Palaeofaeces: A Factual Time Machine

Benzyme Ventures
7 min readMar 10, 2022
  1. Palaeofaeces and its archaeobiological importance

1.1 Faeces and gut microbiota

Faecal samples are used as proxies for gut microbiota. The study of gut microbiome is broad and fascinating, but in brief, it refers to the exploration of the ecosystem of microbes in the gastrointestinal tract. Recent studies have revealed a beguiling link between the gut microbial composition of a person and their health state. Altered gut flora was evident in persons suffering from metabolic disorders, psychological disorders and neurological disorders, pushing us to investigate the evolutionary and ecological history of the gut microbiome (Bull and Plummer, 2014; Pusceddu and Del Bas, 2020). The historical nature of the human gut cannot be studied by observing modern day samples. Therefore, unless we have access to a time machine that allows us to collect ancient stool samples with undamaged DNA, this investigation seems to be close to impossible.

1.2 Palaeofaeces

Palaeofaeces or coprolites are non-mineralised (undecayed) remains of faeces from extant or extinct mammals that are often collected from ancient caves or found within permafrost soil (Kuch and Poinar, 2011). Previously, palaeofaeces were primarily of archaeological importance as they were recipients of studies related to extinct or dead organisms as their DNA composition provides information about the inhabitants of the location and their respective dietary practices. However, the recent research conducted by Wilbowo et al. in 2020, utilized such samples to discover the composition of ancient human gut microbiome and explored the evolutionary history of the human gut microbiota through them. Hence, it is safe to say that they exhibit great potential as a factual time machine!

2. Comparing palaeofaeces to modern-day faeces

2.1 Palaeofaeces and rural faecal samples

Human palaeofaeces samples with well-preserved DNA were obtained from around south-western USA and Mexico. Out of the 498 microbial genomes that were obtained from the samples, 181 genomes were identified as ancient gut microbial genomes. In order to identify the species present, the taxonomic composition was compared with present-day stool samples from urban (industrialised) and rural (non-industrialised) populations. As displayed in figure 1, results showed that the phyla in palaeofaeces samples were more similar to those in rural samples than the phyla present in urban samples, insomuch that the only difference observed between palaeofaeces and rural stool samples was the greater abundance of Spirochaetaceae in palaeofaeces than in the rural samples. Notedly, species of the Spirochaetaceae family such as Treponema succinifaciens are extinct from the urban gut (Obregon-Tito et al., 2015). The suggested reason for its loss is said to be due to its antagonistic behaviour towards Bifidobacterium species which is a probiotic and bio-preservative. With agricultural developments and industrialisation of society, the consumption of dairy and processed food has drastically increased; this could have caused the decline of the species’ survival in the gut environment (Belkacemi et al., 2020).

Microbes from the VANISH (volatile and/or associated negatively with industrialized societies of humans) taxa, which include phyla such as Firmicutes and Proteobacteria were enriched in palaeofaeces and rural stool samples, in comparison to the urban stool samples. Firmicutes phylum has been involved in the stimulation of IgA antibody secretion (Kosiewicz, Zirnheld and Alard, 2011). Further, patients with major depressive disorder possessed a significantly decreased proportion of the phylum (Huang et al., 2018). The increased abundance of Proteobacteria in the ancient gut is related to early colonisation of gut flora. The phylum holds the responsibility of lowering redox potential of the gut environment to suit the growth of anaerobes (Moon et al., 2018).

2.2 Palaeofaeces and urban faecal samples

The urban samples had a higher variety of microbes belonging to the BloSSOM (bloom or selected in societies of urbanization/modernization) taxa in comparison to the taxa from palaeofaeces and rural samples. This includes species from the phylum Bacteroidetes, such as those from the genera Alistipes and Bacteroides and members of the phylum Verrucomicrobia, such as Akkermansia muciniphila. Bacteroidetes members are normal intestinal microflora. However, they can become opportunistic pathogens in the presence of gut dysbiosis. For example, species of Alistipes genus have been isolated from patients with conditions such as acute appendicitis and abdominal and rectal abscess. Contradictingly, such species also exhibit immunotherapeutic characteristics against diseases such as liver fibrosis and cardiovascular disease (Parker et al., 2020). Akkermansia muciniphila too carries many therapeutic properties which has led to it being produced as supplements and probiotics. Higher levels of A. muciniphila have been observed in athletes and lean persons. Furthermore, obese persons treated with the species showed reduction of weight gain and better glucose tolerance (Anonye, 2017).

Figure 1: The distribution of phyla among samples of palaeofaeces, non-industrial (rural) and industrial (urban) samples (Wibowo et al., 2021).

2.3 Unique microbial characteristics of palaeofaeces

Transposases and mobile genetic elements that are responsible for insertional mutagenesis and transgenesis were more profuse in palaeofaeces than in present day samples. This could have aided in the gut colonization and adaptability to seasonal variation, especially during human migrations (Smits et al., 2017). Though the composition of gut microflora were similar between palaeofaeces and rural stool samples, the overall abundance of microbes in the ancient gut was higher than in the present day. Certain strains of Enterococci were found to be enriched in palaeofeces, along with some Firmicutes. Enterococci belong to the order lactic acid bacteria. They benefit the gut by enhancing digestion of lactose. Firmicutes such as Ruminococcus champanellensis, Ruminococcus callidus and Butyrivibrio crossotus are considered ruminal bacteria today. They assist digestion in herbivores by breaking down complex polysaccharides and fibres. Its considerably high numbers present in ancient human gut in comparison to urban and rural samples is possibly due to the plant-based diet with high number of carbohydrates present within the early population. Many studies showcase the potential of these bacteria as probiotics to combat Clostridium difficile infection (diarrhoea) and prevent colorectal cancer (Sou Ohkawara et al., 2006; De Wolfe et al., 2018).

3. Time travelling with palaeofaeces

The evolutionary history of the human gut was interpreted by tip dating Methanobrevibacter smithii. Upon Bayesian inference, it was observed that M. smithii diversified approximately 85,000 years ago within a timeframe of 51,000 to 128,000 years. Interestingly, its sister species Methanobrevibacter oralis was also found to have diversified slightly prior to M. smithii, within the same timeframe. This led to the presumption that the mentioned bacteria have been recurrent in the human gut since the first human migration from Africa to North America about 90,000 to 194,000 years ago. With the many theories of time travel and time machines pitched to us through scientific fiction and concepts of physics, would you have ever imagined that a time portal could be opened via microorganisms present in the defecated matter of early man? Nature and science are slowly unveiling their bizarre, yet laughable secrets and we are not ready for it!

References

  1. ‌Anonye, B. O. (2017). Commentary: Dietary Polyphenols Promote Growth of the Gut Bacterium Akkermansia muciniphila and Attenuate High-Fat Diet-Induced Metabolic Syndrome. Frontiers in Immunology, 8. https://doi.org/10.3389/fimmu.2017.00850
  2. ‌Belkacemi, S., Alou, M. T., Million, M., Levasseur, A., Khelaifia, S., & Raoult, D. (2020). Prevalence of Treponema species in the Gut Microbiome is Linked to Bifidobacterium sp. and Bacteroides sp. https://doi.org/10.21203/rs.3.rs-117420/v1
  3. ‌Bull, M. J., & Plummer, N. T. (2014). Part 1: The Human Gut Microbiome in Health and Disease. Integrative Medicine (Encinitas, Calif.), 13(6), 17–22. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4566439/
  4. De Wolfe, T. J., Eggers, S., Barker, A. K., Kates, A. E., Dill-McFarland, K. A., Suen, G., & Safdar, N. (2018). Oral probiotic combination of Lactobacillus and Bifidobacterium alters the gastrointestinal microbiota during antibiotic treatment for Clostridium difficile infection. PLOS ONE, 13(9), e0204253. https://doi.org/10.1371/journal.pone.0204253
  5. Huang, Y., Shi, X., Li, Z., Shen, Y., Shi, X., Wang, L., Li, G., Yuan, Y., Wang, J., Zhang, Y., Zhao, L., Zhang, M., Kang, Y., & Liang, Y. (2018). Possible association of Firmicutes in the gut microbiota of patients with major depressive disorder. Neuropsychiatric Disease and Treatment, 14(1), 3329–3337. https://doi.org/10.2147/ndt.s188340
  6. Kosiewicz, M. M., Zirnheld, A. L., & Alard, P. (2011). Gut Microbiota, Immunity, and Disease: A Complex Relationship. Frontiers in Microbiology, 2(180). https://doi.org/10.3389/fmicb.2011.00180
  7. Kuch, M., & Poinar, H. (2011). Extraction of DNA from palaeofaeces. Methods in Molecular Biology, 840(1), 37–42. https://doi.org/10.1007/978-1-61779-516-9_5
  8. Moon, C. D., Young, W., Maclean, P. H., Cookson, A. L., & Bermingham, E. N. (2018). Metagenomic insights into the roles of Proteobacteria in the gastrointestinal microbiomes of healthy dogs and cats. Microbiology Open, 7(5), e00677. https://doi.org/10.1002/mbo3.677
  9. Obregon-Tito, A. J., Tito, R. Y., Metcalf, J., Sankaranarayanan, K., Clemente, J. C., Ursell, L. K., Zech Xu, Z., Van Treuren, W., Knight, R., Gaffney, P. M., Spicer, P., Lawson, P., Marin-Reyes, L., Trujillo-Villarroel, O., Foster, M., Guija-Poma, E., Troncoso-Corzo, L., Warinner, C., Ozga, A. T., & Lewis, C. M. (2015). Subsistence strategies in traditional societies distinguish gut microbiomes. Nature Communications, 6(1). https://doi.org/10.1038/ncomms7505
  10. Parker, B. J., Wearsch, P. A., Veloo, A. C. M., & Rodriguez-Palacios, A. (2020). The Genus Alistipes: Gut Bacteria With Emerging Implications to Inflammation, Cancer, and Mental Health. Frontiers in Immunology, 11. https://doi.org/10.3389/fimmu.2020.00906
  11. Pusceddu, M. M., & Del Bas, J. M. (2020). The role of the gut microbiota in the pathophysiology of mental and neurological disorders. Psychiatric Genetics, 30(4), 87–100. https://doi.org/10.1097/ypg.0000000000000255
  12. Smits, S. A., Leach, J., Sonnenburg, E. D., Gonzalez, C. G., Lichtman, J. S., Reid, G., Knight, R., Manjurano, A., Changalucha, J., Elias, J. E., Dominguez-Bello, M. G., & Sonnenburg, J. L. (2017). Seasonal cycling in the gut microbiome of the Hadza hunter-gatherers of Tanzania. Science, 357(6353), 802–806. https://doi.org/10.1126/science.aan4834
  13. ‌Sou Ohkawara, Hideki Furuya, Kousuke Nagashima, & Tsuneo Hino. (2006). Oral Administration of Butyrivibrio fibrisolvens, a Butyrate-Producing Bacterium, Decreases the Formation… ResearchGate; American Society for Nutrition. https://www.researchgate.net/publication/7452162_Oral_Administration_of_Butyrivibrio_fibrisolvens_a_Butyrate-Producing_Bacterium_Decreases_the_Formation_of_Aberrant_Crypt_Foci_in_the_Colon_and_Rectum_of_Mice
  14. Wibowo, M. C., Yang, Z., Borry, M., Hübner, A., Huang, K. D., Tierney, B. T., Zimmerman, S., Barajas-Olmos, F., Contreras-Cubas, C., García-Ortiz, H., Martínez-Hernández, A., Luber, J. M., Kirstahler, P., Blohm, T., Smiley, F. E., Arnold, R., Ballal, S. A., Pamp, S. J., Russ, J., & Maixner, F. (2021). Reconstruction of ancient microbial genomes from the human gut. Nature, 594(7862), 234–239. https://doi.org/10.1038/s41586-021-03532-0

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