Which bacteria are in your poop?

This is a guest post from my friend and former colleague Tami Lieberman. She’s a postdoc in the Kishony Lab in the Department of Systems Biology at the Harvard Medical School, and you follow her on twitter @conTAMInatedsci.

As a recently minted PhD, I study the evolution of bacteria during infection. I want to better understand how they acquire antibiotic resistance and what else they might be adapting to as they try to survive inside of us. It is super fun to think about invisible evolutionary processes happening inside of people.

I also have fun thinking about the few pounds of bacteria in and on my body— which bacteria live there, how they got there, and what that means for my health. And, of course, how my microbiome might be evolving. Maybe you have also been thinking about the invisible ecosystems on you.

So when two different campaigns on Indiegogo offered me the chance to peer at the composition of my microbiome, I was sold. I had my genome profiled by 23andme years ago and this was clearly the next step.

But I was simultaneously cautious, because microbiome profiling is messy (and I’m not just talking about the sample collection). For example, a story broke a few years ago that each of our guts belongs to one of three canonical types, called ‘enterotypes.’ Since then, the notion of discrete enterotypes has come under considerable scrutiny. The problem is that microbiome research is hard. The DNA profiling technologies and analysis methods are imperfect and still developing. There is no gold standard, because we do not know how to grow most gut bacteria in the lab, to check if they are really there. Moreover, our microbiomes are a moving target, changing with age and diet. How much then can I really learn from a snapshot?

Continue Reading...