In the last couple of decades, a lot of medical research has focused on our gut, especially the role that our microbiome – the carefully balanced ecosystem of bacteria, fungi, protozoa, and viruses that live in our bodies – plays in our overall health. It has been hypothesised that the overly processed modern diet of many in the industrialised world has wreaked havoc on this microbiome, possibly contributing to an increase in obesity, diabetes, autoimmune diseases, and other chronic conditions. But, until now, there was no way of directly assessing how this internal ecosystem may have changed through history. In this month’s ‘Science Notes’, we are looking at a recent study from a team of researchers led by Aleksandar Kostic from Harvard Medical School, which analysed examples of palaeofaeces, or coprolites, from the Americas, identifying the species that lived within our ancestors’ guts and comparing the results with modern humans from both industrialised and traditional societies.
Reconstructing our historic microbiome not only provides us with a better understanding of the diet and overall health of people in the past, it also allows us to assess the impact that the industrialisation of food may be having on the natural balance of our digestive systems today. But assessing this historic microbiome is not the easiest task. Previous studies have relied predominantly on a taxonomic approach, examining the microbes that currently reside within our gut and using phylogenetic trees to determine their likely ancestral species. While this approach can be effective in assessing the evolution of these bacteria, fungi, and protozoa, it does not allow us to determine which combination of these species actually made up our microbiome in the past.
The new study is one of the first to take samples of palaeofaeces and conduct aDNA analysis on them in order to isolate specific microbial species. While extracting DNA from such samples is a fairly straightforward task nowadays, thanks to huge advances in technology, determining which ones are actually from our ancient guts and not just contamination from the burial environment or from modern-day handling can be difficult.
To do this, the team took 15 samples from three sites: Boomerang Shelter in south-eastern Utah; Arid West Cave, also in Utah; and La Cueva de los Muertos Chiquitos, near Zape in the state of Durango, Mexico. The samples were first radiocarbon dated to determine that they were, in fact, archaeological specimens – a process that found that the Boomerang samples mainly dated to 2500-1500 BC, with two samples dating to the 1st century AD; the Arid West Cave samples were approximately 500 years younger; and the Zape samples were even more recent, dating to AD 660-1430. The team then performed shotgun metagenomic sequencing, and found that eight of the samples probably came from a human source and were of high-enough quality for further analysis. In order to compare these samples to modern data, the team also analysed 789 present-day stool samples from both industrial and non-industrial populations across eight countries.
From the eight archaeological samples, the team was able to reconstruct 498 medium- to high-quality microbial genomes. To make sure that none of these were from modern contamination, though, they excluded all those with less than 1% of damage. This left them with 209 remaining genomes, 203 of which were deemed to be from the gut, and out of these 203 samples, 181 were classified as likely to be ancient in origin. An astonishing 39% of these were found to represent previously unknown species.
The types of species identified in the palaeo samples were largely similar to those from non-industrial populations. In particular, they were high in both starch- and/or glycogen-degrading CAZymes, which are probably a result of a greater consumption of complex carbohydrates instead of simple sugars. They also had a greater abundance of mobile genetic elements, which allow the gut to adapt to seasonal variation in food resources. In comparison, the industrial microbiomes were much less diverse. Specifically, the bacterium Treponema succinifaciens, as well as others from the Spirochaetes phylum, which were present in both the ancient and non-industrial samples, appear to have completely disappeared from the industrial ones. The industrial samples had a higher prevalence of species with antibiotic-resistant genes, too. Overall, the trend was clear: industrialisation has had a dramatic impact on our gut health.
These results show that not only is aDNA analysis of palaeofaeces possible, but that such studies can successfully be used to analyse the evolution of our microbiome. As the researchers conclude: ‘Similar future studies tapping into the richness of palaeofaeces will not only expand our knowledge of the human microbiome, but may also lead to the development of approaches to restore present-day gut microbiomes to their ancestral state.’