Wednesday, November 7, 2012

Microbiome Part 7: Human Bacterial Partnerships

Note: This program first aired on October 27, 2012.

It should be clear to you, if you’ve been following this show for the past several weeks, that bacteria influence every aspect of life on Earth. Omnipresent, that is how you should think of bacteria. From the endosymbiosis theory of the origins of chloroplasts for photosynthesis, and mitochondria for energy metabolism to the nitrogen fixing role of symbiotic microbes in plant roots, bacteria are intimately involved in all biological processes. They even single handedly support the non photosynthetic ecosystems of the deep ocean hydrothermal vent communities, supporting life without light, something we used to think of as impossible.

I want to turn our gaze inward now, to the cutting edge of medicine and microbiology, to the human microbiome. Our bodies are a vast universe and play host to thousands of different kinds of life forms. There are estimated to be more bacterial cells on and in our bodies than there are human cells, by at least an order of magnitude. It turns out, we’re actually more than the sum of our parts.  We function more like a forest ecosystem or a coral reef than the individuals we once thought we were.

All of these microbes evolved right along with us, over the millions of years of hominid evolution. Our microbiome has been even been described as an additional organ, one we all have that most of us have no awareness of whatsoever. These bacteria we host fill many ecological roles in our bodies, and in return get a stable and generous living environment. They do so much for us in fact, that without them we could scarcely live. Remember when I talked about bacteria as external digesters? Most of them (and certainly all the ones we are talking about now) are heterotrophic and must ingest nutrients from outside their bodies. The two to five pounds of them living in our guts at any given time are doing just that; digesting all that food we swallow. We physically break the food down into smaller pieces, and we even synthesize some enzymes that chemically break down the food molecules into smaller more absorbable bits. What we can’t or don’t digest (primarily certain complex carbohydrates and fibers) we give to our gut flora, that two to five pounds of bacteria we carry around in our intestines. As decomposers, they are able to at least partially break down the less digestible components of the food we eat, and we can benefit from this. That digested food can be absorbed by our cells. Some of the byproducts of this bacterial digestion are the short chain fatty acids that are so critical to many metabolic pathways, and are thought to play a an anti inflammatory role in the body as well. The microbes also synthesize certain essential vitamins and cofactors that are not otherwise found in the food we eat.

From a nutritional standpoint, our gut flora close a loop that we are not capable of closing on our own, we’ve never had to evolve complete chemical digestion because we’ve been co-evolving with our symbiotic microflora for millions of years. In the coming weeks we will look beyond the simple digestive symbiosis, and explore the various other ways the human microbiome affects and improves our quality of life. 


The New York Times did several articles on the human microbiome this summer, in conjunction with the release of the NIH Human Microbiome project report.

Kolata, Gina “In Good Health? Thank your 100 Trillion Bacteria” New York Times, June 13, 2012

Zimmer, Carl “Tending the Body’s Microbial Garden” New York Times, June 18, 2012

Also, from 2010: Zimmer, Carl (he’s a leading American science writer, who’s latest book is on microbes) “How Microbes Defend and Define Us” New York Times, July 12, 2010

Direct from the source: The National Institute of Health’s Human Microbiome webstite:,

“The structure, function and diversity of healthy human microbiome”—one of the seminal articles from the Human Microbiome Project

Small intestinal bacterial overgrowth happens when large bowel bacteria get into the small bowel (think Girls gone wild meets Mardi Gras), and raise havoc. We tend to think of the gut flora as being in the colon, but there are bacteria in the small bowel too, just less of them and of a different type