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Episode 33: From probiotic mechanisms to applications, with Prof. Graciela Lorca PhD

/in Podcast, Season Three /by Laura

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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:

  • Prof. Lorca’s lab is primarily concerned with discovering the mechanisms of action of specific probiotics, including the molecules they produce that can have beneficial effects on a host.
  • Knowing how a probiotic works allows scientists to select strains that are likely to be effective for a certain application.
  • Prof. Lorca’s lab found that L. johnsonii produces extracellular vesicles (EVs) and that a few proteins carried in these EVs may be important markers of where and how they affect the host. She triggered antibodies against these proteins, allowing them to be tracked in the host.
  • EVs are small protrusions from the bacterial membrane, and only some bacteria produce them. Evs have complex cargo, which mostly represents the metabolic state of the cell.
  • Prof. Lorca studied bacteria that appeared to affect autoimmunity in animal models. In humans, administering these bacteria changed immune markers; this intervention is now in a Phase II trial with humans who have Type 1 diabetes. The bacteria may be acting in the small intestine, but they don’t colonize permanently.
  • Extensive data on safety were required to advance the probiotic through to a Phase II trial. Although administering EVs could be an even safer approach, they are difficult to purify from bacteria. Prof. Lorca continues to investigate the bioactive components of these EVs to perhaps administer only those components.
  • Prof. Lorca is also interested in responders versus nonresponders to a probiotic intervention. One of her clinical trials showed that people had either high lactic acid bacteria (LAB) or low LAB at baseline. For those with high levels of LAB, the levels didn’t change much over time. But for those with initially low levels of LAB, the levels increased over time. The latter responded better to treatment. Furthermore, people with high LAB were shown to consume a diet with more long-chain fatty acids, which LAB can utilize. Overall, dietary intake may be a key part of uncovering responders and nonresponders.
  • Over the next ten years in this field, Prof. Lorca believes we will be able to increasingly personalize probiotics according to someone’s genetics and dietary intake. Regulatory aspects are complicated but continue to evolve.

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.

Episode 32: How microbes and mucus interact in the gut

/in Podcast, Season Two /by Laura

How microbes and mucus interact in the gut, With Dr. Mindy Engevik PhD

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How microbes and mucus interact in the gut, With Dr. Mindy Engevik PhD

Episode summary:

In this episode, the ISAPP hosts discuss mucus-microbe interactions in the digestive tract with Dr. Mindy Engevik PhD from the Medical University of South Carolina, USA. They discuss how mucus in the gut is produced and degraded, and different ways that pathogens and commensal microbes interact with the mucus layer. Dr. Engevik describes some different ways that commensal bacteria make use of mucus, as well as dietary influences on gut mucus production.

Key topics from this episode:

  • The gut epithelium has special cells called goblet cells that actively secrete mucus. In the small intestine, mucus forms a light barrier but in the colon, it forms a thicker barrier with two layers: an inner layer free of microbes, and an outer layer where mucus and microbes coexist.
  • Bacteria in the gut make use of mucus in different ways. Many microbes have the capacity to degrade mucus, and it can provide a carbon source for bacteria to survive. Even bacterial quorum sensing can be influenced by mucus.
  • Bifidobacteria increase mucus production. Akkermansia are good at degrading mucus and also increasing mucus production. Pathogens, however, degrade the mucus and cause inflammation so mucus production is suppressed.
  • Several human diseases involve a dysfunctional gut mucus layer – for example, inflammatory bowel disease.
  • Various models are used for studying mucus – for example, traditional cell lines and human intestinal organoids.
  • Dr. Engevik’s work has found interactions between Clostridioides difficile and Fusobacterium nucleatum in the gut: these bacteria can interact to form biofilms that are more antibiotic-resistant than normal.
  • Individual differences exist in gut microbes as well as glycan structure in the gut, so the best insights will likely come from understanding the entire network of microorganisms, metabolites, and mucus. 
  • Dietary components influence the gut microbiota, which influences mucus production in the gut. High dietary fiber increases the amount of mucus produced by the goblet cells. Some bacteria degrade dietary substrates, then switch over to mucus when they don’t get what they need from the diet.
  • Dr. Engvik is an avid science communicator and advocates for scientists being present on social media. She has found science communication a great way to engage with the public as well as fostering scientific collaborations. The Instagram account showing microscopy images from her lab is @the_engevik_labs

Episode links:

About Dr. Mindy Engevik PhD:

Mindy Engevik is an Assistant Professor at the Medical University of South Carolina. She has Ph.D. in Systems Biology & Physiology and an interest in microbe-epithelial interactions in the gastrointestinal tract. Her lab focuses on how commensal friendly bacteria in the human gut interact with intestinal mucus and she tries to leverage this information to treat intestinal disorders. You can follow her on Twitter at @micromindy.

Episode 31: Microbial species and strains: What’s in a name?

/in Podcast, Season Two /by Laura

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The Science, Microbes & Health Podcast 

This podcast covers emerging topics and challenges in the science of probiotics, prebiotics, synbiotics, postbiotics and fermented foods. This is the podcast of The International Scientific Association for Probiotics and Prebiotics (ISAPP), a nonprofit scientific organization dedicated to advancing the science of these fields.

Microbial species and strains: What’s in a name? with Dr. Jordan Bisanz PhD

Episode summary:

In this episode, the ISAPP podcast hosts speak with Dr. Jordan Bisanz PhD, Assistant Professor of Biochemistry and Molecular Biology at Penn State University in State College, USA. They discuss how to define a bacterial strain, the diversity of strains within a species, and how genetic differences correspond with functional differences. They also talk about manipulating microbial communities for insights about health and disease.

Key topics from this episode:

  • Dr. Bisanz says just because strains within a species are genetically related doesn’t mean they do the same things. Bacteria gain and lose genes rapidly, but we don’t yet know what a lot of those genes do.
  • Natural variation in strains can be used as a tool to find out the functions of genes. 
  • Metagenomics illuminates strain-level differences, but that assumes we know what makes a strain. There’s no single accepted definition of a strain.
  • Knowing the mechanisms behind the effects of a strain on a host is important for predicting if closely related strains will have the same effect.
  • Moving forward, it could be useful to have functional information to go along with strains and their taxonomic descriptors.
  • Dr. Bisanz’s lab tests experimentally how microbial genes are gained and lost in vivo, both through wetlab experiments and computational approaches.
  • Experiments on strains are essential – for example, two strains with differences in 1000 SNPs might be functionally the same, while differences in 2-3 key SNPs might make a big difference.
  • When testing probiotic effects, you may be testing something derived from the original microbial genome but not identical. How can this be managed in industry? Understanding the mechanisms is important, strains that function similarly can qualify as the same strain.
  • A microbiome involves multiple microbes working together, acting differently from all the strains in isolation.
  • Dr. Bisanz studies tractable microbial communities: find the microorganisms that are different in a disease state compared to a healthy state, and create a synthetic community of the microbes that are absent. What are the functions of this community?
  • The challenge is that microbiologists need to be able to manipulate the microbes but cannot do this in a whole human fecal sample.
  • Is gut microbiome sequencing useful? At the level of individual, it may not provide value. But putting the data all together, in the future it may provide interesting information. The challenge with interpretation is that the microbiome is driving, but also responding to, dietary inputs.
  • In the microbiome field, gnotobiotic models (using humanized mice) need to be taken a step further than they currently go – specifying not only which microbes established in the host, but also how they could plausibly affect the mechanism.

Episode abbreviations and links:

Additional resources:

About Dr. Jordan Bisanz PhD:

Jordan Bisanz is an assistant professor of Biochemistry and Molecular Biology at the Pennsylvania State University and the One Health Microbiome Center. The Bisanz lab combines computational analyses and wet lab experimentation to understand how gut microbes interact with each other and their host. The lab specializes in coupling human intervention studies with multi ‘omics approaches and gnotobiotic models to understand how host-microbe interactions shape health generating both mechanistic insights and translational targets.

How to navigate probiotic evidence and guidelines for pediatric populations

Episode 20: How to navigate probiotic evidence and guidelines for pediatric populations

/in Podcast, Season Two /by Laura

How to navigate probiotic evidence and guidelines for pediatric populations

 

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The Science, Microbes & Health Podcast 

This podcast covers emerging topics and challenges in the science of probiotics, prebiotics, synbiotics, postbiotics and fermented foods. This is the podcast of The International Scientific Association for Probiotics and Prebiotics (ISAPP), a nonprofit scientific organization dedicated to advancing the science of these fields.

How to navigate probiotic evidence and guidelines for pediatric populations, with Dr. Hania Szajewska

Episode summary:

In this episode, the ISAPP podcast hosts talk about evidence and guidelines for probiotics in pediatric populations, with Prof. Hania Szajewska MD PhD, of the Department of Paediatrics at the Medical University of Warsaw, Poland. They talk about some of the inconsistencies between different medical organizations’ guidelines for pediatric probiotic use, and how clinicians can move forward with recommendations based on the best available evidence.

 

Key topics from this episode:

  • Guidelines exist on probiotic use for gastroenterological issues in children, but there are differences (especially regarding acute gastroenteritis) between guidelines from different medical societies: European Society for Paediatric Gastroenterology Hepatology and Nutrition (ESPGHAN) and The American Gastroenterological Association (AGA).
  • Realistic expectations are necessary when prescribing probiotics. Different probiotics have different benefits, but they are not a ‘magic bullet’. For example, the evidence shows certain probiotics for acute gastroenteritis reduce diarrhea by an average of one day. This could have a big impact on the quality of life of the end user, but for clinicians it may not sound like a lot so they must set expectations accordingly.
  • The market is overflowing with probiotic products, many of which do not have proven efficacy. This makes it difficult for end users and healthcare professionals to distinguish the best products.
  • Always look for evidence-based probiotics with documented efficacy for the indication for which they are intended.
    • Physicians have the ethical duty to prescribe evidence-based products (that is, clinically proven, effective products).
    • The exact strains and doses matter.
  • Formal training and education of healthcare professionals regarding the beneficial effects of microbes, the microbiome, and probiotics are currently lacking.
  • Is it more valuable to know probiotics’ mechanism of action, or to have evidence from clinical trials that they are effective?
    • Ideally we would have both, but since we don’t know the exact mechanism for all probiotics, positive evidence from clinical trials is crucial. 
    • We also need to make clear to healthcare professionals and end users what to expect from taking probiotics. For example, some probiotics reduce the chances of developing antibiotic-associated diarrhea by 50%. For colic, some probiotics can reduce the crying time by half an hour. These are modest benefits but for the affected individual they may be impactful.
  • For vulnerable populations such as preterm infants, we need high-quality products with proven safety and efficacy.

 

Episode abbreviations and links:

 

About Prof. Hania Szajewska: 

Hania Szajewska, MD, is Professor and Chair of the Department of Paediatrics at the Medical University of Warsaw and the Chair of the Medical Sciences Council. Among her various functions, she served as the Editor-in-Chief of the Journal of Pediatric Gastroenterology and Nutrition; a member of the Council and then as the General Secretary of the European Society for Paediatric Gastroenterology, Hepatology and Nutrition (ESPGHAN); the Secretary of the ESPGHAN Committee on Nutrition. Most recently, she joined the Board of Directors of the International Scientific Association for Probiotics and Prebiotics (ISAPP). Prof. Szajewska has broad interests in pediatric nutrition but her research focuses on the effects of early nutritional interventions on later outcome; and the gut microbiota modifications such as with various biotics (probiotics, prebiotics, synbiotics, postbiotics). She is or has been actively involved in several European Union-funded research projects. She is an enthusiastic advocate for the practice of evidence-based medicine. Prof. Szajewska has co-authored more than 400 peer-reviewed publications and 30 book chapters. Citations >18,141. Hirsch index 72 (WoS, March 2023).

Questioning the existence of a fetal microbiome, with Dr. Kate Kennedy

Episode 19: Questioning the existence of a fetal microbiome

/in Podcast, Season Two /by Laura

Questioning the existence of a fetal microbiome, with Dr. Kate Kennedy

 

Podcast: Play in new window | Download

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The Science, Microbes & Health Podcast 

This podcast covers emerging topics and challenges in the science of probiotics, prebiotics, synbiotics, postbiotics and fermented foods. This is the podcast of The International Scientific Association for Probiotics and Prebiotics (ISAPP), a nonprofit scientific organization dedicated to advancing the science of these fields.

Questioning the existence of a fetal microbiome, with Dr. Kate Kennedy

Episode summary:

In this episode, the ISAPP podcast hosts tackle the debate on the existence of a fetal microbiome, with guest Kate Kennedy PhD of McMaster University in Canada. They talk about Kennedy’s recent co-first-authored paper in Nature, which concludes that it is not biologically plausible that the fetus harbors live microorganisms, and that previous microbial sequencing studies on the fetal microbiome did not account for the many sources of contamination.

 

Key topics from this episode:

  • During the last 10 years, a lively debate has emerged on whether humans harbor living microorganisms prior to birth. Some scientists have looked at fetal and placental tissues and amniotic fluid, and have ostensibly detected microbial DNA. But those results are being questioned, with the argument that the signals being found are not biologically plausible.
  • Kennedy et al. published an article in Nature that re-analyzed data and brought in experts from different related fields to help interpret the data. The conclusion is that the fetal microbiome does not exist. Previous studies have likely seen contamination during sampling, since it’s nearly impossible to collect samples in a sterile way following vaginal delivery; contamination can happen at different stages so stringent controls are needed across all these areas of potential contamination. Furthermore, live microorganisms in the fetus does not fit with what we already know in related fields of science.
  • The popularity of microbiome research may have made scientists interested in this topic, although sequencing by itself may not be sufficient to settle the question of whether a fetal microbiome exists.
  • Human cells have Mitochondrial DNA, which is bacterial in origin. In 16S rRNA gene sequencing, there is some overlap in what is amplified, and this could include mitochondrial DNA, giving misleading results. This was not accounted for in some of the initial fetal microbiome studies.
  • Bringing together disparate disciplines is inherently challenging. It’s very important to work to understand each other and understand the host and biological situation you’re dealing with.
  • If there were even small numbers of bacteria present in the fetus it would have huge implications for our understanding of fetal biology and immunology. One question would be: how is the fetus limiting growth of any microbes it harbors?
  • Despite the likelihood that the fetal microbiome does not exist, the fetus is not unprepared for the microbial onslaught after birth. The maternal microbiota and immune system can educate the fetus immunologically in the absence of fetal colonization.

 

Episode abbreviations and links:

 

About Dr. Kate Kennedy: 

Kate completed her PhD on the role of the maternal gut microbiome in perinatal programming in the lab of Dr. Deborah Sloboda at McMaster University. She previously completed her BSc and MSc in Biology at the University of Waterloo. Her research explores host-microbiome relationships in pregnancy, early-life, and aging to understand their role in modulating health and disease risk.  

Are the microbes in fermented foods safe? A microbiologist helps demystify live microbes in foods for consumers

/in Consumer Blog, ISAPP Science Blog /by KC

By Dr. Gabriel Vinderola, PhD,  Associate Professor of Microbiology at the Faculty of Chemical Engineering from the National University of Litoral and Principal Researcher from CONICET at the Dairy Products Institute (CONICET-UNL), Santa Fe, Argentina.

Since very early in my career I was drawn to science communication. I feel that rather than just producing my own results, silently in my lab, I can extend the reach of the science by amplifying other people’s work. At least in the southern cone where budgets for research have been always limited, science communication is a way to be active in science.

Before the pandemic I used my Instagram account mostly to share personal moments with my circle of family and friends. But when the COVID-19 pandemic hit, I saw interest in fermented foods skyrocket. I started sharing tips about how to prepare fermented foods, telling the science behind them, separating myths from facts, making Instagram Live videos with fermentationists, nutritionists, pediatricians and gastroenterologists, and I turned my personal Instagram account into a public one with an outreach of more than 100,000 followers (@gvinde), from Mexico down to Argentina.

During the pandemic, people were largely homebound and concerned about staying healthy.  The idea of healthy food to keep a diverse gut microbiome that had the potential to enhance our gut and respiratory immune systems against coronavirus really resonated with people. I even had the chance to participate in several radio and TV programs discussing these topics as well as making yoghurt, kefir, kombucha, sauerkraut and sourdough bread at home. I saw that people had the time to devote part of their days at home to keep these communities of microbes “cooking” for them. But these activities revealed to me that more people than I realized did not know that we can eat microbes in a safe way and that they may actually be good for us.

In my encounters, I found much confusion about fermented dairy products. People believe that dairy products must be kept refrigerated, but at the same time they see ultrapasteurized milk, powdered milk or hard cheeses marketed at room temperature. People find it difficult to understand why pasteurized milk should go in the refrigerator but not unopened ultrapasteurized milk.

Some hesitancy around bacterial safety exists because Argentina leads the world in annual cases of Uremic Hemolitic Syndrome (UHS), a life-threatening condition for children, especially those under the age of 5 years, caused by shiga-toxin producing Escherichia coli. Almost 400 children get sick in Argentina every year due to UHS. Among other recommendations, pediatricians tell parents not to offer their children unpasteurized dairy products. This leads to the the most common question I receive on Instagram from parents worried about yoghurt safety: Is yoghurt pasteurized?  “No!” I emphasize. “Yoghurt is not pasteurized, but it is made out of pasteurized milk. In fact, yoghurt has viable bacteria.” And this is when the panic begins.

“If yoghurt has live bacteria, then can’t any bacteria grow there, even the bacteria responsible for UHS? If I leave yoghurt outside the refrigerator or in my car too long, won’t this make it more likely that the UHS bacteria will grow?” This is where I try to use an army of arguments to communicate science in the simplest possible way, from more philosophical to more science-based facts.

The first thing I share is that fermentation was invented well before refrigerators. Fermentation was used by people to preserve foods, for periods well longer than the time it takes to take the yoghurt from the supermarket to make it home or than the time a yoghurt sits in the backpack of my child waiting for school lunchtime. I once posted that I ate a yoghurt that was left in my car for one whole day. That generated a lot of debate on social media!

Then I inform them that the fermentation process to make yoghurt causes the pH to drop well below values needed for pathogens to grow. That it is highly unlikely that a pathogen can enter a well-sealed yoghurt, and in the event that it would be possible, the acidic conditions would impair the pathogen from growing to a level that could be life-threating.

People not only worried about yoghurts bought in the supermarket, well-sealed and made under the strictest safety conditions in industry. In the pandemic many parents learned how to make yoghurt at home, and they wanted to know how safe it is. In these cases, I advised the following to assure their homemade yogurt was safe: use a yoghurt from the supermarket to launch your own fermentation, use pasteurized milk, use good quality water to wash your kitchen devices, and wash your hands properly. In addition you can use a domestic pHmeter or pH indicators to make sure pH dropped below 4.5. In a successful fermentation – after about 1 gallon sitting 8-12 hours at a warm temperature – the fluid milk will transform into a gel. If not, you should discard it.

If these arguments are not enough, then I draw their attention to the well-respected product milk kefir. At least in this region, kefir is surrounded by a halo of “something that is good, no matter what”. People are familiar with the process of fermenting milk kefir at room temperature for a full day. So I make this comparison: commercial yoghurt is fermented for 6 hours, then it is refrigerated and taken to the supermarket. If you are OK letting milk kefir ferment for a whole day, shouldn’t yogurt sitting without refrigeration for a few more hours be harmless enough? It likely would only get more acidic because bacteria will resume fermentation. This fermented food would not become a life-threatening food in just a couple of hours. If milk kefir does not in 24 hours, why should yoghurt?

To further argue, I comment that kombucha is fermented at room temperature for 10 days, sauerkraut for 2 weeks and kimchi for several months. And they are all consumed with their microbes alive. They key is that the microbes that flourish make the environment inhospitable to pathogens.

Still I feel that there is a lot of uncertainty among consumers about the safety of fermented foods and this is may be an obstacle to making them more popular. Scientists must meet the challenge to communicate to lay audiences about how to make fermented foods safely at home and how to store them so they are safe. Nothing is ever 100% safe, but the small risks associated with fermented foods are greatly outweighed by the enjoyment of making and consuming fermented foods.

 

Additional reading:

Suggestions for Making Safe Fermented Foods at Home

2022 TEDx talk

2021 Teaching how to make kefir on TV during the pandemic

2019 participation in Argentina’s most famous TV show, featuring the same host for more than 50 years non-stop

What is a strain in microbiology and why does it matter?

/in ISAPP Science Blog /by KC

By Prof. Colin Hill, Microbiology Department and APC Microbiome Ireland, University College Cork, Ireland

At the recent ISAPP meeting in Sitges we had an excellent debate on the topic of ‘All probiotic effects must be considered strain-specific’. Notwithstanding which side of the debate prevailed, it does raise the question: what exactly is a strain? As a card-carrying microbiologist I should probably be able to simply define the term and give you a convincing answer, but I find that it is a surprisingly difficult concept to capture. It is unfortunately a little technical as a topic for a light-hearted blog, but here goes. Let me start by saying that the term ‘strain’ is important largely because we like to name things and then use those names when we share information, but that the concept of ‘strain’ may have no logical basis in nature where mutations and changes to a bacterial genome are constantly occurring events.

Let’s suppose I have a culture of Lactobacillus acidophilus growing in a test-tube, grown from a single colony. This clonal population is obviously a single strain that I will name strain Lb. acidophilus ISAPP2022. That was easy! I am aware of course that within this population there will almost certainly be a small number of individual cells with mutations (single nucleotide polymorphisms, or SNPs), cells that may have lost a plasmid, or cells that have undergone small genomic rearrangements. Nonetheless, because this genetic heterogeneity is unavoidable, I still consider this to be a pure strain. If I isolate an antibiotic resistant version of this strain by plating the strain on agar containing streptomycin and selecting a resistant colony I will now have an alternative clonal population all sharing a SNP (almost certainly in a gene encoding a ribosomal subunit). Even though there is a potentially very important genotypic and phenotypic difference I would not consider this to be a new strain, but rather it is a variant of Lb. acidophilus ISAPP2022. To help people in the lab or collaborators I might call this variant ISAPP2022SmR, or ISAPP2022-1. In my view, I could continue to make changes to ISAPP2022 and all of those individual clonal populations will still be variants of the original strain. So, the variant concept is that any change in the genome, no matter how small, creates a new variant. When I grow ISAPP2022 in my lab for many years, or share it with others around the word, it is my view that we are all working with the same strain, despite the fact that different variants will inevitably emerge over time and in different labs.

Where the strain concept becomes more difficult is when I isolate a bacterium from a novel source and I want to determine if it is the same strain as ISAPP2022. If the whole genome sequence (WGS) is a perfect match (100% average nucleotide identity or ANI) then both isolates are the same strain and both can be called ISAPP2022. If they have only a few SNPs then they are variants of the same strain. If the two isolates only share 95% ANI then they are obviously not the same strain and cannot even be considered as members of the same species (I am using a species ANI cut-off of 96% that I adopted from a recent paper in IJSEM.

Where it gets really tricky is when the ANI lies between 96% (so that we know that the isolates are both members of the same species) and 100% (where they are unequivocally the same strain). Where should we place the cut-off to define a strain? At what point is a threshold crossed and an isolate goes from being a variant to becoming a new strain? Should this be a mathematical decision based solely on ANI, or do we have to consider the functionality of the changes? If it is mathematical then we could simply choose a specific value, say 99.95% or 99.99% ANI, and declare anything below that value is a new strain. Remember that the 2Mb genome size of Lb. acidophilus would mean that two isolates sharing 99.99% ANI could differ by up to 200 SNPs. This could lead to a situation where an isolate with 199 SNPs compared to ISAPP2022 is considered a variant, but an isolate with 201 SNPs is a new strain (even though it only differs from the variant with 199 SNPs by two additional SNPs). This feels very unsatisfactory. But what about an isolate with only 50 SNPs, but one that has a very different phenotype to ISAPP2022 because the SNPs are located in important genes? Or what about an isolate with an additional plasmid, or missing a plasmid, or with a chromosomal deletion or insertion? I would argue we should not have a hard and fast cut-off based on SNPs alone, but we should continue to call all of these variants, and not define them as new strains.

So, by how much do two isolates have to differ before we no longer consider them as variants of one another, but as new strains? I will leave that question to taxonomists and philosophers since for me it falls into the territory of ‘how many angels can dance on the head of pin?’

All this may seem somewhat esoteric, but there are practical implications. Can we translate the findings from a clinical trial done with a specific variant of a strain to all other variants of the same strain? If Lactobacillus acidophilus ISAPP2022 has been shown to deliver a health benefit (and is therefore a probiotic), can we assume that Lb acidophilus ISAP2022-1 or any other variant will have the same effect? What if a variant has only one mutation, but that mutation eliminates an important phenotype required for the functionality of the original strain? I am afraid that at the end of all this verbiage I have simply rephrased the original debate topic from ‘All probiotic effects must be considered strain-specific’ to ‘All probiotic effects must be considered variant-specific’. Looks like we might be heading back to the debate stage in 2023!

Lactobacilli dominate the vagina in Belgian women

/in ISAPP Science Blog /by KC

By Prof. Sarah Lebeer, Research Professor in Microbiology and Molecular Biology, Department of Bioscience Engineering, University of Antwerp, Belgium

A little over a year ago, I wrote an ISAPP blog post about the setup of our Isala citizen science project on women’s health. Now, I can proudly say that we have the first results. Last year, more than 3300 women sent vaginal samples back to our lab, not only from the big cities but also from the smallest villages all over Flanders, Belgium (Figure 1). While Prof. Jack Ravel and many other colleagues have already done pioneering work in the US (e.g., Ravel et al. PNAS & Valencia study), Estonia and Africa, the vaginal microbiome of healthy women was less well mapped in the region where we live in Western Europe (Flanders, Belgium).

Figure 1: Map of Flanders (Belgium) showing regions from which the Isala participants sent their samples, with a gradient for the number of participants.

Last year, we managed to inspire women from a wide age range to donate two vaginal self-sampled swabs: the youngest participants were 18 years old, while a woman of 98 years old even participated. Each participant of Isala showed a unique vaginal microbiome (Figure 2).

Figure 2. Bar chart showing that each Isala participant had a unique vaginal microbiome composition, but also that lots of parallels could be drawn based on the most dominant bacterium.

Through various analyses, we were able to find parallels between the vaginal profiles of the Isala participants. We decided to divide the women in eight groups based on their most dominant microbe. Lactobacillus crispatus was found in 43% of all Isala women as most dominant bacterium, Lactobacillus iners in 28%, Lactobacillus jensenii in 4%, Lactobacillus gasseri in 3%, Gardnerella vaginalis in 12%, Prevotella in 6%, Bifidobacterium in 2% and Streptococcus in 2% of all Isala participants (Figure 3). Last June 2021, all women received this information, with a nice drawing for each bacterium and some interesting facts about these bacteria, as well as the relative abundance of this top 8. (See here.)

Figure 3. Chart showing the proportion of women participating in the Isala project that have a vaginal microbiota dominated by different bacterial genera or species.

Our work has only just begun. My team (see photo below) is now analyzing all the metadata collected via the detailed questionnaires and associating them with these microbiome profiles. The impact of the menstrual cycle, hormonal fluctuations, diet, smoking, sexual activity and other relevant factors is currently being explored. Hopefully, this will allow us to better understand for the vaginal tract what a ‘healthy microbiome’ really is and what action women can take to obtain or preserve  a ‘healthy’ or resilient microbiome. This is challenging to define with our current state of knowledge, but one characteristic of health of the microbiome may be its resilience. At the next annual ISAPP meeting, Karen Scott and I will co-chair a discussion group on ‘What do we really know about the microbiome and health?’. Now, I think it is fair to say that, compared to the gut, associations between specific microbiome members, such as lactobacilli, and health are quite strong for the vaginal tract. These lactobacilli form a protective barrier, are able to keep pathogens out, and prevent overt inflammation, so we could define lactobacilli-dominated vaginal communities as being resilient to many infections and disorders and thus probably ‘healthy’.

However, there is still much we do not know. Can women make certain changes in their lifestyle, diet, anticonception, underwear material etc. to promote lactobacilli such as L. crispatus in their vagina? What are the consequences of normal events in live such as pregnancy and menopause on these lactobacilli? Is a vaginal community with less lactobacilli always less healthy or resilient? On this page, you can get an overview of the different aspects we want to investigate. We hope to submit the first big Isala manuscript by the end of this year and will inform you as soon as possible about the results.

Lebeer lab, University of Antwerp

Behind the publication: Understanding ISAPP’s new scientific consensus definition of postbiotics

/in ISAPP Science Blog /by KC

A key characteristic of a probiotic is that it remains alive at the time of consumption. Yet scientists have known for decades that some non-living microorganisms can also have benefits for health: various studies (reviewed in Ouwehand & Salminen, 1998) have compared the health effects of viable and non-viable bacteria, and some recent investigations have tested the health benefits of pasteurized bacteria (Depommier et al., 2019).

Since non-viable microorganisms are often more stable and convenient to include in consumer products, interest in these ‘postbiotic’ ingredients has increased over the past several years. But before now, the scientific community had not yet united around a definition, nor had it precisely delineated what falls into this category.

An international group of scientists from the disciplines of probiotics and postbiotics, food technology, adult and pediatric gastroenterology, pediatrics, metabolomics, regulatory affairs, microbiology, functional genomics, cellular physiology and immunology met in 2019 to discuss the concept of postbiotics. This meeting led to a recently published consensus paper, including this definition: “a preparation of inanimate microorganisms and/or their components that confers a health benefit on the host”.

Thus, a postbiotic must include some non-living microbial biomass, whether it be whole microbial cells or cell components.

Below is a Q&A with four of the paper’s seven ISAPP-linked authors, who highlight important points about the definition and explain how it will lay the groundwork for better scientific understanding of non-viable microbes and health in the years ahead.

Why was the concept of postbiotics needed?

Prof. Seppo Salminen, University of Turku, Finland:

We have known for a long time that inactivated microorganisms, not just live ones, may have health effects but the field had not coalesced around a term to use to describe such products or the key criteria applicable to them. So we felt we needed to assemble key experts in the field and provide clear definitions and criteria.

Further, novel microbes (that is, new species hitherto not used in foods) in foods and feeds are being introduced as live or dead preparations. The paper highlights regulatory challenges and for safety and health effect assessment for dead preparations of microbes.

Can bacterial metabolites be postbiotics?

Prof. Gabriel Vinderola, National University of Litoral, Argentina:

Postbiotics can include metabolites – for example, fermented products with metabolites and microbial cells or their components, but pure metabolites are not postbiotics.

Can you expand on what is not included in the category of postbiotics?

Dr. Mary Ellen Sanders, ISAPP Executive Science Officer, USA:

The term ‘postbiotic’ today is sometimes applied to components derived from microbial growth that are purified, so no cell or cell products remain. The panel made the decision that such purified, microbe-derived substances (e.g. butyrate) should be called by their chemical names and that there was no need for a single encompassing term for them. Some people may be surprised by this. But microbe-derived substances include a whole host of purified pharmaceuticals and industrial chemicals, and these are not appropriately within the scope of ‘postbiotics’.

For something to be a postbiotic, what kinds of microorganisms can it originate from?

Prof. Gabriel Vinderola, National University of Litoral, Argentina:

A postbiotic must derive from a living microorganism on which a technological process is applied for life termination (heat, high pressure, oxygen exposure for strict anaerobes, etc). Viruses, including bacteriophages, are not considered living microorganisms, so postbiotics cannot be derived from them.

Safety and benefits must be demonstrated for its non-viable form. A postbiotic does not have to be derived from a probiotic (see here for a list of criteria required for a probiotic). So the microbe used to derive a postbiotic does not need to demonstrate a health benefit while alive. Further, a probiotic product that loses cell viability during storage does not automatically qualify as a postbiotic; studies on the health benefit of the inactivated probiotic are still required.

Vaccines or substantially purified components and products (for example, proteins, peptides, exopolysaccharides, SCFAs, filtrates without cell components and chemically synthesized compounds) would not qualify as postbiotics in their own right, although some might be present in postbiotic preparations.

What was the most challenging part of creating this definition?

Dr. Mary Ellen Sanders, ISAPP Executive Science Officer, USA:

The panel didn’t want to use the term ‘inactive’ to describe a postbiotic, because clearly even though they are dead, they retain biological activity. There was a lot of discussion about the word ‘inanimate’, as it’s not so easy to translate. But the panel eventually decided it was the best option.

 Does this definition encompass all postbiotic products, no matter whether they are taken as dietary supplements or drugs?

Prof. Hania Szajewska, Medical University of Warsaw, Poland:

Indeed. However, as of today, postbiotics are found primarily in foods and dietary supplements.

Where can you currently find postbiotics in consumer products, and what are their health effects?

Prof. Hania Szajewska, Medical University of Warsaw, Poland:

One example is specific fermented infant formulas with postbiotics which have been commercially available in some countries such as Japan and in Europe, South America, and the Middle East for years. The postbiotics in fermented formulas are generally derived from fermentation of a milk matrix by Bifidobacterium, Streptococcus, and/or Lactobacillus strains.

Potential clinical effects of postbiotics include prevention of common infectious diseases such as upper respiratory tract infections and acute gastroenteritis. Moreover, fermented formulas have the potential to improve some digestive symptoms or discomfort (e.g. colic in infants). In addition, there is some rationale for immunomodulating, anti-inflammatory effects which may potentially translate into other clinical benefits, such as improving allergy symptoms. Still, while these effects are likely, more well-designed, carefully conducted trials are needed.

What do we know about postbiotic safety?

Dr. Mary Ellen Sanders, ISAPP Executive Science Officer, USA:

Living microbes have the potential, especially in people with compromised health, to cause an infection. But because the microbes in postbiotics are not alive, they cannot cause infections. This risk factor, then, is removed from these preparations. Of course, the safety of postbiotics for their intended use must be demonstrated, but infectivity should not be a concern.

What are the take-home points about the postbiotics definition?

Prof. Seppo Salminen, University of Turku, Finland:

Postbiotics, which encompass inanimate microbes with or without metabolites, can be characterized, are likely to be more stable than live counterparts and are less likely to be a safety concern, since dead bacteria and yeast are not infective.

Read the postbiotic definition paper here.

See the press release about this paper here.

View an infographic on the postbiotic definition here.

See another ISAPP publication on postbiotics here.

Creating a scientific definition of ‘fermented foods’

/in Consumer Blog, ISAPP Science Blog /by KC

By Prof. Maria Marco, Department of Food Science and Technology, University of California Davis, USA

A panel of scientific experts was recently convened by ISAPP to discuss the state of knowledge on fermented foods. While there was much agreement on the underlying microbiological processes and health-related properties of those foods and beverages, our conversation on definitions led to sustained debate. So what exactly is a fermented food?

The word “ferment” originates from fervere, which in Latin means to boil. According to the Merriam-Webster dictionary, the verb ferment is defined as “to undergo fermentation or to be in a state of agitation or intense activity”. Fermentation is defined as both a chemical change with effervescence and as an enzymatically controlled anaerobic breakdown of energy-rich compounds (such as a carbohydrate to carbon dioxide and alcohol or to an organic acid). In biochemistry, fermentation is understood as an ATP-generating process in which organic compounds act as both electron donors and acceptors. In industry, fermentation means the intentional use of bacteria and eukaryotic cells to make useful products such as drugs or antibiotics. As you can see, there are clearly many meanings implied in “ferment” and “fermentation”. We add onto this by defining how those words apply to foods.

As our ISAPP panel began to deliberate the definition of fermented foods, it quickly became clear how difficult reaching consensus can be! Even though many panel members shared similar academic backgrounds and scientific expertise, finding agreement on the definition required several rounds of debate and some consuming of fermented foods and beverages along the way. Finally, we defined fermented foods and beverages as being “foods made through desired microbial growth and enzymatic conversions of food components” (see the published consensus paper here).

Find ISAPP’s infographic on fermented foods here.

This definition is very specific by requiring microbial growth and enzymatic processes for the making of those foods. Activity of the endogenous enzymes from the food components or enzymes added to the food is not enough for a food to be regarded as fermented. Similarly, foods made by only adding vinegar or “pickling” should not be called fermented. The definition acknowledges the essential roles of microorganisms for making fermented foods but does not require their presence or viability at the time of consumption.

On the other hand, our definition does not restrict fermented foods to only those foods and beverages made using microorganisms using metabolic pathways implicit in the strict biochemical definition. Yogurt and kimchi made using lactic acid bacteria relying on fermentative energy metabolism are included as much as koji and vinegar, foods made using fermentation processes that employ fungi and bacteria that perform aerobic respiratory metabolism.

Each word in a definition needs to be carefully calibrated. The best example of this in our definition of fermented foods is the word “desired”. Unlike a food that is spoiled as a result of microbial growth and enzymatic activity, food fermentations generate wanted attributes. Other words such as “intentional”, “desirable”, or “controlled” may also be used to describe this meaning. However, those words also have caveats that not all fermented foods are made “intentionally”, at least in the way that they were first prepared thousands of years ago. Qualities of fermented foods may be “desirable’ in some cultures but not others. While some fermentations are “controlled”, others are spontaneous, requiring little human input.

The process of discussing the definition with a group of scientific experts was enlightening because it required us to deconstruct our individual assumptions of the term in order to reach agreement on descriptions and meaning. With a definition in hand, we can use a shared language to study fermented foods and to communicate on the significance of these foods and beverages in our diets. There will also certainly be more “fermenting” of these concepts to improve our knowledge on the production and health impacting properties of fermented foods for years to come.

Find the ISAPP press release on this paper here.

Read about another ISAPP-led publication on fermented foods here.

Learn more in a webinar on the science of fermented foods here.

Can the microbiota help protect against viral infections? Summary of an ISAPP discussion group

/in ISAPP Science Blog /by KC

By Drs. Karen Scott, University of Aberdeen, and Sarah Lebeer, University of Antwerp

As part of the ISAPP virtual annual meeting 2020, around 85 members of the ISAPP community joined us in a Zoom discussion forum to discuss the topic: “Do our resident microbes help protect against viral infections?” A scientific perspective on this topic is especially important during the COVID-19 pandemic, when many members of the general public are wondering about actions (if any) they can take to protect themselves before a SARS-CoV-2 vaccine becomes widely available.

We introduced the topic and were joined by several invited experts, who also gave short presentations:

  • Joel Dore (INRAE France)
  • Tine Licht (Technical University of Denmark)
  • Mary O’Connell-Motherway (APC Microbiome, Cork)

The ensuing conversation, open to all participants, was wide-ranging, starting with the gut microbiota and expanding to include the microbiota at other body sites, and the effects of the gut microbiota around the body gut via transport of metabolites. Here are some of the main take-home messages from this discussion.

Components of the microbiota (bacteria, fungi, archaea, viruses and others) at a body site interact with each other. Although scientists often study one component of the (gut) microbiota at a time, members of the microbiota from different kingdoms interact with each other in ways that can be positive or negative for the host. In particular, specific activities of bacteria can be widespread, frequent or rare among members of the microbiota – and it is often the rare activities that have important impacts on the course of a disease: e.g. specific antimicrobial agents produced by some bacteria prevent Salmonella infections in pigs and cure mastitis in cows.

Mechanistic work shows bacteria in the microbiota can prevent, eliminate or promote viral infections. Studies have shown some microbes can prevent attachment of viruses to cell surfaces by offering alternative receptors. In contrast, virus particles can utilise other bacterial cells to “mask” them and facilitate entry into host cells. Other bacteria can stimulate the immune system to promote elimination of a viral infection, while under specific circumstances this same immune activation may promote viral infection. When it comes to the microbiota of the respiratory tract, studies have shown its bacterial members play a crucial defensive role. Probiotics that are already shown to be effective against other viral upper respiratory tract infections may have promise for COVID-19 (either for preventing infection or enhancing recovery), and currently studies are underway to investigate these.

Probiotics or prebiotics could be useful adjuncts to vaccination, but they are not likely to become a reality for COVID-19. Scientists are perennially interested in the topic of vaccine efficacy, and some probiotics have been shown to increase efficacy for widely available vaccines in certain populations. But in the current pandemic, developing a safe and effective vaccine (or vaccines) is the primary concern. Testing the possibility of probiotic or prebiotic combination therapies would be secondary, since the necessary testing would take longer in order to evaluate the adjuvant potential of different probiotic strains. Because the expression of cell surface molecules that can mediate adjuvant activity is strain-dependent, screening and selecting the best strains would probably take too long to become a reality for COVID-19. Certainly, participants agreed that introduction of a safe, effective vaccine was the priority, without any delays to test out ‘extras’.

A scientific rationale exists for maintaining gut microbiota diversity in order to reduce the development of diseases which, as “underlying health conditions”, may result in more severe COVID-19 outcomes. It is clear that individuals with certain underlying health conditions—related to the central nervous system and gastrointestinal system, and to metabolic and immunological dysfunction—tend to experience a more severe disease, with worse outcomes, following SARS-CoV-2 infection. Many of these conditions are also associated with a gut microbiota that is different from that of healthy controls. Research consistently shows that individuals with metabolic disease, for example, have a less diverse, lower ‘richness’ microbiota, which is often linked to increased intestinal permeability, higher gut inflammation and more oxidative stress throughout the body. This increased oxidative stress then exacerbates the microbial dysbiosis, causing more inflammation and increased intestinal permeability – creating a vicious cycle effect. This cycle is linked with obesity and metabolic disorders. In healthy individuals who are at risk of developing such conditions, the diversity of the existing resident microbiota may be increased by the application of prebiotics or synbiotics, included within a healthy, diverse, high-fibre diet. These approaches may improve bacterial fermentation in the large intestine, resulting in increased production of important bacterial metabolites that help regulate host metabolism, including short-chain fatty acids.

Until a SARS-CoV-2 vaccine is available, supporting a diverse and complex gut microbiota through diet may contribute to maintaining health in at-risk populations. Despite the intense worldwide scientific efforts and collaborations, it is unlikely that an effective vaccine against COVID-19 will be widely available soon. In the meantime, we have to protect ourselves and our local ‘at-risk’ populations as best we can. We are learning more and more about the mechanisms of dietary fibre’s health effects, in which gut bacteria play a major role. Evidence suggests that keeping our gut microbiota as complex and diverse as possible by consuming a high-fibre diet (supplemented by fermented foods, probiotics and prebiotics) might help mitigate susceptibility to infections in general.

How do probiotics stay alive until they are consumed?

/in Consumer Blog, ISAPP Science Blog /by KC

By Prof. Gabriel Vinderola PhD,  Associate Professor of Microbiology at the Faculty of Chemical Engineering from the National University of Litoral and Principal Researcher from CONICET at Dairy Products Institute (CONICET-UNL), Santa Fe, Argentina

See the Spanish version of this blog post here.

As a professor, most of my days are spent with people from the academic and scientific world. But through some outreach activities, I am also fortunate to interact with many people who are not scientists by training, but have curious, scientific minds. One question I am often asked is, “Is it really possible for probiotics to still be alive when they are dried and in a capsule?” The answer is yes. Let me provide some basic background on probiotics and explain my response.

The idea of consuming live microbes to promote health is not new. Back in 1907, Élie Metchnikoff, a disciple of Louis Pasteur, the father of microbiology, associated the intake of fermented milks containing live lactobacilli, with a prolonged and healthy life in Bulgarian peasants (see here). This idea was later captured by the concept of probiotics: live microorganisms that, when administered in adequate amounts, confer a health benefit on the host (Hill et al. 2014). Four simple and pragmatic criteria allow one to conclude if specific strains of microorganisms qualify as a probiotic for use in foods and dietary supplements. Probiotic strains must be (i) sufficiently characterized; (ii) safe for the intended use; (iii) supported by at least one human clinical trial showing they are effective; and (iv) alive in the product at an efficacious dose throughout shelf life (Binda et al. 2020). Being alive at the moment of consumption is one of the key characteristics of probiotics.

Life is the condition that distinguishes animals and plants from inorganic matter. Life includes the capacity for growth, for reproduction and for metabolic activity. In order to sustain life, certain environmental conditions must be met, but these differ for different organisms. For microbes, the availability of water and nutrients, adequate temperature and pH (acidity), and the absence of growth inhibitors are essential conditions. However, it is possible to manipulate certain conditions to bring about a state where growth may be put in “stand-by mode”, yet the microbe remains alive. We cannot imagine ourselves in a condition where life is preserved even without any metabolic activity, but for microbes it is possible. Probiotics can be in foods (yoghurts, fermented milks, fruit juices, cereal bars) or in food supplements (capsules, compressed pills) in a “hibernation” state, characterized by no growth, no reproduction and no metabolic activity, waiting for the proper conditions to come back to full metabolic life. This occurs when the microbes reach the gut, which has proper temperature, nutrient availability, lack of inhibitors, adequate acidity and water. Thus, in case of microbes, there is an uncoupling of life and metabolic activity. Even without having any metabolic activity, they can still be alive, but in a dormant state.

Open a food supplement containing probiotics and you will probably find a white dry powder. This is what the microbes may look like in their dormant state, due to a technological process called freeze-drying or lyophilization. Freeze-drying is a two-stage process where cells are first quickly frozen at very low temperatures (-40 to -70°C, or less, using liquid nitrogen for example). Then, frozen water is removed by a gentle process of evaporation at low pressure and temperature, called sublimation. This process removes most of the water from around and inside the cells, leaving the microbes in a dormant state. Water activity is scientists’ way of measuring water availability for the microbes. This technological measure ranges from 0 (no water) to 1 (pure water). A water activity close to 0 impairs growth. In food supplements, freeze-drying leaves water activities less to 0.2, ensuring that no metabolic activity will take place during the shelf life of the product.

Bifidobacteria cells (circled in red) freeze-dried in a probiotic powder. This is a scanning electron microscopy image amplified 10,000 times. Cells are embedded in dry polydextrose.

So yes, probiotics in food supplements are alive in their own way. This is the case also for probiotics included in certain foods such as cereal bars. In case of food products with water activities closer to 1, such as yogurts, fermented milks, cheeses or fruit juices containing probiotics, the factor that limits metabolic activity is the low temperature at which these products are stored, combined in certain cases (yogurts, fermented milks, fruit juices) with the low pH (or high acidity) of these products. The combination of low temperature and acidity is effective in maintaining probiotic cells in a dormant state, impairing any metabolic activity that may lead to cell stress and cell death along the shelf life of the product. Yet, even while tightly controlling factors that impair metabolic activity, some cell death may occur during the shelf life of probiotics in the products that deliver them. In this case, responsible manufacturers are sure to add extra probiotic cells so that the necessary amount of viable cells needed to deliver a health effect are present through the end of the shelf life of the product.

In both probiotic foods and food supplements, the number of viable cells is commonly expressed as a certain number of colony forming units, or by the abbreviation “CFU”. As probiotics are present in high concentrations, the number of viable cells often reaches into the billions within a capsule or in a serving of yogurt. To be able to count such enormous numbers of cells, microbiologists must make serial dilutions of the probiotic product. Then, they will put a small drop of a dilution on the surface of a Petri dish containing a culture medium on which probiotics will grow. Each probiotic cell (or clump of cells) will grow in place and form a visible colony that can be observed to the naked eye, and counted.

Agar plate containing colonies of a probiotic bacteria. Cells deposited on the surface of the agar plate duplicated several times until forming a visible amount of cells: a colony.

In brief, live probiotics are present in food and supplements, but in a state of life different to that of higher organisms where metabolic activity is taking place at all times. During shelf life, the metabolic activity of probiotics is stopped by freeze-drying them (food supplements) or by a combination of low temperature and acidity (yogurts and fruit juices, for example). Active growth returns when these microbes enter out gut and find the proper conditions of nutrients, temperature, acidity and water to be active and deliver their health effects.

How some probiotic scientists are working to address COVID-19

/in ISAPP Science Blog, News /by KC

By ISAPP board of directors

With the global spread of COVID-19, the scientific community has experienced an unusual interruption. Across every field, many laboratories are temporarily shuttered and research programs of all sizes are on hiatus. Principal investigators around the world are doing their part to keep their students and local communities safe, and many are donating lab safety equipment to medical first responders who urgently need it.

In this global circumstance of research being put on hold, it is enlightening to consider what some scientists in the fields of probiotics, prebiotics, and fermented foods are working on—or proposing—in the context of understanding ways to combat viral threats. These individuals are rising to the scientific challenge of finding effective ways to prevent or treat viral infections, which may directly or indirectly contribute to progress against SARS-CoV-2.

Here, ISAPP shares words from some of these scientists—and how they have connected the dots from probiotics to coronavirus-related work with potential medical relevance.

Prof. Sarah Lebeer, University of Antwerp, Belgium: Relevance of the airway microbiome profile to COVID-19 respiratory infection and using certain lactobacilli to enhance delivery or efficacy of vaccines

Could the microbes in our upper and lower airways play a role in how we respond to the virus? Significant individual differences exist in the microbes that are prevalent and dominant in our airways. Lactobacilli are found in the respiratory tract, especially in the nasopharynx. They might originate there from the oral cavity via the oronasopharynx, but we have found some strains that seem to be more adapted to the respiratory environment, for example by expressing catalase enzymes to withstand oxidative stress. Currently we have a Cell Reports paper in press that shows certain lactobacilli are more prevalent in the upper respiratory tract of healthy people compared to those with chronic rhinosinusitis. Further investigation of one strain found in healthy people showed it inhibited growth and virulence of several upper respiratory tract pathogens. Our work on other viruses shows that certain lactobacilli can even block the attachment of viral particles to human cells. This raises the possibility that lactobacilli could be supplemented through a local spray to help improve defenses against the inhaled virus. Based on these data, we are initiating an exploratory study with clinicians and virologists on whether specific strains of lactobacilli in the nasopharynx and oropharynx could have potential to reduce viral activity via a multifactorial mode of action, including barrier-enhancing and anti-inflammatory effects, and reduce the risk of secondary bacterial infections in COVID-19.

Another line of exploratory research from our lab pertains to the delivery or efficacy of SARS-CoV-2 vaccines. Currently, many groups are rapidly developing vaccines, which predominantly use the viral spike S protein or its receptor-binding domain as antigen to induce protective immunity. We are exploring the potential of specific strains of lactobacilli with immunostimulatory effects as adjuvants for intranasal SARS-CoV-2 vaccination, or the potential of a genetically engineered antigen-producing organism for vaccine delivery.

At this year’s virtual ISAPP annual meeting, Dr. Karen Scott and I will also be leading an ISAPP discussion group called “How your gut microbiota can help protect against viral infections”. We will discuss previous work that has shown bacteria can have anti-viral effects. For many years, our colleagues, Profs. Hania Szajewska and Seppo Salminen, have studied a different virus, namely rotavirus, that causes acute diarrhea in children, and have found that Lactobacillus rhamnosus GG (new taxonomy Lacticaseibacillus rhamnosus GG) binds rotavirus and disables it, thereby blocking viral infection/multiplication. This may explain why this probiotic reduces the incidence and duration of acute diarrhea in children. Similar findings have been reported for specific probiotics and prebiotics and prevention of upper respiratory tract infections.

Prof. Rodolphe Barrangou, North Carolina State University, USA: Engineering probiotic lactobacilli for vaccine development

Between NC State University and Colorado State University (CSU) there is a historical collaborative effort aiming at engineering probiotics to develop novel vaccines. The intersection of probiotics and antivirals is the focus here with expressing antigens on the cell surface of probiotics to develop oral vaccines. The CSU infectious diseases center is very much fully operational and focused on COVID-19 now, and we recently received a research exception to open our lab for two individuals assigned to this NIH-funded project, and pivot our rotavirus efforts here to coronavirus. We are actively engineering Lactobacillus acidophilus probiotics expressing COVID-19 proteins to be tested as potential vaccines at CSU in the near future, as progress dictates.

Prof. Colin Hill, University College Cork, Ireland: The microbiome as a predictor of COVID-19 outcomes

We have recently proposed a project to examine oral and faecal microbiomes to identify correlations/associations between COVID-19 disease severity and individual microbiome profiles. If funded, we propose to analyse bacterial and viral components of the microbiome from three body sites (nasopharyngeal swabs, saliva, and faeces) in 200 donors and mine the data for biomarkers of disease risk and clinical severity. We will use machine learning to identify microbiome signatures in patients who contract the virus and remain asymptomatic, those who develop a mild infection, or those who have an acute infection requiring admission to an intensive care unit and intubation. This will enable microbiome-based risk stratification of subjects testing positive, and appropriate clinical management and early intervention, and prioritization of subjects for receiving an eventual vaccine.

Dr. Dinesh Saralaya, Bradford Institute for Health Research, UK: A live biotherapeutic product for targeted immunomodulation in COVID-19 infection

The COVID-19 pandemic presents an unprecedented challenge to our healthcare systems and we desperately require the rapid development of new therapies to ease the burden on our intensive care units. As well as its appropriate mechanism of action (targeted immunomodulation rather than broad immunosuppression), the highly favourable safety profile of MRx-4DP0004 makes it a particularly attractive candidate for COVID-19 patients, and may potentially allow us to prevent or delay their progression to requiring ventilation and intensive care.

The trial is a Phase II randomised, double-blind, placebo-controlled trial to evaluate the efficacy and safety of oral Live Biotherapeutic MRx-4DP0004 in addition to standard supportive care for hospitalised COVID-19 patients. Up to 90 subjects will be randomised 2:1 to receive either MRx-4DP0004 or placebo (two capsules, twice daily) for 14 days. The primary endpoint is change in mean clinical status score as measured by the WHO’s 9-point Ordinal Scale for Clinical Improvement, while secondary endpoints include a suite of additional measures of clinical efficacy such as need for and duration of ventilation, time to discharge, mortality, as well as safety and tolerability. The size and design of the trial are intended to generate a meaningful signal of clinical benefit as rapidly as possible.

Drs. Paul Wischmeyer and Anthony Sung, Duke University School of Medicine, USA: Probiotics for prevention or treatment of COVID-19 infection

We are planning several randomized clinical trials of probiotics in COVID-19 prevention and treatment. These trials are based on multiple randomized clinical trials and meta-analyses that have shown that prophylaxis with probiotics may reduce upper and lower respiratory tract infections, sepsis, and ventilator associated pneumonia by 30-50%. These benefits may be mediated by the beneficial effects of probiotics on the immune system. The Wischmeyer laboratory and others have shown that probiotics, such as Lactobacillus rhamnosus GG, can improve intestinal/lung barrier and homeostasis, increase regulatory T cells, improve anti-viral defense, and decrease pro-inflammatory cytokines in respiratory and systemic infections. These clinical and immunomodulatory benefits are especially relevant to individuals who have developed, or are at risk of developing, COVID-19. COVID-19 has been characterized by severe lower respiratory tract illness, and patients may manifest an excessive inflammatory response similar to cytokine release syndrome, which has been associated with increased complications and mortality. We hypothesize that probiotics will directly reduce COVID-19 infection risk and severity of disease/symptoms. Thus, we are proposing a range of trials, the first of which will be:

A Randomized, Double-Blind, Placebo-Controlled Trial of the PRObiotics To Eliminate COVID-19 Transmission in Exposed Household Contacts (PROTECT-EHC). Objective: Prevent infection and progression of illness in household contacts/caregivers of known COVID-19 patients exposed to COVID-19 (who have a >20-fold increased risk of infection). We will conduct a multicenter, randomized, double blind, phase 2 trial of the probiotic Lactobacillus rhamnosus GG vs. placebo to decrease infections and improve outcomes. This trial will include weekly collection of microbiome samples from multiple locations (i.e. fecal, oral). This trial will utilize a commercial probiotic, delivering 20 billion CFU of Lactobacillus rhamnosus GG, and placebo.

We are currently developing protocols to study prevention and treatment of COVID-19 in a range of other at-risk populations including: 1) Healthcare providers; 2) Hospitalized patients; 3) Nursing home and skilled nursing facilities workers. We are seeking additional funding and potential collaborators/trial sites for this work, and encourage interested funders and collaborators to reach out for further information or to join the effort at: Paul.Wischmeyer@nullduke.edu and also encourage you to follow our progress and our other probiotic/microbiome work on Twitter: @paul_wischmeyer

Prof. Gregor Reid, University of Western Ontario, Canada: Documenting anti-viral mechanisms of certain probiotic strains

While our institute is now studying the cytokine storm in COVID-19 patients, the closure of my lab has meant I have turned to surveying the literature: Prof. Glenn Gibson and I have a paper published in Frontiers in Public Health stating a case for probiotics and prebiotics to help ‘flatten the curve’ and keep patients from progressing to severe illness. There is good evidence that certain orally administered probiotic strains can reduce the incidence and severity of viral respiratory tract infections. Mechanistically this appears to be, in part, through modulation of inflammatory responses similar to those causing severe illness in COVID-2 patients, and antiviral activity — which has not been shown against SARS-Co-V2 but has been documented against common respiratory viruses, including influenza, rhinovirus and respiratory syncytial virus. Improving gut barrier integrity and affecting the gut-lung axis may also be part of these probiotics’ mechanism of action. At a time when drugs are being tried with little or no anti-COVID-19 data, probiotic strains documented for anti-viral, immunomodulatory and respiratory activities should be considered for clinical trials to be part of the armamentarium to reduce the burden and severity of this pandemic.

Rapid, collaborative effort

As the world waits in ‘lockdown’ mode, continued scientific progress for coronavirus prevention or treatment is critically important. ISAPP salutes all probiotic and prebiotic scientists who are stepping up to pursue unique solutions. Addressing the important research questions described above will require a rapid collaborative effort, from obtaining ethical approval and involving medical staff to collecting the samples, to recruiting participants as well as experts to process and analyze samples. All of this has to be done in record time – but from our experience of this scientific community, it’s definitely up to the challenge.

Is probiotic colonization essential?

/in Consumer Blog, ISAPP Science Blog /by KC

By Prof. Maria Marco, PhD, Department of Food Science & Technology, University of California, Davis

It is increasingly appreciated by consumers, physicians, and researchers alike that the human digestive tract is colonized by trillions of bacteria and many of those bacterial colonists have important roles in promoting human health. Because of this association between the gut microbiota and health, it seems appropriate to suggest that probiotics consumed in foods, beverages, or dietary supplements should also colonize the human digestive tract. But do probiotics really colonize? What is meant by the term “colonization” in the first place? If probiotics don’t colonize, does that mean that they are ineffective? In that case, should we be searching for new probiotic strains that have colonization potential?

My answer to the first question is no – probiotics generally do not colonize the digestive tract or other sites on the human body. Before leaping to conclusions on what this means for probiotic efficacy, “colonization” as defined here means the permanent, or at least long-term (weeks, months, or years) establishment at a specific body site. Colonization can also result in engraftment with consequential changes to the gut microbiota composition and function. For colonization to occur, the probiotic should multiply and form a stably replicating population. This outcome is distinct from a more transient, short-term (a few days to a week or so) persistence of a probiotic. For transient probiotics, it has been shown in numerous ways that they are metabolically active in the intestine and might even grow and divide. However, they are not expected to replicate to high numbers or displace members of the native gut microbiota.

Although some studies have shown that digestive tracts of infants can be colonized by probiotics (weeks to months), the intestinal persistence times of probiotic strains in children and adults is generally much shorter, lasting only few days. This difference is likely due to the resident gut microbiota that develops during infancy and tends to remain relatively stable throughout adulthood. Even with perturbations caused by antibiotics or foodborne illness, the gut microbiome tends to be resilient to the long-term establishment of exogenous bacterial strains. In instances where probiotic colonization or long-term persistence was found, colonization potential has been attributed more permissive gut microbiomes specific to certain individuals. In either case, for colonization to occur, any introduced probiotic has to overcome the significant ecological constraints inherent to existing, stable ecosystems.

Photo by http://benvandenbroecke.be/ Copyright, ISAPP 2019.

This leads to the next question: Can probiotics confer health benefits even if they do not colonize? My answer is definitely yes! Human studies on probiotics with positive outcomes have not relied on intestinal colonization by those microbes to cause an effect. Instead of colonizing, probiotics can alter the digestive tract in other ways such as by producing metabolites that modulate the activity of the gut microbiota or stimulate the intestinal epithelium directly. These effects could happen even on short-time scales, ranging from minutes to hours.

Should we be searching for new probiotic strains that have greater colonization potential? By extension of what we know about the resident human gut microbiota, it is increasingly attractive to identify bacteria that colonize the human digestive tract in the same way. In some situations, colonization might be preferred or even essential to impacting health, such as by engrafting a microbe that performs critical metabolic functions in the gut (e.g. break down complex carbohydrates). However, colonization also comes with risks of unintended consequences and the loss of ability to control the dose, frequency, and duration of exposure to that particular microbe.

Just as most pharmaceutical drugs have a transient impact on the human body, why should we expect more from probiotics? Many medications need to be taken life-long in order manage chronic conditions. Single or even repeated doses of any medication are similarly not expected to cure disease. Therefore, we should not assume a priori that any observed variations in probiotic efficacy are due to a lack of colonization. To the contrary, the consumption of probiotics could be sufficient for a ripple effect in the intestine, subtly altering the responses of the gut microbiome and intestinal epithelium in ways that are amplified throughout the body. Instead of aiming for engraftment directly or hand-wringing due to a lack of colonization, understanding the precise molecular interactions and cause/effect consequences of probiotic introduction will lead to a path that ultimately determines whether colonization is needed or just a distraction.

The Children of Masiphumelele Township

/in Consumer Blog, featured, ISAPP Science Blog /by Mary Ellen Sanders

Gregor Reid PhD MBA FCAHS FRSC, Professor, Western University and Scientist, Lawson Health Research Institute, London, Canada

Just off the main road from Cape Town, South Africa to Simon’s Town, sits Masiphumelele township where challenges of poverty, malnutrition, HIV and the risk of violence face people every day.

It is also the location for the Desmond Tutu HIV Foundation Youth Centre, a safe haven that provides adolescent-friendly sexual and reproductive health services alongside educational and recreational activities for youth living in Masiphumelele and surrounding areas.

To understand some of the dangers that children face, in 2017, about 270,000 people in South Africa were newly infected with HIV, adding to one of the highest HIV prevalence rates in the world. The Tutu Youth Centre aims at helping educate youth to reduce their risk of becoming another HIV statistic.

I was invited there by University of Cape Town Professor Jo-Ann Passmore, a woman not only recognized for her research but whose passion for helping others is reflected in her warm smile (4th from left in group photo). She asked if I would be interested in holding a workshop to illustrate to the youth how using sachets of probiotic bacteria could empower them. I jumped at the chance. On an afternoon break from the Keystone Symposium, thirty researchers joined me along with Jo-Ann and my wife Debbie, a teacher of children with learning disabilities.

After a tour of the areas where children learn on computers, play games in safety, or have personal discussions about sexual health, everyone filled the room with a stunning backdrop of the Nobel Laureate’s image. Having been privileged to meet the Archbishop when he was hosted by St. Joseph’s Healthcare Foundation in 2008, it was a nerve-tingling experience for me.

Giving a lecture on beneficial microbes is hard enough to peers sitting in the back of the room, but to do so with young South Africans was more somewhat daunting. However, it proved to be a lot of fun especially when we had to identify kids who were good leaders (the boys all pointed to a girl), who liked to make stuff and sell it to others (two boys stood out). By the end, we had picked the ‘staff’ of a new company.

The next step was for four groups to decide on the company’s name, what products they’d make from the probiotic sachets (the options were many including yoghurt, cereals, fruit juices, maize), what marketing tools they would use and who they would target to obtain a respectable income.

Interestingly, several of the conference participants seemed less engaged, as if they had never considered how microbiology research could affect real lives. In front of them were children facing huge challenges on a day-to-day basis. In one group, the kids were quiet until my wife brought out pens and paper, then they went to town designing products, names and labels. A lesson for me on how different people need different stimuli to become engaged. The faculty left early to beat the traffic back to Cape Town, so unfortunately, they did not hear the outcome of the children’s work.

When we re-assembled to present the results, I was impressed with what could be created in such a short time. My favourite was the Amazing Maize, a bottle shaped like a corn cob with the idea it would contain fermented maize. It emphasized the importance of marketing and for products to taste and look good to be purchased.

It has been over ten years since Archbishop Tutu applauded us for the Western Heads East project and thanked us for empowering women and youth and contributing to nutrition in Africa. Since then, thanks to the huge efforts of Western staff and students, and more recently IDRC funding and partnerships especially with Yoba-for-life, Heifer International and Jomo Kenyatta University of Agriculture and Technology, over 260,000 people in east Africa are now consuming probiotic yoghurt every week. The children of the South African townships were maybe too young to join in this new wave of microenterprises, but at least now they have heard about it and the importance of fermented food and beneficial bacteria.

In the background of the workshop several wonderful women committed to start up a new production unit using the Yoba/Fiti sachets developed by Yoba-for-life. I left them some sachets for them to try out the process.

But it was me who left with the biggest lesson on how precious each life is, and how those of us with the knowledge, need to provide the means for others to use their own talents to fulfill the purposes of their lives.

No better way than to start with the children.

live-dead-probiotics

Dead bacteria – despite potential for benefit – are not probiotics

/in featured, ISAPP Science Blog /by Mary Ellen Sanders

Re-posted from an original blog article by Dr. Mary Ellen Sanders, ISAPP Executive Science Officer

At the 2018 International Scientific Association of Probiotics and Prebiotics (ISAPP) meeting in Singapore, two renowned speakers reported unpublished research documenting the health benefits of dead bacteria.

Prof. Hill showed that an inactivated Lactobacillus strain reduced anxious behavior, reduced cortisol levels, and impacted the microbiome in a mouse model. Prof. Patrice Cani showed that heat-killed Akkermansia muciniphila were sufficient to ameliorate obesity and diabetes in mice. Both professors made the point that these microbial preparations were not probiotics.

Prof. Colin Hill is the lead author on the oft-cited and -downloaded (over 40,000 times) ISAPP consensus paper reaffirming the definition of probiotics, which emphasizes that probiotics must be alive when administered. This, of course, does not preclude health effects of dead bacteria. One just must remember that dead bacteria are NOT probiotics. Many different types of microbe-derived substances such as metabolites, cell wall fragments, enzymes, and neurochemicals, can have beneficial physiological effects. A 2016 review by de Almada et al. lists a couple dozen published studies of physiologically active dead bacteria.

Preserving the long-accepted definition of probiotics as ‘live microbes’ is important to the many stakeholders involved in the field. Consumers should be able to purchase a product labeled as ‘probiotic’ and know that it contains an effective level of live microbes. Regulators should know that a product without an adequate level of live microbes is fraudulent if called a probiotic. Scientists should be able to use the term and have reviewers and readers understand that they are referring to functions of live microbes. An agreed-upon definition enables us to be precise when discussing an issue. Saying that because dead bacteria have a health effect and they should be called ‘probiotics’ is like saying that because vitamin D has a health benefit, the term ‘vitamin A’ should include vitamin D.

What are implications of the fact that dead microbes may have health effects?

Stewards of the probiotic field can expect increased frustration with popular press writers. I’ll use a recent example to make this point. The June 2018 Cooking Light Magazine /Special Gut Health Issue included an article that lists sourdough bread as a top probiotic-containing fermented food. When the error about misusing the term ‘probiotic’ to describe a food that contained no live probiotic bacteria was pointed out to the editor by Jo Ann Hattner, MPH RD author of Gut Insight, Cooking Light chose to ignore advice from an expert and justify their mistake by using an irrelevant observation that both live and dead cells in probiotic products may generate beneficial biological responses. Apparently, the expertise she derived from a paper that described the “probiotic paradox” trumped the considered opinions of global expert scientists/researchers and the FAO/WHO, who agree that probiotics must be alive when administered. It’s quite a simple concept. It is true that some dead microbes may have some health benefit (although evidence of such an effect is much lower than that available from controlled human trials on actual probiotics), but they are NOT probiotics.

Confusion. Some audiences will be confused by the idea that probiotics that are killed can have health benefits. Inaccurate writers, such as the Cooking Light author above, will perpetuate this error. This is unfortunate, since the probiotic concept is a long-standing one, backed by much mechanistic and clinical evidence. Conflating probiotics with dead bacteria will lead to confusion over important aspects of an effective probiotic product.

Overages.  It is not uncommon for commercial products to be formulated with live microbes at time of manufacture that far exceed the number claimed on the label. This is to assure that the product meets label claim at the end of shelf life, as probiotics often die to some extent during storage. Sometimes this ‘overage’ can reach 10-fold more than the level guaranteed on the product, although more typically it’s 2- to 5-fold. If over the course of shelf life the viable count drops to label claim, then dead microbes may comprise as much as 90% of the microbes present. We don’t know if these dead bacteria – although no longer probiotics – have physiological benefits, as no studies have been conducted on this form of inactivated cells, but it’s an interesting possibility. When we study a probiotic product, perhaps that product needs to be characterized by both the level of live and dead microbes that are present. Means of inactivation, such as heat, pressure, irradiation, or sonication, may impact the physiological activity of the resulting dead cells.

Opportunity.  Keeping probiotics alive in commercial products is a challenge. Research such as Prof. Cani’s targets an expanded range of microbes – many isolated from the human GI tract – that cannot be easily grown and stabilized in commercial products. Further, these microbes lack the history of safe use that food-associated microbes have, and so administration of high numbers of these next-generation probiotics will require proof of safety. If these microbes can be killed and still deliver health benefits, the commercialization process could be simplified.

ISAPP may need to consider convening another consensus panel to address these newly emerging terms, such as postbiotic and paraprobiotic. Then we can all be on the same page when using these terms, which have important scientific, nutritional and clinical impact. Of course, even if ISAPP does this, authors may still choose to ignore it.

blog foodomics image

Global FoodOmics: A Crowd-Sourced Window Into Microbes In Our Foods

/in Consumer Blog, featured, ISAPP Science Blog /by Mary Ellen Sanders

January 25, 2018. By Mary Ellen Sanders, PhD , Dairy & Food Culture Technologies

Among the factors under our control, diet may be the most important determinant of our gut microbiota. Observations from the American Gut Project suggest that foods containing live microbes increase fecal bacterial diversity, which is generally associated with a healthy gut.

An initiative, Global FoodOmics, was launched earlier this year at the University of California San Diego under the auspices of the American Gut Project to learn more about bacteria in foods and the small molecules they produce. Dr. Julia Gauglitz is the project manager. Food samples (over 2000 have been collected to date) have been analyzed for their small molecule composition and will be tested by 16S rDNA sequencing to determine the bacterial species present. Although currently in its early stages, the aim for this project is to inventory the vast different foods consumed by people around the world.

Although many fermented foods (beer, bread, wine, kefir, many cheeses and others) rely on yeast or molds as fermentation or ripening agents, this project will aim to detect bacterial DNA, but these DNA approaches cannot distinguish between life and dead bacteria.  Labels and other descriptors accompanying submitted food samples may help determine if the species detected are likely to be alive. Fermented foods that retain live bacteria are more likely to influence our colonizing microbiota.

The small molecules being assayed are not limited to the ones produced by microbes. They may be due to microbial growth in the food (by food fermentation microbes or perhaps by spoilage or food poisoning microbes), may be innate to the food, or may be intentional or incidental (e.g., pesticides) additives to foods.

The intent is to turn Global FoodOmics into a crowd-sourced project. It will join the American Gut Project as an avenue for citizens to directly participate in science and enable the project to make all of the data publically available to other researchers and clinicians.

It is notable that this project is not the first attempt to understand the microbial components of food. Food microbiologists for decades have been assaying foods for microbes used to produce food, responsible for food spoilage and linked to food poisonings.  Recently, Prof. Bob Hutkins, University of Nebraska, on behalf of the International Scientific Association for Probiotics and Prebiotics (ISAPP) and with support from the National Dairy Council, embarked on a project to learn the state of knowledge about levels of live microbes in fermented foods. They dug into the published literature and emerged with “A survey of live microorganisms in fermented foods”, In Press at Food Microbiology. This paper gives us a summary of what is known about populations of live microbes in fermented foods, information that is very useful for people wanting to add live microbes to their diet.

Another effort to understand microbes in foods is the Consortium for Sequencing the Food Supply Chain, a partnership between IBM Research and Mars Inc. This project, focused on food safety, aims to develop a baseline of normal microbial communities in foods.

Both Global FoodOmics and the Consortium for Sequencing the Food Supply Chain will leverage modern DNA sequencing technologies to allow us better understand the microbes associated with foods. Global FoodOmics is the first project to understand the microbes and molecules in foods, by pairing small molecule metabolomics measurements with rDNA sequencing.

stool sample for lab

Microbiome Analysis – Hype or Helpful?

/in Consumer Blog, featured, ISAPP Science Blog /by Mary Ellen Sanders

By Karen Scott, PhD, Rowett Institute, University of Aberdeen, Scotland

Since we have realized that we carry around more microbial than human cells, and that these microbial inhabitants are important to maintain our health, searching for the bacterial species that are implicated in causing disease has become the holy grail of microbiology. However, to understand which bacteria are present or absent in a disease state, we first have to understand what constitutes normal. This is hampered by the fact that we are all different – and our microbial communities are also all different. In fact, the faecal bacterial community in samples taken months apart from one person will be identifiable as coming from that specific healthy adult, but the community will be quite distinct from samples from any other healthy adult. In the same way, the microbial community of two individuals suffering from the same disease will be different.

Despite these differences, scientists have managed to establish some facts over the past 15 years. Too many Proteobacteria, which includes Enterobacteria and E.coli, in your large intestine is not generally good news. Firstly, it means that conditions in the large intestine are probably not oxygen-free, as they should be. Secondly, an expansion in these populations usually means a decline in something else – after all food and places to live are finite resources. Bacterial diversity in the adult intestine is also important. The main factor that has been found across many different diseases is that bacterial diversity is lower in diseased individuals than their healthy counterparts. This does not necessarily mean that a low diversity is causing the disease, as various features of the disease (including any antibiotic therapy, inflammation, decreased or increased transit time) may all themselves affect the diversity of the microbiota.

Although scientists have not succeeded in defining a ‘healthy microbiota,’ there is an increasing trend to get your microbiome tested. Microbiome companies are bombarding us with offers to send in a small sample and find out about your gut microbiota, for a price. So, should you?

This really depends why you want to know, and what level of detail of analysis is being offered. Remember the orders of taxonomy? Kingdom, phylum, class, order, family, genus, and species.  Some companies identify the bacteria in your faeces only to the phylum level. This is a taxonomic level above the level needed to differentiate mammals and fish (these are ‘classes’). If you told someone that there were more fish in the Indian Ocean than mammals would this be a surprise? It would be such an expected fact it would be meaningless. This is similar to describing the microbiota at a phylum level – Bacteroidetes numbers versus Firmicutes numbers. Such numbers are meaningless. However, continuing the fish analogy, if you said that there were more mackerel than tuna in the North Atlantic Ocean this becomes a bit more meaningful. The fisherman immediately knows what type of fish he is more likely to catch, and perhaps even which net to use. The same is true of the microbiome. Telling someone that he/she has a lot of Enterobacteria and few Roseburia is actually useful as we know from studies that this represents an abnormal balance of bacteria and something should be done to redress this. Yet the bottom line health consequence of this abnormal balance of bacteria remains to be determined. So getting your gut microbiome sequenced could be useful – depending on what level of information you will receive, and what you are prepared to do about it.

And so we come to the next problem. Having established what your gut microbiota is, how are you going to make it better? And will that make YOU better? At the moment scientists don’t really have a good answer to these questions. Specific prebiotics can certainly be useful to increase the numbers of some bacteria generally assumed to be beneficial – such as Bifidobacterium, Faecalibacterium prausnitzii and even Roseburia species. But it is not really clear what the exact health benefits of such an increase in bacterial numbers would be. Health claims on prebiotics are currently limited to ‘improve intestinal transit’ and ‘lower the glycaemic response’. If you found out that your microbiota had a low diversity, increasing the variety of foods in your diet, in particular the fibre component, could certainly improve this. Our gut microbiota basically relies on our undigested food to survive, so providing a greater amount and more types of food containing fibre and prebiotics will definitely encourage populations of diverse bacteria to expand. In addition to improving digestive health, fibre fermentation by gut bacteria also results in the production of microbial products that have been shown to have health benefits.

So by all means get your gut microbiome analyzed if you want to, but perhaps instead, save your money and just increase your prebiotic and fibre consumption, which will increase levels of the potentially beneficial bacteria that are already there in your gut.

Recommended reading

Why microbiome tests are currently of limited value for your clinical practice

kombucha

Kombucha: Trend or New Staple?

/in Consumer Blog, featured, ISAPP Science Blog /by Mary Ellen Sanders

September 2017. By Prof. Bob Hutkins, Khem Shahani Professor of Food Science, University of Nebraska, Department of Food Science and Technology, Lincoln.

This blog post is adapted from a piece published by the Lincoln Journal Star. The article, first published May 4, 2016 and written by Prof. Bob Hutkins, appeared as a response to a reader’s question: “I keep hearing about kombucha… What is this stuff?”

Kombucha (pronounced kom-BOO-chuh) is made by fermenting sweetened tea using a combination of yeasts and bacteria. This mixture of live cultures that starts the fermentation is called SCOBY, short for “symbiotic colony of bacteria and yeast.” The SCOBY takes the form of a gooey mat that can be re-used for each batch or shared with friends.

Kombucha is one of many trendy fermented foods, like kimchi and kefir, that are now found everywhere. No longer just the fare of hipster cafes and posh restaurants, you can find kombucha at your local grocery store—or even at Walmart.

Kombucha’s origins go back at least 2,000 years, to China; the drink gradually spread throughout Asia and Europe. In the U.S., kits for home-brewing kombucha became available to consumers in the early 1990s, and bottled versions soon appeared on grocery store shelves.

Several factors may explain the popularity of kombucha. First, many people like the flavor: uniquely sweet and sour, with a vinegary overtone. Some ethanol (alcohol) may also be present, although commercial products must contain less than the legal limit of 0.5 percent. The fermentation reaction yields carbon dioxide, which gives kombucha a pleasant fizziness. Flavor combinations are endless, from ginger, mango, and blood orange to lavender and cinnamon.

It’s probably the suggested health properties that are most responsible for the kombucha craze. The live cultures in some blends have antimicrobial activity, which may have been valuable in past eras when antibiotics were not available. However, these properties depend on the particular mix of microbes, which varies from batch to batch or brand to brand. Other suggested health benefits range from improved gut health and digestion to treatment of cancer and other diseases. Unfortunately, there is no scientific evidence to support these health claims.

It may be that kombucha is not for everyone—the acidic nature of the drink may not sit well for some people. Microbiologists have also expressed concern that home-brewed kombucha could possibly contain toxin-producing fungi. (See related post on making safe fermented foods at home.)

Nonetheless, there’s no doubt that many consumers are drinking kombucha. Annual sales in the U.S. are over $500 million, with double-digit growth. Around half of the coveted 25-to-34 age group (i.e. millennials) are kombucha drinkers. Yes, it’s popular now, but it also seems that kombucha is likely to be around for a while.

 

Bob Hutkins is the Food Doc. He is a professor at the University of Nebraska-Lincoln, where he teaches and conducts research in food science and food microbiology. Questions on any topic related to food, food safety, food ingredients and food processing can be sent to the Food Doc at features@nulljournalstar.com.