Podcast Archives - International Scientific Association for Probiotics and Prebiotics (ISAPP)

Episode 35: Investigating gut microbiome links to chronic diseases, with Dr. Purna Kashyap MBBS

April 9, 2024/in Podcast, Season Three /by Laura

Subscribe: Apple Podcasts | Spotify | RSS

In this episode, the ISAPP hosts discuss the gut microbiome’s role in chronic diseases with Dr. Purna Kashyap MBBS, from Mayo Clinic in Rochester, Minnesota, USA. Dr. Kashyap talks about how to discover the complex factors that trigger and perpetuate chronic diseases such as inflammatory bowel disease, zeroing in on the gut microbiome as a contributor to different aspects of gastrointestinal (GI) tract physiology.

Key topics from this episode:

Dr. Kashyap became interested in some of the initial studies linking the gut microbiome to chronic diseases around 2007-2008, and subsequently began to study the molecular mechanisms that underlie changes in GI tract physiology.
How can scientists figure out causality in chronic diseases and the role of gut microbes? Dr. Kashyap sees causality as an ongoing cascade of events in the GI tract, with no single causal factor. Both the initial triggers and the perpetuating factors can be considered part of what causes these diseases.
Microbes can help perpetuate a certain state in the host because once they establish themselves they serve to make the environment more conducive to their survival. In chronic diseases, the factor that triggers the microbial community configuration may not be as important as the factor(s) that perpetuate it on an ongoing basis.
The gut microbiome is changeable but not easy to change. Scientists need to know how the microbial community sustains itself and intervene there to change the community.
Even small microbiome studies can be informative if you look at who responds to the intervention and why. This information can be valuable for informing which treatments might work for which subgroups of people.
Dr. Kashyap encourages combining three types of research: large-scale studies on microbial metabolites and potential drug targets; clinical studies on the metabolites present in various subgroups; preclinical models studying the effects of individual metabolites.
Diet, microbes, and host uptake all contribute to the physiological effects of different metabolites. And for example, if a metabolite is low, knowing which microbes are present is not enough information to explain why it’s low.
In gastroenterology, clinicians primarily care about the gut microbiome in relation to the new treatments it makes possible. Now that FDA-approved treatments exist (standardized fecal microbiota transplants for recurrent C. difficile), clinicians may start paying more attention.
Does Dr. Kashyap recommend interventions to patients based on their gut microbiomes? A high-fiber diet is good for the gut microbiome and also for overall health, so he advises patients to adhere to dietary recommendations for their daily fiber intake.

Episode abbreviations and links:

Article on the microbiome in irritable bowel syndrome: Multi-omics for biomarker approaches in the diagnostic evaluation and management of abdominal pain and irritable bowel syndrome: what lies ahead
Study comparing the effects of gut microbiota from people in the US vs. rural Thailand: Industrialized human gut microbiota increases CD8+ T cells and mucus thickness in humanized mouse gut
Study on the effects of the metabolite tryptamine: Gut Microbiota-Produced Tryptamine Activates an Epithelial G-Protein-Coupled Receptor to Increase Colonic Secretion
GWAS: Genome-wide association studies

Additional resources:

Why researchers need to understand more about the small intestinal microbiome. ISAPP blog.

About Dr. Purna Kashyap:

Dr. Purna Kashyap is practicing gastroenterologist and Professor of Medicine and Physiology, the Bernard and Edith Waterman Director of the Microbiome program, and Director of the germ-free mouse facility in the Center for Individualized Medicine at Mayo Clinic, Rochester, MN. The NIH funded Gut Microbiome laboratory led by Dr. Kashyap is focused on delineating the complex interactions between diet, gut microbiome, and host gastrointestinal physiology. The laboratory uses germ-free mouse models in conjunction with measures of gastrointestinal physiology in vitro and in vivo to investigate effects of gut microbial products on host gastrointestinal function. In parallel, they use a systems approach incorporating multi-omics, patient metadata, and physiologic tissue responses in human studies, to aid in discovery of novel microbial drivers of disease. The overall goal of the program is to develop novel microbiota-targeted therapies. Dr. Kashyap has published nearly 100 peer reviewed articles including journals like Cell, Cell Host Microbe, Science Translational Medicine, Nature Communications, and Gastroenterology. He was inducted to American Society of Clinical Investigation in 2021. He has previously served on the scientific advisory board of American Gastroenterology Association Gut Microbiome Center, and on the council of American Neurogastroenterology and Motility Society. He now serves on the council and the research committee of AGA, in an editorial role for Gut Microbes and as an ad hoc reviewer on NIH study sections.

Episode 34: New evidence on the virome in gut-brain communication and stress, with Nathaniel Ritz and Thomaz Bastiaanssen

March 8, 2024/in Podcast, Season Three /by Laura

Podcast: Play in new window | Download

Subscribe: Apple Podcasts | Spotify | RSS

In this episode, the ISAPP hosts discuss a new study on how the gut virome affects the host during stress, with Nathaniel (Nate) Ritz from the Institute for Systems Biology in Seattle, USA and Thomaz Bastiaanssen from APC Microbiome Ireland. The guests give an overview of the microbiota-gut-brain axis, then delve into a new study they led on the virome and its effects on stress responses in mice.

Key topics from this episode:

The gut and the brain communicate in various ways, and the microbiota play a role in some of these modes of communication. Various studies use animal models to look at mechanisms that might be applicable to humans.
Why would the microbiota affect the human brain? Because we evolved with a ‘background’ of microbes and have relied on them as we evolved. For example, gut microbes produce metabolites the human body is unable to produce by itself.
The newly published paper is titled “The gut virome is associated with stress-induced changes in behaviour and immune responses in mice”.
Most microbiota-gut-brain axis research to date has looked at the bacterial component of the microbiome, but this misses the bigger context. The virome is the collection of viruses in the gut, mostly consisting of bacteriophages (which infect bacteria in the gut). This study focused on the virome and how it influenced the gut bacteriome as well as host behavior.
Bioinformatics challenges exist when working with the virome for several reasons. For one, distinguishing the biology of a bacteriophage from its host can be challenging.
The study used a fecal virome transplant: taking a fecal sample, removing the cellular organisms and small particulates so that the bacteriophages were left over, and then concentrating them and administering them. The researchers took this entire virome from a mouse, then transferred it back to the same individual mouse while it was undergoing stress.
After stress, differences were seen in the mouse gut bacteriome and virome. The mice had higher anxiety- and depression-like behaviour, plus changes in their immune systems. But after the fecal virome transplant, some of their behaviours were improved.
Do the viruses impact the host nervous system directly, or do they only affect the host by way of the bacteriome? This is not fully known, but there appears to be very little interaction of the bacteriophages with the host.
Analysis of the gut bacteriome or virome must respect the compositional nature of the data. The types of measurements used to analyze the microbiome and virome are confounded by compositional effects, and in the field this is not respected as much as it should be.
The next step after this study is to explore the changes in microbiome function in the mice, perhaps pinpointing which bacterial groups need to be changed to normalize the mouse behaviours.

Episode links:

Study showing how bacteriophages in the gut are associated with inflammation: Expansion of Bacteriophages Is Linked to Aggravated Intestinal Inflammation and Colitis
The idea of gut microbiota volatility: Volatility as a Concept to Understand the Impact of Stress on the Microbiome
Two-part microbiome bioinformatics analysis guidebook by Thomaz Bastiaanssen (See supplementary data for an in-depth, reproducible tutorial in R): Part 1, Part 2
Information on John Aitchison’s work on compositional analysis: Aitchison’s Compositional Data Analysis 40 Years on: A Reappraisal

About Nathaniel Ritz:

Dr. Nathaniel Ritz completed his PhD in Prof. John Cryan’s lab at APC Microbiome Ireland where he studied the role of the bacteriome and the virome in social and stress-related disorders. His interests lie in elucidating microbiota-host interactions and establishing microbiota causality within the microbiota-gut-brain axis. Nathaniel has recently moved to Seattle, Washington, USA, to join the lab of Dr. Sid Venkatesh as a postdoctoral fellow at the Institute for Systems Biology to further unravel the mechanisms underpinning microbe-host interaction. Outside of the lab, Nathaniel is an avid rock climber, dog walker, and partner to fellow scientist Dr. Minke Nota. More details and current position can be found at https://venkatesh.isbscience.org/

About Thomaz Bastiaanssen:

Dr. Thomaz Bastiaanssen is the lead bioinformatician in Prof. John F. Cryan’s microbiota-gut-brain axis group in Cork, Ireland. He is interested in the ecological dynamics governing host-microbe communication and how this complex interplay can impact human well-being. He will soon transition to a new role at Amsterdam UMC, the Netherlands, where he will continue to study the microbiome gut-brain axis. Besides working on multi-omics analyses, he enjoys horror stories, tabletop games and spending time with his wife, son, and corgi. His website can be found at: https://thomazbastiaanssen.github.io/

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

February 16, 2024/in Podcast, Season Three /by Laura

Podcast: Play in new window | Download

Subscribe: Apple Podcasts | Spotify | RSS

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:

Article on how bacterial EVs may have effects on type 1 diabetes: Internalization of extracellular vesicles from Lactobacillus johnsonii N6.2 elicit an RNA sensory response in human pancreatic cell lines
Tracking bacterial EVs in the host: Identification of Biomarkers for Systemic Distribution of Nanovesicles From Lactobacillus johnsonii N6.2
Clinical trial showing feasibility of using a probiotic strain in applications related to type 1 diabetes: Lactobacillus johnsonii N6.2 Modulates the Host Immune Responses: A Double-Blind, Randomized Trial in Healthy Adults
Using diet to predict levels of bacteria in the gut: Identification of food and nutrient components as predictors of Lactobacillus colonization
Master of Science degree at University of Florida: Microbiome in Health and Disease

Additional resources:

New paper outlines the value of studying probiotics in the small intestine. ISAPP blog.

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

November 24, 2023/in Podcast, Season Two /by Laura

Podcast: Play in new window | Download

Subscribe: Apple Podcasts | Spotify | RSS

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?

November 7, 2023/in Podcast, Season Two /by Laura

Podcast: Play in new window | Download

Subscribe: Apple Podcasts | Spotify | RSS

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:

Review on strain diversity co-authored by Dr. Bisanz: Challenges and opportunities of strain diversity in gut microbiome research
Computational and experimental resources for mapping phenotypes to genes: A Genomic Toolkit for the Mechanistic Dissection of Intractable Human Gut Bacteria
Example of mechanistic insights: Human gut bacteria produce ΤΗ17-modulating bile acid metabolites
Research highlight on complex synthetic microbial communities: Making gut microbiomes from scratch
Description of a defined complex microbial community: Design, construction, and in vivo augmentation of a complex gut microbiome

Additional resources:

What is a strain in microbiology and why does it matter? ISAPP blog post by Prof. Colin Hill PhD

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.

Episode 30: A systems biology perspective on the gut microbiome

October 19, 2023/in Podcast, Season Two /by Laura

Podcast: Play in new window | Download

Subscribe: Apple Podcasts | Spotify | RSS

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.

A systems biology perspective on the gut microbiome, with Dr. Sean Gibbons PhD

Episode summary:

In this episode, the ISAPP hosts discuss the microbiome and systems biology with Dr. Sean Gibbons PhD, Associate Professor at the Institute for Systems Biology in Seattle, USA. Prof. Gibbons talks about exploring and manipulating the complex ecology of the microbiome with the aim of engineering outputs of this system. He describes the utility of artificial intelligence in microbiome science and how the microbiome will play a role in personalized medicine in the future, including in the delivery of probiotics and prebiotics.

Key topics from this episode:

Dr. Gibbons’ lab primarily focuses on designing bioinformatic tools for exploring and manipulating the complex ecology of the microbiome, and trying to shape the outputs of the system. He emphasizes the need for computational tools alongside traditional microbiological techniques, which are needed to validate computational findings.
From the work so far, he says probiotics appear to be efficacious but context-specific, so the effects may appear dampened in trials with heterogeneous participants.
He underlines that artificial intelligence (AI) is needed to integrate complexity and predict emergent outputs of a biological system that includes a microbiome. Reductionist approaches are somewhat limited because each component of a complex system may behave differently on its own.
Diet is a key way to deliberately manipulate the gut microbiome. Researchers are working on how to push the system in a predictable direction. One approach is to create orthogonal niches for organisms: for example, an item in the diet (such as seaweed) that could support an organism that wouldn’t otherwise be there. His lab is working on tools that predict the likelihood of engraftment of a particular organism in a complex community.
Reliable tools are needed to map taxonomic composition onto functional outputs.
Two branches existed in the history of AI: (1) extracting new knowledge using approaches such as neural nets, and (2) A symbolic AI family of modelling, in which you already have knowledge and you can use it to make predictions about a system (making use of knowledge graphs).
Dr. Gibbons says microbiome measurements will likely be a part of clinical medicine in the future, because the microbiome accounts for individuals’ personalized responses to some interventions that cannot be explained by any other known factor.
In the future, we will be able to develop tools for precision prebiotic, probiotic, and dietary interventions through metabolic modelling work.
Many probiotics have great efficacy in a particular context – so one challenge ahead is to find a rational way to deploy these organisms and to prove they work well. We will need to address the regulatory challenges inherent in personalized approaches as well.

Episode links:

DGGE: Denaturing Gradient Gel Electrophoresis
Paper on correlation analyses: Use and abuse of correlation analyses in microbial ecology
Comment on a new approach to clinical trials required for precision medicine: Personalized medicine: Time for one-person trials
Paper on the gut microbiome and statin response: Heterogeneity in statin responses explained by variation in the human gut microbiome
Paper on developing niches in a microbial ecosystem: Orthogonal dietary niche enables reversible engraftment of a gut bacterial commensal
Paper on horizontal gene transfer in the gut microbiome: Elevated rates of horizontal gene transfer in the industrialized human microbiome

About Dr. Sean Gibbons PhD:

Sean Gibbons earned his PhD in biophysics from the University of Chicago in 2015. He completed his postdoctoral work at MIT in 2018. Sean is now an associate professor at the Institute for Systems Biology, in Seattle. His lab studies the ecology and evolution of microbial communities. In particular, Sean is interested in how host-associated bacterial communities influence the health and wellness of the host organism. His group designs computational and wet-lab tools for studying these complex systems. Ultimately, the Gibbons Lab aims to develop strategies for engineering the ecology of the gut microbiome to improve human health.

Episode 29: Human milk oligosaccharides in the infant gut

October 6, 2023/in Podcast, Season Two /by Laura

Podcast: Play in new window | Download

Subscribe: Apple Podcasts | Spotify | RSS

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.

Human milk oligosaccharides in the infant gut, with Dr. Simone Renwick PhD

Episode summary:

In this episode, the ISAPP hosts discuss human milk and the infant gut with Dr. Simone Renwick PhD from Mother-Milk-Infant Center of Research Excellence (MOMI CORE) at UC San Diego, USA. Dr. Renwick talks about her work investigating how communities of microbes versus individual microbes in the infant gut metabolize human milk oligosaccharide (HMO) structures, and what we know about the origin and functions of the microbes contained in human milk.

Key topics from this episode:

Dr. Renwick studies how components of human milk foster the development of the infant gut microbiota. These components include HMOs (special sugars found in human milk) and the milk microbiota.
HMOs cannot be metabolized by the human body, but when microbes in the infant gut break them down, it has health benefits for the infant (because infants who receive no human milk are predisposed to a range of diseases).
Dr. Renwick used in vitro models to mimic infant microbiota communities, and found that these communities rapidly degraded the HMOs. This metabolism increased microbes associated with health and suppressed potentially pathogenic microbes.
Although most research on HMOs focuses on bifidobacteria that are specially equipped to break them down, she looked at individual strains within the infant gut community and found approximately 100 species capable of directly degrading HMOs.
Once breastfeeding ceases, some microbes in the infant gut adapt to different sources of sugars, but others greatly decrease in abundance.
Microbes act differently in a community than on their own. Within a complex community, microbes that are better equipped to degrade the HMOs will act quickly, producing byproducts that are then are available to other members.
All of the different in vitro models have their advantages and disadvantages. The spatial relationships of the human body are often missing in in vitro models.
Humans appear to have the highest concentration of milk oligosaccharides of any mammal.
The milk microbiota is another active area of investigation. Live microbes are present in the mammary gland, but their source is still unknown. They tend to resemble the composition of the microbiota on the skin as well as the infant oral cavity, but curiously, anaerobic bacteria are also found in the milk microbiota. Somehow these microbes may move from the mother’s gut to the milk. These microbes may not directly metabolize HMOs. (See this paper.)
Formula companies are beginning to put HMO structures into their products – mainly 2′-Fucosyllactose.

Episode links:

About Dr. Simone Renwick PhD:

Dr. Simone Renwick is the Milk & Microbes postdoctoral fellow at the Mother-Milk-Infant Center of Research Excellence (MOMI CORE) at the University of California, San Diego, USA. Her research focuses on understanding the role of human milk components, such as the human milk oligosaccharides (HMOs) and milk microbiota, in fostering the developing infant gut microbiota. She is also interested in the potential therapeutic applications of milk components in diseases that affect adults. Currently, Simone is supervised by Drs. Lars Bode, Rob Knight, Pieter Dorrestein, and Jack Gilbert. Prior to her postdoc, Simone completed her PhD in Molecular and Cellular Biology (MCB) at the University of Guelph, Canada, under the supervision of Dr. Emma Allen-Vercoe.

She was the recipient of the Students and Fellows Association poster prize at the ISAPP 2023 meeting in Sitges, Spain.

Episode 28: Lactobacilli in the microbiomes of the gut, skin, reproductive tract and more

September 21, 2023/in Podcast, Season Two /by Laura

Podcast: Play in new window | Download

Subscribe: Apple Podcasts | Spotify | RSS

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.

Lactobacilli in the microbiomes of the gut, skin, reproductive tract and more, with Prof. Kingsley Anukam PhD

Episode summary:

In this episode, the ISAPP podcast hosts cover a range of topics related to lactobacilli and health with Prof. Kingsley Anukam PhD from Nnamdi Azikiwe University in Nigeria. Prof. Anukam has a special interest in lactobacilli, and studies lactobacilli in microbiomes across many different contexts: fermented foods, skin, gut, and reproductive tract sites. He talks about the wide range of research he has led in Nigeria using diverse sources of funding.

Key topics from this episode:

Prof. Anukam describes his collaboration with Prof. Gregor Reid PhD early in his career, prompted by a paper claiming that African women did not have vaginal microbiomes dominated by lactobacilli. Subsequent work showed this was not the case – confounding factors contributed to the initial result.
He cautions researchers against making conclusions about race or ethnicity when geographical variations or other factors could better account for the differences between groups. In studies it’s important to specify the geography as well as the other factors (dietary, cultural) that may impact the gut microbiome in these populations.
There is a long history of fermented foods in Africa but not a lot of research has been done on them. In a 2009 paper with Prof. Reid, Prof. Anukam reported isolated lactic acid species from a fermented food called okpeye produced in Eastern Nigeria. The isolates showed potential for industrial applications.
Most of his research studies are funded from outside Nigeria, with different sources of funding.
‘Parachute’ science is common in Africa, where researchers come into an African country, obtain samples and leave. He encourages researchers to involve local scientists to build capacity and allow them to do the analysis.
Prof. Anukam describes a clinical trial he led on the skin microbiome and malodor in Nigerian youth. He found the skin microbiome in the armpit was altered if individuals used deodorants and antiperspirants; and these individuals kept having the same malodor issues. Individuals with less odor were found to have more lactobacilli on the skin, with differences in composition between men and women. They developed a topical cream to use as an intervention for 14 days, and found that lactobacilli on the skin increased and less odor was reported.
The microbiome(s) of the male reproductive organs have not been studied very much. Semen has a microbiome, and this is shown by both culture and non-culture methods. It is dominated by lactobacilli, and this corresponds with semen quality. The evidence is mixed on the existence of testes and prostate microbiomes. A gut-testes connection may exist, however, as shown in mouse studies.
Prof. Anukam says in a study of subjects seeking reproductive healthcare, different microbiomes were observed both in males and females having difficulty conceiving.
The semen microbiome could play a significant role in reproduction – for example, it may produce metabolites that could affect the female reproductive tract and influence the environment for conception to take place. When doing in vitro fertilization, evidence has shown that if the samples are contaminated by pathogens, it can be difficult to achieve conception.

Episode links:

Paper from 2009 on fermented foods: African traditional fermented foods and probiotics
Paper from 2021 on skin malodor: Topical cream containing live lactobacilli decreases malodor-producing bacteria and downregulates genes encoding PLP-dependent enzymes on the axillary skin microbiome of healthy adult Nigerians
Paper from 2021 on reproductive microbiomes: Microbiome Compositions From Infertile Couples Seeking In Vitro Fertilization, Using 16S rRNA Gene Sequencing Methods: Any Correlation to Clinical Outcomes?

About Prof. Kingsley Anukam PhD:

Kingsley C Anukam is a research scientist in human microbiome and biotherapeutics with over 20 years experience. He shares his time between Canada and Nigeria as an adjunct professor at Nnamdi Azikiwe University where he assists in the training and supervision of post graduate students working in the area of probiotics, fermented foods, human microbiome, infectious diseases, laboratory diagnostics, human genomics and forensic DNA analysis. He had his graduate education in Nigeria and post doctorate training in Dr. Gregor Reid’s Lab at Lawson Health Research Institute and Department of Microbiology and Immunology, Western University, Canada. He is the first from Africa to show that vaginal microbiome of healthy Nigerian women is similar to women from other populations irrespective of geographical location. He has sequenced and annotated the full genome of over 10 Lactobacillus species of African origin mainly from the reproductive tract and African fermented foods in collaboration with Prof. Sarah Lebeer. He played a significant role in the formation of the DORA project, an ISALA-inspired citizen science for vaginal health in Nigeria. He has over 80 scientific research publications in peer-reviewed journals and listed among first 10 most cited researcher at Nnamdi Azikiwe University by Google Scholar. He is currently the Chief Editor, Journal of Medical Laboratory Science, and a peer-reviewer of several international journals.

Episode 27: Investigating the benefits of live dietary microbes

September 7, 2023/in Podcast, Season Two /by Laura

Podcast: Play in new window | Download

Subscribe: Apple Podcasts | Spotify | RSS

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.

Investigating the benefits of live dietary microbes, with Prof. Colin Hill PhD and Prof. Dan Tancredi PhD

Episode summary:

In this episode, the ISAPP podcast hosts themselves are the experts: Prof. Colin Hill PhD from APC Microbiome Ireland / University College Cork and Prof. Dan Tancredi PhD from University of California – Davis talk about their recent work investigating the health benefits from consuming higher quantities of live dietary microbes – and not just microbes that meet the probiotic criteria.

Key topics from this episode:

Profs. Hill and Tancredi were involved with others in a recent series investigations & 3 published papers on whether there should be a recommended daily intake of live microbes.
Prof. Hill started by writing a blog, prompted by the finding that meta-analyses on probiotics tended to show some general benefits for health. Would this apply to any safe, live microbes – even those that do not meet the probiotic criteria?
Various hypotheses (hygiene hypothesis, old friends hypothesis, missing microbes hypothesis) posit that a lack of microbes is associated with poorer health.
Clean water and clean food have reduced the burden of infectious disease. But at the same time, across populations there has been an increase in chronic diseases. Could a lack of live dietary microbes be contributing to this increase in chronic disease, because the immune system lacks adequate inputs? Or in other words, could there be a general health benefit for healthy people in consuming high quantities of live microbes?
To address the hypothesis scientifically: they investigated the health status of people who eat large vs. small numbers of safe live microbes in their diets. Starting with NHANES data in the US, the researchers classified foods into categories of high / medium / low numbers of live microbes.
Note that not all fermented foods contain live microbes, but some contain high numbers of live microbes. A possible confounding factor in the analysis was that high microbe foods tend to be healthier foods.
The researchers published a series of 3 papers. The 3rd paper showed an association between intake of live microbes and various (positive) measurements of health. Consistent, modest improvements were seen across a range of health outcomes.
This is an association, but statistically the team did use regression analysis to statistically adjust for effects on health that could be due to other factors besides the live microbial intake.
The take-home is not to eat unsafe or rotten food, but rather to eat more high-microbe or fermented foods, and in general eat a healthy diet.

Episode links:

Additional Resources:

Live Dietary Microbes: A role in human health. ISAPP infographic.

About Prof. Colin Hill PhD:
Colin Hill has a Ph.D in molecular microbiology and is a Professor in the School of Microbiology at University College Cork, Ireland. He is also a founding Principal Investigator in APC Microbiome Ireland, a large research centre devoted to the study of the role of the gut microbiota in health and disease. His main interests lie in the role of the microbiome in human and animal health. He is particularly interested in the effects of probiotics, bacteriocins, and bacteriophage. In 2005 Prof. Hill was awarded a D.Sc by the National University of Ireland in recognition of his contributions to research. In 2009 he was elected to the Royal Irish Academy and in 2010 he received the Metchnikoff Prize in Microbiology and was elected to the American Academy of Microbiology. He has published more than 600 papers and holds 25 patents. More than 80 PhD students have been trained in his laboratory. He was president of ISAPP from 2012-2015.

About Prof. Dan Tancredi PhD:
Daniel J. Tancredi, PhD, is Professor in Residence of Pediatrics in the University of California, Davis School of Medicine. He has over 25 years of experience and over 300 peer-reviewed publications as a statistician collaborating on a variety of health-related research. A frequent collaborator on probiotic and prebiotic research, he has attended all but one ISAPP annual meeting since 2009 as an invited expert. In 2020, he joined the ISAPP Board of Directors. Colin Hill and Daniel co-host the ISAPP Podcast Series “Science, Microbes, and Health”. On research teams, he develops and helps implement effective study designs and statistical analysis plans, especially in settings with clusters of longitudinal or otherwise correlated measurements, including cluster-randomized trials, surveys that use complex probability sampling techniques, and epidemiological research. He teaches statistics and critical appraisal of evidence to resident physicians; graduate students in biostatistics, epidemiology, and nursing; and professional scientists. Dan grew up in the American Midwest, in Kansas City, Missouri, and holds a bachelor’s degree in behavioral science from the University of Chicago and masters and doctoral degrees in mathematics from the University of Illinois at Chicago. He lives in the small Northern California city of Davis, with his wife Laurel Beckett (UC Davis Distinguished Professor Emerita), their Samoyed dogs Simka and Milka, and near their two grandkids.

Episode 26: The role of microbes in gut-brain communication

August 1, 2023/in Podcast, Season Two /by Laura

Podcast: Play in new window | Download

Subscribe: Apple Podcasts | Spotify | RSS

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.

The role of microbes in gut-brain communication, with Prof. Emeran Mayer MD

Episode summary:

In this episode, ISAPP podcast host Prof. Dan Tancredi PhD welcomes guest Prof. Emeran Mayer MD, a gastroenterologist and researcher at University of California Los Angeles. They talk about the microbiota-gut-brain axis, covering its evolutionary origins and how this complex system works in the human body to support overall health.

Key topics from this episode:

Microbiota-gut-brain communication has a long evolutionary history: microbes have been around for billions of years and they stored a lot of information in their genes. At some point in evolution microbes got inside the digestive tube of a primitive marine animal called hydra and it proved advantageous for this animal.
The hydra shows the origin of the human enteric nervous system (ENS): microbes live inside this tube and transfer genes to the nerve cells of this digestive tube, showing the origin of neurotransmitters.
Today in humans the neurotransmitters influence gene expression of microbes and change the microbial behaviors; the metabolites produced feed back to the brain.
Prof. Mayer’s initial interest as a gastroenterologist was the ENS and how it regulates motility. Subsequently the ENS was found to regulate many gut functions. The gut also houses a large part of the immune system and a complex hormonal system, and all these systems are connected with each other and communicate with the brain.
There is an increasing understanding that many chronic diseases relate to Inappropriate engagement of the immune system, starting in the gut.
When Prof. Mayer started in the field, the term “gut health” did not exist. Now it’s a ubiquitous term which has associations with wellbeing, acknowledging the gut has influence on many other body systems.
The associations between gut (microbiota) and brain health started with provocative animal experiments from Cork, Ireland, in which researchers manipulated the gut microbiome and found changes in emotion-like behaviors of animals. However, it has been difficult to translate to human interventions.
How do microbiome-targeted dietary interventions affect the brain? We do know the “Standard American Diet” (deficient in fiber) has changed the gut microbes in a way that compromises the production and maintenance of the gut barrier.
There are many misconceptions about “leaky gut”, but basically contact between beneficial microbes and immune system sensors stimulate the immune system of the gut to low-grade inflammation. This can alter the tight junctions, making the gut more permeable, and ultimately this can affect the brain. Diet can affect the role of microbes in maintaining an effective gut barrier.
Prof. Mayer describes how he ended up studying the microbiota-gut-brain axis – he would not have predicted how important and popular this field would become.
In the future, there will be more sophisticated and personalized interventions. He sees a paradigm shift happening from reductionist approaches in medicine to systems biological approaches. This field is making us acknowledge that diet will play a major role.

Episode links:

Prof. Mayer’s first academic book, Basic and Clinical Aspects of Chronic Abdominal Pain (Pain Research and Clinical Management)
Prof. Mayer’s first book for the general public, The Mind-Gut Connection
Review on microbiota-gut-brain axis: The Microbiota-Gut-Brain Axis: From Motility to Mood
Review on the impact of diet on intestinal permeability: Influence of a high-fat diet on gut microbiota, intestinal permeability and metabolic endotoxaemia
Review on microbiota-dependent interactions between diet and the immune system: Human nutrition, the gut microbiome, and immune system: envisioning the future

About Prof. Emeran Mayer MD:

Emeran A Mayer is a Gastroenterologist, Neuroscientist and Distinguished Research Professor in the Department of Medicine at the David Geffen School of Medicine at UCLA, the Executive Director of the G. Oppenheimer Center for Neurobiology of Stress & Resilience and Founding Director of the Goodman Luskin Microbiome Center at UCLA. He is one of the pioneers and leading researchers in the bidirectional communication within the brain gut microbiome system with wide-ranging applications in intestinal and brain disorders. He has published 415 scientific papers, co edited 3 books and has an h-index of 125. He published the best selling books The Mind Gut Connection in 2016, the Gut Immune Connection in June 2021, and the recipe book Interconnected Plates in 2023. He is currently working on a MasterClass and a PBS documentary about the mind gut immune connection. He is the recipient of numerous awards, including the 2016 David McLean award from the American Psychosomatic Society and the 2017 Ismar Boas Medal from the German Society of Gastroenterology and Metabolic Disease.

Episode 25: The effects of metabolites in the colon

July 18, 2023/in Podcast, Season Two /by Laura

Podcast: Play in new window | Download

Subscribe: Apple Podcasts | Spotify | RSS

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.

The effects of metabolites in the colon, with Prof. Kristin Verbeke PhD

Episode summary:

In this episode, the ISAPP podcast hosts talk about colonic metabolites with Prof. Kristin Verbeke PhD, from KU Leuven, Belgium. She talks about characterizing microbial metabolism in the colon and the consequences of producing various metabolites, both beneficial ones (such as short-chain fatty acids) and potentially detrimental ones.

Key topics from this episode:

Prof. Verbeke is a pharmacist by training, and now leads hospital breath testing and carries out research on microbial metabolites in the gastrointestinal tract, including how prebiotics and probiotics can change bacterial metabolism.
The majority of protein in the diet is digested in the small intestine, but about 5% of animal protein and 10-15% of plant protein reaches the large intestine to be fermented by the microbiota. This produces metabolites, which are shown in vitro to be toxic. However, in vivo there is less evidence of toxicity; the negative effects of these metabolites may be reduced by the interactions of different compounds in the colon.
Short-chain fatty acids (SCFAs) are produced when the body digests dietary fiber, and Prof. Verbeke’s group and others are investigating whether they are responsible for the benefits of eating fiber.
Most SCFAs are quickly absorbed in the large intestine, and they serve as an energy source for the cells. They then travel to the liver via portal circulation, where they have additional functions. What’s left over reaches systemic circulation.
The difficulty is knowing how many SCFAs are produced in the colon, and how many reach systemic circulation. In one experiment, they labeled the SCFAs that were administered to the colon via capsule; 36% ended up in systemic circulation. Further, when SCFAs were administered at physiological doses the subjects receiving them (compared to placebo) showed a lower cortisol response to stress.
SCFAs also affect fat oxidation and fat synthesis in the liver. Their relevance to non-alcoholic fatty liver disease are being investigated.
It’s important to eat fiber, and lots of different types. After fiber consumption, SCFAs increase in a sustained manner and take about 8h to get back to baseline. But with SCFA delivery via capsule they spike quickly and then disappear.
As for coatings to deliver to the colon, some coatings are time-dependent, pH dependent, etc. and this is an area for further exploration.

Episode links:

Study on protein fermentation: Modulation of protein fermentation does not affect fecal water toxicity: a randomized cross-over study in healthy subjects
Study on SCFAs: Systemic availability and metabolism of colonic-derived short-chain fatty acids in healthy subjects: a stable isotope study
Review: Coated dosage forms for colon-specific drug delivery

About Prof. Kristin Verbeke PhD:

Kristin Verbeke graduated from the KU Leuven, Belgium as a pharmacist in 1991. She obtained a PhD in Pharmaceutical Sciences at the Laboratory of Radiopharmaceutical Chemistry in 1995 and subsequently spend a postdoctoral period in developing radioactively labelled compounds. In 2002, she was appointed at the department of gastroenterology of the Medical Faculty of the Leuven University where she got involved in the use of stable isotope labelled compounds to evaluate gastrointestinal functions. Within the University Hospitals Leuven, she is responsible for the clinical application of diagnostic 13C- and H2-breath tests. Her current research interest specifically addresses the microbial bacterial metabolism in the human colon. Her team has developed several analytical techniques based on mass spectrometry and stable isotope or radioisotope technologies to evaluate several aspects of intestinal metabolism and function in humans (transit time, intestinal permeability, carbohydrate fermentation, protein fermentation, metabolome analysis). Collaborative research has allowed showing an aberrant bacterial metabolism in patient groups with end stage renal failure, inflammatory bowel diseases, irritable bowel disorders and alcohol abuse. These collaborations all have resulted in high quality peer-reviewed papers. In addition, she showed the impact of dietary interventions (modulation of macronutrient composition, pre- or probiotic interventions) on the microbial metabolism and its impact on health. As a PI, she acquired grant support from the university and different funding bodies and successfully completed these projects. Similarly, she supervised several PhD projects that all resulted in the achievement of a PhD degree. Her research resulted in over 200 full research papers. Together with colleague Prof. J. Delcour, she was the beneficiary of the W.K. Kellogg Chair in Cereal Sciences and Nutrition (2010-2020). She is the president of the Belgian Nutrition Society, the vice-chair of the Leuven Food Science and Nutrition Center, and the co-chair of the Prebiotic task force at ILSI Europe. Furthermore, Kristin Verbeke is the editor of the journal Gut Microbiome and member of the editorial board of Gastrointestinal Disorders. Kristin joined the ISAPP Board of Directors in 2023.

Episode 24: Reflections on the probiotic field and ISAPP’s role

July 4, 2023/in Podcast, Season Two /by Laura

Podcast: Play in new window | Download

Subscribe: Apple Podcasts | Spotify | RSS

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.

Reflections on the probiotic field and ISAPP’s role, with Dr. Mary Ellen Sanders PhD

Episode summary:

In this episode, the ISAPP podcast hosts talk about how the probiotic field has evolved over the past 20 years with Dr. Mary Ellen Sanders PhD, ISAPP’s outgoing executive director. She describes how ISAPP is a unique organization advancing the science in the field, highlights what she has enjoyed about being a part of the ISAPP community, and looks ahead to the future of the field.

Key topics from this episode:

Sanders describes her career path and how it led to her role with ISAPP.
Both ISAPP and Sanders’ role have changed over time, but she always appreciated two things: great scientific discussions, and interacting with an excellent board of directors.
ISAPP has always been dedicated to following the science, highlighting where the evidence is but also the shortcomings of the evidence.
The development of microbiome science changed the field of probiotics but it remains important to focus on what probiotics can do for health, rather than what they can do for the microbiome.
Mechanisms are important to elucidate, but the most important thing is whether a product impacts health.
Sanders says regulations are needed and in the future she hopes regulators will reach out to the expert scientists more frequently and be clear about the standards they expect for a claim.
ISAPP meetings are unique–both scientifically enlightening and a lot of fun. Longtime ISAPP board member Gregor Reid had the initial idea for the successful ‘discussion groups’ held every year.
In the future, Sanders thinks probiotics will be used more precisely, like medicines. But also the concept of live dietary microbes may become more popular, with quantities of safe microorganisms being consumed for health benefits.

Episode links:

Read about Todd Klaenhammer, a well-known food microbiologist who supervised Sanders as a graduate student.
Early paper by Mary Ellen Sanders (1993): Effect of Consumption of Lactic Cultures on Human Health
An overview of ISAPP activities is found here.
The ISAPP-linked scientific papers on live dietary microbes:
Should There Be a Recommended Daily Intake of Microbes?
A Classification System for Defining and Estimating Dietary Intake of Live Microbes in US Adults and Children
Positive Health Outcomes Associated with Live Microbe Intake from Foods, Including Fermented Foods, Assessed using the NHANES Database

About Dr. Mary Ellen Sanders PhD:

Mary Ellen Sanders, PhD has served in several roles within ISAPP. She was the founding president, executive science officer and executive director and has retired from ISAPP as of June 30, 2023. She is also a consultant in the area of probiotic microbiology. She works internationally with food and supplement companies to develop new probiotic products and offers perspective on paths to scientific substantiation of probiotic product label claims. She is the current chair of the United States Pharmacopeia’s Probiotics Expert Panel, was a member of the working group convened by the FAO/WHO that developed guidelines for probiotics and serves on the World Gastroenterology Organisation Guidelines Committee preparing practice guidelines for the use of probiotics and prebiotics for gastroenterologists.

Episode 23: Studying microbial ecosystems and how they support health

June 15, 2023/in Podcast, Season Two /by Laura

Podcast: Play in new window | Download

Subscribe: Apple Podcasts | Spotify | RSS

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.

Studying microbial ecosystems and how they support health, with Prof. Emma Allen-Vercoe PhD

Episode summary:

In this episode, the ISAPP podcast hosts talk about microbial ecosystems with Prof. Emma Allen-Vercoe PhD from the University of Guelph in Canada. Prof. Allen-Vercoe describes how her lab brings together information from microbial sequencing and culturing to learn about the human gut microbiome and how it supports health. She discusses what we know about the industrialized gut microbiome and possible ways to improve health by manipulating it.

Key topics from this episode:

What the microbiome is and the suite of tools that are typically used to study it.
Allen-Vercoe does both sequencing and culturing in her lab as well as metabolomics, proteomics, and transcriptomics to discover on a molecular level at what the microbes are doing. They have a model system called “Robogut” to study microbial ecosystems.
Culturing is still crucial and it’s important for trainees in microbiology to gain experience culturing organisms that are less straightforward to grow. The late Sydney Finegold inspired others to try culturing more challenging microorganisms.
The challenge of culturing is matching the techniques in the lab to what happens in nature when it grows. Her lab builds metagenome-associated genomes to be able to predict the particular substrates that a certain microbe needs to grow.
The “missing microbes” hypothesis is that the human microbiome has been depleted over a few generations in people from industrialized societies, and this correlates with an increase in chronic diseases.
The Yanomami people from South America have very diverse gut microbiomes and they share certain species with other non-industrialized societies very distant from them around the world, which are not found in industrialized populations. People in industrialized societies are never exposed to these microbes, but even if they were, the microbes might not stick around because the substrates needed to sustain them (e.g. through the diet) are absent.
The industrialized microbiome is not necessarily ‘bad’ but we do have to find out more about whether the lack of certain microbes has health effects. This is possible through the Robogut system, which can perturb microbial ecosystems and look at their behavior without affecting people’s health.
Fecal transplants have limitations, so they’ve started to work on therapeutic ecosystems. These are “clean” or defined ecosystems that can be administered therapeutically.

Episode links:

Paper on the Robogut system: The Robogut: A Bioreactor Model of the Human Colon for Evaluation of Gut Microbial Community Ecology and Function
Allen-Vercoe mentioned the work of Sydney (Sid) Finegold in tackling difficult-to-culture microorganisms.
2009 review by Blaser and Falkow: What are the consequences of the disappearing human microbiota?
Book by Martin Blaser: Missing Microbes – How the Overuse of Antibiotics Is Fueling Our Modern Plagues
Paper on Yanomami gut microbiomes: Gut Microbiome Biomarkers and Functional Diversity Within an Amazonian Semi-Nomadic Hunter-Gatherer Group
Paper from Allen-Vercoe lab: Culturing Human Gut Microbiomes in the Laboratory

About Prof. Emma Allen-Vercoe PhD:

Emma obtained her BSc (Hons) in Biochemistry from the University of London, and her PhD in Molecular Microbiology through an industrial partnership with Public Health England. Emma started her faculty career at the University of Calgary in 2005, with a Fellow-to-Faculty transition award through CAG/AstraZeneca and CIHR, to study the normal microbes of the human gut. In particular, she was among the few that focused on trying to culture these ‘unculturable’ microbes in order to better understand their biology. To do this, she developed a model gut system to emulate the conditions of the human gut and allow communities of microbes to grow together, as they do naturally. Emma moved her lab to the University of Guelph in late 2007, and has been a recipient of several Canadian Foundation for Innovation Awards that has allowed her to develop her specialist anaerobic fermentation laboratory further. This has been recently boosted by the award of a Tier 1 Canada Research Chair in Human Gut Microbiome Function and Host Interactions. In 2013, Emma co-founded NuBiyota, a research spin-off company that aims to create therapeutic ecosystems as biologic drugs, on a commercial scale. The research enterprise for this company is also based in Guelph.

Episode 22: Biotics in animal and human nutrition

May 9, 2023/in Podcast, Season Two /by Laura

Podcast: Play in new window | Download

Subscribe: Apple Podcasts | Spotify | RSS

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.

Biotics in animal and human nutrition, with Prof. Kelly Swanson

Episode summary:

In this episode, the ISAPP podcast hosts join guest Prof. Kelly Swanson PhD from University of Illinois at Urbana-Champaign, to discuss the role of biotics in animal and human nutrition. They review the criteria for prebiotics and synbiotics, then discuss how we gain knowledge about nutrition and the role of biotics in animals compared to humans.

Key topics from this episode:

A good argument can be made that biotics are essential for our diet; they are beneficial even if efficacy is sometimes difficult to prove.
Nutrients have an impact on the host’s health and simultaneously on the host-associated microbes.
Health benefits are essential to the FDA definition of fiber.
Antibiotics’ effect on the microbiota: short-term effects may be minor, but we still don’t know the long-term effects.
The synbiotics definition, criteria for products to meet this definition, and the health outcomes from using these biotic substances.
The difference between complementary and synergistic synbiotics.
When studying biotics in companion animals (cats and dogs), can results from one host be extrapolated to another host? Final studies should be in the target host.
Biotics are important in veterinary medicine and a popular topic of study.
Predictions about the future of nutrition science as informed by the microbiome.

Episode links:

US FDA: United States Food and Drug Administration
Randomized, controlled trial from Swanson lab on a potential prebiotic: 454 pyrosequencing reveals a shift in fecal microbiota of healthy adult men consuming polydextrose or soluble corn fiber.
Prebiotic definition: Expert consensus document: The International Scientific Association for Probiotics and Prebiotics (ISAPP) consensus statement on the definition and scope of prebiotics.
Synbiotic definition: The International Scientific Association for Probiotics and Prebiotics (ISAPP) consensus statement on the definition and scope of synbiotics.
Review on antibiotic use in agriculture: Antibiotics Overuse in Animal Agriculture: A Call to Action for Health Care Providers.

Additional resources:

Synbiotics. ISAPP infographic.
New synbiotic definition lays the groundwork for continued scientific progress. ISAPP blog post.
Synbiotics: Definitions, Characterization, and Assessment. ISAPP webinar.

About Prof. Kelly Swanson:

Kelly Swanson is the Kraft Heinz Company Endowed Professor in Human Nutrition at the University of Illinois at Urbana-Champaign. His laboratory studies the effects of nutritional interventions, identifying how diet impacts host physiology and gut microbiota. His lab’s primary emphasis is on gastrointestinal health and obesity in dogs, cats, and humans. Much of his work has focused on dietary fibers and ‘biotics’. Kelly has trained over 40 graduate students and postdocs, published over 235 peer-reviewed manuscripts, and given over 150 invited lectures at scientific conferences. He is an active instructor, teaching 3-4 nutrition courses annually, and has been named to the university’s ‘List of Teachers Ranked as Excellent by Their Students’ 30 times. He serves on advisory boards for many companies in the human and pet food industries and non-profit organizations, including the Institute for the Advancement of Food and Nutrition Sciences and International Scientific Association for Probiotics and Prebiotics.

Episode 21: Genetically modified microorganisms for health

April 24, 2023/in Podcast, Season Two /by Laura

Podcast: Play in new window | Download

Subscribe: Apple Podcasts | Spotify | RSS

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.

Genetically modified microorganisms for health, with Dr. Carlos Gómez-Gallego

Episode summary:

In this episode, ISAPP podcast host Dan Tancredi joins guest Carlos Gómez-Gallego PhD, from University of Eastern Finland, to discuss genetically modified microorganisms. They go over what genetically modified microorganisms are, their potential benefits over non-modified microorganisms, and how they might improve human health–in particular, diseases of the metabolic and immune systems.

Key topics from this episode:

Genetically modified microorganisms are those that have been modified using genetic engineering, giving them abilities they do not normally have. Functions can be either conferred or deleted. Different genetic engineering tools can be used – e.g. to make them produce therapeutic compounds, or make them increase degradation of toxins or harmful compounds.
One advantage over non-modified microorganisms is the potential to have continuous delivery of a therapeutic compound, and the potential to deliver it to a localized area in order to avoid unwanted interactions.
Genetically modified microorganisms have promise in metabolic and immune-linked disorders such as non-alcoholic fatty liver disease (NAFLD).
In NAFLD, genetically modified E. coli Nissle can secrete hormones that are under-regulated or under-expressed. His group modified bacteria by introducing a plasmid that allowed it to produce aldafermin, an analog of the human hormone fibroblast growth factor 19 (FGF19).
With genetically engineered microorganisms, we must consider the benefits but also the risks. However, if it’s a therapeutic for a disease with few or no alternatives, there’s a strong case for developing them.
To increase efficacy and safety of these microorganisms, it’s possible to introduce sensors that produce the therapeutic in response to different stimuli. Also, it’s important to modify the bacteria so their use is controlled and they cannot spread. They can also be modified to avoid transmission of genes.
Are there market-approved genetically modified microorganisms? No approved ones yet, but some are in Phase 1 and Phase 2 clinical trials.

Episode links:

Review on manipulating bacteria for cancer treatment — Tweak to Treat: Reprograming Bacteria for Cancer Treatment

About Dr. Carlos Gómez-Gallego:

I am a Senior Researcher at the Institute of Public Health and Clinical Nutrition (University of Eastern Finland). I have completed two university degrees, one in Biology and another in Food Science and Technology, and an MSc in Nutrition and Health. I subsequently completed a Ph.D. from the University of Murcia, where I investigated the effect of infant formula processing on the content of polyamines and bioactive peptides, and their impact on intestinal microbiota and immune system development during lactation.

My research and interests are primarily focused on advancing the understanding of the impact of diet, food, and bioactive compounds on human microbiota and their association with human health. As part of the BestTreat project (https://besttreat.eu/index.html), I have co-supervised two PhD students (Johnson Lok and Valeria Ianone) who evaluated the potential use of engineered E. coli Nissle 1917 producing human hormones for the treatment of non-alcoholic fatty liver disease (NAFLD) in a mouse model. The first publication has already been submitted, and the second is currently in process.

More info about my publications:
Research Gate https://www.researchgate.net/profile/Carlos-Gomez-Gallego
UEF connect https://uefconnect.uef.fi/en/person/carlos.gomez-gallego/#information

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

April 5, 2023/in Podcast, Season Two /by Laura

Podcast: Play in new window | Download

Subscribe: Apple Podcasts | Spotify | RSS

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:

The website for the European Society for Paediatric Gastroenterology Hepatology and Nutrition (ESPGHAN): https://www.espghan.org/
See here for a primer on evidence-based medicine: The Centre for Evidence-Based Medicine.
The new ESPGHAN guidelines on probiotics: Probiotics for the Management of Pediatric Gastrointestinal Disorders: Position Paper of the ESPGHAN Special Interest Group on Gut Microbiota and Modifications.
Important clinical trial on a probiotic for acute gastroenteritis: Lactobacillus GG administered in oral rehydration solution to children with acute diarrhea: a multicenter European trial.
Recently published clinical trial co-authored by Prof. Szajewska on prevention of antibiotic-associated diarrhea: Multispecies Probiotic for the Prevention of Antibiotic-Associated Diarrhea in Children: A Randomized Clinical Trial.
This paper co-authored by Prof. Szajewska shows an example of actionable evidence: Lactobacillus reuteri to Treat Infant Colic: A Meta-analysis.
Paper by ESPGHAN on the need for independent verification of probiotic quality: Commercial Probiotic Products: A Call for Improved Quality Control. A Position Paper by the ESPGHAN Working Group for Probiotics and Prebiotics. Also see Improving End-User Trust in the Quality of Commercial Probiotic Products.

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

March 21, 2023/in Podcast, Season Two /by Laura

Podcast: Play in new window | Download

Subscribe: Apple Podcasts | Spotify | RSS

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:

Kennedy, et al. paper published in Nature: Questioning the fetal microbiome illustrates pitfalls of low-biomass microbial studies
Kennedy refers to two papers in 2021 with differing conclusions: Fetal meconium does not have a detectable microbiota before birth and Microbial exposure during early human development primes fetal immune cells.

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.

Episode 18: The definition of postbiotics

March 6, 2023/in Podcast, Season Two /by Laura

Podcast: Play in new window | Download

Subscribe: Apple Podcasts | Spotify | RSS

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.

The definition of postbiotics, with Dr. Gabriel Vinderola and Prof. Seppo Salminen

Episode summary:

In this episode, the ISAPP podcast hosts join guests Gabriel Vinderola, PhD, Principal Researcher at the
National Scientific and Technical Research Council (CONICET) and Associate Professor at University of Litoral in Argentina, and Seppo Salminen, PhD, Professor at University of Turku in Finland, to discuss the relatively recent definition of postbiotics and what kinds of substances are included in this category. They talk about the criteria for something to qualify as a postbiotic, common mechanisms of action for postbiotics, and how postbiotic science has brought new perspectives on the study of probiotics.

Key topics from this episode:

What are postbiotics? Dr. Vinderola and Prof. Salminen dive deep into the definition of postbiotics created in 2021 and what it entails.
Postbiotics, similar to probiotics, prebiotics, and synbiotics, must provide health benefits to the host.
The nature of the postbiotic preparation is important for its health benefits. When the inactivation process is changed, this can lead to altered health benefits, and clinical studies must be repeated to ensure the desired health benefits are maintained.
They explain why “inanimate” was chosen to describe the microorganisms / components in a postbiotic preparation.
What is the mode of action, or how do postbiotics work?
- Postbiotics show similar mechanisms of action to probiotics, except for ones requiring viability, since postbiotics will not grow and produce metabolic byproducts in the host.
- Postbiotics can benefit the host via physical interaction with the host epithelial and immune cells.
- A primary mechanism of action is likely to be through activation of the immune system, through which postbiotics can affect inflammation and some disease conditions.
- Postbiotics may also affect the microbiome composition and ability to inhibit pathogens.
From a regulatory point of view, inanimate microorganisms may represent an easier category to prove safe for users. For industry, postbiotics may be more convenient with a longer shelf life.
Some controversy still exists around the ISAPP-led postbiotic definition, and this has led to valuable discussions that are crucial to scientific progress. So far the authors of the definition have defended their stance.

Episode abbreviations and links:

ISAPP scientific consensus definition of postbiotics, published in Nature Reviews Gastroenterology & Hepatology: The International Scientific Association of Probiotics and Prebiotics (ISAPP) consensus statement on the definition and scope of postbiotics
Study on a postbiotic for addressing chronic stress in students: Health Benefits of Lactobacillus gasseri CP2305 Tablets in Young Adults Exposed to Chronic Stress: A Randomized, Double-Blind, Placebo-Controlled Study
Study using live bifidobacteria to address irritable bowel syndrome: Randomised clinical trial: Bifidobacterium bifidum MIMBb75 significantly alleviates irritable bowel syndrome and improves quality of life–a double-blind, placebo-controlled study
Study using dead bifidobacteria (same strain as above) to address irritable bowel syndrome: Heat-inactivated Bifidobacterium bifidum MIMBb75 (SYN-HI-001) in the treatment of irritable bowel syndrome: a multicentre, randomised, double-blind, placebo-controlled clinical trial
Opinion from the European Food Safety Authority (EFSA) Panel on Nutrition, Novel Foods and Food Allergens (NDA) on pasteurized Akkermansia muciniphila as a novel food (NF) pursuant to Regulation (EU) 2015/2283: Safety of pasteurised Akkermansia muciniphila as a novel food pursuant to Regulation (EU) 2015/2283

Additional Resources:

Postbiotics. ISAPP infographic (also available in Japanese and Spanish).

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

Definition of postbiotics: A panel debate in Amsterdam. ISAPP blog post.

About Dr. Gabriel Vinderola:

Gabriel Vinderola graduated at the Faculty of Chemical Engineering from the National University of Litoral (Santa Fe, Argentina) in 1997. He obtained his Ph.D. in Chemistry in 2002 at the same University. He collaborated with several research teams in Canada, Spain, France, Italy, Germany, Brazil and Finland. He is presently Principal Researcher of the National Scientific and Technical Research Council (CONICET) and Associate Professor at the Food Engineering Department of his home Faculty. He participated in 1999 in the development of the first commercial cheese carrying probiotic bacteria in Latin America. In 2011, he was awarded the prize in Food Technology for young scientists, by the National Academy of Natural, Physic and Exact Sciences from Argentina. He published more than 120 original scientific publications in international refereed journals and book chapters. From 2020 to present, he serves as a member of the board of directors of the International Scientific Association for Probiotics and Prebiotcis (ISAPP). He is engaged in science communication to the general public through Instagram (@gvinde).

About Prof. Seppo Salminen:

Seppo Salminen, MSc, MS, PhD, is a Senior Advisor, Functional Foods Forum (FFF) at the University of Turku. His areas of expertise are gut microbiota, probiotics and prebiotics, nutrition and food safety, and EU regulations. Seppo teaches the topics of lactic acid biotechnology, functional foods and EU legislation and conducts research into food and health, intestinal microbiota, probiotics, prebiotics, functional foods, food legislation, health claims, and novel foods.

Episode 17: Using metabolomics to learn about the activities of gut microbes

February 23, 2023/in Podcast, Season Two /by Laura

Podcast: Play in new window | Download

Subscribe: Apple Podcasts | Spotify | RSS

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.

Using metabolomics to learn about the activities of gut microbes, with Dr. Anisha Wijeyesekera

Episode summary:

In this episode, the ISAPP podcast hosts address the topic of metabolomics with Dr. Anisha Wijeyesekera, PhD, a Lecturer in the Department of Food and Nutritional Sciences at the University of Reading, United Kingdom. Dr. Wijeyesekera gives an overview of how metabolic profiling works, including the information provided by different biological samples, and discusses how metabolomics can be used to piece together the contributions of microbes to host health.

Key topics from this episode:

Dr. Wijeyesekera introduces the field of metabolomics and describes it as an essential part of systems biology. Metabolic profiling provides a real-time snapshot of the multiple metabolic processes going on in a system at the time the sample was collected.
Metabolites are the end products of metabolism; the gut microbiota is the most metabolically active of the microbiomes in the human body.
Methodology depends on what information you hope to uncover from your samples. Different biological samples (e.g. stool, urine, plasma) provide different pieces of information; this is cross-referenced with information on metabolic pathways.
One application of metabolomics is in identifying biomarkers that can predict patient outcomes. Identifying differences in microbes as well as metabolites could lead to the development of dietary-based supplements for patients to take alongside clinical treatments.
Changes in microbial composition may not be that meaningful if the bugs that change are doing the same thing in the end; this is what metabolomics helps uncover.
Metabolomics gives you insights into mechanisms when you have a probiotic or prebiotic trial with clinical outcomes.
Short-chain fatty acids are metabolites that are frequently associated with health; changes in these is a clue that the gut microbiota has been impacted by the intervention.
Bile acids are metabolites that come from diet. Microbes convert primary bile acids to secondary, which circulate throughout the body. You can measure bile acids to see how gut microbiota are affected by an intervention.
Metabolomics is very promising and may be used in more probiotic and prebiotic studies in the future.

Episode abbreviations and links:

Reviews on metabolic phenotyping: Metabolic phenotyping in clinical and surgical environments and Metabolic Phenotyping in Health and Disease.
Dr. Wijeyesekera’s research on how critical illness affects the gut microbiota: Multi-Compartment Profiling of Bacterial and Host Metabolites Identifies Intestinal Dysbiosis and Its Functional Consequences in the Critically Ill Child and Profiling Gut Microbiota and Bile Acid Metabolism in Critically Ill Children
Papers on how metabolic phenotyping is helping us to better understand the gut microbiota: Gut microbiota composition and activity in relation to host metabolic phenotype and disease risk and Genome-microbiome interplay provides insight into the determinants of the human blood metabolome and The fecal metabolome as a functional readout of the gut microbiome.

About Dr. Anisha Wijeyesekera:

Anisha is a Lecturer in the Department of Food and Nutritional Sciences at the University of Reading, United Kingdom. She previously worked at Imperial College London, where she also obtained her PhD (in Biochemistry). Anisha’s research applies a combined microbial and metabolic phenotyping approach, to better understand the tripartite relationship between diet, gut microbiota and human health. At the University of Reading, she conducts in vitro and in vivo studies for functional assessment of the gut microbiota, particularly in response to prebiotics and probiotics. The ultimate aim is to use this information to tailor nutritional or other interventional therapy to improve health outcomes.

Episode 16: The honey bee microbiome and potential for probiotics

February 6, 2023/in Podcast, Season Two /by Laura

Podcast: Play in new window | Download

Subscribe: Apple Podcasts | Spotify | RSS

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.

The honeybee microbiome and potential for probiotics, with Dr. Brendan Daisley

Episode summary:

In this episode, the ISAPP podcast hosts cover the honey bee microbiome with Brendan Daisley, PhD, who is currently a post-doctoral fellow at the University of Guelph in Canada. Daisley explains how the honeybee microbiome is unique, why it’s important for bee health, and the potential for probiotic applications as well as the practicalities of how live microorganisms are delivered to hives.

Key topics from this episode:

Daisley’s research is motivated by declining bee populations and finding ways to find ways to stop this.
He originally researched how probiotics could have detoxification functions in humans; this led to the question of whether probiotics could help reduce the toxicity of pesticides in bees and possibly affect resistance to infectious diseases.
Each individual bee has a microbiome of its own. Unlike other insects, bees have a core, defined microbial community in their guts.
Surprisingly, no one has successfully derived a completely germ-free honey bee. Microbiota-depleted bees do exist, however.
Research is ongoing on how microbes may even enable life in bee species — e.g. the recent finding that pupation in stingless bees is triggered by fungi.
Bees are affected by pesticides; many pesticides also have antimicrobial effects, but regulatory agencies do not track these effects.
Supplementing bees with beneficial strains of microbes can improve bee health and resistance to infectious diseases. However, no good baseline studies have been done on the bee gut, so it’s difficult to know what’s ‘normal’ and what is missing. The Canadian Bee Gut Project aims to determine this.
It’s possible to try finding bees that may have had less exposure to pesticides, but it’s difficult to determine past exposure because bees are traded and sent all over the world.
Wolbachia is a valuable endosymbiont for bees, and acts like a ‘secondary mitochondria’ in their cells. Currently it is hardly ever found in honey bees, possibly because of chronic exposure to tetracycline.
Probiotics can be delivered to bees using a “BioPatty” or a spray-based formula; the delivery method is very important. Supplementing the hive with certain probiotics can suppress outbreaks of American Foulbrood disease when they happen.
Daisley and colleagues used 3 probiotic strains, which remain present in the bee host for several weeks.
As far as potential prebiotics for bees, it has been observed that pollen fibers can beneficially modulate the honey bee microbiome.
The healthy honey bee microbiome should be dominated by lactic acid bacteria.

Episode abbreviations and links:

This is the first paper on American foulbrood (AFB), caused by the spore-forming bacterium Paenibacillus larvae, that Daisley and colleagues captured: Novel probiotic approach to counter Paenibacillus larvae infection in honey bees
In this paper, the group showed LX3 supplementation in the BioPatty formula can decrease AFB load to near undetectable levels: Lactobacillus spp. attenuate antibiotic-induced immune and microbiota dysregulation in honey bees. This paper showed the LX3 strains can mitigate some of the negative health side effects of antibiotic exposure. Another paper from the California study, directly comparing the BioPatty and the new BioSpray, is in press.
See these reviews related to the honey bee microbiome: Missing microbes in bees: how systematic depletion of key symbionts erodes immunity, and Deteriorating microbiomes in agriculture – the unintended effects of pesticides on microbial life
Check out the website for the Canadian Bee Gut Project. The project aims to define what constitutes a “healthy” microbiome in honey bees by performing country-wide sampling in coordination with beekeepers across Canada.

About Dr. Brendan Daisley:

Dr. Brendan Daisley is a postdoc at the University of Guelph (Allen-Vercoe lab) and the current President of the Students and Fellows Association of ISAPP. He graduated from his PhD in Microbiology & Immunology at Western University in 2021 (supervisor: Dr. Gregor Reid), during which he received several national awards including the Armand Frappier Outstanding Student Award, adjudicated by The Canadian Society of Microbiologists. Brendan has a broad range of experience in environmental application of probiotics to honey bees and, notably, he was the first to introduce the theory of ‘missing microbes’ within the field of honey bee microbiome research. During his PhD, he helped coordinate several large field trials across North America (mostly in Ontario and California) showing that supplementation of probiotic lactobacilli strains to honey bees could improve colony-level health outcomes. During his postdoc work, he has developed a microbiome database tool (BEExact) for improved detection of uncultivated ‘microbial dark matter’, established a bioreactor model of the honey bee gut microbiome (the RoBEEgut), and co-founded the Canadian Bee Gut Project (https://beegutproject.uoguelph.ca) – a nationwide crowdsourcing initiative that aims to deeply sequence thousands of bee microbiome samples to increase our knowledge on the multifactorial drivers of honey bee mortality.

Episode 15: A primer on prebiotics

January 24, 2023/in Podcast, Season Two /by Laura

Podcast: Play in new window | Download

Subscribe: Apple Podcasts | Spotify | RSS

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.

A primer on prebiotics, with Dr. Karen Scott

Episode summary:

In this episode, the ISAPP podcast hosts talk about prebiotics with Karen Scott, PhD, who is an ISAPP board member and Senior Research Fellow at Rowett Institute, University of Aberdeen, Scotland. Scott describes what prebiotics are, as well as the latest thinking about how they fit within an overall healthy diet and how they confer health benefits through the gut microbiota.

Key topics from this episode:

Dr. Scott and colleagues at the Rowett Institute began many years ago by working on anaerobic bacteria from the rumen of animals, then started to focus on the bacteria in the human large intestine.
Prebiotics (see definition below) stimulate the growth of beneficial bacteria in the human gut, and in doing so, benefit host health.
Prebiotics alone cannot guarantee health: they must be consumed in addition to a healthy regular diet, which helps support thediversity of all gut microbes.
Prebiotics are not necessarily supplements; they are found in high amounts in many foods such as bulb-based vegetables, banana, and plantain. Around 5g of prebiotic per days is beneficial for health.
Not all prebiotics are equal: they each stimulate the growth of particular groups of bacteria. By definition, they must be selectively utilized (that is, some bacteria but not others must use them), and this differentiates prebiotics from fiber.
Some prebiotics are shown to improve gut transit (i.e. reduce constipation). One common example of the benefit of prebiotics has to do with bone health: metabolism of prebiotics in the colon tends to lower the pH; this increases calcium absorption for supporting bone health. Other benefits involve the production of short-chain fatty acids.
Bifidobacterium have traditionally been a group of bacteria targeted by prebiotics. Some Bifidobacterium produce lactate, and other bacteria produce butyrate (important for colonic health) from lactate. In healthy adults, there are bacteria that are equally or more important than bifidobacteria, however.
Prebiotics can target other body sites besides the gut.
Prebiotics that can be used by a bacteria in pure culture are not necessarily used by those bacteria within the ecosystem of the human gut.
New experimental platforms exist to see which bacteria are producing specific compounds on the growth of a specific substrate. But a model may not represent what is happening in the host, so this must be specifically tested.
Human milk oligosaccharides are a great example of how prebiotics are important to human health. Formula is often supplemented with prebiotics because of ample evidence that oligosaccharides (naturally present in human milk, but mimicked synthetically) enable growth of specific bacteria in the baby’s gut that are very important for immunity and other aspects of health.
Overall, to support bacteria in your gut and overall health, Dr. Scott recommends consuming a diverse diet: “eat a rainbow”. If you cannot, a prebiotic supplement is advisable.*

Episode abbreviations and links:

Dr. Karen Scott works at the Rowett Institute, a renowned centre focused on nutrition and human health.

ISAPP published the scientific consensus definition of prebiotics.

An early review co-authored by Dr. Scott, covering gut microbiota functions and their impact on host health via diet.

A review on prebiotics to support calcium absorption and therefore bone health.

Dr. Scott refers to a new tool: the Exploris 240 Orbitrap mass spectrometer, which is interfaced with an atmospheric pressure matrix assisted laser desorption ionisation (AP-MALDI) source and direct infusion. This theoretically allows scientists to measure the distribution and composition of complex gut bacterial communities, whilst simultaneously assessing metabolite production from the constituent microbes, allowing them to better understand the cooperation and competition between different human gut microbiota species.

Additional resources:

Prebiotics. ISAPP infographic.

Understanding prebiotics and fiber. ISAPP infographic.

The many functions of human milk oligosaccharides: A Q&A with Prof. Ardythe Morrow. ISAPP blog post.

About Dr. Karen Scott:

Dr. Karen Scott is a Senior Research Fellow at the Rowett Institute, University of Aberdeen. She leads a research team investigating the (molecular) mechanisms by which key members of the gut microbiota interact with the diet and host, at different life-stages. The fermentation products of gut bacteria contribute to gut health, and are differentially expressed on different substrates, including prebiotics. In vitro bacterial growth studies utilising our large culture collection of gut anaerobes (in pure culture, mixed culture, fermentor systems, and also with human cells) and bioinformatic analyses illustrate niche-specific processes and bacterial interactions. Resident bacteria are also an important reservoir of transferable antimicrobial resistance genes, and other work investigates the evolution and spread of resistance from farm to fork.

Episode 14: Evidence on probiotics for preterm infants

November 1, 2022/in Podcast, Season One /by KC

Podcast: Play in new window | Download

Subscribe: Apple Podcasts | Spotify | RSS

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 Prebiotic (ISAPP), a nonprofit scientific organization dedicated to advancing the science of these fields.

Evidence on probiotics for preterm infants, with Dr. Geoffrey A. Preidis

Episode summary:

In this episode, the ISAPP podcast hosts talk about probiotics for preterm infants with Geoff Preidis, MD, PhD, a pediatric gastroenterologist and researcher at Baylor College of Medicine & Texas Children’s Hospital. Predis describes the evidence on probiotics for prevention of necrotizing enterocolitis, the challenges in interpreting the evidence that exists, and using the evidence to make clinical decisions.

Key topics from this episode:

Dr. Preidis works mostly with preterm infants, a population that didn’t exist just a few decades ago.
In the totality of evidence on probiotics for treating or preventing certain health conditions, the largest body of evidence is on whether probiotics can prevent negative health outcomes in preterm infants. Large meta-analyses (>15,000 preterm infants, >60 RCTs) conclude that overall, probiotics reduce the risk of necrotizing enterocolitis (NEC) by ~50%.
Probiotics do not appear to increase the risk of sepsis. In one case, contamination during the manufacturing process led to a severe infection and death. Although there is a very low risk of this happening, it highlights that a pharmaceutical grade probiotic is not available to give infants.
Many caveats accompany these findings, however. Trials use a wide range of products, as well as different strains, doses, durations of treatment, preterm infant populations, etc. Trials vary in their quality.
The body of evidence on probiotics for preventing NEC is convincing but far from perfect. Future trials need to continue reporting details on safety.
Some leading professional societies have issued guidelines that contradict each other.
How should clinicians make a decision, then? One way of choosing one therapy over another is to use network meta-analysis, which ranks therapies according to which product might have greater efficacy than another. However, the most studied therapies tend to rank higher.
Another way to make a decision is to consider looking at mechanisms. This is challenging with NEC, since we don’t know exactly what causes it.
Dr. Preidis is doing research on the association between early life undernutrition and increased risk of metabolic disorders later in life, what is known as the “thrifty phenotype” hypothesis. The mechanism may involve an epigenetic switch, whereby early life nutritional insult affects gene expression and metabolism in a long-lasting way.

Episode abbreviations and links:

This 2020 Cochrane Library review of probiotics for preventing NEC, mortality, and invasive infection (i.e. sepsis), found that “Combined analyses showed that giving very preterm and very low birth weight infants probiotics may reduce the risk of necrotizing enterocolitis, and probably reduces the risk of death and serious infection,” but also noted important concerns about the quality of the trials used to support these conclusions, that, “further, large, high-quality trials are needed to provide evidence of sufficient quality and applicability to inform policy and practice.”

Study in JPGN showing metabolites and fecal microbiota in preterm infants are modulated according to the probiotics they are exposed to.

Network meta-analysis on how probiotics affect morbidity and mortality in preterm infants.

A recent commentary by Dr. Preidis on rational selection of a probiotic for preventing necrotizing enterocolitis

Additional resources:

Probiotics and Necrotizing Enterocolitis. ISAPP infographic.

Probiotics to Prevent Necrotizing Enterocolitis: Moving to Evidence-Based Use. ISAPP blog.

About Dr. Geoff Preidis:

Dr. Preidis received his undergraduate degree in Physics from Harvard University, then completed his medical degree, residency in Pediatrics, fellowship in Pediatric Gastroenterology, Hepatology & Nutrition, and Ph.D. in Translational Biology and Molecular Medicine from Baylor College of Medicine. Now an Assistant Professor at Baylor College of Medicine and Texas Children’s Hospital, Dr. Preidis leads the Nutritional Physiology Research Laboratory and serves as an attending physician on both the Neonatal Gastroenterology, Hepatology & Nutrition Consultation Service and the Transplant Hepatology Service.

Dr. Preidis’s laboratory seeks to define mechanisms through which early life malnutrition impairs intestinal and liver function, leading to both short-term and long-term medical problems. Current studies focus on how malnutrition slows gastrointestinal motility, alters the gut microbiome, and inhibits the liver’s ability to synthesize important substances including bile acids – all of which adversely impact child growth. This research aims to help children suffering from nutritional deficiencies caused by a wide range of medical and socioeconomic factors, including premature newborns in the neonatal intensive care unit.

Episode 13: The history of ISAPP

October 17, 2022/in Podcast, Season One /by KC

Podcast: Play in new window | Download

Subscribe: Apple Podcasts | Spotify | RSS

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 Prebiotic (ISAPP), a nonprofit scientific organization dedicated to advancing the science of these fields.

The history of ISAPP, with Drs. Glenn Gibson, Mary Ellen Sanders and Irene Lenoir-Wijnkoop

Episode summary:

In this episode, the ISAPP podcast hosts talk about the history of the ISAPP organization with the organization’s three co-founders: Glenn Gibson, Mary Ellen Sanders and Irene Lenoir-Wijnkoop. The three guests recount the origins of ISAPP and the state of probiotic and prebiotic science 20 years ago when the organization was founded. They speak about some of the successes and challenges they encountered along the way, and highlight what they see as some of the key achievements of ISAPP.

Key topics from this episode:

The origin of the idea for ISAPP back in 1999: an organization dedicated to the science of pro- and prebiotics.
The annual meeting proved a key mechanism to gathering the multi-disciplinary scientists together to talk about and advance the science.
How ISAPP walks the line between receiving funding from industry members yet protecting scientific credibility.
The value that ISAPP has provided to industry members and the academic scientific community over the years.
How research in the field developed in the last 20 years and the questions that remain unanswered.
How industry members understood the importance of science 20 years ago and still do today, respecting the line between science and marketing.
Challenges from the last 20 years and where the field is going.

About Irene Lenoir-Wijnkoop:

Irene Lenoir-Wijnkoop is affiliated with the Utrecht University, specialized in public health nutrition and she provides independent consultancy services in related areas. She acts as associate editor in the Drugs Outcomes Research & Policies section of Frontiers. Through her passion for tackling preventable food-related diseases, which jeopardize healthcare resources, societies and human equity, she pioneered the field of nutrition economics.

After a first experience in clinical nutrition, she successively held assignments at the Dutch and the French subsidiaries of The Upjohn Company. When food industries initiated clinical research activities, she joined management and executive positions at the Danone Group. Besides her responsibilities, she got actively involved in ILSI Europe, in many international societies and advisory boards, primarily in the field of probiotics. She co-conceived ISAPP by enabling the first -seminal- meeting in 1999 in New York. In 2010 she was awarded with the Elie Metchnikoff Prize of Recognition.

About Mary Ellen Sanders:

Mary Ellen Sanders, PhD serves as the Executive Science Officer for the International Scientific Association of Probiotics and Prebiotics. She is also a consultant in the area of probiotic microbiology (www.mesanders.com). She is the current chair of the United States Pharmacopeia’s Probiotics Expert Panel, was a member of the working group convened by the FAO/WHO that developed guidelines for probiotics, and co-chairs the World Gastroenterology Organisation Guidelines Committee for practice guidelines for the use of probiotics and prebiotics for gastroenterologists. She lives in Colorado with her husband, where she enjoys her 2 grandchildren, hiking and riding her aging Morgan horse.

About Glenn Gibson:

Born in an ambulance parked on a roundabout outside Littlethorpe Maternity Hospital near Sunderland, UK (his dad fainted). Failed scientist at school – a trait he has successfully continued to this very day. Has poked around in people’s faeces for over 30 years and as a result, has published over 500 research papers but do not waste your time reading any of them, as you will learn nothing. Before that he did a PhD on sediment microbiology and learnt a lot about what the great population (or poopulation) of Dundee flush down their toilets.

He has supervised over 80 PhD students and 40 postdocs, who all said he was an absolute pleasure to work with and they wished their projects had lasted 10 times as long as they did. He is a compulsive fantasist. He thinks h-factor is a hat size. Has not done a day’s work in the last decade, largely because he spends all his time reading refereeing requests from journals he has never heard of, or grant bodies wanting reviews after spending decades bouncing every single one of his*, or conference organisers asking him to travel across the world (at his own expense) to give a talk or chair a session on anything whatsoever. Helped Mary Ellen, Irene and Gregor found the organisation most people call EYE-SAPP.

Episode 12: Postbiotics and probiotics in Japan: A researcher’s perspective

October 6, 2022/in Podcast, Season One /by KC

Podcast: Play in new window | Download

Subscribe: Apple Podcasts | Spotify | RSS

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 Prebiotic (ISAPP), a nonprofit scientific organization dedicated to advancing the science of these fields.

Postbiotics and probiotics in Japan: A researcher’s perspective, with Prof. Akihito Endo

Episode summary:

In this episode, ISAPP podcast host Dan Tancredi talks with food microbiologist Prof. Akihito Endo from Tokyo University of Agriculture in Japan, who was an author on the published ISAPP scientific consensus definition of postbiotics. Endo describes the unique properties of fructophilic lactic acid bacteria, and talks about the landscape of probiotic and postbiotic products in Japan.

Key topics from this episode:

Prof. Tomotari Mitsuoka originally introduced the concept of probiotics, prebiotics, and “biogenics” in Japan – the latter are similar to postbiotics.
Japan is a leading country in postbiotic applications, with many companies actively producing postbiotic products with killed bacterial cells.
Endo has done research on fructophilic lactic acid bacteria (FLAB), which favor fructose instead of glucose; they are found in flowers, fruits, fermented foods, and honeybee guts.
Novel species of FLAB have been discovered recently, and Endo found novel bacteriocin-producing FLAB. The bacteroicins may be active against pathogens.
Dead cells of FLAB are present in fermented foods so they have a history of safe consumption. There is one postbiotic product with FLAB in Japan at present.
Endo tested fresh honey and found it has viable FLAB. After 2 weeks they die because of antimicrobials present in honey. But there’s a safe consumption history even of the viable cells, albeit at low levels. He is interested in exploring them as probiotics in food products.
The Japanese regulatory environment has two health claim systems for ‘biotics’: FOSHU, FFC. FOSHU is more restricted, while FFC can have more diverse health claims.
A large variety of postbiotic products are available in Japan.
One mechanism by which FLAB confer health benefits is through IgA induction (i.e. influencing immune activity).

Episode abbreviations and links:

The International Scientific Association of Probiotics and Prebiotics (ISAPP) consensus statement on the definition and scope of postbiotics

Mitsuoka T. 1998. Functional Food: Probiotics, Prebiotics, Biogenics. Intestinal Flora and Probiotics.

Mitsuoka. 2011. History and Evolution of Probiotics. Japanese Journal of Lactic Acid Bacteria.

Background on fructophilic lactic acid bacteria: Are fructophilic lactic acid bacteria (FLAB) beneficial to humans?

Viable fructophilic lactic acid bacteria present in honeybee-based food products

Japanese categories for health benefit claims on foods (for more details, see ISAPP consensus statement):

FOSHU – Food for Specialized Health Use
FFC – Food with Functional Claims

On Kikunae Ikeda’s discovery of umami: Glutamate: from discovery as a food flavor to role as a basic taste (umami)

Additional resources:

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

Postbiotics. ISAPP infographic

What is a postbiotic? ISAPP video

About Prof. Aki Endo:

Akihito Endo is a research professor at Department of Nutritional Science and Food Safety, Faculty of Applied Bioscience, Tokyo University of Agriculture, Japan. He obtained a PhD degree of Fermentation Science with a topic on Lactic Acid Bacterial Diversity during Shochu Fermentation at Tokyo University of Agriculture in 2005. After he studied as a postdoc in Stellenbosch University (South Africa) and in University of Turku (Finland), he started to work in Tokyo University of Agriculture in 2013. His research themes are ecology and food application of fructophilic lactic acid bacteria and oligosaccharide metabolism in human gut anaerobes. He is a member of Subcommittee on the taxonomy of Bifidobacterium, Lactobacillus and related organisms, International Committee on Systematics of Prokaryotes since 2011 and a board member of Japanese Society for Lactic Acid Bacteria since 2021.

Episode 11: How to build a satisfying scientific career and make a difference

September 20, 2022/in Podcast, Season One /by KC

Podcast: Play in new window | Download

Subscribe: Apple Podcasts | Spotify | RSS

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 Prebiotic (ISAPP), a nonprofit scientific organization dedicated to advancing the science of these fields.

How to build a satisfying scientific career and make a difference, with Prof. Gregor Reid

Episode summary:

In this episode, the ISAPP podcast hosts talk about how to succeed as a scientist in the fields of probiotics and prebiotics with Gregor Reid, professor emeritus at Western University, Canada. Prof. Reid, who is ISAPP’s former president and host of the first ISAPP meeting 20 years ago, tells about his career path and shares ways to make a difference outside of the scientific laboratory.

Key topics from this episode:

The importance of keeping a sense of humor as a scientist
Sometimes it pays to do something unconventional: early in his career, Reid decided to work with a urologist who had a hunch that lactobacilli were important in women’s health; they had difficulty getting funding to investigate further but they persisted over a number of years and eventually published some landmark work
Reid (with others) investigated on how biofilms impacted clinical antibiotic treatments
When clinical problems drive the research, it can have great impact on people’s lives, yet it can take many years to progress from observation to mechanism to better clinical treatments
Probiotics are “an ecological approach to an ecological problem” but often the structures (funding, regulatory, etc.) are not in place for scientists to study them or pursue them as interventions in industry
Prof. Reid has worked in South Africa, led by local people, helping them obtain tools for making fermented yogurt (Yoba-For-Life)
For early career scientists who want to make a difference in science beyond publishing papers, it’s important to be proactive and go after what you want
The right lab and the right environment are essential
Reflect on the personal connection to your work that “makes you almost unstoppable”
Partnerships are key for international impacts
Those involved in ISAPP can champion a cause that’s important to them within the organization
Flexibility will be key for probiotics (and other ‘biotics’) companies in the future
The field is poised to expand; all kinds of organisms will benefit from probiotics in the future

Episode abbreviations and links:

Landmark papers related to vaginal lactobacilli, biofilms and health:

Recurrent urethritis in women

Bacterial biofilm formation in the urinary bladder of spinal cord injured patients

Bacterial biofilms: influence on the pathogenesis, diagnosis and treatment of urinary tract infections

Ultrastructural study of microbiologic colonization of urinary catheters

Additional resources:

Reflections on a career in probiotic science, from ISAPP founding board member Prof. Gregor Reid. ISAPP blog

The Children of Masiphumelele Township. ISAPP blog

About Prof. Gregor Reid:

Gregor Reid is a Fellow of the Royal Society of Canada and Canadian Academy of Health Sciences, and Distinguished Professor Emeritus at Western University.

Born and raised in Scotland, he did his PhD in New Zealand and immigrated to Canada in 1982. His research, most recently at Lawson Health Research Institute, has focused on the role of beneficial microbes in the health of humans and other life forms. He has produced 32 patents, 586 peer-reviewed publications cited over 50,000 times, has a Google Scholar H index of 116 and has given over 650 talks in 54 countries. He is ranked #3 in Canada and #59 in the world for Microbiology Scientists by research.com. In 2001, he chaired the UN/WHO Expert Panel that defined the term probiotic. In 2004, he helped introduce probiotic yoghurt to East Africa as a means for women to create microenterprises that by 2019 reached 260,000 adults and children.

He has received an Honorary Doctorate from Orebro University, Sweden, a Distinguished Alumni award from Massey University, New Zealand, a Canadian Society for Microbiologists Career Award and Western University’s highest accolade of Distinguished Professor. He is Chief Scientific Officer for Seed, a Californian start-up.

The Science, Microbes & Health Podcast

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

The Science, Microbes & Health Podcast

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

The Science, Microbes & Health Podcast

A systems biology perspective on the gut microbiome, with Dr. Sean Gibbons PhD

The Science, Microbes & Health Podcast

Human milk oligosaccharides in the infant gut, with Dr. Simone Renwick PhD

The Science, Microbes & Health Podcast

Lactobacilli in the microbiomes of the gut, skin, reproductive tract and more, with Prof. Kingsley Anukam PhD

The Science, Microbes & Health Podcast

Investigating the benefits of live dietary microbes, with Prof. Colin Hill PhD and Prof. Dan Tancredi PhD

The Science, Microbes & Health Podcast

The role of microbes in gut-brain communication, with Prof. Emeran Mayer MD

The Science, Microbes & Health Podcast

The effects of metabolites in the colon, with Prof. Kristin Verbeke PhD

The Science, Microbes & Health Podcast

Reflections on the probiotic field and ISAPP’s role, with Dr. Mary Ellen Sanders PhD

The Science, Microbes & Health Podcast

Studying microbial ecosystems and how they support health, with Prof. Emma Allen-Vercoe PhD

The Science, Microbes & Health Podcast

Biotics in animal and human nutrition, with Prof. Kelly Swanson

The Science, Microbes & Health Podcast

Genetically modified microorganisms for health, with Dr. Carlos Gómez-Gallego

The Science, Microbes & Health Podcast

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

The Science, Microbes & Health Podcast

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

The Science, Microbes & Health Podcast

The definition of postbiotics, with Dr. Gabriel Vinderola and Prof. Seppo Salminen

The Science, Microbes & Health Podcast

Using metabolomics to learn about the activities of gut microbes, with Dr. Anisha Wijeyesekera

The Science, Microbes & Health Podcast

The honeybee microbiome and potential for probiotics, with Dr. Brendan Daisley

The Science, Microbes & Health Podcast

A primer on prebiotics, with Dr. Karen Scott

The Science, Microbes & Health Podcast

Evidence on probiotics for preterm infants, with Dr. Geoffrey A. Preidis

The Science, Microbes & Health Podcast

The history of ISAPP, with Drs. Glenn Gibson, Mary Ellen Sanders and Irene Lenoir-Wijnkoop

The Science, Microbes & Health Podcast

Postbiotics and probiotics in Japan: A researcher’s perspective, with Prof. Akihito Endo

The Science, Microbes & Health Podcast

How to build a satisfying scientific career and make a difference, with Prof. Gregor Reid

Contact Us

Follow Us

Subscribe to our science newsletter