You Are What You Eat—And So Are They: Microbes in Your Gut

—by Roxy Bergeron

For years we have heard that fiber plays an important part of a healthy diet. But thanks to advances in genetics and modern science, the role of not just fiber but the whole gamut of goodness found in fruits and vegetables is becoming ever more clear. And that has to do with the care and feeding of the multitude of microorganisms that call our bodies home.

Between one and three pounds of “us” is actually “them”—the 100 trillion microbes that live both in and on us. We carry around about two pounds’ worth of bacteria in our gut alone. And along with other microfriends that inhabit our skin, tongue, and various other places, cell for cell, our ratio of microbe cells to human cells is ten to one—ten of theirs to one of ours.1

Space may indeed be the Final Frontier, but classifying the creatures dwelling deep in the depths of our own bodies is the current New Frontier. The genetic analysis of the microorganisms inhabiting our gut, skin, tongue, and other sundry bodily areas is a burgeoning scientific field of study, made possible by advances in genomic technology.2

Genomes, ours and theirs

Our “first” genome is our human genome, the so-called genetic blueprint that makes each of us a unique individual. The genes making up our microbiome—the microscopic critters living in and on our bodies—make up our “second genome.” 

According to a report posted on the National Institute of Health website in 2012 called “The Human Microbiome: Our Second Genome,” “(t)he human microbiome is a source of genetic diversity, a modifier of disease, an essential component of immunity, and a functional entity that influences metabolism and modulates drug interactions.”2

(A “microbiota” is defined as all the microbes in a given community; a “microbiome” is the sum total of all their genes.)1

So, how did they get there?

Acquisition of our unique gut microbiome is highly matriarchal, since those of us who passed through our mother’s birth canal on our way to life have sterile guts and are initially infused with bacteria from her vaginal and intestinal microbes. Babies born via cesarean section pick up microbes from the skin of the people around them. 

At first, babies have a special microbial community. Weaning and eating solid foods brings about changes in microbe population, so that by the time a child is about three years old, its microbes have settled into a population that is a lot like that of its parents.1 Over the course of our lives, our microbiome shifts and changes through our contact with food, places, people, and circumstance.

In a recent article that ran in the New York Times Sunday Magazine, author and food guru Michael Pollan describes his odyssey of learning the identity and important details concerning his very own gut microbiome through his participation in the American Gut Project. Along the way, he learned that our little symbiotic friends live with us as commensal helpmates and play a critical role in training and modulating our immune system.1  

The microbes also perform “ecosystem services,” including occupying space and establishing an alimentary environment that dissuades potential invaders. They also manufacture neurotransmitters (the gut has its own nervous system), enzymes, vitamins B and K, and essential nutrients such as amino acids and short-chain fatty acids. Molecules that affect our immune and metabolic systems are also created there. Obesity, diabetes, and metabolic disease are diseases singled out as being affected by the status of one’s gut microbiome—particularly obesity.2 

Diversity in our microbiome’s makeup makes it possible for the creatures, which breed a new generation every 20 minutes, to adapt quickly to threats by swapping genes and bits of DNA and meet whatever threat has appeared.

Mike and Ike

Under a microscope, a colony of microbes looks a lot like, well, a pile of really, really tiny Mike and Ike candy pieces. These rod-shaped creatures coevolved along with our historic ancestors and digest for us the things we cannot—such as the fibrous parts of the plants we eat and the sugar in mother’s milk.

In the human gut, the main types of creatures are Bacteroidetes and Firmicutes, along with a variety called Prevotella (just giving them a shout-out). It’s a savvy setup for us and them, since they get to eat, and we receive the benefits of the byproducts of their actions, such as fermentation.

Fermentation’s byproduct is short-chain fatty acids that help prevent inflammation and nourish the epithelial cells lining our gut , which act as a barrier to keep toxins from leaking into our bloodstream. The process also lowers the gut’s pH, and this is a good thing. A lower intestinal pH improves the gut barrier, promotes colonic health, provides pathogen resistance, and can decrease the number of evil proteobacteria. The more plants the gut gets to ferment, the lower the pH.3

So, what’s for dinner?!

The clarifying light of definitive scientific knowledge is not yet shining on the question of what constitutes a healthy gut biome or what the most beneficial course of action regarding diet might be.  But a reasonable take-away, if you will, is to eat a diet that does not cause inflammation and that encourages fermentation by desirable microbes. 

One idea is to hedge your bets and eat a diet rich in fruits and vegetables to get all three kinds of fiber: resistant starch found in foods such as beans, oats, and bananas; soluble fiber in onions, roots, and nuts, to name a few; and insoluble fibers such as the kinds found in whole grains and avocado. Then your friends down under can happily percolate away doing what they were born to do—ferment your food.4  

Another idea is to eat probiotic foods to enrich and fortify your existing microbiome. The main probiotic food (a food that contains live cultures of beneficial bacteria) consumed in the standard Western diet is yogurt. Borrowing from the menus of other cultures, kefir, miso, sauerkraut, coconut water, sour pickles, and kimchi all have probiotic creatures to help keep a gut happy and healthy and biodiverse.

Foods rich in prebiotics include banana, garlic, asparagus, Jerusalem artichoke, honey, leeks, and onions; these will help feed your symbiont buddies. Avoid processed foods (which are notorious for being low in fiber and high in calories and fat), eat prebiotic fermented foods, and consume whole grains and plants to ensure a variety of polysaccharides and fiber—lots of fiber—to maintain a healthy fermentation process in the gut.

I must admit to feeling a little bit as if I’m following in Pollan’s footsteps and thinking of myself as not “me” but “us.” It rather appeals to my maternal side! I take seriously my position as food source for my commensals and am eating a lot more salads and fresh food. Party on, guys!


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Additional resources

1. A very nice “meet your microbes” article from Mother Jones: <www.>.

2. The role the gut colonies may be playing in obesity is fascinating. This article from Mother Jones does a nice job discussing the research: <>.

3. Learn more about the American Gut Project at <>, including how you can participate in this citizen science project. Visit <>.

4. Another gut microbiome citizen science research project is Ubiome at <>.  

5. For a fee, you can have your own gut biome tested through either of these projects.

[Roxy Bergeron is a volunteer cashier at HPC. She contributes regularly to the newsletter; her last article was about gardening in a drought-leaning world.]