The microbes that live in our gut are less diverse than they were 2,000 years ago.
This is one of the key findings from the genomic analysis of fossilized human feces from rock shelters in North America and Mexico. Eight samples dating back 1,000 and 2,000 years ago reveal microbes that are completely new to science, as well as others that are completely absent from the intestinal microbiome today.
In contrast, the modern intestinal microbiome contains significantly more antibiotic-resistant microbes than those of our ancestors. These findings can help us understand the link – if any – between our reduced microbiome and the higher current incidence of “industrial” chronic diseases such as diabetes and obesity.
The human microbiome is a fascinating and complex machine, and in recent years scientists have discovered that it plays a much more important role in keeping our bodies healthy than we previously realized. But our understanding of how the human microbiome has changed over time is limited.
Introduce petrified feces, scientifically known as coprolites. Although these fossils may seem quite unpleasant, they can be rich sources of information about how ancient animals lived, revealing complex information about diet and intestinal parasites and diseases.
They also contain some of the microbes that arrange the gut, allowing anyone with the right tools to take a snapshot of the microbiome. This was done by an international team of microbiologists, led by the Jocelyn Diabetes Center in the United States, with the greatest details about each ancient human microbiome in the gut.
Researchers have taken coprolites, perfectly preserved in three rock shelters ̵
These coprolites were validated as humans by dietary analysis and dated by radiocarbon analysis. The scientists then performed the complex work of extracting valuable preserved DNA that can identify microbes.
The researchers successfully reconstructed 498 microbial genomes; of these, 181 are most likely derived from human intestines rather than the surrounding soil.
Of these sequences, 158 appear to represent a separate species of microbial species. They were then compared to 789 microbiomes from today’s communities, both industrial and non-industrial communities.
The results were astounding. Ancient microbiomes were not only more similar to those of modern non-industrial communities, but they contained species not found in any modern microbiome. Of the 158 genomes, 61 were completely unknown to science – almost 40 percent.
This diversity in the microbiome, researchers say, may have something to do with dietary diversity.
“In ancient cultures, the foods you eat are very diverse and can maintain a more eclectic collection of microbes,” said microbiologist Alexander Kostic of the Diabetes Center in Jocelyn.
“But as you move toward industrialization, and more toward a nutritious diet, you’re losing a lot of nutrients that help maintain a more diverse microbiome.”
There were also some fascinating microbial differences. They had fewer genes associated with antibiotic resistance, but they also had fewer genes to produce proteins that break down glycans, the sugar molecules found in mucus.
Degradation of colon mucus has been linked to diseases such as Crohn’s disease, celiac disease and ulcerative colitis.
Ancient microbes also had more transposases, enzymes that can cut and place and replicate elements of DNA, switching things to adapt to changing conditions, among other things.
“We think it could be a strategy for microbes to adapt to an environment that is shifting much more than the modern industrialized microbiome, where we eat the same things and live the same life more or less all year round,” Kostic said.
“While in a more traditional environment, things are changing and microbes need to adapt. They can use this much larger collection of transposases to pick up and collect genes that will help them adapt to different environments.”
It is not clear how the evolving microbiome has changed our health and the sample size is relatively small, but research shows that we can use coprolites to examine the intestines of our ancestors to understand what has changed. In turn, this can lead to better health outcomes in the future.
“Such future research, using the richness of paleofetches, will not only expand our knowledge of the human microbiome, but may also lead to the development of approaches to restore today’s intestinal microbiome to its ancestral state,” the team wrote in a report.
The study was published in Nature.