[A new first-of-its-kind study of DNA recovered from preserved
human feces suggests that over the past thousand years the human gut
has experienced an “extinction event,” losing dozens of species
and becoming significantly less diverse.] [[link removed]]

PILES OF ANCIENT POOP REVEAL ‘EXTINCTION EVENT’ IN HUMAN GUT
BACTERIA  
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Andrew Curry
May 12, 2021
Science Magazine
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_ A new first-of-its-kind study of DNA recovered from preserved human
feces suggests that over the past thousand years the human gut has
experienced an “extinction event,” losing dozens of species and
becoming significantly less diverse. _

"Coprolites" by James St. John, licensed under CC BY 2.0

 

Every meal you eat is digested with the help of the bountiful bacteria
thronging your intestines. When you're done digesting, those bacteria
are also part of what's excreted. Now, 1000-year-old piles of
dried-out poop are offering insights into how the billions-strong
bacterial ecosystems in the human gut have been altered by sanitation,
processed foods, and antibiotics.

In a study published today in _Nature_, researchers analyzed ancient
DNA from coprolites, or preserved feces, found at the back of rock
shelters in Utah and Mexico. The data give scientists their first
good look at ancient gut bacterial communities
[[link removed]], says Stanford
University biologist Justin Sonnenburg. “These paleofeces are the
equivalent of a time machine.”

They suggest that over the past millennium, the human gut has
experienced an “extinction event,” losing dozens of species and
becoming significantly less diverse, says lead author and Harvard
Medical School microbiologist Aleksandar Kostic. “These are things
we don't get back.”

Previous studies have used the gut bacteria of today's
hunter-gatherers and herders as a proxy for the ancient microbiome.
Their microbial diversity far exceeds that of people in industrial
societies, and researchers have linked low diversity to higher rates
of “diseases of civilization,” including diabetes, obesity, and
allergies. But it wasn't clear how much today's nonindustrial people
have in common with ancient humans. “We really wanted to be able to
go back in time and see when those changes [in the modern gut
microbiome] came about, and what's causing them,” says Harvard
University geneticist Christina Warinner, a co-author on the paper.
“Is it food itself? Is it processing, is it antibiotics, is it
sanitation?”

An international team analyzed eight ancient coprolites preserved by
dryness and stable temperatures in three rock shelters in Mexico and
the southwestern United States. Researchers radiocarbon dated the
samples, some of which were excavated almost 100 years ago and stored
in a museum, to between 0 C.E. and 1000 C.E. Meradeth Snow, a
molecular anthropologist at the University of Montana, Missoula, then
rehydrated tiny bits of feces, recovering longer DNA strands than
previous paleofeces analyses.

Earlier attempts to analyze the ancient gut microbiome had been
thwarted by the challenge of sorting ancient gut bacterial DNA from
that of microbes invading from the surrounding soil, says Marsha
Wibowo, a Ph.D. student at Harvard's Joslin Diabetes Center, who
analyzed the DNA. She singled out the ancient gut species by focusing
on DNA that had been damaged by time, and on sequences from bacteria
known to be associated with the mammalian gut. Some of the ancient DNA
was unfamiliar, however, evidently representing never-before-seen
kinds of extinct bacteria.

The coprolites yielded 181 genomes that were both ancient and likely
came from a human gut. Many resembled those found in nonindustrial gut
samples today, including species associated with high-fiber diets.
Bits of food in the samples confirmed that the ancient people's diet
included maize and beans, typical of early North American farmers.
Samples from a site in Utah suggested a more eclectic, fiber-rich
“famine diet” including prickly pear, ricegrass, and grasshoppers.

But the ancient microbiomes also stood apart from their modern
counterparts, for example lacking markers for antibiotic resistance.
And they were notably more diverse, including dozens of unknown
species. “In just these eight samples from a relatively confined
geography and time period, we found 38% novel species,” Kostic says.

_Treponema_ bacteria, for instance, are virtually unknown in the
industrialized gut microbiome and appear only occasionally in people
living nonindustrial lifestyles today. But, “They're present in
every single one of the paleofeces, across all the geographic
sites,” Kostic says. “That suggests it's not purely diet that's
shaping things.” He hopes future experiments on coprolites from
other time periods will make it possible to isolate when the biggest
shifts took place and what prompted them.

The findings echo another study of much older samples by Warinner and
colleagues published this week, which reported DNA from previously
unidentified microbes on the teeth of Neanderthals and early modern
humans.

The new data from old poop show no one on the planet today has been
spared changes to their microbiome. “Nonindustrial populations,
including their microbiomes, shouldn't be considered proxies for our
ancestors,” says Massachusetts Institute of Technology geneticist
Mathieu Groussin.

The findings also suggest we've lost a lot of microbial helpers in the
recent past, and our bodies may not have had time to adapt. “This
study gives us a gold standard to check on what species we've lost,”
Sonnenburg says.

Because feces aren't considered human remains under U.S. law, Warinner
says, there was little discussion early on about the ethics of the
research. But when the group reached out to several dozen tribes in
the Southwest, some said the samples were a link to their ancestors
and were upset they hadn't been consulted earlier. The study now
includes an ethics statement, a first for a paleofeces paper.

University of California, San Diego, geneticist Keolu Fox says the
team didn't go far enough. Insights into the ancient gut could someday
inform commercial efforts to reshape modern microbiomes, he says. That
raises complex questions of who owns such data. “It's supposedly
waste, but it contains DNA and profiles of microbial diversity. Maybe
that poop is literally gold,” Fox says. “We're getting into a
whole new gray area.”

Posted in: 

* Archaeology [[link removed]]
* Evolution [[link removed]]

doi:10.1126/science.abj4390

_Andrew Curry is a journalist in Berlin. Twitter
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