Gut Microbiome

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True   Likely   Speculative
Human Uniqueness Compared to "Great Apes": 
Relative Difference
Human Universality: 
Individual Universal (All Individuals Everywhere)
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In a recent comparison of gut microbial diversity from 160 wild chimpanzees, 70 wild bonobos, 186 wild gorillas, and >500 humans, across five different populations ranging from urban to hunter-gatherer lifestyles, it was found that humans have lost microbial diversity compared to the wild great apes. This change is hypothesized to be the result of increased consumption of meat.

Background Information: 

The gut bacteria of mammals are highly diverse and generally the composition of a mammal's gut microbes reflects their diet.  For instance, herbivores harbor more similar suites of bacteria compared to carnivores. The richness of the gut microbiota is also related to diet, with herbivores generally harboring the most complex microbial assemblages (highest number of "species" of microbes), and carnivores the least.  This presumably reflects the need for microbial assemblages to work together to break down complex polysaccharides from plants, whereas richer, simpler diets comprised of meats are more easily broken down and do not require specialized enzymes or thermodynamically-based microbial symbioses. There is an additional force shaping the gut microbial communities of mammals: animals with similar gut physiologies tend to have similar microbial communities (eg, foregut fermenters vs hindgut fermenters).  In this context, chimpanzees and humans have similar diet, gut structures and thus both species have grossly similar gut microbial assemblages typical of omnivorous primates.

The Human Difference: 

Humans and the Great apes share a core set of bacterial genera and co-occurance patterns across those taxa were highly consistent. However, the relative abundance of Bacteroides, which are associated with diets rich in animal meat, are increased five fold in humans. Conversely, Methanobrevibacter and Fibrobacter, both involved in the degradation of plant matter, are greatly reduced in humans.

Universality in Human Populations: 

Humans are by far the most studied animal, and this is true for the characterization of the microbial assemblages in the gut as well. Comparison of >500 humans from lifestyles that include urban US and Europe, rural Malawi, preindustrial southern Amazon rainforest, and hunter-gatherer in Tanzania found that all groups showed lower levels of microbial diversity than that of wild apes.

Mechanisms Responsible for the Difference: 

As carnivores show the least microbial diversity, increased meat consumption could explain the loss of microbial complexity.

Implications for Understanding Modern Humans: 

Since the gut microbes are implicated in energy balance, and in contributing to the body weight of the host, a greater understanding of the differences between humans and their close relatives may shed light on whether gut microbes helped shape the evolution of humans and in particular if they played a role in the proposed trade-off bewteen large gut and large brain.

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Referenced By:
Title Certainty
Cuisine Speculative
Detoxifying/Removing Antinutrients Likely
Milk Composition True

References

  1. A great-ape view of the gut microbiome, Nishida, Alex H., and Ochman Howard , Nature Reviews, 2019/01/08, (2019)
  2. Gut microbiome composition is associated with cardiac disease in zoo-housed western lowland gorillas (Gorilla gorilla gorilla)., Krynak, Katherine L., Burke David J., Martin Ryan A., and Dennis Patricia M. , FEMS Microbiol Lett, 2017 Aug 15, Volume 364, Issue 15, (2017)
  3. Seasonal cycling in the gut microbiome of the Hadza hunter-gatherers of Tanzania, Smits, Samuel A., Leach Jeff, Sonnenburg Erica D., Gonzalez Carlos G., Lichtman Joshua S., Reid Gregor, Knight Rob, Manjurano Alphaxard, Changalucha John, Elias Joshua E., et al. , Science, 2017/08/24, Volume 357, Issue 6353, p.802, (2017)
  4. Captivity humanizes the primate microbiome, Clayton, Jonathan B., Vangay Pajau, Huang Hu, Ward Tonya, Hillmann Benjamin M., Al-Ghalith Gabriel A., Travis Dominic A., Long Ha Thang, Van Tuan Bui, Van Minh Vo, et al. , 2016/08/29, (2016)
  5. Cospeciation of gut microbiota with hominids, Moeller, A. H., Caro-Quintero A., Mjungu D., Georgiev A. V., Lonsdorf E. V., Muller M. N., Pusey A. E., Peeters M., Hahn B. H., and Ochman H. , Science, 07/2016, Volume 353, Issue 6297, p.380 - 382, (2016)
  6. Gut Microbiome of Coexisting BaAka Pygmies and Bantu Reflects Gradients of Traditional Subsistence Patterns., Gomez, Andres, Petrzelkova Klara J., Burns Michael B., Yeoman Carl J., Amato Katherine R., Vlckova Klara, Modry David, Todd Angelique, Robinson Carolyn A. Jost, Remis Melissa J., et al. , Cell Rep, 2016 Mar 8, Volume 14, Issue 9, p.2142-53, (2016)
  7. Insights into human evolution from ancient and contemporary microbiome studies, Schnorr, Stephanie L., Sankaranarayanan Krithivasan, Jr. Cecil M. Lewis, and Warinner Christina , Genetics of human origin, 2016/12, Volume 41, p.14 - 26, (2016)
  8. Metagenome Sequencing of the Hadza Hunter-Gatherer Gut Microbiota., Rampelli, Simone, Schnorr Stephanie L., Consolandi Clarissa, Turroni Silvia, Severgnini Marco, Peano Clelia, Brigidi Patrizia, Crittenden Alyssa N., Henry Amanda G., and Candela Marco , Curr Biol, 2015 Jun 29, Volume 25, Issue 13, p.1682-93, (2015)
  9. Subsistence strategies in traditional societies distinguish gut microbiomes., Obregon-Tito, Alexandra J., Tito Raul Y., Metcalf Jessica, Sankaranarayanan Krithivasan, Clemente Jose C., Ursell Luke K., Xu Zhenjiang Zech, Van Treuren Will, Knight Rob, Gaffney Patrick M., et al. , Nat Commun, 2015, Volume 6, p.6505, (2015)
  10. Rapid changes in the gut microbiome during human evolution., Moeller, Andrew H., Li Yingying, Ngole Eitel Mpoudi, Ahuka-Mundeke Steve, Lonsdorf Elizabeth V., Pusey Anne E., Peeters Martine, Hahn Beatrice H., and Ochman Howard , Proc Natl Acad Sci U S A, 2014 Nov 18, Volume 111, Issue 46, p.16431-5, (2014)
  11. Evolution of mammals and their gut microbes., Ley, Ruth E., Hamady Micah, Lozupone Catherine, Turnbaugh Peter J., Ramey Rob Roy, J Bircher Stephen, Schlegel Michael L., Tucker Tammy A., Schrenzel Mark D., Knight Rob, et al. , Science, 2008 Jun 20, Volume 320, Issue 5883, p.1647-51, (2008)