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Ancient human faeces reveal gut microbes of the past

The microbial cells that inhabit the human gut, collectively called the gut microbiota or microbiome, have key influences on our metabolic and immune-system biology1,2. Many microorganisms are passed down over the generations3,4. However, the gut microbiota (tracked by analysing the microbial DNA in faeces) can be radically reshaped within days to months of certain events, such as immigration into a different country5 or antibiotic treatment6. Defining which microbes were once part of our evolutionary history and have since been lost might provide a key to understanding the relationship between microbes and human health. Writing in Nature, Wibowo et al.7 address this issue by turning to a microbial ‘time machine’: palaeofaeces. By using DNA sequencing to study the microbiomes of human stool samples that are 1,000–2,000 years old, this study provides valuable insights into gut microbes from a time before industrialization.

The human microbiome is a malleable component of our biology that adapts to specific circumstances, for example displaying seasonal variation corresponding to food availability8. Although this malleability offers a potential avenue for the treatment of human diseases linked to microbiota, it is also a vulnerability. Many aspects of industrialized life, such as antibiotic use and a fibre-deficient Western diet9,10, have a negative effect on gut microbes.

Which core microbes and microbial functions from the pre-industrial microbiota were lost as societies became industrialized? Certain broad bacterial groups (referred to as ‘volatile and/or associated negatively with industrialized societies of humans’ (VANISH) taxa) are highly prevalent in present-day Indigenous populations living traditional lifestyles, but are rare or absent in industrialized populations10. There are also numerous bacterial taxa (referred to as ‘bloom or selected in societies of urbanization/modernization’ (BloSSUM) taxa) that have the opposite pattern10. Whether present-day non-industrialized populations have microbiotas that are similar to those of humans who lived thousands of years ago has remained an open question, until now.

Wibowo et al. report DNA-sequencing analysis of 15 samples of palaeofaeces collected from the southwestern United States and Mexico. Seven of these samples were excluded for further study because of poor-quality DNA or evidence of soil contamination, or because the sample was found to come from a canine host. The age of the eight remaining samples was determined using carbon dating, and analysis of DNA damage revealed hallmarks that confirmed the antiquity of the material (ancient DNA has specific characteristics of degradation). The human origin of these samples was validated by microscopic analysis of dietary remains present in the palaeofaeces and by evidence of human mitochondrial DNA.

The high quality of the data generated enabled the authors to detect known microbial species and to discover previously unknown microbes through the reconstruction of microbial genomes. A total of 181 of the 498 reconstructed microbial genomes were classified as gut derived and had extensive DNA damage, consistent with an ancient origin, and 39% of the ancient genomes offered evidence of being newly discovered species.

Wibowo and colleagues compared their data from the ancient gut samples with data from a collection of previously sequenced stool samples from present-day populations with industrialized and non-industrialized lifestyles. The species Treponema succinifaciens, a microbe in the Spirochaetaceae family shown to be lost from industrial populations8, was present in palaeofaeces, as were other VANISH taxa that were absent in industrialized samples and prevalent in non-industrialized samples. BloSSUM taxa, including the species Akkermansia muciniphila (which degrades human mucus), were more abundant in the industrialized samples than in the non-industrialized samples and the palaeofaeces. Together, these results support the idea that features of non-industrialized microbiomes are similar to the microbiomes of our human ancestors, and that industrialized populations have diverged from this microbial signature (Fig. 1).

Figure 1

Figure 1 | A comparison of ancient and modern human gut microbes. Wibowo et al.7 analysed the DNA of gut microbes found in 1,000–2,000-year-old human palaeofaeces, and compared this with the DNA of gut microbes in faecal samples from present-day individuals from industrialized and non-industrialized societies. The authors used a statistical method called principal component analysis to compare the patterns of bacterial species present in the samples from each individual. This approach distributes data points corresponding to each individual’s sample along two axes, termed PC1 and PC2. Samples that are more similar to each other are grouped more closely together on the graph. This analysis reveals that the samples of palaeofaeces are distributed among those from individuals living in non-industrialized societies, indicating a similarity of gut-microbe profiles between ancient humans and modern humans living traditional lifestyles — both of which are distinct from the microbial profile of people in industrialized societies. (Figure based on Fig. 1b of ref. 7.)

The authors moved beyond focusing on species identity: they compared the genes, and the predicted functions of the proteins encoded by those genes, for the microbes in palaeofaeces with those found in present-day samples. Both the industrialized and the non-industrialized present-day samples had a greater prevalence of antibiotic-resistance genes than did the palaeofaeces, a finding consistent with the ancient microbes being from before the era of antibiotic use. Palaeofaeces had a high prevalence of genes encoding proteins that can degrade the molecule chitin, a component of insect exoskeletons. This finding is consistent with human consumption of insects, known to be a component of ancestral diets. Insect ingestion was confirmed by the authors’ microscopy analysis of material in the palaeofaeces. The authors report many genes that were particularly prevalent in industrialized samples, including those involved in the degradation of mucus in the human gut.

Wibowo and colleagues’ study is a remarkable technical achievement. They were able to recover high-quality DNA from microbial organisms that lived thousands of years ago, probably because of the good preservation possible in the dry desert environment in which the samples were located. Multiple independent lines of evidence authenticated the sample age and the human origin of the faeces. Having these ancient DNA sequences available in the public domain will undoubtedly benefit scientists for years to come.

However, DNA-sequence-based analyses do have limitations when the results are not paired with validation by other types of laboratory experiment. Using computational tools to predict information about proteins encoded by DNA is an imperfect method under ideal conditions, and is particularly tricky when analysing gene functions for previously unknown organisms, such as those discovered in this study. Moreover, microbiomes are highly variable between individuals and between populations. Analyses of more palaeofaeces from a wider range of timescales and locations will be needed to better understand general and population-specific features of ancient human gut microbiomes.

The authors found notable differences in the composition and function of microbes in palaeofaeces compared with those of microbes in present-day faeces. The higher prevalence of mucus-degrading species and genes in industrialized microbiomes than in ancient and non-industrialized ones is probably driven by Western diets, which often lack sufficient dietary fibre to support once-numerous fibre-degrading microbial species11,12. Given the links between the microbiome and the immune system, these differences might be connected to the rising rates of autoimmune, inflammatory and metabolic disorders in industrialized populations9,10.

Wibowo and colleagues’ work indicates that there are now two viable alternatives to time travel for understanding the composition of ancient microbiomes. Palaeofaeces enable the direct investigation of ancient microbiomes, but the sample age limits the further measurements and experiments that can be performed. Importantly, this study validates that present-day Indigenous populations living traditional lifestyles have similar microbiome compositions to those of ancient humans. It is essential to acknowledge that most of these present-day populations are marginalized, lead a vulnerable existence, and require exceptional protections to ensure they are not exploited. With ethically conducted research, these modern populations might open a window on our microbial past.

Nature 594, 182-183 (2021)

doi: https://doi.org/10.1038/d41586-021-01266-7

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Competing Interests

The authors declare no competing interests.

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