What ancient feces can tell us about our modern diet

Attempts to return to a more “natural” way of eating are on trend in the diet world. It’s a hazy concept defined by diets like paleo and keto.

But despite being sold as a return to how humans should eat, new research suggests modern people will never reclaim a critical piece of the puzzle: the exceptionally different gut microbiome of ancient people, and the advantages that came with it.

“Under the hypothesis of the ‘disappearing microbiome,’ if you start reintroducing some of these, quote-unquote ‘lost or disappeared’ microbes, you could see health benefits,” Aleksandar Kostic tells Inverse. Kostic is the senior author of the study and an assistant professor of microbiology at Harvard Medical School.

Research from Kostic and his team published in Nature on Wednesday uses microbial DNA to tell the story of how diet has shaped the human gut microbiome over time. It’s a story that starts with ancient feces and may end with the development of new medical treatments.

Ancient guts and “disappearing microbiota”

As studies of ancient microbiomes emerge, they’ve confirmed what some scientists expected: pre-industrial diets yielded more diverse guts.

Gut diversity is good. A wealth of bacteria helps break down food into nutrients, protects us from pathogens, and prevents inflammatory diseases that weaken our digestive system. When beneficial bacteria are hurt by antibiotics or dietary patterns, we can be susceptible to illness.

According to Kostic, our gut microbiomes weren’t always the way they are now.

“One hallmark of the nonindustrial microbiome is the higher diversity — the many more organisms that are present — but no one's really kind of taken a trip in time to see what the ancient prehistoric microbiome looks like, particularly before the introduction of industrialization,” Kostic says.

Scientists think it has a lot to do with how the way we eat has changed over time. While shoppers in modern-day industrialized nations may have a world of options to choose from at the grocery store, non-industrialized diets historically yielded more gut diversity. Today, there’s “not that much diversity,” Kostic says.

“Everything is kind of based on a relatively small ingredients list, particularly compared to people that were hunter-gatherers and literally making use of everything that they saw growing around them,” he says.

And while what we eat shapes the kinds of microbes in our gut, there’s also a lot outside of our control.

The “disappearing microbiota” hypothesis posits that disappearing microbes have led to an increase in chronic disease over time. It argues beneficial gut bacteria were simply erased over time due to increased use of antibiotics and a transition to a Western diet rich in processed foods, red meat, sugars, and fats.

Based on this idea that our gut has lost bacterial diversity — and this loss may be associated with chronic disease — Kostic and colleagues set out to compare ancient microbiomes to modern ones.

How they did it — The study team analyzed a small group of 8 ancient fecal samples previously collected from two cave sites in Utah and one north of Durango, Mexico. According to Kostic, the samples are incredibly well preserved because of arid conditions — they look like what you’d imagine feces would look like, but desiccated.

The people behind the samples lived around 1,000 and 2,000 years ago. They farmed, hunted, and gathered.

Using a technique called “metagenome-assembled genomes,” the team was able to piece together DNA that had fragmented over time. The technology fits together sequences of DNA like a puzzle, allowing researchers to paint a picture of a gut microbiome and create a taxonomy of the various bacteria.

The team also compared the profile of the ancient guts with modern data from hundreds of both “non-industrialized” and “industrialized” microbiomes. The non-industrialized gut data came from people in Mexico, Fiji, Peru, Tanzania, and Madagascar, while the industrialized gut data came from the people in the United States, Denmark, and Spain.

The scientists looked for differences in the specific kinds of bacteria, but also differences between parts of genetic sequences and their functions.

Historically, research like this study relies on artifacts excavated by archaeologists and institutions with a long history of neglecting input from the Indigenous peoples, including removing artifacts without permission. The study authors write that “throughout this study, complexities emerged that extend beyond the scientific findings,” adding “we recognize there are Indigenous people who view the palaeofaeces as a cultural connection to their ancestors which should never be overlooked.” In this study, consultations with Indigenous experts did not happen prior to the project, but later “immediate steps” were taken to “initiate an interactive process.”

What they found — Of the 181 microbial genomes that were reconstructed from the ancient samples, almost 40 percent were previously undescribed. Undescribed microbes are those the lost or extinct, but new to us.

They also found that the ancient guts had a lot more in common with today’s non-industrialized communities. For example, a kind of bacteria named Treponema succinifaciens was prevalent in the ancient and modern non-industrialized samples but was completely absent from the modern industrialized ones.

Notably, some gut microbiomes had advantages over the others.

While the ancient DNA had predictably few antibiotic-resistant genes, both the non-industrialized gut genomes and the industrialized ones had more antibiotic-resistant genes. These genes emerge over time from widespread antibiotic use and can make infections harder to treat.

Ancient and non-industrialized gut genomes also had few or no genes associated with mucin-degradation — this is when the protective layer of mucus that covers the surface of the gastrointestinal tract is eaten away by bacteria — compared to the gut genomes of people labeled as industrialized.

Fewer of these genes suggest ancient intestines were better equipped to maintain a mucus barrier between the intestines and stomach and the bloodstream.

Why it matters — Kostic first became interested in the contents of ancient guts because of the rise of diseases like multiple sclerosis, allergies, metabolic diseases, and both types of diabetes.

“For me, it really started with the question of, ‘why are we experiencing such an increase in the incidence of chronic diseases in the Western world?’” Kostic says.

Much research points to the contents of our gut - and how our diet has shaped it.

“More and more data in the microbiome field is emerging that these microbes all play an important role in managing really every aspect of our physiology,” he says.

While the idea that non-industrialized gut microbiomes and industrialized are different isn’t new, few studies have actually explored the ancient gut microbiome and its similarities to modern societies. This new research brings in a novel gene sequencing approach and allows researchers to actually approximate genetic sequences of previously unknown microbes.

What's next — While it’s not unreasonable to assume that eating more like ancient people could fix what ails our own microbiomes, and some argue diets geared toward “whole foods” do just that, returning our guts to their pre-industrial form isn’t that simple.

Many of the microbes spotted in the ancient fecal matter are gone for good, Kostic says — and no diet can restore them.

“Unless you bring those microbes back, you've lost some kind of capacity conferred by the microbiota to receive the maximal benefit from those foods and from that particular more healthy lifestyle,” Kostic explains. “You're kind of shot in the foot from the start.”

But he did add that introducing certain macronutrients — options like non-digestible carbs or fibers that our enzymes can’t break down — are a way to promote a diverse gut microbiome. These include foods like whole grains and vegetables.

This research could also help hasten the development of treatments like fecal transplants from healthier gut microbiomes for various chronic problems. Transplants like these have proved successful for hard-to-treat clostridium difficile infections, which can be caused by antibiotics and harms the colon. They’re even used with some cancer therapies to make them more effective.

There’s a chance they could be even more effective if they incorporated the bacteria identified in this study as beneficial — even if it’s unclear, for now, how this ancient bacteria could be reintroduced.

“Potentially working with this more ancient microbiome, you could see better results,” said Kostic. “And maybe if they can't be reintroduced at some wider level, we could [at least] start seeing a decrease in this epidemic of chronic diseases that have become so problematic and is continuing to grow around the world.”

Abstract: Loss of gut microbial diversity1–6 in industrial populations is associated with chronic diseases, underscoring the importance of studying our ancestral gut microbiome. However, relatively little is known about the composition of pre-industrial gut microbiomes. Here we performed a large-scale de novo assembly of microbial genomes from palaeofaeces. From eight authenticated human palaeofaeces samples (1,000–2,000 years old) with well-preserved DNA from southwestern USA and Mexico, we reconstructed 498 medium- and high-quality microbial genomes. Among the 181 genomes with the strongest evidence of being ancient and of human gut origin, 39% represent previously undescribed species-level genome bins. Tip dating suggests an approximate diversification timeline for the key human symbiont Methanobrevibacter smithii. In comparison to 789 present-day human gut microbiome samples from eight countries, the palaeofaeces samples are more similar to non-industrialized than industrialized human gut microbiomes. Functional profiling of the palaeofaeces samples reveals a markedly lower abundance of antibiotic resistance and mucin-degrading genes, as well as enrichment of mobile genetic elements relative to industrial gut microbiomes. This study facilitates the discovery and characterization of previously undescribed gut microorganisms from ancient microbiomes and the investigation of the evolutionary history of the human gut microbiota through genome reconstruction from palaeofaeces.