Microbiologists have a new way to tell whose sh-t is dirtying the waters. A survey of sewage across the United States shows that every city has a distinct microbial character that can reveal signs of health, such as how obese its residents tend to be. Dozens of the microbes identified in the survey are common throughout the United States, and could provide better ways to tell whether bacterial pollution comes from humans.
The human gut is filled with microbes that are proving ever more important to health and disease. To understand the diversity of these bacteria—collectively called the gut microbiome—and how their numbers and types vary through time, microbiologists have isolated and sequenced DNA from stool samples of hundreds of individuals. But Mitchell Sogin, a molecular evolutionist at the Marine Biological Laboratory in Woods Hole, Massachusetts, and Sandra McLellan, a microbiologist at the University of Wisconsin, Milwaukee, wanted to take a much broader view and study the microbiomes of entire human communities. In addition, they were looking for a better indicator of human fecal pollution.
To do that, they needed to figure out how to assess the microbiomes of large numbers of people at once. They recruited wastewater treatment plant operators from 71 U.S. cites to collect more than 200 samples of incoming sewage. They then sequenced DNA in the samples and determined its origin. About 15% of the isolated sewage DNA belonged to microbes found in humans, Sogin and McLellan’s team reported online last week in mBio. Many of the rest are microbes that live in sewer pipes. Using a technique developed by Sogin and his colleagues, which can more precisely determine which bacteria are present in a large sample of feces, the researchers identified about 60 types of bacteria that were common to people in all of the cities. Because they seem to be found wherever humans are, these 60 may be a more reliable way to determine if human feces are contaminating a waterway, McLellan says.
But the abundance of these and less common bacteria varied from place to place. This variation in the “sewer-wide” microbiomes reflected the variation seen among surveys of microbiomes of individual people. Each city had “a unique signature,” McLellan explains.
Those differences offer hints about the health of cities’ residents. Fat people tend to have a different microbiome from that of lean people, for example. By analyzing the microbes in each city’s sewage, the researchers could tell which had an obesity problem, Sogin says. Denver and Key West, Florida, microbes reflected a leaner population than those from Salina, Kansas, and Memphis, Tennessee, for example. The researchers have not tested whether sewage microbiomes can indicate other health conditions.
“What appeals to me [about this work] is the scale and the novelty,” says Gary Huffnagle, a microbiologist at the University of Michigan Medical Center in Ann Arbor who was not involved with the work. “It’s got the potential to open up a new way to look at large-scale populations for epidemiological analyses.”
Although analyzing the microbiomes of a city’s population as a whole can obscure important individual differences, it also reveals patterns evident only on a broad scale, Huffnagle notes. Besides, it’s much easier to collect poop from sewers than by collecting stool samples from individuals. “We can actually study human beings without all the paperwork.”