What if the biggest mistake we're making with gut health is treating the microbiome like a list of bacteria instead of a living ecosystem?

Your gut is home to trillions of microorganisms that influence inflammation, metabolism, immune function, hormones, brain health, and longevity. But modern life—from ultra-processed foods and antibiotics to pesticides, chronic stress, and inadequate fiber—may be systematically stripping away the microbial diversity we need to stay healthy.

My guest, Kiran Krishnan, is a research microbiologist and microbiome expert who has spent nearly two decades studying these complex microbial ecosystems. He co-founded Microbiome Labs and has helped develop microbiome testing and clinically studied probiotics.

Kiran introduced me to the concept of the holobiome: the idea that we aren't simply human cells and human DNA, but walking ecosystems containing millions of microbial genes that perform essential functions throughout the body.

We explore what's actually damaging that ecosystem, how poor gut health can contribute to leaky gut, endotoxemia, systemic inflammation, and metabolic dysfunction, and most importantly, what we can do to rebuild it.

Kiran breaks down how much fiber we should actually be eating, the difference between soluble and insoluble fiber, why resistant starch and polyphenols matter, what fermented foods really do, and how to think about probiotics and microbiome testing. We also discuss how fasting, sleep, resistance training, outdoor exposure, and even social connection can influence microbial diversity.

In this episode, you'll learn:

• Why microbial diversity may be one of the most important markers of gut health

• How antibiotics, ultra-processed foods, pesticides, and stress can disrupt the gut microbiome

• How leaky gut, endotoxemia, chronic inflammation, and metabolic health are connected

• How fiber, resistant starch, fermented foods, polyphenols, and probiotics support the gut

• Why sleep, fasting, exercise, outdoor exposure, and social connection can help build a more resilient microbiome

We also explore the future of gut health, including the limitations of current microbiome testing and how Kiran is using AI and machine learning to develop targeted probiotic combinations around specific biological pathways.

My biggest takeaway is that gut health isn't something we fix with one supplement. We are guardians of an incredibly complex ecosystem—and the choices we make every day can either support it or slowly dismantle it.

If we want to improve longevity, metabolic health, inflammation, and chronic disease prevention, taking care of our microbiome may be one of the most powerful places to start.

Learn more about Dr. Shah:

Website: www.drshah.com

Clinic: next-health.com

Instagram: @extend_podcast and @darshanshahmd

Learn more about Kiran Krishnan:

Website: biomelc.com

Instagram: @kiranbiome

Special offer from Kiran! Join the free Circe community here to get the FREE Leaky Gut Guide and The 5 Pillars to Building a Resilient Gut.

Thank You To Our Sponsors:

Next Health Longevity Summit: Head to next-health.com/summit to secure your spot at the first ever Next Health Longevity Summit in Nashville on 9/12! Our speakers include Dr. Shah, LeAnn Rimes, Dr. Jeremy London, Dr. Louisa Nicola, Dr. Vonda Wright and many more! This is one day packed with activities like blood tests, recovery modalities, IV's and brands we love that will completely change the way you think about health.

Momentous: Head to livemomentous.com and use code DRSHAH for up to 35% off your first order!

191: Kiran Krishnan: How to Rebuild Your Gut Microbiome & Reduce Inflammation

Extend Podcast with Darshan Shah, MD

191: Kiran Krishnan: How to Rebuild Your Gut Microbiome & Reduce Inflammation