by Cliff Bueno de Mesquita
This month I will switch gears and write about a new topic – the gut microbiome. This is not something we are currently researching in the AMO, but is an important subdiscipline in microbial ecology right now with important implications for human health. Many popular media sources in recent years have picked up on gut microbiome research often reporting on how important gut microbes are for human health. This is true and is backed up by a large and growing body of scientific work. But what are the individual organisms?
The human gut is dominated by three phyla of bacteria: the Firmicutes (Families Lachnospiraceae and Ruminococcaceae), the Bacteroidetes (Bacteroidaceae, Prevotellaceae and Rikenellaceae) and the Actinobacteria (Bifidobacteriaceae and Coriobacteriaceae). These phyla and families are also abundant in the guts of other primates and mammals. One abundant genus is Prevotella, which are Gram-negative bacteria found in the oral, vaginal, and gut microbiota (Figure 1). Prevotella is an important genus to study because it is very abundant in some people and not very abundant in others. In fact, Prevotella was a key taxon driving the idea of “enterotypes” or groupings in humans. In 2011, three enterotypes, dominated by either Bacteroides, Prevotella, or Ruminococcus, were described (1).
Prevotella abundance appears to be linked to long-term diet and is more abundant in a plant-based diet compared to a meat-based diet. Prevotella has been linked to diets high in fiber and carbohydrates while Bacteroides to protein and animal fat (2, 3). This makes sense because Prevotella produce enzymes specifically involved in fiber and carbohydrate degradation. A study comparing the gut microbiota in children from Europe eating a typical western diet compared to children in a rural village in Burkina Faso eating a diet high in fiber, similar to early human diets at the birth of agriculture, showed a huge difference in Prevotella abundance, with the Burkina Faso children averaging 53% Prevotella abundance and the European children averaging 0% Prevotella abundance (4). Additional work has found lower counts of Bacteroides in vegans (5). More broadly, chimpanzees have greater abundances of Prevotella than humans.
1. M. Arumugam, J. Raes, E. Pelletier, D. Le Paslier, T. Yamada, D. R. Mende, G. R. Fernandes, J. Tap, T. Bruls, J. M. Batto, M. Bertalan, N. Borruel, F. Casellas, L. Fernandez, L. Gautier, T. Hansen, M. Hattori, T. Hayashi, M. Kleerebezem, K. Kurokawa, M. Leclerc, F. Levenez, C. Manichanh, H. B. Nielsen, T. Nielsen, N. Pons, J. Poulain, J. Qin, T. Sicheritz-Ponten, S. Tims, D. Torrents, E. Ugarte, E. G. Zoetendal, J. Wang, F. Guarner, O. Pedersen, W. M. De Vos, S. Brunak, J. Doré, J. Weissenbach, S. D. Ehrlich, P. Bork, Enterotypes of the human gut microbiome. Nature. 473, 174–180 (2011).
2. G. D. Wu, J. Chen, C. Hoffmann, K. Bittinger, Y. Chen, S. A. Keilbaugh, M. Bewtra, D. Knights, W. A. Walters, R. Knight, R. Sinha, E. Gilroy, K. Gupta, R. Baldassano, L. Nessel, H. Li, Linking long-term dietary patterns with gut microbial enterotypes. Science (80-. ). 334, 105–109 (2011).
3. A. H. Nishida, H. Ochman, A great-ape view of the gut microbiome. Nat. Rev. Genet. 20, 195–206 (2019).
4. C. De Filippo, D. Cavalieri, M. Di Paola, M. Ramazzotti, J. B. Poullet, S. Massart, S. Collini, G. Pieraccini, P. Lionetti, Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa. Proc. Natl. Acad. Sci. U. S. A. 107, 14691–14696 (2010).
5. J. Zimmer, B. Lange, J. S. Frick, H. Sauer, K. Zimmermann, A. Schwiertz, K. Rusch, S. Klosterhalfen, P. Enck, A vegan or vegetarian diet substantially alters the human colonic faecal microbiota. Eur. J. Clin. Nutr. 66, 53–60 (2012).
Various lab members contribute to the MoM Blog