Microbiome Myths and Misconceptions

April 10, 2020

Microbiome researcher and scholar of integrative gut health Lucy Mailing, PhD. is back on the podcast with me today. Lucy just completed her doctoral degree at the University of Illinois at Urbana-Champaign, where she studied the effects of diet and exercise on the gut microbiome in states of health and disease. She has authored numerous peer-reviewed journal articles and recently won the Young Scientist Award at the International Scientific Conference on Probiotics, Prebiotics, Gut Microbiota, and Health in 2019.

On this podcast, Lucy discusses her recent talk at the 2020 IHH-UCSF Symposium on Nutrition and Functional Medicine. The topic is myths and misconceptions about the microbiome - and some of these are quite surprising! We discuss gut testing methods and why some are better than others. Lucy explains why you consider skipping probiotics after a course of antibiotics and shares what to do instead to support repopulation of a healthy microbiota. She also discusses some of the best and worst gut-health supplements.

Here’s the outline of this interview with Lucy Mailing:

[00:00:30] Why care about the gut microbiome?

[00:01:37] Previous podcast with Lucy: How to Optimise Your Gut Microbiome.

[00:03:52] Unschooling and self-directed learning.

[00:04:40] Book: The Carpenter and the Gardener by Alison Gopnik.

[00:05:45] Podcast on unschooling: How to Support Childhood Cognitive Development, with Josh Turknett, MD.

[00:06:16] Lucy speaking at UCSF: Microbiome Myths & Misconceptions (on Facebook). Slides from her talk.

[00:07:46] Lucy's talk at the Ancestral Health Symposium 2019: Modulating the gut microbiome for health: Evidence-based testing & therapeutic strategies.

[00:09:06] Myth: Culture-based stool testing is accurate.

[00:11:00] Companies currently using 16S: Thryve and BiomeFx.

[00:11:28] Podcast: How to Use Probiotics to Improve Your Health, with Jason Hawrelak.

[00:12:16] Diagnostic Solutions GI-MAP.

[00:14:34] Metagenomics; Onegevity.

[00:14:56] Doctors Data and Genova have now added PCR (polymerase chain reaction) to their tests.

[00:15:33] Parasites Blastocystis and Dientamoeba fragilis.

[00:17:35] Jason Hawrelak’s course: Blastocystis & Dientamoeba: Gastrointestinal Pathogens or Commensal Symbionts?

[00:17:39] Blastocystis.net. Book: Thoughts on Blastocystis, by Christen Rune Stensvold.

[00:18:45] Gut dysbiosis is driven by oxygen leaking into the gut; Study: Rivera-Chávez, Fabian, Christopher A. Lopez, and Andreas J. Bäumler. "Oxygen as a driver of gut dysbiosis." Free Radical Biology and Medicine 105 (2017): 93-101.

[00:19:04] Blastocystis might buffer oxygen influx, preventing the overgrowth of other pathogens. Study: Tsaousis, Anastasios D., et al. "The human gut colonizer Blastocystis respires using Complex II and alternative oxidase to buffer transient oxygen fluctuations in the gut." Frontiers in cellular and infection microbiology 8 (2018): 371.

[00:19:40] Blastocystis colonization correlates with a higher bacterial diversity; Study: Audebert, Christophe, et al. "Colonization with the enteric protozoa Blastocystis is associated with increased diversity of human gut bacterial microbiota." Scientific reports 6 (2016): 25255; And the opposite result: Nourrisson, Céline, et al. "Blastocystis is associated with decrease of fecal microbiota protective bacteria: comparative analysis between patients with irritable bowel syndrome and control subjects." PloS one 9.11 (2014).

[00:20:02] Myth: We know what a “healthy” gut microbiome looks like.

[00:20:06] Lucy's blog on the elusive “healthy microbiome”: A new framework for microbiome research.

[00:22:43] Microbial signatures of dysbiosis.

[00:26:06] Myth: Everyone needs comprehensive gut testing.

[00:27:37] Ivor Cummins and Malcom Kendrick podcasts: Should You get a CAC Heart Scan or Not? Part 1 and Part 2.

[00:28:14] Myth: Breath testing is a reliable way to test for SIBO.

[00:28:27] Lucy's blog posts on testing for SIBO: What the latest research reveals about SIBO and All about SIBO: Small Intestinal Bacterial Overgrowth.

[00:29:40] Culture-based testing methods underestimate the number of bacteria in the small intestine by about a hundredfold; Study: Sundin, O. H., et al. "Does a glucose‐based hydrogen and methane breath test detect bacterial overgrowth in the jejunum?." Neurogastroenterology & Motility 30.11 (2018): e13350.

[00:30:53] Orocecal transit time ranges from ten to 220 minutes; Study: Connolly, Lynn, and Lin Chang. "Combined orocecal scintigraphy and lactulose hydrogen breath testing demonstrate that breath testing detects orocecal transit, not small intestinal bacterial overgrowth in patients with irritable bowel syndrome." Gastroenterology 141.3 (2011): 1118-1121.

[00:32:43] SIBO might not produce enough hydrogen to result in a positive breath test. Sundin, O. H., et al. "Does a glucose‐based hydrogen and methane breath test detect bacterial overgrowth in the jejunum?" Neurogastroenterology & Motility 30.11 (2018): e13350.

[00:34:36] Myth: Most bloating, distension, gas is from SIBO (and we neeed to kill the overgrowth).

[00:34:45] Small intestinal dysbiosis, not bacterial overgrowth is what underlies a lot of gut symptoms; Study: Saffouri, George B., et al. "Small intestinal microbial dysbiosis underlies symptoms associated with functional gastrointestinal disorders." Nature communications 10.1 (2019): 1-11.

[00:36:09] Mark Pimentel's research group.

[00:37:04] How to support the gut ecosystem; serum bovine immunoglobulins (SBI).

[00:38:25] Orthomolecular SBI Protect.

[00:38:38] Myth: A high-fat diet is bad for the gut.

[00:38:52] Misconceptions from the scientific literature on high-fat diets.

[00:39:54] Diet alters the gut microbiome composition within 48 hours; Study: David, Lawrence A., et al. "Diet rapidly and reproducibly alters the human gut microbiome." Nature 505.7484 (2014): 559-563.

[00:41:06] The Hadza hunter-gatherer microbiota cycles with the seasons; Study: Smits, Samuel A., et al. "Seasonal cycling in the gut microbiome of the Hadza hunter-gatherers of Tanzania." Science 357.6353 (2017): 802-806.

[00:42:41] Ketones may support gut barrier function. Study: Peng, Luying, et al. "Butyrate enhances the intestinal barrier by facilitating tight junction assembly via activation of AMP-activated protein kinase in Caco-2 cell monolayers." The Journal of nutrition 139.9 (2009): 1619-1625.

[00:44:45] Myth: More exercise is always better. 

[00:46:05] Zinc carnosine may reduce exercise-induced gut permeability; Study: Davison, Glen, et al. "Zinc carnosine works with bovine colostrum in truncating heavy exercise–induced increase in gut permeability in healthy volunteers." The American journal of clinical nutrition 104.2 (2016): 526-536.

[00:46:45] Myth: You should always take probiotics after antibiotics.

[00:47:51] Probiotics can delay the restoration of the native microbiota after antibiotics; Study: Suez, Jotham, et al. "Post-antibiotic gut mucosal microbiome reconstitution is impaired by probiotics and improved by autologous FMT." Cell 174.6 (2018): 1406-1423.

[00:49:20] A better strategy: supporting the gut epithelial cell with butyrate; Study: Rivera-Chávez, Fabian, et al. "Depletion of butyrate-producing Clostridia from the gut microbiota drives an aerobic luminal expansion of Salmonella." Cell host & microbe 19.4 (2016): 443-454.

[00:51:37] Myth: Prebiotics work the same for everyone and always feed good bacteria.

[00:52:45] Blog post: Resistant Starch: Is it Actually Good for Gut Health?

[00:53:12] Cooking food affects microbiome; Study: Carmody, Rachel N., et al. "Cooking shapes the structure and function of the gut microbiome." Nature Microbiology 4.12 (2019): 2052-2063.

[00:54:27] Variable glycemic responses to Fructooligosaccharide (FOS) and Galactooligosaccharide (GOS); Study: Liu, Feitong, et al. "Fructooligosaccharide (FOS) and galactooligosaccharide (GOS) increase Bifidobacterium but reduce butyrate producing bacteria with adverse glycemic metabolism in healthy young population." Scientific reports 7.1 (2017): 1-12.

[00:55:32] Myth: All herbal antimicrobials are safe and effective.

[00:56:13] Grapefruit seed extract inhibits a broad spectrum of bacteria and is toxic; Study: Heggers, John P., et al. "The effectiveness of processed grapefruit-seed extract as an antibacterial agent: II. Mechanism of action and in vitro toxicity." The Journal of Alternative & Complementary Medicine 8.3 (2002): 333-340. Presentation by Jason Hawrelak, PhD: Phytotherapy in the Treatment of Dysbiosis of the Small and Large Bowel.

[00:57:03] Herbs that have been found to be useful: Atrantil, Iberogast, triphala.

[01:00:44] Current projects: blogging, consultation, creating training courses.

[01:03:02] Lucy’s website, support Lucy’s work on Patreon.