Once the diversity of the microbial world is catalogued… it will make astronomy look like a pitiful science. – Julian Davies

For Neil Armstrong, the giant step for mankind was taken on the moon. For Jeff Leach, it might just be in the colon, at least if he can find the money.

Jeff Leach called me not so long ago to ask me about my colon. Well, that isn’t totally right. He called to tell me about other peoples. Is that worse?

In the colon live trillions of bacteria (though such estimates are guesses as wild as those about the numbers of stars), a universe of planet-sized cells just above the sphincter. These bacteria are important, but uncharted. The most poorly known feature of these beasts is how they vary from one person to the next and why. Your metabolism, immune health, propensity to diabetes and ability to digest seaweed have all, recently, been suggested to depend upon the microbes on or inside you, but on what does the composition of those microbes themselves depend?

This is a version of the belly button mystery I discussed last week—the mystery of what determines just which microbes you have and depend on (or fight). Leach wants to understand what determines the wild life of your colon.

Most readers of Scientific American are aware that their bodies are covered inside and outside with microbes on which his or her life, odor, and much else depend—their cloak of cells. But this consensus is new. In the 1960s Lynn Margulis posited that the mitochondria in our cells and chloroplasts in plant cells were relictual bacteria, evidence of ancient symbioses. She also argued that symbiosis were everywhere, a dominant feature of evolution. She was right on all counts, the founding mother of the microbiome. She was also ignored. Not long after, Carl Woese went into his lab proposing to look at the nucleotides of bacteria to create evolutionary trees of microbes. He was laughed at, but went on to found modern evolutionary biology. Then, in the 1980s, while using LSD and driving around with his girlfriend Kary Mullis had the idea to use the enzymes in an Archaean (a group of microbes that Woese put on a totally unique branch of the tree of life) to amplify DNA and, in essence, produce much more of it for analysis. Together these accomplishments set the stage for the modern field of microbial ecology and evolution. For all of this work, Margulis, Woese and Mullis were regarded as crazy (They were not then, though each of them would ultimately turn to forms of wildness with time. Perhaps when you are once right and no one listens, you can come to believe that every time that no one listens you are right).

Leach wants to take the insights of Margulis and the tools of Woese and Mullis and go big. He is a go big or go home kind of guy. He has the “let’s go kick some butt,” demeanor of a high school wrestling coach one win shy of the state championship. His perspective is that he can only really understand what is going on by seeing samples of feces (from toilet paper wipes) from thousands and thousands of samples. With those samples, Leach wants to study the variation among people in terms of their gut microbes (or at least the ones that end up in feces). With so many samples he might be able to understand the effect of subtle differences among individuals. Are vegan’s microbiomes different from those of vegetarians? Or what effect does having a dog have on your microbiome? Or do probiotics have any effect on the micrbiome at all (they affect rat and mouse microbiomes, but alas rats and mice aren’t the ones buying the stuff)? This sort of ambitiousness is possible only because Leach has teh good fortune to be able to work after the earlier, harder, times. Leach wants to see with the tools he has inherited. Galileo had a telescope. Anton Von Leeuwenhoek had a single-lens microscope. Leach has bundled up pieces of used Charmin, that and modern genetics.

Leach thinks that there are healthy microbial communities and sick ones, that most of us tend to have somewhat to very sick ones and if we understand the variation we might understand how to eat, live, and farm (microbes) in such a way as to favor the healthy ones. He wants to study whole families, including cats, dogs and all the rest. This is an exciting idea, but it, like hundreds of other exciting ideas about gut microbes, still needs to be tested. The field is in its stumbling infancy. The field needs the data; Leach needs the data.

Continue reading at Scientific American