My favorite books about the microbiome

The number of books about the microbiome have exploded in the past few years, but I've tried to read (or at least skim) every book I can find. If you're a newcomer who would like to come up to speed, here's my ranked list of the best books as of today (November 2016).

1. Knight, Rob Follow Your Gut: How the Ecosystem in Your Gut Determines Your Health, Mood, and More

At only 120 pages, this is the most concise summary of what’s known — and not known — about the microbiome. Written by one of the scientists behind the American Gut Project, it’s a readable and fascinating overview of the facts and a great first introduction. If you only read one book, this is it.

1. Sonnenburg, Justin The Good Gut: Taking Control of Your Weight, Your Mood, and Your Long-term Health

Another concise, well-written summary by a top-notch researcher. This one ties for first place because, well, I'm a fan of uBiome and this one doesn't focus on American Gut. The science is first-rate, but there is practical advice too, including an appendix of microbiome-friendly recipes.

2. Spector, Tim The Diet Myth: Why the Secret to Health and Weight Loss is Already in Your Gut

Another excellent one written by a practicing scientist and a good complement to Follow Your Gut. The author's concise writing style packs multiple interesting examples and facts on each page. Divided into chapters based on type of food, I learned about what's proven and what's unknown about the effects of different diets on health.

3. Collen, Alanna 10% Human: How Your Body's Microbes Hold the Key to Health and Happiness

Another great overview that explains to the ordinary person the implications of the microbiome. Well-written, full of interesting facts, but sticks strictly to mainstream science. For example, although the author explains the concept of "leaky gut", she observes it skeptically as an unproven hypothesis, rather than jump whole-hog into diagnoses. Best parts discuss the gut role on behavior ("Mind Control"), with detailed examples from autism research, Whipple's Disease, and more. The book includes a list of the highest-quality references, but unfortunately it's not complete, so many of the facts are hard to follow up.

4. Blaser,Martin Missing Microbes: How the Overuse of Antibiotics Is Fueling Our Modern Plagues

5. Velasquez-Manoff, Moises An Epidemic of Absence: A New Way of Understanding Allergies and Autoimmune Diseases

Another book that explains a provocative idea that our immune systems need regular stimulation by parasites and other infectious agents, or we risk unpleasant side effects in the form of allergies, diabetes, and many other nasty conditions. The remarkable correlation between the hygiene of modernity and the rise of autoimmune diseases makes for powerful evidence that science is far behind in understanding all the consequences of our current lifestyles.

Short, practical summary of what's known about microbial infections, with suggestions for how to manage and treat them. I liked the chapters on the mouth and skin, with practical advice about how to choose toothpaste and soap.

Spector, Tim Identically Different: Why We Can Change Our Genes

Well-written, concise overview of what's known about epigenetics and "Fat Genes", "Gay Genes", "Infidelity Genes", "Bacteria Genes" and more. This is the same author of The Diet Myth discussed above, written before he became aware of the microbiome.

Other Books Worth Having in the Pile

Matthews, Richard The Symbiont Factor: How the Gut Bacteria Microbiome Redefines Health, Disease and Humanity

Heavily researched and footnoted (the last hundred pages are references), it's an overview of the practical side of what's known about the microbiome. When I'm looking for a short summary of particular conditions (Parkinsons, Alzheimers), I reach for Dr. Matthews book first.

My complaint is that it's written by a clinician, not a scientist or journalist, and it's hard to tell when he's writing from opinion (e.g. his rants against GMOs) or whether there's a real scientific consensus on something (e.g. the role of Bifidobacterium).

Not Recommended

Life is short, so to help you be more efficient, here's a list of books that I think are a waste of time.

Mullin, Gerard E. The Gut Balance Revolution: Boost Your Metabolism, Restore Your Inner Ecology, and Lose the Weight for Good!

Although Dr. Mullin has been thinking about the microbiome for years, most of this book is about standard alternative diet advice, with references to Omega-6, FODMAPs, Mediterranean Diet, etc. but not really much specific about the microbiome. Don’t waste your money.

Kellman, Raphael The Microbiome Diet

Includes the typical formulaic suggestions for how to cure a bad microbiome (Remove! Replace! Reinoculate! Repair!) and lots of sweeping, unproven suggestions for what to eat: “Cinnamon balances blood sugar” with absolutely nothing to connect it to the microbiome. There is a nice list of “superfoods” including natural prebiotics like jicama, but again you must take his word for it that this somehow benefits the microbiome. Just google it and save the effort.

Gershon, Michael The Second Brain: The Scientific Basis of Gut Instinct and a groundbreaking new understanding of nervous disorders of the stomach and intestine

Although this was a ground-breaking classic when first published in the 1990s, much of the information is obsolete thanks to new technologies, especially the new sequencing methods that gave rise to our understanding of the microbiome. The more recent book, Gut by Giulia Enders is a more up-to-date description of the anatomical aspects of the digestive system, though Gershon is still worth reading because of its details as well as its outsized influence since its publication.


Just about any new health book from the past few years will touch on the microbiome, but I didn’t find much specifically microbiome-related that was useful or new in books by David Asprey (“The Bulletproof Diet”), Tim Ferriss’ Four Hour Body, or Chris Kresser’s Paleo Code. You may find these books useful for other reasons, like the detailed discussions of specific foods, but you’ll learn little about the microbiome.

The Bulletproof Diet, for example, stresses the now-disproven Firmicutes/Bacteroidetes ratio too much.

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