Computers, poop, and years of research: it’s a combination leading scientists to an unprecedented understanding of the microbial communities in our intestines. But a new paper from researchers in Europe and the UK reveals that when it comes to what’s in our gut, there’s still lots to learn.
The study looked at bacterial genetic information found in almost 12,000 stool samples and turned up 1,952 potential new species. Stack that up against the 273 species of gut bacteria currently identified and cultured in labs, and it represents a whole lot we don’t know about poop.
“There’s still a lot of stuff missing,” says study author Alexandre Almeida, a postdoctoral fellow at the European Bioinformatics Institute. In other words: “a lot of these are species that haven’t yet been grown [in the lab], but we can detect them at the DNA level when we actually look at the stool samples.”
The research, from the UK’s Wellcome Sanger Institute and the European Bioinformatics Institute, relied on a recently-published database of cultivated strains of gut bacteria. “Our goal was to determine how comprehensive their collection was,” says Almeida. The researchers took publically available data sets that give information about the bacterial DNA identified in stool samples and compared them to the bacteria included in the paper published earlier this month. They found what appear to be 200 percent more species of bacteria than were captured in the database.
While this may sound like a smelly task, finding gut bacteria isn’t as simple as putting poop on a microscope slide—and these researchers didn’t handle the samples themselves at all. In order to identify the teeming horde of microbes that ride around inside us, helping to digest our food and (in some cases) causing illness, science has turned to computers. Researchers sequence all of the DNA to be found in a sample, and then set about the complicated work of piecing together the genomes of each microorganism whose DNA is to be found. (It’s called metagenomics.)
As for what they found, “the raw numbers were very surprising,” says Almeida. They’d expected to find fewer unidentified bacteria in the samples, but he has an explanation for why they did find so many. The bacteria they identified are less abundant, meaning there are fewer of them in a given microbiome, and they’re also less frequently found, meaning fewer people in their dataset were carrying them.
“We have significantly extended the known repertoire of genomes in the gut,” says Almeida’s coauthor Robert Finn. Finn, who is affiliated with the European Bioinformatics Institute, is also a coauthor of the paper published earlier this month.
There are two things happening here: first, metagenomic sequencing techniques are always getting better, which means they can spot things at very low concentrations (though Almeida and his co-author Robert Finn caution that they still can’t spot everything); second, the publically available stool data they used is biased toward the available samples, which are predominantly from Europeans and North Americans.
Among the non-European and North American samples they studied, the rarer bacteria were more common and found in higher numbers, says Almeida. This indicates that a good first step for extending knowledge of the human microbiome would be to diversify the sample base.
A broader base, with more knowledge of common and uncommon bacteria across the globe, will also help in identifying medically important bacteria, says Finn. Currently, some of the rare bacteria in their sample may only look rare because of the database skew: it’s possible that those bacteria are correlated with certain diseases common in parts of the world that aren’t included among the samples.