Fossil Feces Analysis Shows How Human Diet Changed Over 2,000 Years

Analysis shows ancient people and nonindustrial societies today have about the same gut bacteria; industrial populations have different biomes, and meanwhile, some bacteria seem to have gone extinct

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Members of the Korubo indigenous people in Brazil's Amazon rain forest.
Members of the Korubo indigenous people in Brazil's Amazon rain forest.Credit: Ricardo Belie / Brazil Photos /

We are what we eat, they say. Or as Hippocrates wrote 2,500 years ago, “Let thy food be thy medicine and medicine be thy food,” resulting in 2,500 years of arguing over how our diet impacts our health.

Indeed, the science of diet and nutrition is bewildering, characterized by contradictory evidence and uninformed anecdotal reports. What works for some doesn’t work for others. One reason for this frustrating inconsistency involves change to the bacteria in our digestive systems.

A new paper in Nature reports on analysis of fossil feces in North America, showing how our microscopic inmates changed from 2,000 years ago to now.

A separate study of the hominin biome in evolution, also published this week, revealed that Neanderthals and Homo sapiens ate pretty much the same diets, including carbs. That had been a surprise.

Now the new study looks at the last couple of thousand years. No question, the human diet has changed radically from the pre-agricultural phase of hunting and gathering, to husbanding animals and growing crops. Then people began to scorn water and fresh foods for coke and Cheetos. It was reasonable to assume these changes would affect our biomes.

They did: The ancient gut bacteria from 2,000 and 1,000 years ago are similar to those of modern nonindustrial societies, the team reports. There are parallels with the biomes of industrial-society people, but there are also key differences.

For example, the bacteria show that the ancients ate more complex carbohydrates – fresh starch – than industrial people do today. We eat more processed foods, containing simple sugars.

Complex carbs take longer to digest and are considered to be a more stable (and natural) source of energy. Simple sugars are small sugar molecules found in table sugar and syrups.

Extinction event

Why would anybody analyze paleo-poo to elucidate the biomes of yore? To better understand our state of health.

Clearly, the diversity of our microbial guests diminished during the industrial era, commensurately with an increase in the incidence of chronic illnesses such as obesity and autoimmune diseases, the authors explain.

So, inquiring minds wondered what our biomes were like before the industrial era.

A hot dog stand in New York last month. Credit: ANGELA WEISS - AFP

Aleksandar Kostic and colleagues managed to reconstruct 498 microbial genomes from mineralized mess found in rock shelters.

“What we were able to find from these paleo feces of course was just small fragments of DNA, on average about 300 base pairs long. On their own each one of these fragments really can’t tell us much, but 300 base pairs is large enough that you can actually start to assemble it, piece these [fragments] together like a puzzle, and start to assemble partial genomic partial genomes and even near complete genomes,” he explains to Haaretz.

That provided them with enough information to align the micro-creatures to existing common human gut bacteria (there are databases of their genomes). And thus they identified 181 genomes as ancient and of human gut origin – of which 39 percent were unknown species of bacteria.

“They are novel species, sometimes even novel at the genus level – higher up on the phylogenetic tree. There is no current known microbe, that is, is the same species,” Kostic explains. “We hypothesize that these may be ‘extinct’ species that no longer exist today.” However, he qualifies that they could exist somewhere in some human population.

Yes, bacterial species can go extinct too, like T-rex and the passenger pigeon.

Could the advent of antibiotics in the mid-20th century have affected our microbiome to such a degree that it would obviate this whole study, from the perspective of causing profound change unrelated to diet? Must the change in biome be related to change in food intake? The team did find an increase in antibiotic-resistance genes in the bacteria.

Before diving into that rabbit hole, note that antibiotic resistance genes didn’t arise with industrial penicillin – they’ve been around for hundreds, thousands and likely millions of years. Why? Because there are creatures out there that naturally produce bactericidal molecules (like penicillin). Here is a link to a story on the prehistory of antibiotic resistance. 

The demon soap

Now back to our story. In fact, three separate elements led to the diminished diversity of our intestinal bacteria in modern times, Kostic explains.

One is sanitation, and medical advances – which includes antibiotics. They’re being massively overprescribed, they definitely cause drastic changes in our microbiome, not just in the short term for individuals but even in the long term, he says. Some microbes will vanish entirely after a course of antibiotics. Plus, our habit of cleaning with soap and bleach may protect us from E. coli infection and other revolting conditions, but it also has the side effect of changing the microbiome. And not all bacteria are bad – some are our friends.

Two is diet, which also has immediate impact on the overall composition of the gut microbiome. The paleo-poo study and separate ones show that the bacterial population of modern nonindustrial communities (not eating processed and pre-processed foods) has much greater capacity to digest carbs – which are complex sugars. Not like the simple sugars in, well, sugar and syrups. These germs actually help us consume carbs we can’t digest. The industrial population has lesser ability to digest complex carbs.

A Waiapi man giving Caxiri, a craft beer made with Manioc, imbibed daily by men, women and children when is not yet sour, in the Manilha village, Brazil.Credit: APU GOMES / AFP

Third is – sorry, folks – exercise. It’s probably less important to our microbiome composition, but it’s worth mentioning, Kostic stresses: “We think that some of the benefit of exercise actually is conferred in a non-direct way via the microbiome.”

In all three things, our lives changed from the pre-industrial era to the industrial, causing change in our microbiome. Industrial societies exercise less and eat more processed foods and lather themselves in antibiotics, certainly compared with the ancient world.

Just to drive home the point, the ancient Romans may have thought they were the acme of purification with their bathhouses, but whatever else they achieved as they splashed in their piscina, they were sharing shared intestinal parasites. Good intentions and all that.

All this could help explain the modern uptick in chronic autoimmune diseases, the authors claim.

Asked if this might be an artifact of improved diagnostics rather than microbiomial morphing, Kostic argues that it’s hard to miss the diagnosis in the case of some metabolic conditions such as obesity and the deadly ones such as type 1 diabetes. Multiple sclerosis is also hard to miss if untreated over time, he adds. So no, he doesn’t think improved recognition is the key factor behind the increase in autoimmune conditions.

Never mind Nemo: Seeking Treponema

Finally, we humans are a variant lot. From bankers on Wall Street to Kalahari hunter-gatherers to vegans in India – is there even such a thing as a generalized human industrial-era biome, that can fairly be compared with prehistoric biomes?

Sort of. “I was a bit surprised in how much actually is shared among industrialized communities across the globe, and also modern nonindustrial communities across the globe, which were distinct from industrialized,” Kostic explains.

One thing that jumped straight out at him, Kostic says, is the genus Treponema, a spirochete. Industrial-type modern humans have zero Treponema, the modern samples showed. Nonindustrial people are awash in it – and there it was in every single paleo-sample: they had eight ancient paleo-poops from various geographic regions and time periods.

Now the story gets kicky. Treponema didn’t go extinct, but somehow the industrial populations lost it.

“We see similar trends with other symbiotic microbes, like the genus Prevotella to a slightly lesser extent, because it is present in some people in the industrialized communities. But it’s also highly prevalent in the nonindustrialized populations and is right there in all the ancient coprolites.”

The opposite also exists: bacteria that industrial folks have and the nonindustrial and ancient ones don’t. Take Akkermansia mucinophila, a rarity in nonindustrial communities and absent in the ancient samples.

Akkermansia mucinophila is a microbe that adores mucin, eating it like we eat candy. Thing is, unlike candy, we need our mucin – think of it as part of the goo coating our cells. When it degrades on the outer surface of our gut cells, it enables other germs to invade more easily. The outcomes can include inflammation; leaky gut syndrome.

The bottom line is that the miraculously preserved ancient poo piles teach that ancient and nonindustrial people had/have a more diverse diet, including some carbs that they couldn’t even digest but their friend the bacterium could. Yay team. We learn that diet is crucial to maintaining our biome, but antibiotics can knock your microbial inmates off balance. Exercise matters too, but you knew that already.