Archive for category: Podcast

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This episode features Dr. Anissa Armet PhD RD from the University of Alberta in Canada, speaking about the impact of diet on both the gut microbiota and overall health. Dr. Armet, a registered dietitian and researcher, says the Western diet along with the associated gut microbiome changes have played a role (amongst other things) in the rise of autoimmune diseases in industrialized societies. Dr. Armet describes a recent dietary study she and her collaborators published, for which they created a very high fiber diet called the Non-Industrialized Microbiome restore (NiMe, pronounced “nee mee”) diet. They created recipes and meal plans based on what some non-industrialized populations in the world typically consume, which included 45 grams of dietary fiber per day, and only small portions of animal proteins and dairy products. The participants in this controlled feeding trial saw substantial cardiometabolic benefits as well as certain changes in the gut microbiota after three weeks on the diet. Interestingly, the diet initially reduced the diversity of participants’ gut microbiota, likely because of increased pH in the gut, but diversity rebounded toward the end of the trial. The researchers also introduced a strain of L. reuteri isolated from the gut microbiota of people in a non-industrialized society, to observe whether it would engraft since the diet was known to contain growth substrates for the bacteria. Although the strain did not engraft in the gut microbiota (except in one participant), the health benefits of the diet overall were still observed. The researchers concluded that the NiMe diet can be used to target the gut microbiome and change community characteristics that are relevant for health.

Episode abbreviations and links:

• Dr. Armet’s Instagram account
• Published study on the NiMe diet (called the “restore diet” in the publication): Cardiometabolic benefits of a non-industrialized-type diet are linked to gut microbiome modulation
• Previous research in Papua New Guinea, which informed the NiMe diet: The Gut Microbiota of Rural Papua New Guineans: Composition, Diversity Patterns, and Ecological Processes
• Review on how the gut microbiome informs knowledge about healthy dietary patterns: Rethinking healthy eating in light of the gut microbiome
• New publication from another research group, which complements the NiMe study findings: Immune and metabolic effects of African heritage diets versus Western diets in men: a randomized controlled trial
• Downloadable NiMe diet book: The NiMe Diet: Scientific Principles and Recipes

About Dr. Anissa Armet PhD RD:

Dr. Anissa Armet is a Registered Dietitian and postdoctoral researcher at the University of Alberta. Anissa completed her PhD in Nutrition and Metabolism in March 2024, then transitioned into her postdoc to research the effects of microbiome-targeted dietary interventions in inflammatory bowel diseases. She uses machine learning to determine if the gut microbiome predicts clinical responses in the context of precision nutrition. Anissa has authored several peer-reviewed publications, including a review on healthy eating in light of the gut microbiome and a dietary intervention trial on microbiome restoration. Being equally passionate about knowledge translation, Anissa co-authored an award-winning, open-access, high-protein cookbook designed to support muscle health, is currently developing a plant-based version, and recently co-authored an open-access ebook, The NiMe Diet: Scientific Principles and Recipes.

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This episode features Dr. Vanessa Leone PhD from the University of Wisconsin – Madison on how gut microbes and eating patterns impact the host circadian system and overall health. In mouse models, Dr. Leone has found that in a 24-hour period, minor changes occur in the composition of the gut microbiota, while more important changes occur in gut microbiota function (that is, metabolite production). However, these changes depend on the type of diet and the timing of meal consumption. Metabolic health is also affected by this interplay. In humans, obesity is correlated with loss of microbiota rhythmicity, although causality remains unclear. One study by Dirk Haller found that a loss of rhythmicity helped predict which people with prediabetes would progress to diabetes. Constantly shifting timezones (or shifting between day and night shifts) appears to be more detrimental to metabolic health than maintaining a constant schedule, and research is ongoing about what might mitigate these effects. In this field of research it’s important to consider people’s chronotype: their tendency to rise early versus stay up late. In the future, Dr. Leone hopes to untangle more about how different factors affect metabolic health: diet, gut microbiota, and the circadian system.

Episode abbreviations and links:

• Paper from the lab of Dirk Haller showing that 13 OTUs lost rhythms in those with prediabetes, predicting who might develop diabetes: Arrhythmic Gut Microbiome Signatures Predict Risk of Type 2 Diabetes
• Review paper: Daily Eating Patterns and Their Impact on Health and Disease
• Paper on the importance of timing in microbiome sample collection: Time of sample collection is critical for the replicability of microbiome analyses
• University of Wisconsin – Madison Leone Lab webpage

About Dr. Vanessa Leone PhD:

Vanessa A. Leone, Ph.D. is an Assistant Professor in the Department of Animal & Dairy Sciences at the University of Wisconsin-Madison, where she also obtained a Ph.D. She performed postdoctoral studies and was an Instructor of Medicine at the University of Chicago in the Section of Gastroenterology, Hepatology, & Nutrition where she examined how the gut microbiome impacts complex metabolic  diseases. Dr. Leone currently studies how day vs. night oscillatory patterns of gut microbes influence the body’s internal clock and metabolism. She hopes to mechanistically define what constitutes a microbial oscillator versus a non-oscillator, examine how host factors impact the broader diurnal structure and functional outputs of the gut microbiome, and to determine how microbial oscillations impact host metabolism. These findings will likely pave the way to identify how timed delivery of pre-, pro-, or postbiotics can be leveraged to promote a balanced gut microbiota and improve host health.

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This episode features Dr. Abigail (Abbey) Thiel PhD, who works remotely (from the US) with Wageningen University to manage a project focused on developing animal-free milk proteins using precision fermentation. Dr. Thiel explains that the motivation for the project is to find alternatives to animal-produced foods using microorganisms to produce key components of dairy products. Her project focuses on producing the protein casein, which is found in milk (and contributes to its structure and stability), to eventually produce a milk substitute or a protein powder that could be used as a food ingredient. A specific yeast is used to produce the casein: the scientists insert directions for making the protein into the yeast, then put it in a bioreactor to produce the protein. After that, they figure out how to purify the protein so it can be used in various applications. The final step is upscaling the process to produce abundant and cost-effective casein. The group has also started initial digestion studies to see how the purified casein is digested. Meanwhile, Dr. Thiel is passionate about food science communication and has a YouTube channel called Abbey the Food Scientist, where she strives to build awareness of food science as a career and also to address myths about food science.

Episode abbreviations and links:

• Book co-edited by Dr. Thiel: Careers in Food Science
• Abbey the Food Scientist YouTube channel

About Dr. Abigail Thiel PhD:

Abigail (Abbey) Thiel is a food scientist, educator, and project manager of research focused on producing milk proteins using yeast. She earned her PhD in Food Science from the University of Wisconsin-Madison and later worked as a postdoctoral researcher at Wageningen University & Research in the Netherlands. Abbey is passionate about making the science behind food accessible to all. She runs a successful YouTube channel with over 1.4 million views, breaking down food science concepts for everyday audiences, and created an online course, Food Science for Beginners. In addition, she develops high school curriculum and educational resources to help students explore food science as a career path.

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This episode features Dr. Paul Cotter PhD of TEAGASC in Ireland, talking about the creation of fermented foods and how they can lead to health benefits. A huge array of foods can be fermented, and historically fermentation was used to extend the shelf life of a food that people had an abundance of. Dr. Cotter’s work in the field originally started with a bacteria-killing bacteriocin that had been isolated from kefir, and later moved toward the microbes in fermented foods. Currently he’s interested in comparing the artisanal approach to fermented foods, which leads to somewhat unpredictable results in the final products, with the industrial approach, which leads to more consistent results. In different artisanal fermented foods, which strains are common and which are unique? Potentially some of the strains can be used to confer a health benefit, and even a benefit that’s personalized to an individual. Dr. Cotter sees the role of fermented foods as possibly targeting pre-disease rather than disease if their ability to confer health benefits can be unravelled further.

Episode abbreviations and links:

• Paper in Cell showing huge microbial diversity in foods: Unexplored microbial diversity from 2,500 food metagenomes and links with the human microbiome
• DOMINO research project website

Additional resources:

ISAPP infographic: Fermented foods

About Dr. Paul Cotter PhD:

Prof Paul Cotter is the Head of Food Biosciences at Teagasc (the Irish Agriculture and Food Development Authority), is a Principal Investigator with the large Irish Research Centres, APC Microbiome Ireland, VistaMilk and Food for Health Ireland and head of microbiology/co-founder of SeqBiome, a microbiome sequencing and bioinformatics service provider. He is a molecular microbiologist, with a particular focus on the microbiology of foods (especially fermented foods), the food systems and of humans, as well as probiotics and postbiotics. Prof Cotter is the author of >400 peer-reviewed, was included in the Clarivate list of highly cited researchers for 2018-2024, received an honorary doctorate from the University of Antwerp in 2024 and is the Field Chief Editor of Frontiers in Microbiology.

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In this episode, ISAPP’s current President Prof. Maria Marco PhD and past President Prof. Dan Merenstein join the podcast hosts for a conversation about highlights in biotic science from the past year. Prof. Marco points out a paper published in Nature Microbiology, the result of an ISAPP discussion group exploring whether diet may be a confounder of biotic effects in clinical studies. The group concluded that scientists should work with dietitians to include data on participants’ habitual diet in future studies on biotics – particularly with on prebiotics. These efforts will help scientists establish causality and understand the basis of individual responses to a biotic intervention. Prof. Merenstein highlighted conversations in 2024 around the role of probiotics in the neonatal intensive care unit (NICU), including ISAPP’s panel on this topic at the annual meeting in Cork, Ireland. Although US regulators have recently warned against the use of probiotics for preterm infants in the NICU setting, the data overwhelmingly points to benefits and this may eventually drive regulatory change. Prof. Marco added that a take-away from ISAPP’s panel was that parents of preterm infants should be included in the decision-making around whether to use probiotics. The guests talked about Prof. Merenstein’s recent appointment to the National Academy of Medicine and his rigorous approach to primary care research. Further highlights in the science this year were ISAPP’s papers exploring evidence for probiotics restoring an antibiotic-disrupted microbiota, and evidence for the benefits of probiotics in healthy individuals – both of which found a lack of conclusive evidence to answer these questions. Many gaps exist in the knowledge around biotics, gut microbiota, and health – for example, another paper this year found that the abundance of microorganisms in a fecal sample is a confounder of microbiome-disease associations. And finally, beyond the scientific advancements, conveying the scientific concepts to the general public requires careful consideration and dedicated effort.

Episode abbreviations and links:

• ISAPP paper calling for dietary data to be included in clinical trials on biotics: Design and reporting of prebiotic and probiotic clinical trials in the context of diet and the gut microbiome
• Blog article on ISAPP’s panel on the use of probiotics for preterm infants: Expert Panel at ISAPP Annual Meeting Addresses Probiotic Use for Premature Infants
• Blog article on Prof. Merenstein’s appointment to the National Academy of Medicine: ISAPP Board Member Prof. Dan Merenstein MD Elected to National Academy of Medicine
• Explanation of ISAPP’s paper exploring whether probiotics restore an antibiotic-disrupted microbiota: ISAPP panel concludes that more evidence is needed to determine whether probiotics help restore an antibiotic-disrupted microbiota
• Paper showing fecal microbial load may confound microbiome-disease associations: Fecal microbial load is a major determinant of gut microbiome variation and a confounder for disease associations

About Prof. Maria Marco PhD

Dr. Maria Marco, PhD, is a Professor in the Department of Food Science and Technology at the University of California, Davis. She earned her bachelor’s degree in microbiology at The Pennsylvania State University and her PhD in microbiology at the University of California, Berkeley. As a postdoc at NIZO food research in The Netherlands, she developed a love for lactic acid bacteria and the importance of these microorganisms in our foods and the digestive tract. Her postdoctoral studies led to the discovery that probiotics are metabolically active in the intestine and responsive to dietary intake. Dr. Marco started her lactic acid bacteria and gut health laboratory at UC Davis in 2008 and has built an internationally-recognized, NIH, USDA, and NSF funded research program on probiotics, fermented foods, and dietary modulation of the gut microbiome. Dr. Marco also consults with and has received funding from international foundations and companies to investigate how certain microbes in foods or supplements may benefit health. She is active with science communication activities such as the EATLAC project and is the instructor for two food microbiology courses. Dr. Marco received the American Society for Microbiology Distinguished Lecturer award in 2012. Recently, she founded the ongoing Gordon Research Conference series on Lactic Acid Bacteria. Dr. Marco attended her first ISAPP meeting as a postdoc and participated as an invited expert before joining the ISAPP Board of Directors in 2019.

About Prof. Dan Merenstein

Dr. Daniel Merenstein, MD, is a Professor with tenure of Family Medicine at Georgetown University, where he also directs Family Medicine research. Dr. Merenstein has a secondary appointment in the undergraduate Department of Human Science, in the School of Health. Dr. Merenstein teaches two undergraduate classes, a research capstone and a seminar class on evaluating evidence based medical decisions. He has been funded by PCORI, NIH, USDA, foundations and industry. The primary goal of Dr. Merenstein’s research is to provide answers to common clinical questions that lack evidence and improve patient care. Dr. Merenstein is a clinical trialist who has recruited over 2,000 participants for 10 probiotic trials since 2006. He is an expert on probiotics, on antibiotic stewardship in outpatient settings, and also conducts HIV research in a large women’s cohort. He sees patients in clinic one day a week. Dan lives in Maryland with his wife and 4 boys.