Bacteroide composition in the gut

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The Bacterial kingdom has played a significant role in Homo sapien evolution. Only ten percent of the cells existing in the body are human. Genetically, we are about 1% human, and 99% bacterial (Xu & Gordon, 2003).

The human colon contains the majority of microorganisms in the body, and 25% of these are species of Bacteroides. Bacteroides species are anaerobic, non-spore forming, gram-negative rods that have adapted to, and now thrive in, the human gut(Wexler, 2007). The relationship between Bacteroides and the host has recently been considered mutual, given that the relationship increases the fitness of both species. Given the long history of coevolution between microbiota and the intestine, it has now been shown that bacteroides function as a multifunctional organ that provides metabolic components we do not contain in our own genome (Xu, 2003). Some of these metabolic traits include carbohydrate fermentation, freeing simplified carbohydrates to be reabsorbed by the large intestine and to be used for energy by the host. Through various metabolic mechanisms, Bacteroides provide simplified amino acids and vitamins, while simultaneously utilizing a wide range of dietary polysaccharides for growth (Hooper, Midtvedt, and Gordon. 2002).

Due to the metabolic role of Bacteroides in carbohydrate fermentation, there has been some evidence showing a correlation between diet, gut flora, and obesity. Given the significant role Bacteroides play in the gut, the effect of diet on their mechanisms of action and composition overall is a relevant topic of analysis (Turnbaugh, 2009). How body flora composition might affect adiposity is particularly crucial in light of the drastic shift in food source in the United States and its consequent growing obesity epidemic.

Genomic and Proteomic Advances

Recently, genomic and proteomic analyses have provided insight into the mechanisms in which microbiota adapt and thrive within varying microenvironments. Sequencing B. thetaiotaomicron and B. fragilis show notable genomic commonalities. These Bacteroides, like eukaryotes, show low gene content for the size of their genome (Xu and Gordon, 2003). A large portion of the their genetic make-up consists of proteins containing over 1,000 amino acids, which, it seems, allow for a vast selection of relevant proteins for gene expression. Putative relevant proteins have been determined by homology to other known proteins. Of the 4779 proteins identified in the B. thetaiotaomicron proteome, 58% were ascribed a supposed function based on other known proteins, 18% were homologous to proteins without a known function, and 24% were not homologous to any protein identified in the public domain (Xu et al., 2003). The variety of functions is presumed to aid Bacteroides species in multiple ways: the proteome induces the mechanism by which some Bacteroides acquire and hydrolyze otherwise indigestible dietary polysaccharides, and includes an environment-sensing apparatus with extracytoplasmic function sigma factors and one- and two-component signal transduction systems (Xu et. al., 2003).

B. thetaiotaomicron contains the capacity to utilize glycans derived from the colon. The majority (61%) of the necessary enzymes (glycohyrolases) potentially exist in the periplasm, and are necessary to the polysaccharide fermentation process that increases energy availability to the host. Other extracellular proteins have been shown to facilitate the binding of starches to the cell surface to be digested by other extracellular enzymes (Xu et al., 2003).

Additionally, B. thetaiotaomicron was shown to contain a significant population of ECF-sigma factors, which according to other identified homologous genes, are cotranscribed with regulatory proteins that respond to external environmental stimulus and act on gene expression accordingly.

The majority of one-component signal transduction systems were shown to be similar to other genes responsible for nutrient utilization, providing further evidence of Bacteroides’ genetically evolved fitness advantage in nutrient acquisition.

Through genomic and proteomic sequencing, some of the mechanism underlying the adaptive capabilities of the Bacteroide species in the human gut have been identified. The expansive array of proteins available to them mediates their ability to respond to their environment, thrive within the rapidly changing microenvironment of the colon, and acquire and ferment complex carbohydrates for their own energy source as well as for the host.

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Electron micrograph of the Ebola Zaire virus. This was the first photo ever taken of the virus, on 10/13/1976. By Dr. F.A. Murphy, now at U.C. Davis, then at the CDC.

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Legend/credit: Electron micrograph of the Ebola Zaire virus. This was the first photo ever taken of the virus, on 10/13/1976. By Dr. F.A. Murphy, now at U.C. Davis, then at the CDC.
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Overall paper length should be 3,000 words, with at least 3 figures with data.

Section 2

Include some current research in each topic, with at least one figure showing data.

Section 3

Include some current research in each topic, with at least one figure showing data.

Further Reading

[Sample link] Ebola Hemorrhagic Fever—Centers for Disease Control and Prevention, Special Pathogens Branch

References

[Sample reference] Takai, K., Sugai, A., Itoh, T., and Horikoshi, K. "Palaeococcus ferrophilus gen. nov., sp. nov., a barophilic, hyperthermophilic archaeon from a deep-sea hydrothermal vent chimney". International Journal of Systematic and Evolutionary Microbiology. 2000. Volume 50. p. 489-500.

Turnbaugh PJ, Ridaura VK, Faith JJ, Rey FE, Knight R, Gordon JI. The Effect of Diet on the Human Gut Microbiome: A Metagenomic Analysis in Humanized Gnotobiotic Mice. Science translational medicine. 2009;1(6):6ra14.

Wexler HM. Bacteroides: the Good, the Bad, and the Nitty-Gritty. Clinical Microbiology Reviews. 2007;20(4):593-621. doi:10.1128/CMR.00008-07.

Xu J, Bjursell MK, Himrod J, et al. A genomic view of the human-Bacteroides thetaiotaomicron symbiosis. Science. 2003;299(5615):2074-6.

Xu J, Gordon JI. Honor thy symbionts. Proceedings of the National Academy of Sciences of the United States of America. 2003;100(18):10452-10459.

Edited by Maggie Schein, a student of Nora Sullivan in BIOL168L S2 (Microbiology) in The Keck Science Department of the Claremont Colleges Spring 2014.