Your poop is a living forest. Seriously! Hundreds of species of microbes thrive inside of you, helping you to live your best life. Everyone’s microbiome differs—yours from your neighbors’, and different populations’ from one another’s. But there is much scientists still don’t know about the human microbiome. And one team of scientists think they’ve made a leap in helping us understand this forest.


An international team of researchers analyzed the poop from 308 men. But rather than analyzing the DNA and the kinds of microbes present in the poop, they looked at the transcriptome—the list of things that each of these bacteria actually do. This can be an important tool for future study to help identify the causes of and potential cures for diseases.

“This is the first large transcriptomic survey,” Curtis Huttenhower, associate professor in computational biology at the Harvard T.H. Chan School of Public Health, told Gizmodo. “That shows what gut microbes are doing in addition to who’s there.”


More and more work is being done to understand the residents of the human gut. Studies have linked problems with the microbiome to inflammatory bowel disease, diabetes, cancer, and other disorders. Our gut bacteria even seems to have a big impact on our mental health. We have data about what species tend to live in the gut, but we don’t know much about what they do there. So the researchers sequenced the fecal microbiomes of 308 older men taking part in the “Health Professionals Follow-Up Study.” They looked at the messenger RNA—essentially photocopies of only the parts of the DNA that the microbes actually uses.

The two studies, both published today in Nature Microbiology, demonstrate that gut residents are performing different functions at different times, depending on their human host. Essentially, the studies suggest that, like different types of human cells, some of the bacteria are always performing different jobs, while others only start working in response to some external factor, like the kind of food you eat.

This study is still just a tool for learning more—it will be a few more years at least before we can say that a problem with bug X causes disease Y. But this work establishes that various bacteria have different functions. Also, it “helps us to detect when something is wrong in the short term,” said Huttenhower, “and in the longer term hopefully we’ll figure out how to fix it when something specific goes wrong.”

Of course there are limitations here—the study included only 308 older men working in the healthcare field, and microbiomes can vary drastically between individuals. Also, working with poop can be also be, well, shitty. “The bad part is that the stool samples have been known to spill, and that’s bad all around,” said Huttenhower.


The world of microbiome research is advancing quickly, and there are lots of ways to get involved, from citizen science programs like the American Gut Project to home testing kits like uBiome. Some are wary of the at-home tests. But maybe one day, doctors will be able to prescribe specific fixes to your microbiome to help you get over disease, rather than just the general probiotic pills you may have seen around.



“When the U.S. set out to restore wolves in Yellowstone, they can’t just parachute in wolves, and can’t just replant a whole forest and import in everything at once,” said Huttenhower. “You have to find the right way to bring wolves and their support system into the ecology. That’s the way it works with microbes at well.”


[Nature Microbiology 1, 2]

