Best Methods for Microbiome Analysis

In this episode I sit down again with microbiome researcher Dr Suzanne Devkota to explore what a healthy microbiome really is and how we can support it. We unpack diversity, early life programming, fibre and microbiota accessible carbohydrates (MACs), plus the genuine role of probiotics, prebiotics and postbiotics.

Suzanne also shares cutting edge research on short chain fatty acids, Akkermansia, inflammatory bowel disease, visceral fat and colon cancer, and helps separate solid science from the noise you see online.

What We Cover

• What the microbiome is and how it differs along the digestive tract
• Why diversity is a key marker of gut health and how chronic disease and diet affect it
• Early life influences on the microbiome, from birth mode to first foods
• The realities of stool testing, different methods, and how to interpret results with care
• Probiotics versus prebiotics versus postbiotics, when each may or may not be useful
• MAC rich foods, short chain fatty acids and why butyrate is so important for gut barrier integrity
• The Akkermansia story, mucus, leaky gut and why focusing on one bug is misleading
• New data on IBD, gut leakiness, bacteria in fat tissue and links to fibrosis and metabolism

I hope this conversation gives you a clearer, more grounded view of gut health and helps you focus on practical, sustainable steps that genuinely support your microbiome.

You can learn more from Dr Suzanne Devkota by following her on Instagram, or by visiting the Cedars-Sinai Human Microbiome Research Institute and the Devkota Lab.

• Intro (00:00:00)
• The Microbiome Conversation (00:01:16)
• How Diversity Shapes Your Gut’s Health and Resilience (00:04:40)
• The First Three Years That Shape a Lifetime (00:08:09)
• What Microbiome Tests Can and Can’t Tell You (00:11:05)
• Probiotics, Prebiotics, Postbiotics (00:18:05)
• The Quiet Power of Short-Chain Fatty Acids (00:34:47)
• The Fiber Controversy and What People Get Wrong (00:47:58)
• How Daily Habits Quietly Reshape Your Microbiome (00:49:28)
• Antibiotics, Resetting, and Rebuilding Your Gut (00:52:07)
• How Early-Life Factors Imprint Your Gut for Decades (00:56:57)
• Why Chronic Inflammation and IBD Connect Back to the Microbiome (01:03:14)
• What We’re Learning About Colon Cancer and the Gut (01:16:13)
• The Future of Microbiome Science and Personalized Gut Care (01:27:45)

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Simon Hill, MSc, BSc (Hons)

• Creator of theproof.com
• Host of The Proof with Simon Hill
• Author of The Proof is in the Plants

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