The Science, Microbes & Health Podcast

This episode features Dr. Aayushi Uberoi PhD from Washington University in St. Louis (USA), speaking about the skin microbiome and various techniques for studying it. The skin is a reactive interface that protects the body, with the skin on various parts of the body looking very different because of stratifications in the epithelial layers and the local nutritional landscape. The skin microbiome in general is nutrient sparse and varies at different body sites. Research has shown that epithelial development, stratification, and differentiation are altered in the absence of the microbiota, showing the active role of the skin microbiota in regulating skin function. Microbes that inhabit the skin are shown to elicit unique immune responses with systemic effects. Communication between skin microbes and human body cells may be happening via metabolites. When conducting skin microbiome experiments, controls are important; the low biomass samples are susceptible to contamination. In the future, knowing more about the nutritional needs of the skin microbes could help guide the development of prebiotics for skin.

Episode abbreviations and links:

Paper showing a humanized mouse model for studying the skin microbiome: Commensal-derived tryptophan metabolites fortify the skin barrier: insights from a 50-species gnotobiotic model of human skin microbiome

Paper on the skin microbiome’s contributions to wound healing: The wound microbiota: microbial mechanisms of impaired wound healing and infection

Paper investigating mechanisms of how skin microbes influence skin function: Commensal Microbiota Regulates Skin Barrier Function And Repair Via Signaling Through The Aryl Hydrocarbon Receptor

Review by Belkaid and Segre: Dialogue between skin microbiota and immunity

About Dr. Aayushi Uberoi PhD:

Aayushi Uberoi is an Assistant professor of Pathology & Immunology and Medicine (Dermatology) in Washington University School of Medicine in Saint Louis. Her lab studies the host-microbe-environment interactions in regulating skin barrier. She has studied interactions between microbes and skin since her Ph.D. research on cutaneous papillomaviruses in Dr. Paul Lambert’s lab at the University of Wisconsin-Madison. While traditional studies of infectious skin diseases have typically focused on singular pathogens within the host, skin is colonized by a diverse array of microbes, which likely exert significant influence on epithelial characteristics. Motivated by this question, Aayushi’s postdoctoral research at the University of Pennsylvania in Dr. Elizabeth Grice’s lab explored the role of the commensal microbiome in regulating the function of the cutaneous barrier. In the lab, Aayushi wears several hats such as conducting research, developing protocols and assays, writing, and making sure the lab has fun equipment.

Aayushi is a recipient of K99/R00 Pathway to Independence award from National Institute of Arthritis & Musculoskeletal & Skin Diseases (NIAMS/NIH), innovator award from Society of Investigative Dermatology, fellowships from Prevent Cancer Foundation and Dermatology Foundation and a Young Investigator Award from the Wound Healing Society.

This episode features two guests from the ISAPP board of directors who led the recently published consensus definition of gut health: Prof. Maria Marco PhD from UC Davis (USA), and Prof. Eamonn Quigley MD from Houston Methodist Hospital (USA). In the paper, the group defines gut health as: “a state of normal gastrointestinal function without active gastrointestinal disease and gut-related symptoms that affect quality of life”. Gut health is a commonly used term that previously had no scientific definition. Initially the group of experts (both scientists and physicians) that met to discuss it had a lot of skepticism, but they became more enthusiastic and engaged as the discussion proceeded and were finally able to reach consensus. The group identified 6 distinct domains that are encompassed under gut health: gut microbiome, gut barrier, gastrointestinal physiology (primarily intestinal secretions and motility), gut-brain axis, immune function, and metabolism. The group hopes it will provide clarity over time about which aspect(s) of gut health are being assessed in a given study (as it’s not realistic to look at all aspects in a single study). One difficulty is that some of the tests available to measure these domains are quite limited and/or invasive. Nor do consistent correlations exist between symptoms and objective measures of the 6 domains. Determinants of gut health are also discussed in the paper, with diet being important among these.

Episode abbreviations and links:

Gut health consensus definition paper: The International Scientific Association for Probiotics and Prebiotics (ISAPP) consensus statement on the definition and scope of gut health

Earlier publication on gut health by Bischoff: ‘Gut health’: a new objective in medicine?

About Prof. Maria Marco PhD:

Dr. Maria Marco PhD, is President of ISAPP’s board of directors and Professor in the Department of Food Science and Technology at the University of California, Davis. She earned her PhD in microbiology at the University of California, Berkeley. Prof. 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. She is currently a fellow in the American Academy of Microbiology.

About Prof. Eamonn Quigley MD:

Dr. Eamonn M M Quigley MD FRCP FACP MACG FRCPI MWGO is David M Underwood Chair of Medicine in Digestive Disorders and Chief of the Division of Gastroenterology and Hepatology at Houston Methodist Hospital. A native of Cork, Ireland, he graduated in medicine from University College Cork. He trained in internal medicine in Glasgow, completed a two-year research fellowship at the Mayo Clinic, and training in gastroenterology in Manchester, UK. He joined the University of Nebraska Medical Center in 1986 where he rose to become Chief of Gastroenterology and Hepatology. Returning to Cork in 1998 he served as Dean of the Medical School and a PI at the Alimentary Pharmabiotic Center. He served as president of the American College of Gastroenterology and the WGO and as editor-in-chief of the American Journal of Gastroenterology.

This special year-end episode, which covers 2025’s highlights in biotic science, features three of the academic scientists who serve on the ISAPP board of directors: Prof. Maria Marco PhD from University of California, Davis (USA), Prof. Sarah Lebeer PhD from University of Antwerp (Belgium), and Dr. Gabriel Vinderola PhD from National University of Litoral (Argentina). After a brief review of ISAPP’s activities, the host, Prof. Colin Hill PhD from University College Cork (Ireland) asks the three guests about the talks that stood out from the ISAPP annual meeting. The guests cited talks by Prof. Howard Bauchner MD on publishing and the scientific communication ecosystem; Dr. Carolina Tropini PhD on factors affecting the gut microbial environment and engineering gut microbes as biosensors; and Dr. Peijun Tian PhD on a microbial metabolite that can signal to the brain to relieve depression through the gut-brain axis. The guests also described some stand-out papers published this year (linked below). Finally, they discussed how science is informing regulatory issues in different parts of the world, and shared some research from their own labs that they’re particularly excited about.

Episode abbreviations and links:

Paper from Dr. Peijun Tian PhD showing a microbial metabolite that signals through the gut-brain axis: Bifidobacteria with indole-3-lactic acid-producing capacity exhibit psychobiotic potential via reducing neuroinflammation

NiMe diet paper: Cardiometabolic benefits of a non-industrialized-type diet are linked to gut microbiome modulation (also see this podcast episode)

Paper on a host colonization factor in L. plantarum: A conserved bacterial genetic basis for commensal-host specificity

Research presented at a congress this year on maternal feces given to infants: Eating a tiny bit of mom’s poop could give C-section babies an immune ‘primer’

Paper from Marco lab on microbial metabolites in sauerkraut: The fermented cabbage metabolome and its protection against cytokine-induced intestinal barrier disruption of Caco-2 monolayers

This episode features Prof. Yvan Vandenplas MD PhD from the University Hospital Brussels and Vrije Universiteit Brussel (Belgium), speaking about the science on probiotics and prebiotics in infant formula. Over the past 20 years in this field, awareness of the importance of the gastrointestinal microbiota has grown, and biotics have been employed to try to shape the gut microbiota of infants formula-fed to resemble that of breastfed infants. In particular, human milk oligosaccharides (HMOs) are prebiotics that are shown to change the microbiota composition, although the clinical benefits of these changes are not yet clear. What clinical benefits are achievable for infants who receive formula with added probiotics or prebiotics? Looking closely at the trials, it’s evident that probiotics and prebiotics are associated with a decrease in infections and antibiotic prescriptions, but researchers need to use these as primary endpoints in their trials to increase the strength of the evidence. In a recent European Society for Paediatric Gastroenterology Hepatology and Nutrition (ESPGHAN) recommendations paper, the probiotic recommendations were challenging because for each specific probiotic intervention the group had difficulty finding two clinical trials with a similar design, limiting their ability to make conclusions. Prof. Vandenplas says more trials need to be done independently to strengthen the evidence. Long-term outcomes from probiotic or prebiotic supplementation in infant formula are possible as well, but much larger longitudinal trials are necessary to establish these outcomes.

Episode abbreviations and links:

ESPGHAN recommendations paper: Recommendations on the health outcomes of infant formula supplemented with biotics by the European Society for Pediatric Gastroenterology, Hepatology, and Nutrition Special Interest Group on Gut Microbiota and Modifications

Trial showing positive outcomes of an infant probiotic and prebiotic intervention in a region with high prevalence of infectious disease: A randomized synbiotic trial to prevent sepsis among infants in rural India

About Prof. Yvan Vandenplas MD PhD:

Yvan Vandenplas did his medical studies at the ”Vrije Universiteit Brussel” (Free University of Brussels) and trained in pediatrics (1981-1986) at the same University. He became Head of the Unit for Pediatric Gastroenterology and Nutrition in 1987 and created the Pediatric Hospital, the KidZ Health Castle, at the University Hospital Brussels (UZ Brussel) of the same university, where he had the Chair of Pediatrics since 1994 up to 2021. He is now Prof. Emeritus and consultant at the same hospital. He is associate editor of Nutrients.

This episode features Dr. Eirini Dimidi PhD RD from King’s College London (UK), speaking about the recently published British Dietetic Association’s guidelines for dietary management of chronic constipation. Constipation can be a major concern for patients, but evidence around some of the most common dietary recommendations for addressing it has remained unclear. After a thorough review of evidence from randomized, controlled trials, Dr. Dimidi and colleagues found evidence for specific foods / beverages improving certain symptoms of constipation. In addition, some supplements such as psyllium, certain probiotics, and magnesium oxide have evidence for efficacy. A high-fiber diet is a commonly recommended dietary strategy for chronic constipation, but the guideline shows that the evidence to date is insufficient to support this recommendation. (However, a high fiber diet has many other benefits.) Probably the effective foods’ key mechanism of action in relieving symptoms of constipation is the fiber they contain, but future studies need to confirm this. Regarding probiotics, so far the evidence is ambiguous around which strains and which durations of treatment are the most effective so the authors were unable to make a confident conclusion. However, for practical reasons they included the expert opinion that patients should be advised to take a probiotic of their choice for at least 4 weeks in addressing chronic constipation.

Episode abbreviations and links:

2025 guidelines: British Dietetic Association Guidelines for the Dietary Management of Chronic Constipation in Adults

2019 review on fermented foods & gastrointestinal outcomes: Fermented Foods: Definitions and Characteristics, Impact on the Gut Microbiota and Effects on Gastrointestinal Health and Disease

LinkedIn profile for Dr. Dimidi

About Dr. Eirini Dimidi PhD RD:

Dr Eirini Dimidi is an Associate Professor in Nutritional Sciences at King’s College London. She is a registered dietitian and nutritionist since 2011, after completing a BSc in Nutrition and Dietetics and a MSc in Clinical and Public Health Nutrition. This was followed by the completion of a PhD from King’s College London where she investigated the effectiveness of probiotics in people with chronic constipation.

She is leading research on nutrition-based interventions, including fibre, prebiotics, probiotics, plant foods, and plant-based diets in gut function and dysfunction. She is also investigating the mechanisms through which nutritional interventions may affect immune and mental health via the gut microbiome. Dr Dimidi led the development of the first ever UK national dietary guidelines for the management of chronic constipation, which have been endorsed by the British Dietetic Association.

Dr Dimidi was awarded the 2023 Cuthbertson Medal by the Nutrition Society, and the 2022 ISAPP Glenn Gibson Early Career Research Prize for her research on the effect of diet in gut health. She also received the 2021 Rising Star and 2020 Elizabeth Washington awards by the British Dietetic Association.