Ancient microbiome study discovers unknown types of gut bacteria

Ancient microbiome study discovers unknown types of gut bacteria
University of Montana researcher Meradeth Snow holds a vial containing ancient human DNA
University of Montana researcher Meradeth Snow holds a vial containing ancient human DNA
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University of Montana researcher Meradeth Snow holds a vial containing ancient human DNA
University of Montana researcher Meradeth Snow holds a vial containing ancient human DNA

A new study published in the journal Nature is reporting on the broadest genomic analysis of ancient poo ever conducted. The research reveals clues to ancient gut bacteria compositions, detecting microbial species never before seen in modern microbiomes.

The study focused on eight authenticated human feces samples found in dry caves in southwestern USA and Mexico. Carbon dating indicated the samples were between 1,000 and 2,000 years old.

Nearly 500 microbial genomes were reconstructed as part of the study, with the researchers confident around 180 could be strongly associated with ancient human microbiomes. Amazingly, 39 percent of those microbial genomes were previously unknown, having never been detected in any modern human microbiome.

Aleksandar Kostic, senior author on the study, says the incredible microbial diversity in ancient gut microbiomes may be due to dietary variations. Industrialized agriculture has led to a lack of variety in crops, meaning our gut bacteria simply does not need to be as diverse as it was in the past.

"In ancient cultures, the foods you're eating are very diverse and can support a more eclectic collection of microbes," says Kostic. "But as you move toward industrialization and more of a grocery-store diet, you lose a lot of nutrients that help to support a more diverse microbiome."

To compare these findings to modern microbiomes the researchers gathered several hundred fecal samples from humans today. Half of the modern samples came from those in the US or Europe eating a Western diet and the other half were gathered from more isolated indigenous communities in places such as Tanzania, Peru and Mexico.

One intriguing finding was the presence of a bacterium called Treponema succinifaciens in every single ancient sample, however, it was not found in any modern Western microbiome. Previous research has detected this bacterium in the microbiome of isolated indigenous communities and it has been hypothesized to be a sign modern industrial human gut microbiomes have diverged from more traditional states.

Another interesting finding was the ancient microbiomes displayed a higher volume of enzymes called transposases, which essentially aid genetic adaptability to dynamic environmental conditions.

“We think this could be a strategy used by the microbes to adapt in an environment that shifts a lot more than the modern industrialized microbiome, where we eat the same things and live the same life more or less year-round,” explains Kostic. “By contrast, in an environment marked by change, the microbes might use this much larger collection of transposases to grab and collect genes that could help them adapt to the different environments.”

And while overall microbial diversity was higher in the ancient microbiome samples, there seemed to be some microbes conspicuously absent in the old poo. Akkermansia muciniphila, for example, was absent from all ancient samples and only rarely detected in non-Western modern samples. Prior studies have found increased volumes of Akkermansia muciniphila in people eating diets high in processed meat and sugar. This microbe is known to produce endotoxins associated with inflammation.

Meradeth Snow, a University of Montana anthropologist working on the study, says this kind of research offers important insights into diseases that affect people in modern Western societies.

"It's a symbiotic relationship,” says Snow. “But when we study people today – anywhere on the planet – we know that their gut microbiomes have been influenced by our modern world, either through diet, chemicals, antibiotics or a host of other things. So understanding what the gut microbiome looked like before industrialization happened helps us understand what's different in today's guts."

The next step for some of the researchers working on the project will be to investigate what the possible metabolic functions were for some of these ancient bacterial species. Kostic speculates it could be possible to use these newly reconstructed ancient genomes to resurrect some of these extinct species and work out how they were influencing ancient humans.

“If we can grow them in the lab, we can understand the physiology of these microbes much, much better,” says Kostic.

The new study was published in the journal Nature.

Sources: Harvard Medical School, University of Montana

1 comment
1 comment
Every now and again science makes exceptional discoveries - and in this case, leads (ledes?) with some questionable premises. If everything discovered is absolutely true, then this is a remarkable finding and in 50 years time maybe we'll have learned how to alter our biome depopulating colonies of Akkermansia muciniphila among others. Certainly the cave crappers of 1-2K years ago ate fruits - high in fructose - and used fermented beverages that reduce the sugar content of libations - why then with such in their diet (and the traditions of pemmican & jerky production in the traditions) did they escape colonization of those pro-inflammatory bacteria?
And as far as my casting shade on the premise of human scat - there are clues in the scat that signify human waste - but given the conditions in the cave, how can scientists be certain the scat was not contaminated by other bacteria from other sources? Animals explore caves, smell deposits, those they don't eat they may "mark" and any liquid contact may allow contaminating colonies to invade old scat.