Our guts are teeming with trillions of microbes. They fight, form alliances, gobble our food, spew chemicals, and hack our immune systems. These hidden happenings in our innards hold sway over our health. Yet the key microbial players and their affairs vary considerably from person-to-person. And, overall, these communities remain a mystery to scientists.

This week, three studies published in the journal Science offer new glimpses of what’s going on in the black box that is our guts. While they all provide insights into these complex communities, they also highlight just how much we still have to learn.

Two studies dug into people’s health and, literally, their poop looking why there is so much variation in gut microbiome. Factors the studies hoped might explain that variation include diet, medication, disease, and stool types—from hard lumps to mushy piles according to the Bristol stool scale. The studies looked at samples from 1,135 Dutch and 1,106 Belgian volunteers. Researchers found that such factors account for only 18.7 percent and 7.6 percent, respectively, of variation. What differences account for the rest are complete unknowns.

The third study tracked the microbial aftermath of five fecal transplants. As the name implies, a fecal transplant aims to replace an out-of-whack gut community with microbe-rich fecal matter from the bowels of a healthy donor. Which old microbes hung on and which new ones took root in the recipients varied from case to case, according to the study. For one participant, the transplant failed completely, with very few of the donor’s microbes settling into their new digs.

“A 'one-stool-fits-all' model currently supported by standardized donor stool banks may not be clinically appropriate,” the authors of that study concluded. Researchers don’t know why there doesn’t seem to be a universal poop, but the answer may lie with the unknowns that create variation in our microbiomes to begin with.

Still, there were some big takeaways from the studies that may guide future research into the microbiome.

First, the two bigger surveys both noted that medications and stool type seemed to have strong links to the composition of the gut microbiome. The authors of the Belgian study noted the looser stools had larger numbers of microbes considered “core” microbiome members—species that seem to be universal players in gut communities.

Researchers also noted that medications have strong influences on the microbiome. Drugs like antibiotics and laxatives may not be unsurprising influences. However, the researchers also found that antihistamines, antidepressants, acid reflux drugs, and the type 2 diabetes drug, metformin, had strong links to changes in the microbiome as well.

Researchers conducting the Dutch study found a number of specific food links. Red wine, coffee, and tea were associated with boosted microbial diversity in the gut. On the other hand, sugary sodas and western-style diets—defined as high energy intakes, snacking, and drinking high-fat milk—were linked to lower bacterial diversity. Preferences for dark over milk chocolate also seemed to alter which microbes were present.

Interestingly, both groups failed to find a link between microbiome composition and early life factors, such as delivery type (vaginal vs. Cesarean section) and feeding (breast vs bottle). The authors were careful to note that the data does not suggest that these factors aren’t important—in infant microbiome development or later disease development. But, rather, may just indicate that they may not influence the adult microbiome.

Science, 2016. DOI: 10.1126/science.aad3369 (About DOIs).

Science, 2016. DOI: 10.1126/science.aad3503

Science, 2016. DOI: 10.1126/science.aad8852