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.
Understanding the gut microbiome in dogs and other pets, with Prof. Jan Suchodolski DACVM PhD
/in Podcast, Season Three /by LauraPodcast: Play in new window | Download
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This episode features Prof. Jan Suchodolski DACVM PhD from Texas A&M University, discussing the gut microbiome in dogs and other companion animals as part of our series on the role of biotics in animal health. Prof. Suchodolski’s lab focuses on understanding gastrointestinal (GI) diseases in pets and developing diagnostic tests for research and clinical practice. His lab works on building a model of what’s happening with animal health, combining microbiome measures with measures of host health. For example, they found that severe gut microbiome dysbiosis in dogs reflected a greater extent of mucosal damage, contributing to the big picture of GI disease. Certain microbiome features when combined with metabolites are promising biomarkers of GI disease in pets. Test reproducibility is highly important, and treatment tends to be multi-modal. Prof. Suchodolski cautions against direct-to-consumer pet microbiome tests, noting that unvalidated assays are very common.
Episode abbreviations and links:
Additional resources:
ISAPP infographic: Prebiotics and probiotics for pets
ISAPP blog post: Are prebiotics good for dogs and cats? An animal gut health expert explains
ISAPP blog post: Using probiotics to support digestive health for dogs
About Prof. Jan Suchodolski DACVM PhD:
Jan S. Suchodolski is a professor, Purina PetCare Endowed Chair for Microbiome Research, associate director and head of microbiome sciences at the Gastrointestinal Laboratory at Texas A&M University. He received his DrVetMed from the University Vienna, Austria and his PhD in veterinary microbiology from Texas A&M University. He is board certified in immunology by the American College of Veterinary Microbiologists (ACVM). His research is focused on developing biomarkers for gastrointestinal disease and therapeutic approaches for the modulation of the intestinal microbiota. He has authored or co-authored more than 400 peer-reviewed articles in the area of veterinary gastroenterology and microbiome research. In 2024, he received the AVMA career achievement in canine research award.
Prebiotics: Does Delivery Format Matter?
/in ISAPP Science Blog /by KCBy 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.
Biotics for agricultural animals, with Prof. Steve Ricke PhD
/in Podcast, Season Three /by LauraPodcast: Play in new window | Download
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This episode, part of a series on the role of biotics in animal health, is a broad-ranging conversation on biotics for agricultural animals, with Prof. Steve Ricke PhD from University of Wisconsin-Madison. Prof. Ricke explains some of the different applications of biotics for poultry as well as swine and ruminants: rapid growth, efficient use of feed, and reducing inflammation. Biotics may also have a role in food safety as it relates to agricultural animals, with research showing how microbiome diversity shapes the impact of pathogens. Animal genetics, diet, and microbiome interactions are extremely complex and fortunately the tools to study these interactions have improved in the past several decades. Prof. Ricke urges scientists to take into account the microbial ecology surrounding the animal – and not to forget the potential impact of the animal on its environment.
Episode abbreviations and links:
Additional resources:
ISAPP podcast with Prof. George Fahey PhD, a mentor of Prof. Ricke: Prebiotics for animal health
About Prof. Steve Ricke PhD:
Prof. Steven C. Ricke received his B.S. and M.S. from the Univ. of Illinois, Champaign-Urbana, IL. and Ph.D. from the Univ. of Wisconsin, Madison, WI. Prof. Ricke was a USDA-ARS postdoctorate in the Microbiology Department at North Carolina State Univ. then joined Texas A&M Univ. as a professor in the Poultry Science Dept. In 2005, he became the first holder of the new Donald “Buddy” Wray Endowed Chair in Food Safety and Director of the Center for Food Safety at the University of Arkansas (UA) and was a faculty member of the Dept. of Food Science and Cellular/ Molecular Graduate program. In 2020 he became the Director of the Meat Science and Animal Biologics Discovery Program in the Animal and Dairy Sciences Dept. at the University of Wisconsin-Madison. Prof. Ricke’s lab conducts studies on the growth, survival, and pathogenesis of pathogens in the poultry gut and their interactions with gut microbiota.
Postbiotics: A global perspective on regulatory progress
/in ISAPP Science Blog /by KCBy 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.
Welcoming ISAPP’s newest board member, Dr. Geoffrey Preidis MD PhD
/in News /by KCAt the 2024 annual scientific meeting in Cork, Ireland, the ISAPP board welcomed its newest member, Dr. Geoffrey Preidis MD PhD of Baylor College of Medicine and Texas Children’s Hospital.
ISAPP President Prof. Maria Marco PhD says, “We are thrilled to have Dr Preidis on our board. He is a great colleague and brings scientific excellence along with the extensive clinical experience needed to translate scientific advancements to patient populations and stakeholder groups.”
Dr. Preidis holds degrees from Harvard University and Baylor College of Medicine (BCM), and is a board-certified Pediatric Gastroenterologist and Associate Professor of Pediatrics at BCM. His research focuses on intestinal microbiome development in extremely premature infants and how probiotics may reduce the risk of necrotizing enterocolitis, sepsis, feeding intolerance, growth failure, and death.
Dr. Preidis says, “I’m excited for this opportunity to work with the distinguished experts on the ISAPP board to help advance the science of biotics and ultimately improve clinical care for children with gastrointestinal disorders.”
ISAPP Board Welcomes New President, Prof. Maria Marco PhD
/in News /by KCAt the ISAPP 2024 annual meeting in July, the ISAPP board of directors ushered in the beginning of the next leadership term, with the role of President being taken on by Prof. Maria Marco PhD from UC Davis (USA). Prof. Marco had served the previous three years as Vice President while Prof. Dan Merenstein MD served as President.
“Maria is a born leader, who has continued to push the board and me to think about what we want from ISAPP,” says Prof. Merenstein. “I’m excited to see where she helps take us in the next three years.”
Prof. Marco leads a lab at UC Davis that focuses on the role of microorganisms, and particularly lactic acid bacteria, in food microbiomes and gut health. The lab’s objectives are to investigate how probiotics alter intestinal function and to improve diets with foods that rely on microorganisms either during production (such as fermented foods) or within the digestive tract (such as dietary fibers). Meanwhile, Prof. Marco is also involved in many outreach activities to spread awareness about fermented foods and health. See one of her recent interviews about fermented foods here.
Prof. Marco has more than 120 publications to her name, and has mentored over 100 students, postdocs, and visiting scientists in her lab. In addition to being President of the ISAPP board of directors, she serves on numerous advisory and editorial boards.
The entire ISAPP board of directors welcomes Prof. Marco into the President role with full confidence that her leadership will help advance the fields of biotics and fermented foods.
Prof. Marco says, “I am so honored for this opportunity to lead the ISAPP board of directors. I have regarded ISAPP as the leading voice in probiotics and prebiotics research since starting in this field over 20 years ago. With our outstanding board and leadership team, we have tremendous momentum to continue to build ISAPP for advancing biotic science.”
I come to praise ISAPP, not to bury it: Reflections on 15 years as a board member
/in ISAPP Science Blog /by KCBy 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
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
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.
Expert Panel at ISAPP Annual Meeting Addresses Probiotic Use for Premature Infants
/in ISAPP Science Blog /by KCBy 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
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
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.
Episode 38: Microbes that break down mucus and milk to benefit the host, with Dr. Clara Belzer PhD
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We discuss microbes, mucus, and milk with Dr. Clara Belzer PhD from Wageningen University in the Netherlands in this episode. Dr. Belzer, a molecular geneticist, specializes in studying the microorganisms that are equipped to break down the glycans in mucus and human milk within the host environment.
Key topics from this episode:
Episode abbreviations and links:
About Dr. Clara Belzer PhD:
Dr. Clara Belzer is Associate Professor Microbiology at the Laboratory of Microbiology of Wageningen University. The Belzer group is called ‘Microbes Mucus and Milk’ and the research is focused on the interaction of the gut microbiome with host mucus and milk. After obtaining her PhD at the Erasmus Medical Center Dr. Belzer did a postdoc at Harvard medical school. By now Dr. Belzer has years of experience on gut microbiome studies on anaerobes, including synthetic communities and different biotic concepts, with a special interest for the Akkermansia muciniphila. The group of Dr. Belzer works on several microbiome HMO and mucus related topics funded by national and international grants, some also in collaboration with medical centers and industry.
Should everyone take a probiotic? Assessment of evidence of probiotics for healthy people
/in ISAPP Science Blog /by KCBy 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:
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:
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 KCBy 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.
Episode 37: Targeting the gut microbiome in inflammatory bowel disease, with Prof. Harry Sokol MD PhD
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The ISAPP hosts discuss the microbiome in inflammatory bowel disease (IBD) with leading expert Prof. Harry Sokol MD PhD, who is Professor of Gastroenterology at Saint Antoine Hospital and has positions with Sorbonne University and the Micalis Institute, INRAE in Paris, France. Sokol talks about the specific gut bacteria that seem to be important in IBD, as well as the challenge of targeting the gut microbiome for therapeutic effects.
Key topics from this episode:
Episode abbreviations and links:
Additional resources:
About Prof. Harry Sokol MD PhD:
Harry Sokol is Professor in the Gastroenterology department of Saint-Antoine Hospital (APHP, Sorbonne Université, Paris, France). the co-director of the Microbiota, Gut & Inflammation team (INSERM CRSA UMRS 938, Sorbonne Université, Paris), group leader in Micalis institute (INRAE) and coordinator of the “Paris Center for Microbiome Medicine” (www.fhu-pacemm.fr/). He is an internationally recognized expert in the inflammatory bowel disease (IBD) and gut microbiota fields, in which he has published more than 330 papers in major journals. He is the current president of the French group of Fecal Microbiota Transplantation, and the head of the APHP Fecal Microbiota Transplantation Center. His work on the role of gut microbiota in IBD pathogenesis led to landmark papers, including the identification of the pivotal role of the commensal bacteria Faecalibacterium prausnitzii in gut homeostasis and IBD. Currently, his work focuses on deciphering gut microbiota–host interactions in health and disease to better understand their role in pathogenesis and develop innovative treatments. Harry received two grants from the European Research Council (ERC) in 2016 and 2022, and he is a member of the International Organization for the Study of IBD (IOIBD). Since 2020, he is recognized as a Highly Cited Researcher (Clarivate, Web of Science). Harry Sokol is currently Associate Editor for Gastroenterology. Harry Sokol co-founded Exeliom biosciences (https://www.exeliombio.com/).
Find Harry on X/Twitter: @h_sokol
Can prebiotics benefit brain health in older adults? ISAPP experts weigh in on a recent study
/in ISAPP Science Blog /by KCWith 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?
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.
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.
Episode 36: Uncovering the mechanisms of sorbitol intolerance, with Dr. Jee-Yon Lee MD PhD
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This episode features Jee-Yon Lee MD PhD, assistant project scientist at the University of California Davis, USA, speaking about a recent paper on the mechanisms of sorbitol intolerance and the contributions of the gut microbiota. Dr. Lee explains how gut microbes in the large intestine can drive sorbitol intolerance, and how their research group designed a probiotic intervention to ameliorate it in a mouse model.
Key topics from this episode:
Episode abbreviations and links:
About Dr. Jee-Yon Lee MD PhD:
Jee-Yon Lee is an Assistant Project Scientist in Dr. Andreas Baumler’s lab at UC Davis, focusing on studying host-microbial interactions and their impact on human health and non-communicable diseases. She earned her MD and PhD from Yonsei University College of Medicine and served as a family medicine physician in South Korea until 2017. She joined Dr. Andreas Baumler’s lab in 2017 as a visiting scholar and completed her postdoctoral research there. Dr. Lee’s long-term research goal is to elucidate the ecological causes of dysbiosis, its consequences on the development of human diseases, and to find potential therapeutics targeting the microbiome.
Should bacteriophages be considered as a member of the biotic family?
/in ISAPP Science Blog /by KCBy 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’.
Episode 35: Investigating gut microbiome links to chronic diseases, with Dr. Purna Kashyap MBBS
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In this episode, the ISAPP hosts discuss the gut microbiome’s role in chronic diseases with Dr. Purna Kashyap MBBS, from Mayo Clinic in Rochester, Minnesota, USA. Dr. Kashyap talks about how to discover the complex factors that trigger and perpetuate chronic diseases such as inflammatory bowel disease, zeroing in on the gut microbiome as a contributor to different aspects of gastrointestinal (GI) tract physiology.
Key topics from this episode:
Episode abbreviations and links:
Additional resources:
Why researchers need to understand more about the small intestinal microbiome. ISAPP blog.
About Dr. Purna Kashyap:
Dr. Purna Kashyap is practicing gastroenterologist and Professor of Medicine and Physiology, the Bernard and Edith Waterman Director of the Microbiome program, and Director of the germ-free mouse facility in the Center for Individualized Medicine at Mayo Clinic, Rochester, MN. The NIH funded Gut Microbiome laboratory led by Dr. Kashyap is focused on delineating the complex interactions between diet, gut microbiome, and host gastrointestinal physiology. The laboratory uses germ-free mouse models in conjunction with measures of gastrointestinal physiology in vitro and in vivo to investigate effects of gut microbial products on host gastrointestinal function. In parallel, they use a systems approach incorporating multi-omics, patient metadata, and physiologic tissue responses in human studies, to aid in discovery of novel microbial drivers of disease. The overall goal of the program is to develop novel microbiota-targeted therapies. Dr. Kashyap has published nearly 100 peer reviewed articles including journals like Cell, Cell Host Microbe, Science Translational Medicine, Nature Communications, and Gastroenterology. He was inducted to American Society of Clinical Investigation in 2021. He has previously served on the scientific advisory board of American Gastroenterology Association Gut Microbiome Center, and on the council of American Neurogastroenterology and Motility Society. He now serves on the council and the research committee of AGA, in an editorial role for Gut Microbes and as an ad hoc reviewer on NIH study sections.
The gut-brain axis in livestock animals: Is there a place for biotics in changing pig behavior?
/in ISAPP Science Blog /by KCBy 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.
A guide to the new FDA Qualified Health Claim for yogurt
/in ISAPP Science Blog /by KCFermented 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:
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.
Episode 34: New evidence on the virome in gut-brain communication and stress, with Nathaniel Ritz and Thomaz Bastiaanssen
/in Podcast, Season Three /by LauraPodcast: Play in new window | Download
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In this episode, the ISAPP hosts discuss a new study on how the gut virome affects the host during stress, with Nathaniel (Nate) Ritz from the Institute for Systems Biology in Seattle, USA and Thomaz Bastiaanssen from APC Microbiome Ireland. The guests give an overview of the microbiota-gut-brain axis, then delve into a new study they led on the virome and its effects on stress responses in mice.
Key topics from this episode:
Episode links:
About Nathaniel Ritz:
Dr. Nathaniel Ritz completed his PhD in Prof. John Cryan’s lab at APC Microbiome Ireland where he studied the role of the bacteriome and the virome in social and stress-related disorders. His interests lie in elucidating microbiota-host interactions and establishing microbiota causality within the microbiota-gut-brain axis. Nathaniel has recently moved to Seattle, Washington, USA, to join the lab of Dr. Sid Venkatesh as a postdoctoral fellow at the Institute for Systems Biology to further unravel the mechanisms underpinning microbe-host interaction. Outside of the lab, Nathaniel is an avid rock climber, dog walker, and partner to fellow scientist Dr. Minke Nota. More details and current position can be found at https://venkatesh.isbscience.org/
About Thomaz Bastiaanssen:
Episode 33: From probiotic mechanisms to applications, with Prof. Graciela Lorca PhD
/in Podcast, Season Three /by LauraPodcast: Play in new window | Download
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This episode, we discuss how to advance from probiotic mechanisms to human applications, with Prof. Graciela Lorca PhD at the University of Florida in Gainesville, USA. Prof. Lorca talks about her experiences seeking out the mechanisms of action of a probiotic – including which molecules from bacteria may have beneficial effects – and bringing a probiotic through drug trials for use in Type 1 diabetes. They also discuss probiotic responders versus nonresponders and how dietary intake may provide clues about who will respond to an intervention.
Key topics from this episode:
Episode links:
Additional resources:
About Prof. Graciela Lorca PhD:
Dr. Graciela Lorca is currently a Professor in the Department of Microbiology and Cell Science at the University of Florida. She completed her Licentiate in Genetics studies at the National University of Misiones and later received her doctoral degree in Food Technology at the National University of Tucuman in Argentina. She completed her postdoctoral studies at the University of California San Diego in Molecular Microbiology and at the University of Toronto in Structural Biology and Gene Regulation. Since joining the Department of Microbiology and Cell Science at the University of Florida in 2007, Dr. Lorca has focused on the identification of environmental signals that modulate host-microbe interactions. Using multiomic approaches, her laboratory is investigating the bacterial components such as extracellular vesicles that target host pathways involved on those beneficial interactions in vitro and in vivo. Furthermore, Dr. Lorca’s laboratory is currently conducting human trials to evaluate the use of Lactobacillus johnsonii Type 1 Diabetes patients. Dr. Lorca currently teaches a graduate and undergraduate level Probiotics course. She is also in charge of the new concentration on Microbiome in health and disease within the Online Master program at Department of Microbiology and Cell Science.
Fermented Food Microbiology Researcher in Mohali, India Receives 2024 Gregor Reid Award for Outstanding Scholars in Developing Nations
/in News /by KCISAPP’s board of directors is happy to announce the 2024 winner of the Gregor Reid Award for Outstanding Scholars in Developing Nations: Dr. Rounak Chourasia PhD, a research associate at the National Agri-food Biotechnology Institute in Mohali, Punjab (India).
Dr. Chourasia’s work focuses on discovering microorganisms with specific properties that contribute to the enhanced health benefits of a traditional cheese called chhurpi from Sikkim Himalaya (a state in Northeast India). He has developed a process for the production of milk cheese using selected strains of lactic acid bacteria, resulting in the release of novel bioactive peptides with potential nutraceutical applications. Furthermore, he has applied selected microbial strains to develop bioactive peptide-enriched novel soybean cheese suitable for those with lactose intolerance. The research has not only contributed to knowledge about the functional properties of chhurpi, but has also provided a foundation for helping local farmers expand their entrepreneurial opportunities.
Dr. Chourasia received both a Bachelor and Master of Science in microbiology from the University of North Bengal, India, followed by a PhD in biotechnology in 2023 from the Institute of Bioresources and Sustainable Development (DBT-IBSD), regional centre, Sikkim, and Kalinga Institute of Industrial Technology (KIIT) University under the guidance of Dr. Amit Kumar Rai and Prof. Dinabandhu Sahoo.
The 2024 committee selected Dr. Chourasia from among the many qualified candidates for the Gregor Reid Award for Outstanding Scholars in Developing Nations in this inaugural year. ISAPP established the award in honor of Dr. Gregor Reid PhD, for the purpose of recognizing and supporting early career researchers within low and middle income countries (LMICs). Dr. Reid is a founding board member of ISAPP, former President of ISAPP, and founder of the ISAPP Students and Fellows Association (SFA), whose work in LMICs throughout his career showed his commitment to scientific excellence, innovation, and community development.
Dr. Chourasia will receive an award plaque and will speak about his work at the ISAPP annual meeting in July, 2024.
Microbiota-Gut-Brain Axis Researcher in Belgium Receives ISAPP’s 2024 Glenn Gibson Early Career Researcher Award
/in News /by KCThe ISAPP selection committee for the Glenn Gibson Early Career Researcher Award is pleased to announce that Dr. Boushra Dalile PhD, a postdoctoral fellow at KU Leuven (Belgium), is the recipient of this year’s award.
Dr. Dalile is a researcher who moved from studying psychology and cognitive neuroscience into biomedical sciences, completing her PhD in 2021. She now focuses on the gut-brain axis – specifically, the mechanistic role of colonic short-chain fatty acids (SCFAs) as mediators of prebiotic effects on stress-related mental disorders. In one of her group’s most recent studies, she used colon-delivery capsules to approximate the metabolic effects of prebiotic administration, and found that direct delivery of SCFAs successfully reduced physiological stress response (as measured by cortisol) in humans. She is interested in continuing to explore the potential of butyrate for modulating fear as well as anxiety-related learning and memory processes.
A multilingual researcher who lived in Germany and Sweden before coming to KU Leuven, Dr. Dalile currently has a postdoc project supported by The Research Foundation – Flanders, titled “INTERFEAR – Investigating the endogenous metabolite butyrate as an epigenetic modulator of fear memory”.
The 2024 award committee, composed of ISAPP board members and affiliates, identified Dr. Dalile as making important contributions in the biotics field early in her scientific career. The award is given annually to a researcher who is no more than five years past their terminal degree, in a field of study related to probiotics, prebiotics, synbiotics, postbiotics or fermented foods. She will receive a cash prize and a speaking slot at the ISAPP annual meeting in July, 2024.
Inaugural Sanders Award for Advancing Biotic Science Goes to Argentinian Researcher who leads YOGURITO program
/in ISAPP Science Blog /by KCThe 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 KCBy 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 KCBy 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.