This is a new field, so much of the written literature remains in academia, but hopefully the following summary of items to read will be helpful.
Here are my suggestions for additional reading.
My list of people who regularly write interesting comments about the microbiome is here:
These people write extensively on the Microbiome, and you’ll find just about anything valuable if their name is attached:
GERMS ARE US Bacteria make us sick. Do they also keep us alive? BY MICHAEL SPECTER
Read more about Toxoplasma Gondii
The Atlantic: How Your Cat Is Making You Crazy (Feb 6, 2012)
http://www.microbiomedigest.com/ A daily digest of scientific microbiome papers, by Elisabeth Bik, laboratory of David Relman, Stanford University – Twitter: @microbiomdigest
Gut Guardians by Grace Liu and Matt Peppin
Gut Check: Exploring Your Microbiome from Coursera
Wild Fermentation: The Flavor, Nutrition, and Craft of Life Culture Foods by Sandor Katz
Diet and nutrition
The Paleo Manifesto: Ancient Wisdom for Lifelong Health by John Durant
The best summary so far of the motivation and principles of ancestral health. The author is a student of Steven Pinker’s, from Harvard, and writes with a general, more academic orientation rather than as a how-to manual. The basic principle, that the modern world is not our natural habitat, makes much sense, and I like the way he applies that rule to diet and exercise, plus sleep and much more.
Paleofantasy: What Evolution Really Tells Us about Sex, Diet, and How We Live Zuk, Marlene Although it tries to debunk ancestral diets with proof that ancient humans had too much variation, this book targets mostly a straw man caricature of the paleo movement, and rarely addresses the real issues.
Why We Get Fat: And What to Do About It
Taubes, Gary A well-researched, easy to read, but thorough discussion of obesity that concludes that carbohydrates, not calories, are key. The simple, seemingly obvious belief that a person’s weight is a function of “calories in and calories out” will seem much less obvious and mostly wrong by the end of this book.
All Natural: A Skeptic's Quest for Health and Happiness in an Age of Ecological Anxiety
Although frustratingly equivocal with recommendations, I liked the survey of the advantages and disadvantages of “mainstream” versus “alternative” approaches to health, on everything from childbirth, vaccinations, and raw milk.
Eating on the Wild Side: The Missing Link to Optimum Health
By Jo Robinson
A highly practical summary of fruits and vegetables: which are good for you and why. Every page is full of interesting, often counter-intuitive tips to eat more healthily. Examples: frozen blueberries are just as healthy as fresh, but broccoli loses most of its nutrition within hours after picking. Carrots cooked with butter are much healthier than raw.
In Defense of Food: An Eater's Manifesto
Pollan, Michael If you’re confused about diet, this is the best advice yet: “Eat food. Not too much. Mostly plants”.
Far out theories
Plague Time: The New Germ Theory of Disease Ewald, Paul Published in 2002, this book raises the intriguing possibility that most (perhaps all) serious diseases are caused by infections. Certain types of cancers (e.g. HPV) are already known to have viral origins, but imagine how our thinking would change if — when — someday science discovers infectious agents behind other cancers and heart disease. Reading this with other books about the role of microbes has made me far more sensitive to the possibility that science and medicine could one day undergo a huge shift in the way that diseases are diagnosed and treated.