Microbiome Medics

Have you ever wondered what microbiome testing looks like? In this episode, co-hosts Dr Siobhan McCormack and Dr Sheena Fraser chat to guest Dr Alena Pribyl from Microba Life Sciences, after sending off their poo samples to be analysed.

*Please note* - We apologise for the audio quality in this episode. We are changing hosting platforms and aim to smooth out the quality in future releases.

What We Cover:

• The process start-to-finish of both co-hosts testing journey: the sample taking, mailing, storage and breaking down the process that is used to analyse their samples
• Metagenomic analysis at Microba Life Sciences and the positives and pitfalls in the industry
• The expansion of this field, how it's developed and grown over the years and things to look out for if you are interested in testing
• Dr Alena Pribyl's expertise and input at every stage of process
• The publications and science behind the process and beyond

Dr Alena Pribyl is Lead Scientist at Microba Life Sciences, a microbial genomics company based in Brisbane, Australia, specialising in high-resolution analysis of the human gut microbiome. Alena has worked in the human gut microbiome field for more than 10 years, with a focus on translating complex microbiome science into meaningful insights.

She completed her PhD in physiology and molecular biomarkers of stress before moving into microbial ecology and human gut microbiome research at the Australian Centre for Ecogenomics at the University of Queensland. In 2018, she became part of the founding team at Microba Life Sciences, where she now leads the science team.

Her work focuses on the scientific development and evidence base behind microbiome testing, including how metagenomic analysis can help us better understand the gut microbial community, its functional potential, and its links with health.

Relevant Microba publications:

• Benchmarking of our community profiler (bioinformatic analysis):https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2021.643682/full
• Validation of our sample collection method: https://academic.oup.com/ismecommun/article/1/1/14/7462904
• Validation of pathogen detection using metagenomics: https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2026.1759322/full

Some recent key papers demonstrating that metagenomics can provide meaningful analyses:

• IBD prediction: https://www.nature.com/articles/s41591-024-03280-4
• Functional/taxonomic changes in active vs inactive IBD: https://www.nature.com/articles/s41586-019-1237-9
• CRC prediction: https://www.cell.com/cell-host-microbe/fulltext/S1931-3128(26)00223-4
• Immunotherapy response: https://www.nature.com/articles/s41591-024-02823-z, https://www.nature.com/articles/s41564-025-01930-y
• Type 2 diabetes prediction: https://diabetesjournals.org/care/article/45/4/811/141052/Gut-Microbiome-Composition-Is-Predictive-of
• Drug-microbiome interactions: https://www.nature.com/articles/s41586-019-1291-3
• Pathogen identification: https://www.thelancet.com/journals/lanmic/article/PIIS2666-5247(23)00244-6/fulltext,
• Diet-microbiome associations: https://www.nature.com/articles/s41591-026-04312-x
• Microbiome-based stratification for lifestyle interventions: https://link.springer.com/article/10.1186/s40168-023-01604-z
• Healthy ageing prediction: https://www.nature.com/articles/s43587-024-00678-0,

Also some publications on the inaccuracy of using the F:B phyla ratios:

• F:B ratio debunking: https://febs.onlinelibrary.wiley.com/doi/10.1016/j.febslet.2014.09.039, https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0084689,. https://journals.asm.org/doi/10.1128/mbio.01018-16

This podcast is brought to you in collaboration with the British Society of Lifestyle Medicine.

Disclaimer: The content in this podcast is not intended to be a substitute for professional medical advice, diagnosis, or treatment. Always seek the advice of your doctor or qualified healthcare provider. Never disregard professional medical advice or delay in seeking it because of something you have heard on this podcast.

Disclaimer: In this episode, Alastair shares his enthusiasm and passion for postbiotics. Please note that while this is a rapidly evolving area of microbiome research, the scientific evidence is still building. The Microbiome Medics team advises that there is currently insufficient evidence to support specific health claims regarding postbiotics. We have enclosed some high-quality references below for listeners interested in further reading.

What are postbiotics, and why might they be the next massive breakthrough in gut health? In this episode of the Microbiome Medics Podcast, Dr. Sheena Fraser is joined by Alastair Jessel, founder of The Postbiotic Company (AYA BIOME™), for an eye-opening dive into the world of post-fermentation microbial science.

Using a clever "beer factory" analogy, Alastair breaks down exactly how postbiotics differ from prebiotics and live probiotics, explaining why these stable, inanimate metabolites might bypass the common pitfalls of live probiotic supplements, like dying on the shelf or in stomach acid. The conversation explores the patented fermentation of turmeric, sharing compelling insights from clinical trials regarding inflammation, weight management, and systemic health, alongside striking anecdotal evidence for skin conditions like rosacea.

Dr. Fraser grounds the discussion with clinical nuance, emphasizing the foundational importance of a whole-food, plant-based diet and natural fermented foods, while exploring how targeted postbiotic supplements could support patients recovering from antibiotic use or managing chronic metabolic issues.

Tune in to learn:

• The fundamental differences between prebiotics, probiotics, and postbiotics.
• Why shelf stability and bioavailability are the biggest hurdles for gut supplements.
• The clinical evidence behind fermented turmeric and its 550+ active metabolites.
• The potential role of postbiotics in post-antibiotic gut recovery, skin health, and metabolic function.
• Why Dr. Fraser advocates for a "food first" approach alongside emerging microbiome therapies.

(Guest Info: Alastair Jessel is the founder of AYA BIOME™ and publishes commentary on the gut health industry via his Substack, @amanofkent.)

Scientific References & Further Reading:

• Braga, J. D., et al. (2024). Gamma-aminobutyric acid as a potential postbiotic mediator in the gut-brain axis. Science of Food, 8(16).
• Higova, E. (2024). Postbiotics as metabolites and their biotherapeutic potential. International Journal of Medical Sciences, 25, 5441.
• Liang, B., & Xing, D. (2023). The current and future perspectives of postbiotics. Probiotics and Antimicrobial Proteins.
• Ma, L., et al. (2023). Postbiotics in human health. Nutrients, 15, 291.
• The Postbiotic Company. Research, Clinical Studies & Trials.

This podcast is brought to you in collaboration with the British Society of Lifestyle Medicine.

Disclaimer: The content in this podcast is not intended to be a substitute for professional medical advice, diagnosis, or treatment. Always seek the advice of your doctor or qualified healthcare provider. Never disregard professional medical advice or delay in seeking it because of something you have heard on this podcast.

While "gut health" is a ubiquitous buzzword in the wellness industry, it has historically lacked a clear scientific definition. In this episode, host Dr. Siobhan McCormack sits down with world-renowned expert Professor Maria Marco from UC Davis and the International Scientific Association for Probiotics and Prebiotics (ISAPP).

They discuss the new scientific consensus defining gut health, the crucial differences between fermented foods and probiotics, and what we can actually learn from direct-to-consumer stool tests. Plus, Siobhan gets a behind-the-scenes look at a rigorous clinical trial investigating the health impacts of kimchi.

What We Cover:

• Defining Gut Health: How a global expert panel established the first consensus definition, moving beyond just the microbiome to include six complex domains.
• Symptoms vs. Biomarkers: Why you can still achieve "gut health" even with a chronic but well-managed gut disorder.
• The Microbiome Testing Reality Check: The limitations of commercial stool tests and why they currently lack the clinical utility to guide personalized medical treatment.
• Fermented Foods vs. Probiotics: The true distinction between foods fermented for taste and preservation, versus specific live microbial strains proven to deliver targeted health benefits.
• Inside the Marco Lab: A look at the complexities of nutritional science, including an ongoing clinical trial comparing the physiological effects of kimchi to unfermented cabbage.

Scientific References & Further Reading:

• Marco, M., et al. (2025). Consensus panel definition of gut health. Nature Reviews.
• Marco, M., et al. (2026). 'The impact of fermented dairy on gastrointestinal health and associated biomarkers'. Nutrition Reviews.
• Bischoff, S. (2011). "Gut health": a new objective in medicine? Perspective Paper.

This podcast is brought to you in collaboration with the British Society of Lifestyle Medicine.

Disclaimer: The content in this podcast is not intended to be a substitute for professional medical advice, diagnosis, or treatment. Always seek the advice of your doctor or qualified healthcare provider. Never disregard professional medical advice or delay in seeking it because of something you have heard on this podcast.

While we often think of sleep and diet as separate pillars of health, our internal biological clocks and gut microbiome intricately connect them both. In this episode, co-hosts Dr. Siobhan McCormack and Dr. Sheena Fraser dive into the fascinating, bidirectional relationship between circadian rhythms, sleep quality, and gut health.

They discuss how our physiology adapts to 24-hour light and dark cycles, the metabolic havoc caused by social jet lag and shift work, and how our gut microbes actually operate on their own daily schedules. Plus, Siobhan and Sheena share practical, evidence-based chrononutrition strategies and explore how targeted dietary patterns, probiotics, and fermented foods can significantly boost your mood and sleep architecture.

What We Cover:

The Circadian Symphony: How light, dark, and our body's internal peripheral clocks orchestrate everything from hormone release (like cortisol and melatonin) to digestion.

Sleep Architecture & Mental Health: The critical role of REM and deep sleep, and how just one night of sleep deprivation increases impulsivity and degrades mood.

Chrononutrition: Why when you eat is just as important as what you eat, and how meal timing acts as a major environmental cue for your gut microbes.

Social Jet Lag & Shift Work: The metabolic consequences of disrupted sleep cycles, including increased risks for Type 2 Diabetes, and actionable strategies to regain circadian balance.

Nutrients & Microbes for Sleep: Exploring the science behind specific dietary protocols, the power of Lactobacillus, and how fermented foods support restorative rest.

• Conti, F. (2025). ‘Dietary protocols to promote and improve restful sleep: A narrative review’. Nutrition Reviews
• Dobielska, M. et al. (2025). ‘Association between fermented food consumption and sleep quality under psychological stress: Prospective cohort study’. Food Science & Nutrition.
• Scott, A.J., Webb, T.L., Martyn-St James, M., Rowse, G., & Weich, S. (2021). 'Improving sleep quality leads to better mental health: A meta-analysis of randomised controlled trials'. Sleep Medicine Reviews
• Hepsomali, P., & Groeger, J.A. (2021). 'Diet, sleep and mental health: Insights from the Uk Biobank Study'. Nutrients
• Reid, M., Omlin, X., Espie, C., Sharman, R., Tamm, S., & Kyle, S. (2022). 'The effect of sleep continuity disruption on multimodal emotion processing and regulation'. Journal of Sleep Research
• Marx, W., Manger, S.H., et al. (2023). 'Clinical guidelines for the use of lifestyle-based mental health care in major depressive disorder'. World Journal of Biological Psychiatry
• Vetter, C. et al. (2018). 'Night Shift Work, Genetic Risk, and Type 2 Diabetes in the UK Biobank'. Diabetes Care

This podcast is brought to you in collaboration with the British Society of Lifestyle Medicine.

Disclaimer:

The content in this podcast is not intended to be a substitute for professional medical advice, diagnosis, or treatment. Always seek the advice of your doctor or qualified healthcare provider. Never disregard professional medical advice or delay in seeking it because of something you have heard on this podcast.

While the gut microbiome often steals the spotlight, the microorganisms residing in our respiratory tract play a vital role in our health and immunity. In this episode, Dr. Sheena Fraser sits down with microbial ecologist Dr. Michael Cox to explore the fascinating, complex, and relatively uncharted territory of the lung microbiome.

They discuss how the lung microbiome fundamentally differs from the gut, the daily flux of bacteria entering and leaving our airways, and the profound impacts of environmental factors like air pollution, smoking, vaping, and household cleaning products. Plus, Dr. Cox shares the massive challenges scientists face when studying these deep-tissue microbes and what the future of respiratory medicine might look like.

What We Cover:

• From Seawater to Sputum: Using marine ecology techniques to decode human respiratory biology.
• Exploring the lungs' dynamic balance of microaspiration and mucociliary clearance.
• Meet the core lung bacteria (Streptococcus, Prevotella, Veillonella) and the puzzle of anaerobes in an oxygen-rich space.
• Environmental Disruptors: How pollution, smoking, and vaping inflame and alter the lung microbiome.
• Hidden Dangers of VOCs: The silent impact of everyday cleaning sprays and aerosols on respiratory health.
• Diet, Exercise, & Epigenetics: The systemic benefits of a high-fiber diet and fitness for chronic lung conditions like COPD and asthma.

About

Dr. Michael Cox is a microbial ecologist and the PGR Lead for the Institute of Microbiology and Infection at the University of Birmingham. His research focuses on the bacteria that reside in the respiratory tract in the context of respiratory diseases (such as COPD and Cystic Fibrosis). His lab works to understand the function of the respiratory microbiome, translate these findings for clinical benefit, and expand our understanding of the respiratory ecosystem beyond just bacteria.

Connect with Dr Michael Cox:

• University of Birmingham

• Cumming, K. J. (2018). "Long term effects of cleaning on the lungs." American Journal of Respiratory and Critical Care Medicine, 197(9):1099-1101.
• Hussain, S., et al. (2024). "Unlocking the secrets: VOCs and their devastating effects on lung cancer." Pathology - Research and Practice, 255:155157.
• Welsh, H. A., et al. (2026). "The effect of vaping on the human lung microbiota." Inhalation Toxicology, Vol 38, Iss 1.

This podcast is brought to you in collaboration with the British Society of Lifestyle Medicine.

Disclaimer:

The content in this podcast is not intended to be a substitute for professional medical advice, diagnosis, or treatment. Always seek the advice of your doctor or qualified healthcare provider. Never disregard professional medical advice or delay in seeking it because of something you have heard on this podcast.

Join Dr. Siobhan McCormack as she welcomes one of the top early-life microbiome scientists in the field, Professor Chris Stewart. Discover the origins of your gut microbiome, the biological superpowers of breast milk, and how lab-grown "organoids" are uncovering surprising ways to protect preterm babies.

What We Cover:

• The Genesis of You: How birth mode and early feeding shape our microbial foundations.
• Inside the Stewart Lab: Using lab-grown human "organoids" to study host-microbe interactions in real-time.
• The Magic of HMOs: Why mothers produce complex sugars (Human Milk Oligosaccharides) that feed gut microbes instead of the baby.
• The "Good" Clostridium: Groundbreaking research on a specific Clostridium perfringens strain that thrives on HMOs to protect preterm infants from gut diseases.
• Probiotics & Preemies: Navigating FDA regulations and the future of personalized medicine in neonatal care.

About

Professor Stewart leads human microbiome research at Newcastle University. His lab combines computational biology with innovative wet-lab human organoid models to study global health issues, focusing primarily on the early-life gut microbiome and protecting vulnerable infants.

Connect with the Stewart Lab:

• Newcastle University Profile
• Google Scholar
• Twitter
• Newcastle Neonatal Nutrition and NEC Research (N4)

• Stewart CJ, et al. (2018). Temporal development of the gut microbiome in early childhood from the TEDDY study. Nature, 562(7728):583–8.
• Chapman JA, et al. (2026). Clostridia from preterm infants metabolize human milk oligosaccharides to suppress pathobionts and modulate intestinal function in organoids. Nat Microbiol, 1–20.
• Masi AC, et al. (2021). Human milk oligosaccharide DSLNT and gut microbiome in preterm infants predicts necrotising enterocolitis. Gut, 70(12):2273–82.
• Beck LC, et al. (2022). Strain-specific impacts of probiotics are a significant driver of gut microbiome development in very preterm infants. Nat Microbiol, 7(10):1525–35.
• UNICEF UK: Breastfeeding in the UK

This podcast is brought to you in collaboration with the British Society of Lifestyle Medicine.

Disclaimer:

The content in this podcast is not intended to be a substitute for professional medical advice, diagnosis, or treatment. Always seek the advice of your doctor or qualified healthcare provider. Never disregard professional medical advice or delay in seeking it because of something you have heard on this podcast.

Join Dr. Siobhan McCormack and the "fibre-fabulous" Dr. Emily Leeming, a former superyacht chef turned King's College London microbiome scientist and registered dietitian. Discover why fibre is the overlooked "Cinderella nutrient," how it fuels your gut microbiome, and practical, delicious ways to hit your 30-gram daily target without the bloat.

What We Cover:

1. The Chef-to-Scientist Pipeline: Dr. Leeming's journey from the high seas to gut health research.
2. The "Blue Poo" Study: What transit time actually is and what it reveals about your digestion.
3. Disease Prevention: How feeding your gut microbiome protects against colorectal cancer and heart disease.
4. Simple Food Combos: Chef-approved tips to easily sneak more whole grains, nuts, and beans into your busy day.

About

Dr. Leeming is a scientist at King's College London, a dietitian, and part of the Harvard-led PROSPECT team investigating early colorectal cancer. She is the bestselling author and writes the popular Second Brain newsletter for over 30,000 subscribers.

Resources Mentioned:

1. Genius Gut: The Life-Changing Science of Eating for Your Second Brain by Dr. Emily Leeming
2. Fiber Power by Dr. Emily Leeming (Releasing May 21st)
3. Gut by Giulia Enders
4. The Psychobiotic Revolution by Scott C. Anderson, John F. Cryan, and Ted Dinan

Scientific References Discussed:

1. O’Keefe SJD, et al. (2015). Fat, fibre and cancer risk in African Americans and rural Africans. Nature Communications.
2. Asnicar F, Leeming ER, et al. (2021). "Blue Poo: Impact of Gut Transit Time on the Gut Microbiome Using a Novel Marker." Gut.
3. Burkitt D, Trowell H. (1975). Refined Carbohydrate Foods and Disease.

This podcast is brought to you in collaboration with the British Society of Lifestyle Medicine.

Disclaimer:

The content in this podcast is not intended to be a substitute for professional medical advice, diagnosis, or treatment. Always seek the advice of your doctor or qualified healthcare provider. Never disregard professional medical advice or delay in seeking it because of something you have heard on this podcast.

In this insightful episode, Dr. Sheena Fraser welcomes back Dr. Anastasia Theodosiou and introduces Baroness Natalie Bennett to discuss the Consumer Products (Control of Biocides) Bill. They unpack the hidden dangers of unregulated antimicrobial chemicals found in everyday items, from toothpaste to treated textiles, and the urgent need to protect our microbiomes from this "chemical cocktail". The trio discusses the critical distinction between medical antibiotics and consumer biocides, advocating for a shift from a "war on microbes" to a system that prioritizes planetary and human health.

Key Topics:

1. Defining biocides and distinguishing them from regulated medical antibiotics
2. The concept of "microbiotoxicity" and the impact of disinfectants on oral and gut health
3. The environmental consequences of biocide runoff and the rise of antimicrobial resistance
4. Why we need systemic regulation rather than relying solely on individual consumer choices

You can find out more about the Women's Environmental Network at https://www.wen.org.uk/

This podcast is brought to you in collaboration with the British Society of Lifestyle Medicine.

Disclaimer:

The content in this podcast is not intended to be a substitute for professional medical advice, diagnosis, or treatment. Always seek the advice of your doctor or qualified healthcare provider. Never disregard professional medical advice or delay in seeking it because of something you have heard on this podcast.

In this deeply personal episode, Dr. Sheena Fraser speaks with her lifelong friend, Katherine Saville, about her transformative journey through breast cancer recurrence and holistic healing. From high-stress corporate life to finding stillness, Katherine shares how she used lifestyle medicine, specifically diet, exercise, and microbiome health, to support her treatment and recovery.

Key Topics:

1. Navigating the isolation and fear of a cancer diagnosis.
2. The hidden dangers of chronic stress and "soldiering on."
3. Practical tips for gut-friendly nutrition during chemotherapy.
4. Finding new purpose and building community after illness.

You can find out more about Cancer Support Netherlands at https://cancersupportnetherlands.nl/

This podcast is brought to you in collaboration with the British Society of Lifestyle Medicine.

Disclaimer:

The content in this podcast is not intended to be a substitute for professional medical advice, diagnosis, or treatment. Always seek the advice of your doctor or qualified healthcare provider. Never disregard professional medical advice or delay in seeking it because of something you have heard on this podcast.

From the viral moment on The Traitors to the biology of the "silent but deadly," this episode is an unashamed deep dive into flatulence. Drs Siobhan and Sheena are joined by Julie Thompson, Lead Dietitian at Guts UK Charity, to break the stigma around passing wind. We discuss what normal gas looks like, why fiber makes us farty (and why that's a good thing!), and the truth about the Low FODMAP diet for IBS sufferers. Plus, we answer the important questions: Do spiders fart? And do charcoal underpants actually work?

Featured Guest:

Julie Thompson is a Gastroenterology Specialist Dietitian with over 16 years of experience supporting people with digestive diseases. She has a particular interest in disorders of gut-brain interaction, such as Irritable Bowel Syndrome (IBS).

A leading voice in her field, Julie contributed to the British Dietetic Association’s (BDA) dietary guidelines for IBS and has delivered the BDA’s Low FODMAP diet training to dietitians across the UK. She currently serves as the Information Manager at the charity Guts UK and sits on the BSG Gut Microbiota for Health Expert Panel.

References and resources:

• Guts UK Charity: https://gutscharity.org.uk/
• Book: Fartology by Stefan Gates
• Book: Does It Fart? by Nick Caruso & Dani Rabaiotti
• The Physics of Farts: Ancalle, D., et al. (2021). "Physics of flatulence." The Journal of the Acoustical Society of America.
• What is a "Normal" Amount of Gas? Modesto, A., et al. (2021). "Meta-Analysis of the Composition of Human Intestinal Gases." Digestive Diseases and Sciences.
• Microbes & Metabolism: Rowland, I., et al. (2018). "Gut microbiota functions: metabolism of nutrients and other food components." European Journal of Nutrition. (See the excellent section on intestinal gas & microbes!)
• Carb Intolerance: Fernández-Bañares, F. (2022). "Carbohydrate Maldigestion and Intolerance." Nutrients.
• The "Bean Study": Winham, D., & Hutchins, A. (2011). "Perceptions of flatulence from bean consumption among adults in 3 feeding studies." Nutrition Journal. (Evidence that the gas often goes away after a few weeks!)
• Symptoms in the UK: Thomson, C., Garcia, A., & Edwards, C. (2021). "Digestive symptoms, diet and demographics in UK adults." Proceedings of the Nutrition Society.
• Global Gas Survey: Palsson, O.S., et al. (2025). "Gas-Related Symptoms in the General Population: Prevalence, Impact and Associated Factors." Neurogastroenterology & Motility.

This podcast is brought to you in collaboration with the British Society of Lifestyle Medicine.

Disclaimer:

The content in this podcast is not intended to be a substitute for professional medical advice, diagnosis, or treatment. Always seek the advice of your doctor or qualified healthcare provider. Never disregard professional medical advice or delay in seeking it because of something you have heard on this podcast.