What Our Guts are Telling Us — The Human Microbiome, Evolution and Biodiversity Loss

Nousheen Mahmud
Oct 30, 2018 · 5 min read

The gut microbiome consists of all the bacteria living in an individual’s intestinal tract. Without these bacteria, we would not be able to digest and process the food we eat. They live in an extreme environment and are known to have coevolved with hominids. In one study, 33 mammalian gut microbiomes were compared to find that the two main factors which dictate gut microbiome diversity are phylogeny and diet. In the figure below published by Nature in 2017, you can observe that ancestral gut microbiomes were more severely affected by their diets, whereas today the lineage is almost entirely correlated with host phylogeny.

Published in Nature Communications section of the online Nature magazine in 2017. Works cited #3.

In recent years, there has been a lot of research on human gut microbiomes and how their diversity can affect our health. There are many factors that influence our gut microbiome diversity, such as diet quality, exposure to food and water-borne pathogens, and use of antibiotics (Carrera-Bastos and Fontes-Villalba 2011). We have seen a loss of diversity in Western populations, where antibiotic use is widespread and diets are more homogenous compared to non-industrialized countries such as Malawi and Venezuela, which have been exposed to more pathogens through food and water and subsist on a varied diet (Davenport and Sanders 2017) The loss of gut microbiome diversity can be linked to several diseases and is a growing issue which requires further research.

Comparing gut microbiomes between humans and closely related primates could provide insight to changes in behavior that alter diversity. “In contrast to African apes, humans have lower gut microbiota diversity, increased relative abundances of Bacteroides, and reduced relative abundances of Methanobrevibacter and Fibrobacter” (Davenport E.R and Sanders J.G 2017) These three bacteria are related to carnivory in other mammals, which may explain the evolutionary change in our microbiome to adjust to eating more meat. The difference in gut microbiome species can be vastly different in current humans. In a population studied in Malawi, a lineage of Bacteroidaceae was found which is completely nonexistent in populations from the United States. (Moeller H.A et al 2016) A possible cause of this is the difference in diet between Malawians and Americans. Where people from Malawi have a varied diet, a large portion of the United State consumed processed food on a regular basis. Antibiotic use is also very widespread in more urbanized countries which can lower the diversity of bacteria in an individual for the rest of their life (Francino M.P 2015) Another article states that the difference in microbiomes of US humans and people from Malawi is greater than those between people from Malawi and bonobos (Moeller H.A et al 2014) Compared to apes, where a variety of different bacteria coexisted at low frequencies, individual humans tend to have fewer dominant taxa at greater rates (Moeller H.A et al 2014) This can be seen in the figure published by PNAS in 2014. These findings could point to a major loss in diversity. The possibility that entire lineages of gut bacteria can disappear points to bigger issues. If this continues, we may lose our ability to digest certain types of food.

Figure 2, published in the Proceedings of the National Academy of Sciences of the United States of America. Works cited #7.

So how do we go about reversing the effect of improper diet, antibiotics and the other factors in our lives that alter our microbiome? One step would be to eat healthier, whole foods rather than processed foods. Since the bacteria we are discussing reside in the digestive system and live off of the food humans eat, it makes sense that consuming food that is good for the person will also promote more stable levels of gut bacteria. People who consume high protein and low carbohydrate diets tend to have less Roseburia in their bodies, which is also common in people with irritable bowel syndrome (Singh R.K et al 2017) There are also links to microbes that are promoted by consuming red meat and the levels of a compound produced which increases the risk of cardiovascular disease (Singh R.K et al 2017) Besides eating well, lowering use of antibiotics if possible would also help maintain a healthy microbiome. Many antibiotics are unavoidable as they are found in farm animals and crops. However, broad spectrum antibiotics can affect the abundances of 30% of the bacteria in the gut community (Francino M.P 2015) Overall, people should be more aware of the way that their diet and lifestyle choices can harm their gut flora. Further research needs to be done on the direct impact of antibiotics and diet on gut intestinal flora and the diseases caused by lack of diversity.

Works Cited

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2. Davenport, E.R., Sanders, J.G (2017) The human microbiome in evolution. Biomed Central Biology, 15:127


3. Francino M.P e(2015) Antibiotics and the human gut microbiome: Dysbioses and accumulation of resistances. Frontiers in Microbiology 6:1543


4. Groussin, M. et al. (2017) Unraveling the processes shaping mammalian gut microbiomes over evolutionary time. Nat. Commun. 8:14319

doi: 10.1038/ncomms14319

5. Heiman, M. L., and Greenway, F. L. (2016). A healthy gastrointestinal microbiome is dependent on dietary diversity. Molecular Metabolism 55:317–320.

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7. Moeller, H.A. et al. (2016) Cospeciation of gut microbiota with hominids. Science Magazine 380–382


8. Moeller, H.A. et al. (2014) Rapid changes in the gut microbiome during human evolution. Proceedings of the National Academy of Sciences of the United States of America 16431–16435


9. Mosca, A., Leclerc, M., and Hugot, J. P. (2016). Gut microbiota diversity and human diseases: Should we reintroduce key predators in our ecosystem? Frontiers in Microbiology 7:455. http://doi.org/10.3389/fmicb.2016.00455

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11. Singh, R.K et al (2017) Influence of diet on the gut microbiome and implications for huma health. Journal of Translational Medicine 15:73


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