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What can fossil excrements tell us about the evolution of the gut microbiome

July 20th, 2021  

Research into how the composition of the gut microbiome affects human health continues to advance. Now, between 1,000 and 2,000 year old human faeces found in dry caves in northern Mexico and Utah have been analysed. The data is an important resource for studying bacterial evolution and the biological spread of chronic diseases throughout history. The study, published in the journal Nature, is the first to uncover new species of microbes.

Ancient microbiome – the answer to current questions?

The microbiome is the collection of the trillions of microorganisms that live in and on our bodies. It consists primarily of bacteria, but also contains fungi, viruses and primordial bacteria. The gut microbiome can be passed down through many generations – but it can be changed by external influences such as antibiotic treatments or dietary changes (1, 2). 

On the one hand, this flexibility of the microbiome is advantageous because it offers a potential avenue for the treatment of diseases related to the microbiome. However, it also presents a vulnerability: Industrial life, which is predominantly characterised by a low-fibre and one-sided diet, changes the gut microbiome for the worse (3, 4). The diversity of bacteria in industrial populations is decreasing, which is closely linked to chronic diseases such as obesity and autoimmune diseases (5).

The diversity of gut bacteria in industrial populations is decreasing

How has the gut microbiome changed over time?

The analysis of fossil faeces, which was possible through the use of DNA sequencing, provides valuable insights into the bacterial composition from a time before industrialisation. The research team reconstructed faeces that are between 1,000 and 2,000 years old and compared them with present-day samples from industrialised and non-industrialised populations.

Is the human microbiome threatened with extinction?

Previous research has shown that what was healthy for us hundreds of years ago is still healthy today. Indigenous peoples living away from civilisation continue to feed on diverse plants and fibres. Due to this diversity of food, their gut flora also has a much higher diversity. Many studies have shown that a diverse microbiome is beneficial and can prevent diseases. Low diversity, on the other hand, has been associated with various diseases, such as obesity or diarrhoea. (6)

An interesting example of a microbiome with high diversity is the Hadza – a primitive people from Tanzania. They are one of the last hunter-gatherer societies on earth, consuming mainly seasonal food. Not only the diet, but also the gut bacteria change cyclically and adapt. The Hadza’s gut flora is extremely diverse. 

Civilisation diseases do not occur at all or only rarely among this people. The key to this composition apparently lies in the diet. It turned out that the gut in industrialised countries is populated quite differently – less diverse. Since we are not dependent on the seasonal food supply, the microbial ecosystem in the gut remains the same – throughout the year. There is evidence that a less diverse gut community poses a higher risk for such diseases. (7)

The myBioma microbiome analysis enables you to find out how your microbial composition is and which bacteria live in your gut. You get an overall picture of your gut universe and significant insights into how your health is doing. According to your results you will receive dietary recommendations, e.g. to optimise your diversity & species richness.

Reconstruction of the fossil human gut microbiome

To analyse the fossil kit, tiny pieces were rehydrated to obtain better bacterial traces. A total of 498 microbial genomes were reconstructed, 181 of which actually came from the gut. 158 of the genomes could in turn be assigned to a specific gut bacterial species, which the researchers compared with 789 gut microbiomes of modern humans.

The result: although the fossil microbiome was more similar to that of non-industrialised populations, it also contained 61 genomes that had previously been completely unknown to science. 39 percent of the fossil gut microbiome was not found at all in today’s stool samples.

Lower diversity – higher risk of disease? 

Might the loss of diversity in the modern gut microbiome be one reason why diseases of civilisation such as chronic inflammatory bowel disease, obesity, asthma, diabetes and allergies are on the rise?

Quite possibly. Because the evidence suggests that a species-poorer gut composition poses a higher risk for such diseases. And as more and more people worldwide are drawn to cities and to a modern lifestyle, this trend could intensify in the future.

Future studies are needed to gain a better understanding of the human microbiome, which could help in the discovery of new treatments for diseases. The studies could also help in developing approaches to restore today’s gut microbiome to its original, species-appropriate state. We are excited!


Reconstruction of ancient microbial genomes from the human gut:

  1. Tett A, Huang KD, Asnicar F, Fehlner-Peach H, Pasolli E, Karcher N, Armanini F, Manghi P, Bonham K, Zolfo M, De Filippis F, Magnabosco C, Bonneau R, Lusingu J, Amuasi J, Reinhard K, Rattei T, Boulund F, Engstrand L, Zink A, Collado MC, Littman DR, Eibach D, Ercolini D, Rota-Stabelli O, Huttenhower C, Maixner F, Segata N. The Prevotella copri Complex Comprises Four Distinct Clades Underrepresented in Westernized Populations. Cell Host Microbe. 2019 Nov 13;26(5):666-679.e7. doi: 10.1016/j.chom.2019.08.018. Epub 2019 Oct 10. PMID: 31607556; PMCID: PMC6854460.
  2. Sonnenburg ED, Sonnenburg JL. The ancestral and industrialized gut microbiota and implications for human health. Nat Rev Microbiol. 2019 Jun;17(6):383-390. doi: 10.1038/s41579-019-0191-8. PMID: 31089293.
  3. Kang DD, Li F, Kirton E, Thomas A, Egan R, An H, Wang Z. MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies. PeerJ. 2019 Jul 26;7:e7359. doi: 10.7717/peerj.7359. PMID: 31388474; PMCID: PMC6662567.
  4. Parks DH, Rinke C, Chuvochina M, Chaumeil PA, Woodcroft BJ, Evans PN, Hugenholtz P, Tyson GW. Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life. Nat Microbiol. 2017 Nov;2(11):1533-1542. doi: 10.1038/s41564-017-0012-7. Epub 2017 Sep 11. Erratum in: Nat Microbiol. 2017 Dec 12;: PMID: 28894102.
  5. Blaser MJ. The theory of disappearing microbiota and the epidemics of chronic diseases. Nat Rev Immunol. 2017 Jul 27;17(8):461-463. doi: 10.1038/nri.2017.77. PMID: 28749457.
  6. Bäckhed F, Fraser CM, Ringel Y,et al. Defining a healthy human gut microbiome: current concepts, future directions, and clinical applications. Cell Host Microbe. 2012;12(5):611-22.
  7. Smits SA, Leach J, Sonnenburg ED, Gonzalez CG, Lichtman JS, Reid G, Knight R, Manjurano A, Changalucha J, Elias JE, Dominguez-Bello MG, Sonnenburg JL. Seasonal cycling in the gut microbiome of the Hadza hunter-gatherers of Tanzania. Science. 2017 Aug 25;357(6353):802-806. doi: 10.1126/science.aan4834. PMID: 28839072; PMCID: PMC5891123.


Über den Autor

Listen to your gut!

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