and exercise counseling for the prevention of cardiovascular risk in healthy people received only a level C recommendation. As one would expect for recommendations for healthy people, the USPSTF imposes a high bar for required evidence. This group of experts aimed to apply a similar high bar for evidence on probiotic indications.  

Meeting the strict criteria for an effective preventative measure

We reviewed data for indications where there were compelling studies on essentially healthy individuals showing some benefit from probiotics. But we wanted to determine if it was plausible that this body of evidence would meet a USPSTF-level of evidence for a recommendation for all healthy people. We recognized that there is sufficient evidence of efficacy to consider using specific probiotics for some indications for certain people. For example, evidence reviews have found that certain probiotics can be effective to prevent necrotizing entercolitis, reduce incidence of antibiotic associated diarrhea, reduce crying time in breast-fed colicky infants, improve therapeutic effectiveness of antibiotics to treat bacterial vaginosis, reduce risk for Clostridioides difficile infections, treat acute pediatric diarrhea, and manage symptoms of constipation. However:

Sufficient evidence of benefit to support the recommendation that “everyone should take a probiotic” is not yet available.

At ISAPP 2024 (held July 9-11), we heard from experts about the promise of probiotics for our skin as we age, for social anxiety, for immune function in children and for helping undernourished kids thrive. Those who understand the evidence level for probiotics recognize the proven and potential role for probiotics in health. Our paper does not change that. There is evidence for many individuals to take daily probiotics due to conditions they have. Interestingly, after our discussion group, the FDA approved a qualified health claim that can be used on yogurt. The claim relates to the impact of yogurt on the risk of developing diabetes. Allowed language for this claim includes:

  • “Eating yogurt regularly, at least 2 cups (3 servings) per week, may reduce the risk of type 2 diabetes. FDA has concluded that there is limited information supporting this claim.” 
  • “Eating yogurt regularly, at least 2 cups (3 servings) per week, may reduce the risk of type 2 diabetes according to limited scientific evidence.”

This claim relied on evidence of correlative associations in humans. For our analysis, we required a higher level of evidence from randomized, controlled trials. Further, this claim applies to yogurts that may or may not contain added probiotics in addition to the yogurt starter cultures. However, it is an important preventative endpoint and supports the idea that healthy people may benefit from probiotic-containing foods.  

Evidence to date suggests that with additional investment in well-designed research, the future may see probiotics reach the high standard of evidence needed for preventative recommendations in healthy people.

 

Further Reading

Do probiotics really benefit healthy people? from NewsMedical

Can we estimate prebiotic effects from short-chain fatty acid production?

/in ISAPP Science Blog /by KC

By Prof. Kristin Verbeke PhD, KU Leuven

Short-chain fatty acids (SCFA), primarily acetate, propionate and butyrate, are the most abundant anions in the large intestine. They are mainly produced from bacterial fermentation of undigested carbohydrates. Since SCFA were found to activate the orphan G-protein coupled receptors GPR-41 and 43 (renamed as free fatty acid receptor ffar-3 and ffar-2), research into their physiological effects on human health has increased exponentially.

SCFA production is proposed to be a mechanism for several health benefits associated with intake of dietary fiber and prebiotics, not only via local effects in the gut but also on distant organs. Molecular mechanisms explaining SCFA effects have mainly been elucidated in cell-based in vitro experiments and animal studies. However, studying the impact of SCFA on human physiology is complicated by the kinetics of these molecules.

Although fecal concentrations of SCFA are relatively easy to measure, consensus has grown that they provide little information. Fecal SCFA do not adequately reflect the production of SCFA in the proximal colon and only represent the fraction of SCFA that has been produced and not used. The capacity of the anion transporters,mainly the monocarboxylate transporter-1 (MCT-1) and sodium-coupled monocarboxylate transporter 1 (SMCT-1), that absorb SCFA into the colonocytes does not seem to be a limiting factor. More bacterial SCFA production results in more uptake of SCFA but not necessarily in a higher fecal excretion. For instance, when we administered colon-delivery capsules containing SCFA in a dose of 250 mmol (equivalent to what is produced from 20 g of fermentable fiber), fecal SCFA concentrations did not increase, indicating nearly complete absorption into the colonocytes (1).

Quantification of SCFA in serum or plasma provides a more relevant alternative, particularly for understanding effects of SCFA on distant organs. Systemic SCFA concentrations are about a 1000-fold lower than fecal concentrations, requiring more sophisticated analytical protocols for measurement. Currently, both GC-MS or LC-MS/MS protocols with or without prior derivatization are available for accurate and reliable SCFA quantification (2). However, it is important to be aware of the ubiquitous nature of acetate and to take sufficient precautions to avoid contamination. For instance, the type of blood tubes used for blood collection should be considered since EDTA-tubes induce contaminations with acetate while separator tubes result in propionate and butyrate concentrations. Also, the type of water used during sample preparation can be a source of acetate contamination, necessitating the measurement of blanks in every run to check for background acetate.

Beyond analytical challenges, uncertainties about when to measure systemic SCFA concentrations also hamper their interpretation in humans. SCFA have a plasma half-life in the order of a few minutes, causing plasma SCFA to vary during the day in response to food intake, particularly fiber. Indeed, postprandial plasma SCFA start to rise about 4 hours after the consumption of a breakfast rich in fermentable fiber and return back to baseline by the end of the day. Measured concentrations therefore depend significantly on the composition and timing of the last meal. Even when using fasting blood samples, it remains important to standardize the evening meal of the previous day to avoid residual fermentation of that meal, known as the second meal effect. Due to their short plasma half-life, SCFA do not accumulate in the circulation, explaining the lack of differences in fasting SCFA concentrations from before to after prebiotic interventions. Additionally, interindividual variation in fasting SCFA concentrations is substantial as shown in a cross-sectional study in 160 individuals (3). The factors contributing to this variability require further investigation but may include dietary habits, microbiota composition, exercise levels or host genetics. In our lab, we prefer measuring postprandial SCFA concentrations during the day and calculating the area-under-the concentration vs time curve as a measure of SCFA production rather than relying on fasting concentrations, despite the increased burden on the participants involved in clinical trials and the associated cost and effort of sample analysis.

Importantly, SCFA production may explain part of the prebiotic activity, but it likely does not provide the complete picture. For example, while the interaction of prebiotics with the immune system may be partly explained by activation of ffar2 and ffar3 receptors on immune cells by SCFA, some prebiotics such as human milk oligosaccharides or specific pectin structures directly activate immune cells via interaction with toll-like receptors 2 and 4 (4). Additionally, by altering the microbiota composition, prebiotics also indirectly alter the microbe-immune interaction. Such effects also need consideration when evaluating prebiotic interactions with host health.

Studies, preferably conducted in the target host (e.g. humans), that aim to elucidate the qualitative and quantitative contribution of SCFA to the host health benefits of prebiotics (i.e. dose-effect relationships, fraction of health benefit explained by SCFA) are highly warranted. Only then can we establish the value of SCFA as markers of prebiotic activity.

Can prebiotics benefit brain health in older adults? ISAPP experts weigh in on a recent study

/in ISAPP Science Blog /by KC

With increasing age and frailty come changes in the gut microbiota – leading scientists to ask whether targeting the gut microbiota using prebiotics could contribute to healthier aging. Of particular interest is whether prebiotics have the potential to affect brain health and cognitive performance in older adults.

An intervention study led by researchers at King’s College London (UK) explored prebiotics’ effects on both physical health and cognition in older adults. In the study, 72 adults (twin pairs) aged 60 and up consumed either a prebiotic supplement or a placebo every day for 12 weeks. The prebiotic supplement contained a mixture of inulin and fructo-oligosaccharides (FOS) totalling 7.5 grams. All participants also did resistance exercises and took a supplement containing protein components (branched-chain amino acids, or BCAAs).

The results were promising: while participants in both groups overall showed improvements in their physical strength (as measured by chair rise time), the individuals in the prebiotic group performed better than the placebo group on cognitive tests (from a computer-based battery of tests called the CANTAB) measuring executive function and memory. The result is consistent with the idea that prebiotics benefit brain health in some situations.

Two ISAPP board members and prebiotic experts, Dr. Anisha Wijeyesekera PhD and Prof. Kristin Verbeke PhD, give their perspectives on this area of research and what’s added by this recent study.

Why are prebiotics of interest for benefits to brain health?

Wijeyesekera: There is growing evidence (and interest) in the link between the gut and the brain. There are several health conditions such as irritable bowel syndrome and autism spectrum disorder where this gut-brain link is evident, as patients experience symptoms that relate to both gut and brain health. Hence, for many researchers, gut microbiota targeted dietary interventions such as prebiotics and probiotics offer an approach to improve health outcomes such as cognitive function through targeted modulation of the gut microbiota.

 

What’s known about the mechanisms by which prebiotics might improve cognition?

Wijeyesekera: This is still being studied but most likely the production of microbial metabolites (such as short-chain fatty acids, or SCFAs) are playing a crucial role here. These microbially derived small molecules enter into host physiological processes, resulting in altered metabolic mechanisms that may be contributing to the changed health outcomes.

Verbeke: The mechanisms for gut-brain signaling have been studied mainly in in vitro and animal studies. Several potential pathways have been proposed, including metabolic (SCFA production that affects the hypothalamic-pituitary-adrenal axis), endocrine (microbial production of neurotransmitters and hormones), immune (release of anti-inflammatory mediators) or neural (vagus nerve stimulation) signaling. It is hard to say whether they are all equally important in humans or whether one of those mechanisms is primary. We assume it is a combination of all those effects.

In the current study, do you think the protein intake and exercise were necessary for the beneficial effects?

Verbeke: I assume that the protein (BCAA) supplement and the exercising was intended to improve the muscle strength, which was the primary outcome of the study. Indeed, the chair rise time improved in both groups but the prebiotic did not confer an additional benefit. With respect to cognition, there was a slight effect in the placebo group that only received the protein/exercise(although it is not indicated whether that difference is statistically significant) but addition of the prebiotic significantly increased the effect. So if the effect of protein/exercise alone was not significant, the result would have been the same without that intervention; if the effect was significant, the effect of prebiotic alone might have been a bit smaller but would probably still be there.

A combination of inulin and FOS were used in the study. Do you think a different type of prebiotic would have had the same results?

Verbeke: As long as we do not know the exact working mechanism, it is hard to predict what the effect of a different prebiotic would be. I do not expect that other prebiotics would have no effect at all but the extent of the effect may (slightly) differ from one prebiotic to another. For instance, it is possible that a prebiotic that yields a different ratio of SCFA upon fermentation may have a different effect, or that a prebiotic that more selectively stimulates bacteria secreting different amounts of neurotransmitters such as GABA may also have a different effect.

What are some gaps in what researchers know about how prebiotics affect brain function?

Wijeyesekera: It would have been great if the metabolic phenotypes had also been characterised in the study, as this would be able to identify alterations to metabolic pathways as a result of the intervention. This may shed more light on the activity of the microbes that were identified to have been altered as a result of the intervention, and also the impact of the protein and exercise in general on metabolic mechanisms.

Verbeke: The effect of prebiotics/fiber on cognitive function is likely confounded by a number of individual host factors such as the baseline diet, age, lifestyle, and baseline cognitive function level. We need much more research to understand the interaction between all these factors and to be able to identify the people that would benefit most from a prebiotic/fiber intervention.

Should bacteriophages be considered as a member of the biotic family?

/in ISAPP Science Blog /by KC

By Prof. Colin Hill PhD DSc, University College Cork, Ireland

ISAPP has provided consensus definitions for a number of biotics that confer a health benefit on the host. These include prebiotics, probiotics, synbiotics and postbiotics, but here I want to put forward an argument that bacteriophages (phages) could qualify as a new member of the ‘biotic’ family.

 

Phages are bacterial viruses that infect and replicate within their bacterial victim before bursting the cell and releasing many new copies of the original virus. Phages can also integrate into the bacterial chromosome and co-exist with the living bacterium, but always with the threat that it can excise and initiate another replication-and-burst cycle. Phages are probably the most abundant biological entities on earth and are found wherever bacteria are present in the body. They are an important component of the microbiome of humans, plants and animals, and play a role in regulating bacterial community composition and function.

If phages are to fit neatly within the existing biotic family they would have to qualify as a biotic and also be shown to provide health benefits. The Oxford English Dictionary defines biotics as ‘of or relating to living organisms; caused by living organisms’. Bacteriophages (phages) are not considered as living organisms in themselves, but they easily fit within the biotic definition as they are completely dependent on living bacterial cells for their own propagation and as such certainly ‘relate to living organisms’.

There is also a significant body of evidence that some phages can confer health benefits on a host. Most of this evidence is based on using phage therapy to treat bacterial infections. This has been done in Russia for almost a century, and while the evidence may not always conform to western regulatory standards there is little doubt that phages can bring benefits such as limiting or clearing infections at various body sites. In a recent example, a randomised, controlled, blinded trial on burn wounds was conducted in Belgium and France with Pseudomonas aeruginosa as the target (1). A topically applied preparation consisting of low titres of a 12-phage cocktail was used. While the efficacy did not reach that of the standard-of-care sulfadiazine silver emulsion cream treatment, the phage treatments did lead to sustained reductions in bacterial burdens.

Phages can also be potentially used to modulate microbiomes to impact host health, as shown in a recent study I was involved in performed by Nate Ritz in the John Cryan lab where faecal virome transplants (FVT) changed the bacterial community and thus reduced the impact of stress-induced changes in behaviour and immune responses in mice (2). This paper was the topic of a recent ISAPP podcast for anyone interested in hearing more about that story. FVT has also been reported to work against Clostridioides difficile infections in humans in a small trial in Germany (3).

The term phagebiotic is perhaps the most fitting for this new type of biotic. I have always argued that we should not invent new terms for things that already have names, so why not just stick to bacteriophages or phages? It is because the term phagebiotic would be reserved for a very specific sub-category of phages. Just as all probiotics are microbes, but not all microbes are probiotics, I would suggest that phagebiotics should only be used to refer to specific phage preparations that have been shown to convincingly confer a health benefit in an appropriate properly controlled trial.

Mirroring the probiotics definition I would start with a suggested definition something like this; ‘phagebiotics are bacteriophages that, when administered in adequate amounts, confer a health benefit on the host’.

 

  1. Jault P., Leclerc T., Jennes S., Pirnay J.P., Que Y.A., Resch G., Rousseau A.F., Ravat F., Carsin H., Le F.R., et al. Efficacy and tolerability of a cocktail of bacteriophages to treat burn wounds infected by Pseudomonas aeruginosa (PhagoBurn): A randomised, controlled, double-blind phase 1/2 trial. Lancet Infect. Dis. 2019;19:35–45. doi: 10.1016/S1473-3099(18)30482-1
  2. Ritz, N.L., Draper, L.A., Bastiaanssen, T.F.S. et al. The gut virome is associated with stress-induced changes in behaviour and immune responses in mice. Nat Microbiol 9, 359–376 (2024). https://doi.org/10.1038/s41564-023-01564-y
  3. Ott, S. J., Waetzig, G. H., Rehman, A., Moltzau-Anderson, J., Bharti, R., Grasis, J. A., et al. (2017). Efficacy of sterile fecal filtrate transfer for treating patients with Clostridium difficile Gastroenterology 152, 799.e797–811.e797. doi: 10.1053/j.gastro.2016.11.010

 

pigs in mud

The gut-brain axis in livestock animals: Is there a place for biotics in changing pig behavior?

/in ISAPP Science Blog /by KC

By Prof. Seppo Salminen PhD, University of Turku, Finland

When pigs are kept as livestock, ‘manipulative behaviour’ is relatively common and it most often consists of biting, touching, or close contact with ears or tails of pen mates, without always resulting in visible wounds. Such pig behavior can cause stress and sometimes results in physical injuries. Chronic stress, nutritional deprivation, diet formulation, health problems, environmental discomfort, high stocking density and competition over resources are among the reported risk factors for tail biting in pigs. However, the precise factors behind behavioral problems in domesticated pigs remain poorly understood. It has been suggested that manipulative behavior may be associated with gut microbiota composition and activity via the gut-brain axis, with potential influence from the metabolites produced by gut microbes.

A multidisciplinary team of researchers recently assessed manipulative pig behaviour and gut microbiota interrelations (König et al. 2024). The aim was to identify pigs performing tail and/or ear manipulation (manipulator pigs) and to compare their fecal microbiota with that of control pigs not manifesting such behaviour. The study was conducted by analyzing video recordings of 45-day-old pigs. Altogether 15 manipulator-control pairs were identified (n = 30). Controls did not receive nor perform manipulative behaviour.

Rectal fecal samples of manipulators and controls were compared on two parameters: (1) culturable lactobacilli, and (2) microbiota composition. 16S PCR was used to identify Lactobacillaceae species after culture isolation, and 16S amplicon sequencing was used to determine fecal microbiota composition. The researchers found fewer culturable Lactobacillaceae species in fecal samples of pigs performing manipulative behaviour, with seven culturable Lactobacillaceae species identified in control pigs and four in manipulator pigs. Manipulators (p = 0.02) and female pigs (p = 0.005), however, expressed higher overall counts of Lactobacillus amylovorus, and the researchers found a significant interaction (sex * status: p = 0.005) with this sex difference being more marked in controls. Manipulator pigs tended to express higher total abundance of Lactobacillaceae but lower alpha diversity. A tendency for an interaction was seen in Limosilactobacillus reuteri (sex * status: p = 0.09). The results add to the findings of an earlier study reporting that intestinal microbiota was changed and lactobacilli were more abundant in a negative control group compared with biting pigs (Rabhi et al. 2020). Taken together, these studies suggest that specific lactobacilli  as well as low diversity of Lactobacillaceae may be factors impacting manipulative behavior.

Manipulative behavior is an important challenge in swine production as it impacts animal welfare and health and the economics and safety of the pork meat supply chain. With emerging information on the gut-brain axis in various animals, scientists are exploring the potential contributions of intestinal microbiota to such behaviors. With recent studies suggesting that there may be a link between observed low diversity in species of Lactobacillaceae and the development of manipulative behaviour, perhaps specific biotics could be used to increase and modulate lactobacilli (selected species and diversity) to control tail and ear biting in pigs. Studies in the future may investigate this possibility.

References

König E, Heponiemi P, Kivinen S et al. Fewer culturable Lactobacillaceae species identified in faecal samples of pigs performing manipulative behaviour. Sci Rep. 2024;14:132. doi: 10.1038/s41598-023-50791-0.

Rabhi N, Thibodeau A, Côté JC, Devillers N, Laplante B, Fravalo P, Larivière-Gauthier G, Thériault WP, Faucitano L, Beauchamp G, Quessy S. Association Between Tail-Biting and Intestinal Microbiota Composition in Pigs. Front Vet Sci. 2020 Dec 9;7:563762. doi: 10.3389/fvets.2020.563762.

Woman holding yogurt. In the US, yogurt now has an approved Qualified Health Claim.

A guide to the new FDA Qualified Health Claim for yogurt

/in ISAPP Science Blog /by KC

Fermented foods such as yogurt, kimchi, and fermented pickles have traditionally been associated with health benefits in countries around the world, but the science that backs these health benefits is relatively new.

Amidst a growing number of scientific studies examining the health benefits of specific fermented foods, a new Food and Drug Administration (FDA) announcement in the US marks an advance in how the potential benefits of fermented foods can be portrayed to the general public.

In response to a petition by Danone North America, the FDA announced that it will allow the first Qualified Health Claim related to a fermented food – yogurt. The new Qualified Health Claim is worded as follows:

Eating yogurt regularly, at least 2 cups (3 servings) per week, may reduce the risk of type 2 diabetes. FDA has concluded there is limited information supporting this claim.

Or Eating yogurt regularly, at least 2 cups (3 servings) per week, may reduce the risk of type 2 diabetes according to limited scientific evidence.

The claim was announced in a letter of enforcement discretion on March 1st, and can be applied to any yogurt product on the US market that meets the FDA’s standards of identity.

Qualified Health Claims and why they’re important

A Qualified Health Claim is a statement that makes a connection between a substance and a disease-related or health-related condition, is supported by scientific evidence, but does not meet the more rigorous “significant scientific agreement” standard required for an Authorized Health Claim.

Currently, approximately one dozen Authorized Health Claims and around 30 Qualified Health Claims exist in the US for different nutritional and food substances. For example, an Authorized Health Claim exists for soluble fiber from whole oats; Qualified Health Claims exist for walnuts, green tea, and a list of other foods.

To ensure that these claims are not misleading, they must be accompanied by a disclaimer or other qualifying language to accurately communicate to consumers the level of scientific evidence supporting the claim.

According to Bob Hutkins, Professor Emeritus at the University of Nebraska-Lincoln, such claims are important when considered within the context of what Americans currently eat.

He says, “We come nowhere close to eating the recommended amounts of fiber, whole grains, and fruits and vegetables. Indeed, according to the USDA Healthy Eating Index, the average consumer scores a 60 on a 100 point scale. When considering our overall eating habits in the US, I don’t know that this one claim will actually move the needle very much. But in my view, health claims, whether ‘Authorized’ or ‘Qualified’, may help nudge consumers to make informed decisions when deciding what to eat.”

The path to Qualified Health Claim

Dr. Miguel Freitas PhD, VP Health and Scientific Affairs at Danone North America, whose team led the petition, says the company’s efforts were motivated by the observation that, over time, evidence supporting the potential of yogurt to reduce the risk of type 2 diabetes grew more and more compelling.

In December 2018, Danone North America first submitted the Qualified Health Claim petition to the FDA. The petition was put on hold during the height of the COVID-19 pandemic and the evidence was reviewed again in 2023 by the FDA.

In total, more than 85 related studies were considered in support of the claim, with 30 being deemed high or moderate quality.

The FDA gave recognition of the claim in March 2024. Dr. Freitas says, “Now that the claim has been announced, our hope is that it will give consumers simple, actionable information they can use to reduce their risk of developing type 2 diabetes through an easily achievable, realistic dietary modification.”

Scientific support

Prof. Hutkins says the FDA has a high bar even for Qualified Health Claims, requiring a substantial level of scientific evidence to support them. He says that regarding this yogurt claim, “The FDA conducted an exhaustive review of studies that were included in the petition. Many of the studies were not considered rigorous enough and were excluded. In my view, they were very conservative in their analysis of the data.”

Both intervention studies and observational studies were considered in the FDA’s evaluation of the evidence linking yogurt and type 2 diabetes. Pro. Hutkins says that while randomized, controlled trials (RCTs) are considered the gold standard, well-conducted observational studies in large human cohorts can be very informative. The latter ended up being the sole basis of the FDA decision.

“The FDA identified 20 relevant intervention studies, but none were considered sufficiently rigorous to draw meaningful conclusions,” he says. “The FDA identified 28 relevant observational studies, which were then critically reviewed. Ultimately they concluded there was sufficient credible data to suggest associations of yogurt consumption on reduced incidence type 2 diabetes.”

The language for Qualified Health Claims includes any relevant qualifications indicated by the evidence. The FDA claim wording does not differentiate between sweetened and unsweetened yogurt products, with the evaluation noting that the beneficial association was observed irrespective of fat or sugar content. Nevertheless, Prof. Hutkins advises paying attention to the overall nutritional profile of different yogurt products, “In my view consumers could gain the benefits of yogurt without the extra calories and refined carbohydrates by choosing unsweetened yogurts.”

Implications for the food industry

Dr. Freitas says, “Our hope is that this new Qualified Health Claim will inspire the food industry as a whole to increase its focus on yogurt innovation and research, to continue unlocking the full extent of its potential benefits.”

Meanwhile, Prof. Hutkins hopes to see more RCTs on yogurt in the future. “It should be possible to design RCTs that would satisfy the FDA,” he says. “I hope funding agencies will agree.”

Prof. Seppo Salminen PhD, from University of Turku (Finland), says this approval may mark the beginning of a trend in developing claims for individual fermented foods. Such is the goal of a European project called Promoting Innovation of ferMENTed fOods (PIMENTO), which acknowledges the high consumer interest in fermented foods and the potential benefits of these foods for nutrition, sustainability, and more. Prof. Salminen points out that yogurt is leading the way, given the new US claim as well as the existing European Union claim regarding yogurt with live cultures and improved lactose digestion.

Inaugural Sanders Award for Advancing Biotic Science Goes to Argentinian Researcher who leads YOGURITO program

/in ISAPP Science Blog /by KC

The ISAPP board of directors is pleased to share that the winner of the inaugural Sanders Award for Advancing Biotic Science is Dr. Maria Pía Taranto PhD, a researcher at the Center of Reference for Lactobacilli at the National Scientific and Technical Research Council (CERELA-CONICET) in Argentina.

Dr. Taranto leads the YOGURITO program, established in 2010, which delivers yogurt and other foods enriched with a probiotic to more than 200,000 lower income schoolchildren through a collaboration between scientists, government, industry, and the local community. For this program, Dr. Taranto and colleagues initially assessed candidate strains and selected L. rhamnosus CRL1505, and then led several preclinical and clinical studies demonstrating how it improves immune function. She and her team then developed the partnerships needed to deliver the foods (yogurt, chocolate milk, fresh cheese, and dehydrated powder) free of charge to children in public schools. Dr. Taranto has showed remarkable tenacity and resourcefulness to lead and maintain this program for over a decade in an environment where funding is limited and irregular and where inflation is high. Today the program has a tangible impact on the lives of hundreds of thousands of children per year who may otherwise be at risk of malnutrition.

Dr. Taranto has advanced the biotics field by translating the science and demonstrating real-world impact, using probiotics as a tool to support health in communities with limited resources. In the future she hopes to be able to measure the effects of the probiotic intervention on health and academic outcomes in the children.

After receiving her undergraduate degree in biochemistry and her PhD from National University of Tucuman, Dr. Taranto came to work as a researcher at CERELA-CONICET in 2001. Besides the YOGURITO program, she is involved in research on metabolic and technological aspects of lactic acid bacteria, characterizing new strains for future applications such as in metabolic diseases.

The Sanders Award for Advancing Biotic Science was established in 2023 thanks to the generous contributions of ISAPP community members, to honor the legacy of ISAPP’s former Executive Science Officer, Mary Ellen Sanders PhD. This annual award recognizes someone who has helped advance the biotics field, including probiotics, prebiotics, synbiotics, postbiotics and fermented foods. This year’s committee, composed of ISAPP board members, an industry member representative and Dr. Sanders, selected Dr. Taranto from among the many deserving nominees. Dr. Taranto will receive a cash award and will speak about her work at the ISAPP annual meeting in July, 2024.

2023 in Review: Highlights in the Field of Biotic Science

/in ISAPP Science Blog /by KC

By Kristina Campbell, Prof. Colin Hill PhD, Prof. Sarah Lebeer PhD, Prof. Maria Marco PhD, Prof. Dan Merenstein MD, Prof. Hania Szajewska MD PhD, Prof. Dan Tancredi PhD, Prof. Kristin Verbeke PhD, Dr. Gabriel Vinderola PhD, Dr. Anisha Wijeyesekera PhD, and Marla Cunningham

Biotic science is an active field, with over 6,600 scientific papers published in the past year. The scientific work that emerged in 2023 covered many diverse areas – from probiotic mechanisms of action to the use of biotics in clinical populations. In parallel with the scientific advancements, consumer interest in gut health and biotics is at an all-time high. A recent survey showed that 67 percent of consumers are familiar with the concept of probiotics and 51 percent of those who consume probiotics do so with the aim of supporting gut health.

Several ISAPP-affiliated experts took the time to reflect on 2023 and identify the most important directions in the fields of probiotics, prebiotics, synbiotics, postbiotics, and fermented foods. Below are these experts’ picks for the top developments in biotic science and application during the past year.

Increased recognition of biotics as a category

After ISAPP’s publication of the recent synbiotics and postbiotics definitions in 2020-2021, board members and others began referring to probiotics, prebiotics, synbiotics, and postbiotics collectively as “biotics”. 2023 has seen the term being used more widely (for example, in article headlines and communications from major organizations) to refer to these substances as a broad group.

Steps forward and steps back in the regulation of live microbial interventions

The actions of regulators have a profound impact on how biotic science is applied and how products can reach consumers. On the positive side, 2023 heralded the regulatory approval of two live microbial drug products for recurrent C. difficile infection by the US Food and Drug Administration (FDA). Both products are derived from fecal samples, but one is delivered to the patient gastrointestinal (GI) tract by enema, and the other is delivered orally.

Meanwhile, a case of fatal bacteremia in a preterm infant who had been given a probiotic product prompted the FDA to issue a warning letter to healthcare practitioners about probiotics in preterm infants, as well as warning letters to two probiotic manufacturers. These actions had the concerning effect of reducing access to probiotics for this population, despite the accumulated evidence that probiotics effectively prevent necrotizing enterocolitis in preterm infants. As outlined in ISAPP’s scientific statement on the FDA’s actions, the regulatory decision weighting the risks of commission over omission did not reflect the wealth of evidence for probiotic efficacy in this population and the low risk of harm.

Wider awareness of the postbiotic concept and definition

Scientific discussions on postbiotics continued throughout 2023, with several debates and conference sessions devoted to discussion of the postbiotic concept – including the status of metabolites in the definition. According to ISAPP board member Dr. Gabriel Vinderola PhD, who was a co-author on the definition paper and an active participant in many of these debates, the ISAPP definition is gaining traction and the debates have been useful in pinpointing further areas of clarification for the sake of regulators and other stakeholders. As shared with the audience at Probiota Americas 2023 in Chicago, Health Canada became the first regulatory agency to address the definition, and has started considering the term postbiotics under the ISAPP definition.

Advances in technologies for analyzing different sites in the digestive tract

When studying how biotics interface with the host via the gut microbiota, the science has relied mainly on analysis of fecal samples, with the majority of the GI tract remaining a ‘black box’. But a 2023 paper by Shalon et al., which was discussed at the ISAPP meeting in Denver, describes a device able to collect intestinal samples from different regions in the GI tract. Analysis of the metabolites and microbes indicated clear regional differences, as well as marked differences between samples in the GI tract versus fecal samples (for example, with respect to bile acids); an accompanying paper revealed novel insights into diet and microbially-derived metabolites. Efforts are underway across the world to develop smart pills or robotic pills that take samples all along the GI tract. Some devices have sensors that immediately signal to a receiver and others have been engineered to release therapeutic contents. Although these technologies may need more validation before they are useful in research or clinical contexts, they may greatly expand knowledge of the intestinal microbial community and how it interacts with biotic substances.

First convincing evidence linking intake of live microbes with health benefits

When an ISAPP discussion group in 2019 delved into the question of whether a higher intake of safe, uncharacterized live microbes had the potential to confer health benefits, it spurred a program of scientific work to follow. Efforts of this group in subsequent years led to the publication of an important study in 2023: Positive Health Outcomes Associated with Live Microbe Intake from Foods, Including Fermented Foods, Assessed using the NHANES Database. Researchers analyzed data from a large US dietary database and found clear but modest health benefits associated with consuming higher levels of microbes in the daily diet.

The benefits of live dietary microbes are being explored further in the scientific literature (for example, here, here, and here) and are likely to remain an exciting topic of study in the years ahead, building evidence globally for the health benefits of consuming a higher quantity of live microbes.

Increased interest in candidate prebiotics

Polyphenols have long been studied for their health benefits, but newer evidence suggests they may have prebiotic effects, achieving their health benefits (in part) through interactions with the gut microbiota. A theme at conferences and in the scientific literature has been the use of polyphenols to modulate the gut microbiota for specific health benefits. More than a dozen reviews on this topic were published in 2023, and several of them focused on how polyphenols may achieve health benefits in very specific conditions, such as diabetes or inflammatory bowel disease.

Another substrate receiving much attention for its prebiotic potential are human milk oligosaccharides (HMOs). HMOs, found in human milk, support a nursing infant’s health by encouraging the growth of beneficial gut microbes. Several articles in 2023 have delved into the mechanisms of HMO metabolism by the gut microbiota, and explored its potential as a dietary intervention strategy to improve gut health in adults.

Sharper focus on evidence for the health and sustainability benefits of fermented foods

Fermented foods are popular among consumers, despite only early scientific knowledge on whether and how they might confer health benefits (see ‘First convincing evidence linking intake of live microbes with health benefits’, above). ISAPP board member Prof. Maria Marco PhD co-authored a review led by Dr. Paul Cotter PhD in Nature Reviews Gastroenterology and Hepatology on the GI-related health benefits of fermented foods. The paper clearly lays out the potential mechanisms under investigation and identifies gaps to be addressed in the ongoing study of fermented foods.

As calls for reducing carbon footprints continue across the globe, plant-based fermented foods are being singled out as an area for innovation and expansion. One example of how these foods are being explored is through the HealthFerm project, a 4-year, 13.1 million Euro project involving 23 partners from 10 countries, which is focused on understanding how to achieve more sustainable, healthy diets by leveraging fermented foods and technologies.

Novel findings related to lactic acid bacteria

Lactic acid bacteria (LAB) are some of the most frequently-studied microbial groups, but scientists have only begun to uncover the workings of this diverse group of bacteria and how they affect a variety of hosts. These bacteria are used as probiotics and are often beneficial members of human and animal microbiomes, and they are also essential to making fermented foods. This year marked the first ever Gordon Research Conference on LAB in California, USA. Attendees showcased the diversity of research on lactic acid bacteria, and the meeting was energized by the early investigators present and by the interest in LAB in other disciplines including medicine, ecology, synthetic biology, and engineering. One example of a scientific development in this area was the further elucidation of the mechanism of Lactiplantibacillus plantarum’s extracellular electron transfer.

Progress on the benefits and mechanisms of action for probiotics to improve the effectiveness of cancer immunotherapies

Researchers have known for several years that the gut microbiota can be a determinant of the efficacy of cancer immunotherapy drugs that involve immune checkpoint blockade, but interventions that target the gut microbiota to improve response to immunotherapies have been slower to develop. This year saw encouraging progress in this important area, with probiotic benefits and mechanisms of action being demonstrated in several papers. Two of the most highly cited probiotics papers of the year centered on this topic: one showing how a tryptophan metabolite released by Limosilactobacillus reuteri (formerly Lactobacillus reuteri — see this ISAPP infographic) improves immune checkpoint inhibitor efficacy, and another paper that reviewed how gut microbiota regulates immunity in general, and immune therapies in particular.

Updated resource available on probiotics and prebiotics in gastroenterology

This year the World Gastroenterology Organisation (WGO) guidelines on probiotics and prebiotics were updated to reflect the latest evidence, with contributions from ISAPP board member Prof. Hania Szajewska MD PhD and former board member Prof. Francisco Guarner MD PhD. The guideline lists indications for probiotic and prebiotic use, and how the use of these substances may differ in pediatric versus adult populations. Find the guideline here.

Statistical considerations for the design of randomized, controlled trials for probiotics and prebiotics

/in ISAPP Science Blog /by KC

By Prof. Daniel Tancredi, UC Davis, USA

The best evidence for the efficacy of probiotics or prebiotics generally comes from randomized controlled trials. The proper design of such trials should strive to use the available resources to achieve the most informative results for stakeholders, while properly accounting for the consequences of correct and incorrect decisions. It is crucial to understand that even well-designed and -executed studies cannot entirely eliminate uncertainty from statistical inferences. Those inferences could be incorrect, even though they were made rigorously and without any procedural or technical errors. By “incorrect”, I mean that the decisions made may not correspond to the truth about those unknown population parameters. Those parameters involve the distribution of study variables in the entire population, but our inferences are inductive and based on just the fraction of the population that appeared in our sample, creating the possibility for discordance between those parameters and our inferences about them. Although rigorous statistical inference procedures can allow us to control the probabilities of certain kinds of incorrect decisions, they cannot eliminate them.

For example, consider a two-armed randomized controlled trial designed to address a typical null hypothesis, that the probability of successful treatment is the same for the experimental treatment as for the comparator. Depending on the analytical methods to be employed, that null hypothesis could also be phrased as saying that the difference in successful treatment probabilities between the two arms is zero or that the ratio of the successful treatment probabilities between the two groups is one. Suppose the study sponsor has two possible choices regarding the null hypothesis, either to reject it or fail to reject it. (The latter choice is colloquially called “accepting the null hypothesis”, but that is a bit of an overstatement, as the absence of evidence for an effect in a sample typically does not rise to the level of being convincing evidence for the absence of an effect in the population.)

With these two choices about the null hypothesis, there are two major types of “incorrect decisions” that can be made: the null hypothesis could be true for the population but the study data led to a decision to reject the null hypothesis, a result conventionally called a “Type-1” error. Or the null hypothesis could be false for the population but the study data led to a decision not to reject the null hypothesis, conventionally called a “Type-2” error. Conversely, there are also two potentially correct decisions. One could fail to reject the null hypothesis when the null hypothesis is true for the population, a so-called “true negative”, or one could reject the null hypothesis when the null hypothesis is not true, a so-called true positive.

The consequences of these four different decision classifications vary from one stakeholder to another, and thus it is unwise to rely solely and simply on commonly used error probabilities when planning studies. The wiser approach is to set the error probabilities so that they properly account for the relative gains and losses to a stakeholder that arise from correct and incorrect decisions, respectively. From long experience assessing the design of clinical trials for probiotics and prebiotics, I recommend that stakeholders in the design phase of studies give thought to the following three statistical considerations.

Pay attention to power

Power is the probability of avoiding a type-2 error—in other words, under the condition that an assumed true effect exists in a study population and that the type-1 error has been controlled at a given value, power is computed of the probability of avoiding the incorrect decision to fail to reject the null hypothesis. Standard practices are to set the type-1 error at 5% and to determine a sample size that achieves 80% power for an assumed alternative hypothesis, one stating that the true effect is of a specific given magnitude, one corresponding to a so-called meaningful effect size. That effect size is typically called a ‘minimum clinically significant difference’ (MCSD) or something similar, because ideally the assumed effect size would be the smallest of the values that would be clinically important, although as a practical matter — because the higher the magnitude of the effect size, the lower the sample size requirements and thus the better the chance of the study being perceived as “affordable” to study sponsors — the MCSDs used to power studies are often larger than some of the values that would also be clinically significant. Nevertheless, let’s consider what it means for the sponsor to accept that the study should be powered at merely the conventional 80% level. Under the assumptions that the true effect in the population is the MCSD and that the study achieves its target sample size, a sponsor of a study that has only 80% power is taking a 1-in-5 chance that the sample results would not be statistically significant (and that the null hypothesis would fail to be rejected).  Such an incorrect decision could have major adverse implications for the sponsor (and for potential beneficiaries of the intervention), particularly given the investments that have been made in the research program and the implications the incorrect decision could have for misinforming future decisions regarding the specific intervention and indeed related interventions.  A 20% risk may not be worth taking.

All other considerations being equal, the risk of a type-2 error could be lowered by increasing the sample size. Under regular asymptotic assumptions that generally apply, increasing the target sample size by about one-third would cut a 20% type-2 error risk in half, to 10%. Increasing the target sample size by two-thirds reduces it all the way to 5%.

Define the true minimum clinically significant effect size applicable to your study

Another important question is where to set the minimum clinically significant effect. Often that effect is based on prior studies without any adjustment—but this can neglect key considerations. Prior effects of an intervention are typically biased in a direction that overstates the benefits of the intervention, especially if the intervention emerged from smallish early-phase studies. More fundamentally, from the perspective of decision theory the estimated effects seen in prior studies do not specifically address what could truly be the minimum clinically meaningful effect when one considers the possible benefits, risks, and costs of the intervention. Probiotics and prebiotics are typically relatively benign interventions in terms of adverse events, so it could be that even more modest favorable impacts on health than were seen in prior studies are still worthwhile.

Powering your study based on what truly is a minimal clinically meaningful effect may lead to a better overall strategy for optimizing net gains, while giving the intervention an appropriately high chance of showing that it works. Although the smaller the assumed effect size, the larger the required sample size needed to detect it (all other factors being the same), a proper assessment of the relative risks and benefits of the intervention and, also, of correct and incorrect decisions about the intervention, may provide a strong basis for making that investment.

In addition, there is another important but often overlooked aspect when deciding on what is a worthwhile improvement. We frequently turn to clinicians to determine what would be a worthwhile improvement, and it is natural for a clinician to address that question by considering what would be a meaningful improvement for a patient who responds to the intervention. Keep in mind, though, that an intervention could be worthwhile for a population if it achieves what would be a worthwhile improvement for a single patient–say, a mean improvement of 0.2 SD on a quality-of-life scale—in only a fraction of the patients in the overall population, say 50%. There are many conditions for which having an intervention that works for only large subsets of the population could be valuable in improving the population’s overall health and wellness. Using this example, where the worthwhile improvement for an individual is 0.2 SD and the worthwhile responder percentage is 50%, then the worthwhile improvement that should be used to power the study would be 0.1 SD, which is equal to (0.2 SD * 50%) + (0 SD * 50%), with the latter product quantifying an assumed absence of a benefit in the non-responders. What should be gleaned from this example is that the minimum clinically important effect for a population is typically less than the minimum clinically important effect for an individual. The effect used to power the study should be the one that applies to the relevant population. Again, that effect should be chosen so that it balances benefits relative to the costs and harms of the intervention while accounting also for variation in whether and how much individuals in the population may respond. When study planners fail to account for this variation, the result is a study that is underpowered for detecting meaningful population-level effects.

Improving the signal-to-noise ratio

In general, effect sizes can be expressed analogously to a mean difference divided by a standard error, and thus can be thought of as a signal-to-noise ratio. Sample size requirements depend crucially on this signal-to-noise ratio. Typically, standard errors are proportional to outcome standard deviations and inversely proportional to the square root of the sample size. The latter is key because it means that in case an expected signal would be cut in half, the noise would also need to be cut in half to maintain the signal-to-noise ratio, which means that if you cannot alter the outcome standard deviation, then you would need to quadruple the sample size. This also applies in the opposite direction, happily: if you can double the expected signal-to-noise ratio, you would only need one-fourth the sample size to achieve the desired power, all other things being equal.

Signal-to-noise ratios can be optimized by designing a trial for a judiciously restricted target population (of potential responders) and by using high-quality outcome measurements for the trial to reduce noise. Although research programs may eventually aim to culminate in large pragmatic trials that show meaningful improvements associated with an intervention even in populations of individuals with wide variations in their likelihood and amount of potential response, it is generally wise up to that stage in a research program to focus trials so that they give accurate information as to whether the intervention works in populations targeted for being more apt to be responsive to an intervention. To do that, for example, the trial methods should include accurate assessments for whether potential recruits are currently experiencing, say, symptoms from whatever condition the intervention is intended to address and whether the recruit would be able to achieve the desired dose of whatever the trial assigns to them. For a truly beneficial intervention, it is easier to continue a research program advancing the development of that intervention if the intervention sustains a consecutive string of “true positive” results from when it began to undergo trials, avoiding a potentially fatal type-2 error (“false negative”).

Careful attention to the above considerations can lead to better trials, ones that combine rigor and transparency with a tailored consideration of the relative costs and benefits of potentially fallible statistical inferences, so that the resulting evidence is as informative as possible for stakeholder decision-making.

New paper outlines the value of studying probiotics in the small intestine

/in ISAPP Science Blog /by KC

Even though the human digestive tract extends from the mouth down through the small and large intestines, the study of probiotics and their activities has tended to focus on the colon. While the colon (or perhaps more accurately its proxy, the faecal sample) is relatively accessible and easy to study, recently some researchers have argued that crucial information can be gained from looking at another digestive tract site: the small intestine.

A recent paper published in Cell Reports Medicine, titled Small intestine vs. colon ecology and physiology: Why it matters in probiotic administration, laid out the differences between probiotic actions and interactions in the small intestine versus the large intestine. The paper was the result of work by an expert group of the International Life Sciences Institute (ILSI) Europe – the Probiotics Taskforce.

The authors of the paper say the duodenum (the first part of the small intestine) is the most dynamic part of the digestive tract. The small intestine as a whole is the site where most of the body’s digestion and absorption takes place, it is also a site of high immune activity. Even though ingested materials move through this area more rapidly than the large intestine, the small intestine allows closer interaction between host and microbes because it has a lower rate of mucus secretion and looser gut barrier junctions. The microbiota of the small intestine is primarily shaped by the digestion and resulting abundance of simple carbohydrates and amino acids, whereas the colonic microbiota is driven by the metabolism of the remaining complex carbohydrates. These factors and others create very different environments for probiotic interaction and activity.

While the most relevant clinical question for a probiotic strain may be what health benefit it confers in the host, researchers may also be interested in gut microbiota manipulation via probiotics to transform host-microbe interactions at discrete locations in the digestive tract – potentially yielding new or improved benefits for the host. The paper raises the possibility of novel probiotics discovered or developed in the future to specifically target the small intestine.

Accessibility of the small intestine, however, remains a challenge. While animal and in vitro models can lead to valuable insights, the authors of the paper point to the need for more sensitive and cost-effective tools for sampling the small intestine in human study participants.

See this Q&A with the paper’s lead author, Dr. Arthur Ouwehand PhD, Global Health & Nutrition Sciences, International Flavors & Fragrances, Finland.

Why is it important to think about how probiotics interact at sites other than the colon?

Nutrient absorption, entero-hepatic circulation, and energy regulation are all happening in the small intestine and have a major impact on our health. Even some forms of diarrhoea originate from the small intestine. So, we should be better aware what happens in the small intestine and how probiotics may influence these processes.

What clues do we have that the small intestine is an important site for probiotic activity?

The most common argument is that the microbial numbers in the small intestine are much smaller and hence (with less competition) probiotics can better exert an effect there. Is that true? We don’t know yet, because small intestinal samples have been difficult to collect. We need to better understand what is happening in the human small intestine.

Do small intestinal interactions depend on the specific probiotic?

Very likely. Also interesting is how diet would shape the effects of the probiotic in the various parts of the small intestine.

What are some of the main questions researchers still need to address regarding how probiotics act in the small intestine?

  • What is the microbiota in the small intestine and how is it influenced?
  • What do these changes in composition and activity mean?
  • How can the small intestinal microbiota be influenced in a meaningful way?

How do you think researchers will overcome the challenges of gathering information about the small intestine?

Capsules that sample the small intestine are nothing new. They were already developed in the 1960s. Better and more affordable capsules are now coming on the market, so minimally invasive sampling of the human small intestine will soon be much more feasible. These new technologies should expand our understanding of the microbiota in different parts of the small intestine, and how probiotics interact in this environment.

Bridging the Gap Between Probiotic and Microbiome Research

/in ISAPP Science Blog /by KC

By Prof. Sarah Lebeer PhD, University of Antwerp, Belgium

September was an eventful month for me, as I had the privilege of participating in various scientific gatherings. These include co-organizing the 14th Symposium on Lactic Acid Bacteria (LAB14) in the Netherlands (LAB symposium), attending the European Helicobacter and Microbiota Study Group workshop (EHMSG) in my hometown of Antwerp, joining the Human Microbiome Symposium at EMBL Germany, and participating in the 7th International Conference on Microbial Diversity conference in Parma. These events provided me with valuable opportunities to share insights from our Isala vaginal microbiota project (https://isala.be/en) and to engage with leading scientists in the fields of the human microbiome, fermented foods, and probiotics, such as Martin Blaser, Maria Gloria Dominguez-Bello, Curtis Huttenhower, Jeroen Raes, Peer Bork, Rob Knight, Gene Tyson and Paul Cotter, just to name a few.

Reflecting on these recent interactions, I find it intriguing that the term ‘probiotics’ is relatively infrequently used in discussions at typical microbiome conferences or sessions. It has struck me that a descriptive microbiome study in a specific cohort or patient group often garners more scientific recognition than a human intervention study involving probiotics, which target the microbiome to induce a particular change in health parameters. It’s worth noting that many large-scale solid microbiome papers are published in high-impact journals, whereas probiotic studies tend to find their home in journals with lower impact factors. This discrepancy exists even when most associations observed in microbiome studies are primarily descriptive rather than causal. I must admit to this bias in our own work, having recently published a substantial cohort study (the Isala study) on the vaginal microbiome with over 3300 participants in Nature Microbiology, while our probiotic studies typically appear in lower-impact journals (e.g. this study). Although our Isala study yielded valuable insights, it could only associate 10.4% of questionnaire responses with features of the microbiome composition, with associations rather than causal relationships identified. Nevertheless, we plan to explore these findings further through intervention studies (including probiotic, dietary, and lifestyle interventions) and more mechanistic research (https://isala.be/en ). Similarly, the extensive gut microbiome cohort study conducted by Jeroen Raes’ team in Belgium and published in Science could explain only 7.6% of the associations with the extensive metadata collected.

While we do all acknowledge the value and strength of such large microbiome cohort studies, probiotic intervention studies offer a unique advantage in investigating causality. In such studies, live microorganisms (or mixtures thereof) are deliberately administered in specific formulations and evaluated for their health benefits to the host. Probiotics often do not work via (gut) microbiome modulation (as more broadly discussed in this ISAPP podcast episode), but undoubtedly interact in the same complex environment. ISAPP has long championed the importance of rigorous and well-controlled clinical trials to assess the value of interventions, but the results, while scientifically valuable, are seldom sensational. This shouldn’t come as a surprise because modifying the health status of a living host with a single intervention, be it a probiotic or a single drug molecule, is a complex task. If you’ve ever listened to a lecture or read a paper by ISAPP President Dan Merenstein (if not, check this ISAPP podcast episode), you’ll recall his emphasis on the high number-needed-to-treat (NNT) in many traditional drug interventions. If these NNTs are compared for some drugs with probiotics, probiotics actually do not perform badly, and often outperform other interventions in terms of safety.

Probiotics, by their nature, have a multifaceted mode of action, attributed to their status as live microorganisms with an average of 3000 genes and probably even more bioactive molecules expressed. Their effects in a living host are diverse and context-dependent, involving complex modulation of biochemical, immune, and other pathways. While I haven’t conducted the statistical calculations myself, the likelihood of detecting a significant and large-scale effect in probiotic intervention studies does not appear high, especially given that the average probiotic intervention study involves around 74 participants, rarely exceeding 200 participants .

This limitation has contributed to an underwhelming reputation for the science behind probiotics despite the many health benefits demonstrated, as these trials are typically small in scale and constrained by limited budgets and limited number of parameters under investigation. Most of these studies are carried out by university and food company researchers with budgets significantly smaller than those in the pharmaceutical industry, where studies can cost around $40,000 per participant. The microbiome therapeutics and live biotherapeutics (LBPs) field, which includes probiotic products for therapeutic indications and routes, is gradually moving towards more expensive pharmaceutical-style trials, with some FDA-approved trials featuring GMP-produced LBPs. Success stories like REBYOTATM (from Ferring and Rebiotix) and VOWST (formerly SER-109, from Seres) have demonstrated significant benefits in specific conditions (C. difficile infection), which have reduced heterogeneity from the host side. Yet, participant numbers in these trials remain in the same range as many probiotic intervention studies.

Given the available funding from both private and public sources, organizing large clinical trials with specifically designed probiotics as LBPs for all promising health conditions under stringent pharmaceutical conditions is an unrealistic prospect. If probiotic strains can be delivered orally as food supplements, it is likely that current trial practices will continue to be preferred due to budget, logistical, and regulatory considerations, even though they may have limitations in claiming health benefits under less rigorous conditions. These studies, if conducted and analyzed diligently, can still yield valuable and meaningful results.

As scientists actively engaged in both the microbiome and probiotic fields, we should seek greater unity. We must recognize that the science of how live microbes interact with a living host is inherently complex and rarely boils down to a single mode of action resulting in spectacular effects. Although the intended use of probiotics and LBPs differs, both share similar scientific challenges. ISAPP’s definition of probiotics is a valid attempt to embrace this complexity and can apply to most microbial therapeutics or LBPs if the administered microorganisms are well-characterized and quality-controlled.

Let’s acknowledge that, despite their challenges, probiotic trials have already contributed and will likely continue to contribute) unique insights into the intricate world of host-microbe interactions, and these insights can be harnessed to improve human health.

Why responders and non-responders may not be the holy grail for biotics

/in ISAPP Science Blog /by KC

By Prof. Dan Merenstein MD, Georgetown University Medical Center, USA

In September the New York Times published an article titled “What Obesity Drugs and Antidepressants Have in Common“. It was written by a physician who had personally struggled with weight issues and depression. In his personal journey with these health challenges, he hesitates to undergo any treatments. But he eventually does and experiences much relief from them. Why would a practicing physician hesitate to use approved drugs?

The article opens with this viewpoint: “We like to think we understand the drugs we take, especially after rigorous trials have proved their efficacy and safety. But sometimes, we know only that medications work; we just don’t know why.” He goes on to discuss selective serotonin reuptake inhibitors (SSRIs) and  the recently approved weight loss drugs, such as glucagon-like peptide-1 (GLP-1) receptor agonists. The former have been widely used for over 40 years, while the weight loss drugs are more recent. For both classes of drugs, we have some ideas how they work but the exact mechanisms have not been elucidated. While this knowledge gap has not prevented wide usage, the author of the article was skeptical about using the drugs if he did not know exactly how they worked. 

When I started studying probiotics 15 years ago, I began to interact with a different group of scientists than I was used to. My new collaborators were basic and applied scientists, not just clinicians. I had opportunities to attend conferences that covered bench science more than clinical evidence.  My perspective as a clinical researcher was different from most of the others in attendance. I was somewhat surprised to learn how much emphasis those scientists placed on understanding mechanisms. On the one hand, intuitively it makes sense. If you know how something functions, you have a lot more confidence that it will do what you expect it to do, and more assured that it can be used safely. You also have a sense that it should work for you. But on the other hand, knowing an intervention is effective is more important than knowing how it achieves its effectiveness.

This emphasis on understanding mechanisms of action for interventions reminds me of the development of beta-blockers, a class of medicines that block epinephrine, and cause the heart to beat slower and with less force. One of the most common test questions I was asked when I was a medical student and resident is: What class of blood pressure medicines are never permissible for a patient with congestive heart failure (CHF)? Well it was obvious to all of us that the answer was clearly beta-blockers, as you wouldn’t want to slow the heart rate and reduce the force of the heart in a patient already suffering from a poorly performing heart. Yet after clinical trials were completed, beta-blockers were shown to be effective treatment for CHF patients and are now a mainstay of CHF treatment. This was counterintuitive considering the drug’s mechanism of action. So in fact, a drug’s mechanism of action does not always lead in a straightforward way to knowledge about which conditions can be treated or which individuals will respond.

Beyond mechanisms of action and individual response

In clinical medicine, we use two important statistics to capture efficacy and safety of an intervention: number needed to treat (NNT) and number needed to harm (NNH). NNT is the number of patients that need to be treated in order to have an impact on one person, while the NNH is the number of patients who must be treated with an intervention before one patient is harmed.  All interventions have both an NNT and NNH. Obviously, the goal is  a very low NNT and a high NNH. But we are rarely so fortunate. Take for example statins, a medicine many of us take. In patients at low risk of cardiovascular disease, the NNT is 217, which means 1 person out of 217 avoided a nonfatal heart attack by taking statins. Meanwhile, NNH for muscle pain is 21 and for developing diabetes is 204.

NNT and NNH are rarely considered in the biotics field. Yet I commonly encounter discussions about the importance of identifying responders versus non responders to biotic intervention and the need to elucidate the mechanism(s) of action for biotic substances. I believe this is because many of the scientists doing research in biotics come not from a clinical background but more bench research, where the questions really are those of mechanism. Many seem to believe that such knowledge is the Holy Grail of biotics – if only scientists could have such a good grasp of mechanism that they could figure out why certain people responded while others do not. There is nothing inherently wrong with wanting to identify reasons for differences in individual response. It is what we do in clinical practice every day. When I give someone blood pressure medicine and they don’t respond to it, I wonder – Is it a compliance issue? Is the patient’s blood pressure caused by something that the medicine does not impact? Is the patient taking the medication at the wrong time, with the wrong diet, or with other interfering medicines?  Clinicians always must think about who is responding and who is not responding. However, NNT and NNH for biotics are worth prioritizing.

Data have shown that certain probiotics can get people better from an upper respiratory tract infection 26 hours earlier, or can treat infantile colic, or improve irritable bowel syndrome symptoms with a NNT respectively of 20, 15 and 100, while having a very high NNH. These are great products. But instead what I often hear at conferences is that we need to figure out why some people respond to the probiotics and others do not. I agree, go ahead and figure it out. But have realistic expectations. If two of the most widely used medicines, SSRIs and GLP-1 agonists, have an unclear mechanism, and if statins have an NNT of 217, be realistic about the impact of your probiotic. When a doc prescribes you Lipitor, he doesn’t say, “Good luck –  I hope you are the 0.4% in which it helps and aren’t the 5% that gets muscle cramps.” The hope is that for you, the NNT is 1. And when your strain or product does have an impact, feel free to find ways to improve efficacy but celebrate the impact it has. If possible, maybe compare your NNTs to standard of care, or if no comparison look at your NNT versus NNH to really better understand what your biotic can do.

Probiotic Administration in Preterm Infants: Scientific Statement

/in ISAPP Science Blog /by KC

Board of Directors, International Scientific Association for Probiotics and Prebiotics

in collaboration with

Dr. Geoffrey Preidis MD PhD, Pediatric Gastroenterology, Hepatology & Nutrition

Prof. Andi L Shane MD MPH MSc, Pediatric Infectious Diseases

A recent report of a fatality in an extremely premature infant recipient of a probiotic product has resulted in a warning letter from the United States Food & Drug Administration (FDA) to healthcare practitioners about probiotic supplementation in preterm infants and a warning letter to the probiotic product manufacturer.

Publicly available information suggests that this fatality was the direct consequence of bacteremia resulting from ingestion of the probiotic organism Bifidobacterium longum subsp. infantis delivered in medium chain triglyceride oil. This situation differs from case reports of adverse events that resulted from extrinsic probiotic product contamination (1, 2). This is an important distinction, as the potential risks and mitigation strategies differ between etiologies. As complete details of this most recent fatality have not been released, specific factors that may have contributed to the adverse outcome are unknown. However, it is worth considering the context of this case report within the broader literature available on probiotic use in this population, including the wealth of data available on sepsis incidence.

Evidence from systematic reviews

Premature infants, especially those of <32 weeks gestation and with a birth weight <1500 g, are a vulnerable population at significant risk of morbidity and mortality.  Necrotizing enterocolitis (NEC) is highly prevalent (5-10% incidence) among very preterm infants, with mortality rates of 20-30% and high morbidity among survivors, including short gut syndrome, parenteral nutrition-associated liver disease, and neurocognitive delay.

A large body of literature exists on the use of probiotics in hospitalized preterm infants, with particular focus on the prevention of NEC. At least 85 randomised clinical trials (RCTs) (3) have been conducted to evaluate the use of probiotics in preterm infants for the prevention of diseases associated with prematurity, and a number of systematic reviews with meta-analyses have analysed these data in recent years. Most RCTs conducted in the neonatal intensive care unit (NICU) designate sepsis as one of the main outcome measures.

The most recent meta-analysis was published online October 2 in JAMA Pediatrics (3). This study included 106 trials on probiotic, prebiotic, synbiotic and lactoferrin interventions for either preterm infants <37 weeks and/or those with low birth weight (<2500 g). Administration of probiotics containing multiple strains were found to be most effective in the reduction of all-cause mortality (31% reduction), with a 62% decrease in incidence of severe NEC compared to placebo (moderate and high certainty evidence). Single strain probiotics combined with lactoferrin provided greatest efficacy in the reduction of late-onset sepsis incidence (67% risk reduction with moderate certainty evidence). It was noted that none of the included studies reported cases of probiotic-induced sepsis.

Other authors including groups from the Cochrane Collaboration, American Gastroenterological Association (AGA) and the European Society for Paediatric Gastroenterology Hepatology and Nutrition (ESPGHAN) have found similar results, and studies can be reviewed here:

Probiotics to prevent necrotising enterocolitis in very preterm or very low birth weight infants – Sharif, S – 2023 | Cochrane Library

Probiotics Reduce Mortality and Morbidity in Preterm, Low-Birth-Weight Infants: A Systematic Review and Network Meta-analysis of Randomized Trials – Gastroenterology (gastrojournal.org)

Probiotics for Preterm Infants: A Strain-Specific Systematic… : Journal of Pediatric Gastroenterology and Nutrition (lww.com)

No meta-analysis has attributed increased risk of sepsis to probiotic use in preterm infants – rather, in many cases a protective effect (or a trend toward protection) was reported. However, it is important to acknowledge the real but rare risk of probiotic-induced bacteremia in this population. In a recent review of case reports of probiotic-associated invasive infections in children, probiotic-induced bacteremia in premature infants were found to have resolved in most cases with use of effective antimicrobial therapy (4).

With data collected on over 10,000 preterm infants, substantial benefits demonstrated and a low level of risk identified, promise to improve outcomes in preterm infants who receive a probiotic product currently exists. Based on the evidence currently available, hospitals and NICUs across the globe have already adopted practices relating to probiotic use in preterm infants, some with significant health impacts (5, 6).

Risk benefit analysis and considerations for healthcare implementation

Further work needs to be done to support probiotic administration in the NICU. Collaborative efforts include recommendations for practical steps to improve probiotic product quality assurance specifically for NICU use, published in July 2023 in JAMA Pediatrics (7).

It is important to note that few (or possibly no) effective interventions are without an adverse event profile, and probiotics are no exception. Even food has a safety standard of reasonable certainty and on a regular basis, individuals suffer fatal foodborne infections. When considering the clinical indications for any intervention for an individual patient or a population of individuals, a thorough comparison of all available data on both the potential risks and the potential benefits is warranted.

The American Gastroenterological Association (8) and other major societies (including ESPGHAN and the World Gastroenterology Organisation) (9, 10) endorse probiotic products for the prevention of NEC among preterm low birth weight infants. The societies’ guidelines agree that the recommendation to use probiotics is conditional. Conditional recommendations are sensitive to patients’ values and preferences, and to the guideline panel’s perception of risk-benefit balance.  However, the recent FDA letter does not acknowledge these recommendations and further, recommends against probiotic use in preterm infants despite the robust efficacy data. With interventions such as probiotic administration, ideally shared clinical decision-making with patient and clinician would ensue. Regulatory warnings inform the risk-benefit calculation but typically do not invalidate a clinical recommendation.

Summary

  • Probiotic administration to preterm infants has been demonstrated to significantly reduce the risk of NEC, sepsis and death in large systematic reviews with meta-analyses.
  • Meta-analyses have not identified significant adverse events or safety concerns, although rare case reports have documented sepsis attributed to probiotics.
  • Stringent manufacturing standards are recommended for probiotics in vulnerable populations such as preterm infants.
  • Standardized comprehensive safety reporting across probiotic intervention studies is needed, along with funding for the conduct of long term studies.
  • The risks and benefits of probiotic administration should be considered in both the specific population and individual patients, with regulatory frameworks to enable implementation.
  • More information about this fatality should be immediately released so healthcare professionals and researchers can learn from this experience and continue to provide optimal evidence-based patient care.

To inquire about expert academic physicians available for media comment, please contact ISAPP’s Executive Director, Marla Cunningham, at marla@nullisappscience.org

See also:

NEC Society: Statement on FDA Warning of Probiotics in Preterm Infants

References

(1) Vallabhaneni S, Walker TA, Lockhart SR, et al. Notes from the field: Fatal gastrointestinal mucormycosis in a premature infant associated with a contaminated dietary supplement–Connecticut, 2014. MMWR Morb Mortal Wkly Rep. 2015;64(6):155-156.

(2) Bizzarro MJ, Peaper DR, Morotti RA, Paci G, Rychalsky M, Boyce JM. Gastrointestinal Zygomycosis in a Preterm Neonate Associated With Contaminated Probiotics. Pediatr Infect Dis J. 2021;40(4):365-367.

(3) Wang Y, Florez ID, Morgan RL, et al. Probiotics, Prebiotics, Lactoferrin, and Combination Products for Prevention of Mortality and Morbidity in Preterm Infants: A Systematic Review and Network Meta-Analysis. JAMA Pediatr. 2023 Oct 2:e233849.

(4) D’Agostin M, Squillaci D, Lazzerini M, et al. Invasive Infections Associated with the Use of Probiotics in Children: A Systematic Review. Children (Basel). 2021 Oct 16;8(10):924.

(5)  Rath CP, Athalye-Jape G, Nathan E, et al. Benefits of routine probiotic supplementation in preterm infants. Acta Paediatr. 2023 Jul 28.

(6) Bui A, Johnson E, Epshteyn M, Schumann C, Schwendeman C. Utilization of a High Potency Probiotic Product for Prevention of Necrotizing Enterocolitis in Preterm Infants at a Level IV NICU. The Journal of Pediatric Pharmacology and Therapeutics 2023;28(5):473–475.

(7)  Shane AL, Preidis GA. Probiotics in the Neonatal Intensive Care Unit-A Framework for Optimizing Product Standards. JAMA Pediatr. 2023 Sep 1;177(9):879-880.

(8) Su GL, Ko CW, Bercik P, et al. AGA Clinical Practice Guidelines on the Role of Probiotics in the Management of Gastrointestinal Disorders. Gastroenterology. 2020 Aug;159(2):697-705.

(9) WGO Practice Guideline: Probiotics and Prebiotics. Available from: https://www.worldgastroenterology.org/guidelines/probiotics-and-prebiotics

(10) van den Akker CHP, van Goudoever JB, Shamir R, et al. Probiotics and Preterm Infants: A Position Paper by the European Society for Paediatric Gastroenterology Hepatology and Nutrition Committee on Nutrition and the European Society for Paediatric Gastroenterology Hepatology and Nutrition Working Group for Probiotics and Prebiotics. J Pediatr Gastroenterol Nutr. 2020 May;70(5):664-680.

Microbiota from a surprising source—baby kangaroos—might decrease cattle methane production

/in ISAPP Science Blog /by KC

By Prof. Seppo Salminen, University of Turku, Finland

One of the major contributors to greenhouse gas production is the final stage of anaerobic fermentation in the rumen (pre-stomach compartment) of cattle, which produces methane. The process is the top agricultural source of greenhouse gases worldwide. In addition, the formation of methane is associated with approximately 10% energy loss in animals.

To ameliorate the drawbacks of methanogenesis, scientists at Washington State University explored the potential of homoacetogenic microbes (i.e. those that promote the production of acetate),  and especially Acetobacterium woodii, to outcompete methanogens and thereby reduce methane production in the rumen of production animals.

For this purpose, original inoculum of rumen samples were obtained from freshly slaughtered cows and developed into stable consortia of methanogens. Meanwhile, homoacetogenic cultures were developed from baby kangaroo droppings obtained from a wallaby ranch in Washington State. The original baby kangaroo sample had no methanogens present. Rumen bioreactors were inoculated with the bovine study samples and kangaroo gut microbes, and monitored for methane production and kinetics.

The investigators reported that acetogens are dominant in kangaroos, and in their presence methanogens are generally inhibited. The researchers suggested that kangaroos have interesting novel acetogens that utilize hydrogen, which rumen fermentation produces. These acetogens are potential probiotics, once they are well characterized and the benefits to rumen fermentation are documented.

This study also suggests that a variety of kangaroo acetogens should be further explored for their potential use in controlling rumen fermentation and reduction of greenhouse gas production. At the same time, additional benefits of acetogens from other marsupials could be explored and new findings are possible for potential biotic (pro-, pre-, syn- and postbiotic) development.

 

 

 

 

 

Clarifying the role of metabolites in the postbiotic definition

/in ISAPP Science Blog /by KC

By Dr. Gabriel Vinderola PhD, Instituto de Lactología Industrial (CONICET-UNL), Faculty of Chemical Engineering, National University of Litoral, Santa Fe, Argentina and and Prof. Colin Hill PhD, School of Microbiology and APC Microbiome Ireland, University College Cork, Cork, Ireland

ISAPP published a definition for the term postbiotics in 2021 that states that “a postbiotic is a preparation of inanimate microorganisms and/or their components that confers a health benefit on the host” (Salminen et al., 2021). This 19-word definition had to distill the content of the accompanying article that ran to over 9,000 words (not including references) and so obviously a lot of nuance was lost. A reading of the full paper should dispel any misconceptions, but we thought it might be timely to discuss what is perhaps the most common misunderstanding.

Some of the previous definitions included metabolites (purified or semi-purified) under the postbiotic concept. We did not agree with this interpretation. For us, the term postbiotics refers to preparations that consist largely of intact microbial cells, or preparations that retain some or all of the microbial biomass contained in microbial cells. This latter concept was captured in the phrase “and/or their components” The first column of page 3 of Salminen et al., 2021 elaborates on this; “The word ‘components’ was included because intact microorganisms might not be required for health effects, and any effects might be mediated by microbial cell components, including pili, cell wall components or other structures. The presence of microbial metabolites or end products of growth on the specified matrix produced during growth and/or fermentation is also anticipated in some postbiotic preparations, although the definition would not include substantially purified metabolites in the absence of cellular biomass. Such purified molecules should instead be named using existing, clear chemical nomenclature, for example, butyric acid or lactic acid”. So, taken in context, the scope of the ISAPP definition covers inanimate, dead, non-viable microbes; either as intact whole dead cells or in the form of “their components”. We do not consider microbial metabolites to be postbiotics. Such an interpretation would, for example, make butyrate or other end-products of fermentation postbiotics (once shown to have a health benefit). The ISAPP definition does not exclude the likelihood that microbial metabolites will be present in a postbiotic preparation, but it does require that dead microbes or microbial cell fragments or structures should be present to qualify as a postbiotic.

Why did the ISAPP definition exclude purified or semi-purified metabolites in the absence of cellular components? We fully accept that metabolites or other microbe-generated functional ingredients such as lactate, butyrate, bacteriocins, defensins, neurotransmitters, and similar compounds can be present in a postbiotic preparation. But as you can see from this list, these compounds already have names that are clearly understood. The ISAPP definition of postbiotics focuses on the beneficial role of inanimate microbes and/or their components, a category that did not have a clear definition. Postbiotics are simply one category of substances that provide microbe-associated health benefits. In terms of semantics, dictionaries define the prefix ‘post’ as meaning ‘after’ and the word ‘biotic’ as meaning ‘living things’, and so a postbiotic in that context is something that was living and is now after-life, or inanimate. Metabolites are derived from living things, but never had an independent ‘life’ of their own. As a thought experiment, let us imagine a microbe that has been shown to have a health benefit and therefore qualifies as a probiotic. If the same microbe is inactivated and continues to show a health benefit, this new formulation is no longer a probiotic and qualifies as a postbiotic. If this postbiotic preparation can be further purified and it is shown that a metabolite or metabolites in the absence of cells or their components can provide the same health benefit it ceases to be a postbiotic and becomes a health-promoting metabolite. We could imagine microbially-produced vitamins as an example.

Ideally, definitions should be clear without supplemental explanation. But short, simply worded definitions that describe complex concepts must be read in a context. There is a background, they have a scope, there are things that are covered by that definition and things that are not, and of course definitions have their limitations. It would be hard, if not impossible, to include the scope, the background, the coverage and the limitations in a 19-word definition. For instance, the 15-word probiotic definition is “live microorganisms that, when administered in adequate amounts, confer a health benefit on the host” (Hill et al, 2014). This does not include the idea that probiotics are strain-dependent, a fact that is widely accepted by the field. Other criteria for probiotics not stated in the definition include the fact that that they may be of any regulatory category, that their health benefits must be demonstrated in well-controlled trials in the target host, and that they must be safe (Binda et al. 2020).

In closing, we believe that the postbiotic concept can be an incredibly important scientific, regulatory and commercial concept. That is why we spent the time and effort to arrive at what we hope is a workable definition. We accept that the definition is not perfect but we do think it is useful, and we urge those interested in the future of this important field to read the accompanying paper carefully and to place the definition in its proper context.

See ISAPP’s Postbiotics infographic here.