As Mathilde Poyet ushers me through the Global Microbiome Conservancy’s laboratory in Kiel, Germany, I’m met with all sorts of state-of-the-art equipment. It’s an impressive facility, with typical lab apparatus, such as incubators, the latest sequencing devices and anaerobic chambers for culturing bacteria. But the most important stuff in the lab is stored in a freezer at −80 ºC. The samples are so crucial that there is a back-up battery system — if the electricity to the freezers goes off, the materials will remain intact. These test-tube samples aren’t some immortality serum or cancer-fighting bacteria: they’re faeces.
To be precise, they’re suspended stool samples and bacteria that have been cultured from faeces. But at one point, this was poo that Poyet and her colleagues, including her partner Mathieu Groussin, had collected as part of their work for the Global Microbiome Conservancy (GMbC), of which Groussin is a co-founder. Poyet likes to call the project their “first baby” (one of their real babies, their infant daughter Aelis, joins us in their office as we speak).
“We’ve seen all sorts of poop across the Bristol stool scale — all shapes, all sizes, all colours,” says Poyet, referring to the stool classification chart physicians use to assess digestive issues.
Poyet and Groussin’s work is predicated on the idea that faeces provide an ideal snapshot of the human gut microbiome: the genetic content of the community of organisms found in intestines. This differs across populations1 and can serve as a health indicator. Most research on the human gut microbiome focuses on populations of European descent. But the GMbC solicits samples that are more globally representative. The samples in the freezer come from as far afield as Ghana, Tanzania, Finland and Thailand.
Samples being collected and frozen for the GMbC’s biobank of waste products.Credit: F. Rondon/Global Microbiome Conservancy
Over the past nine years of the programme, the team has sampled 50 populations spanning 19 countries. Its members have worked with local scientists, ethics boards and communities to collect the samples, and have taken cars, boats, helicopters and even quadbikes to sample sites. Back in the lab, researchers analyse the stool content, sequence the genetic material of bacteria cultured from samples and store the live samples in their biobank.
To outsiders, taking stool samples constantly might seem — and smell — disgusting. In Kiel, the scientists occasionally make “poop soup”, using a vessel called a bioreactor to see the effects of different scenarios on procured bacteria. They do this only a few times a year, because the process can be long and expensive, and the aromas pungent, prompting their more-conventional floor mates to give the workspace the nickname “smelly lab”.
But faeces provide a remarkable window into human health. “It’s our best way to interrogate what’s in the gut from healthy people,” says Groussin. “It’s a little bit gross, but that’s just our best way to access this incredible and important biodiversity.”
A treasure trove for science
With the microbiome a buzzy research topic, other scientists around the globe are taking samples to study it themselves. And as seen during the COVID-19 pandemic, wastewater analysis is a valuable public-health tool — providing scientists with the means to monitor pathogens in the population before an infection surges.
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