Reasons for differences in microbiome composition among different populations

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Introduction


In recent research of the human microbiome, studies have found that the composition of the microbiota can have large effects on the health of individuals. The human microbiome is the collection of microbial species that live in different anatomical places on the human body (Pflughoeft and Versalovic 2012). The microbial populations have shown to have large effects on human disease (Pflughoeft and Versalovic 2012). This shows a possible connection between the differences in disease rates among different populations of people and differences in the microbial populations present in the microbiome. It is important to know the causes for differences in human microbiome among different populations. The composition of the microbiome may depend on “health, genotype, diet, and hygiene” (Pflughoeft and Versalovic 2012; 100). There is currently a debate over whether the makeup of the microbiome depends more on genetics or environmental location. Some studies are finding that nutrition and water quality in the first year of life show are most important for forming the microbiome (Pflughoeft and Versalovic 2012). Recent studies are attempting to determine which factors are most important in determining the composition if the microbiome.



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Genetic factors influencing microbiomes


Many studies comparing different geographical populations of humans and studies comparing different animal species have come to the conclusion that genetic differences play a large role in the composition of the microbiome. One study of tilapia, toads, geckos, quail, and mice tested changes in the microbiota of the colon and cecum after periods of fasting (Kohl et al. 2014). Interestingly this study found that in tilapia, toads, and mice, there was more genetic diversity in the colon microbiome during a fast than while well nourished (Kohl et al. 2014). This shows that the environmental factor of diet is not the only factor that keeps the microbiota thriving but that other factors are at play that may have to do with genetics. In the same study, tests of the cecum found that in tilapia and toads, although there were initial changes in genetic diversity after the start of the fast, the microbiotic species returned to normal later in the fast (Kohl et al. 2014). This shows that the microbiota of the cecum is able to regulate itself without any nutrient input from the environment. The samples from the ceca of mice showed no changes in the microbiotic species (Kohl et al. 2014). In this case it appears that the microbiota was completely controlled by a factor other than diet which may have a genetic origin. A study comparing the saliva microbiome of Alaskans, Africans, and Germans claimed that environment did not always play an important role in the makeup of the microbiotic species. This study stated that Germans may have less microbiotic diversity because ancestrally they come from a more specific area as opposed to Alaskans and Africans who come together from more diverse areas (Li et al. 2014). This suggests that the makeup of the microbiota of the saliva may be dependent on the genetic similarities of the people involved rather than on the characteristics of the environment they live in. Other human studies sough to determine how microbiota differ between related and unrelated individuals. A study of human twins analyzed fecal samples from each twin pair. This study found that twins have a more similar microbiota than individuals that are not related (Goodrich et al. 2014). This may indicate that genetics plays a role in the microbiome composition; however, the similarities may also be due to the environment. This study, however, also found that twin pairs who were monozygotic have more similarities in their microbiome samples than do twins who were dizygotic (Goodrich 2014). This demonstrates that the identical DNA of the monozygotic twins does affect the similarity of the gut microbiome.

Environmental Factors influencing Microbiomes


Although many studies give evidence for genetics playing an important role in differences in the microbiome among populations, there are also recent studies that demonstrate how the microbiome is affected by environmental factors. One study focused on eight different fish species with different feeding habits. This study found that in the fish with plant based diets the main bacterial species were of the phyla of Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria. In carnivorous, however, the main bacteria found in the microbiome were different (J. Li et al. 2014). This studies shows that the environmental factor of diet does play a role in the make-up of the microbiome. The differences in microbiotic composition among fish with different diets may be a result of the ability of certain microbes to aid in the digestion of different macronutrients (J. Li et al 2014). This evidence can be related to differences in the human microbiome because it suggests that diets of different populations can result in difference a microbiome composed of different species. In the human study above where samples of saliva were analyzed from Alaskans, Africans, and Germans, further analysis looked at different groups within these three. For the Alaskans and the Africans, subgroups within these were analyzed and some contradictory evidence was found. In the Alaskan subgroups, there were no significant differences in the microbiomes of the different groups even though the groups have different geographic locations and different diets. In the African subgroups, however, one subgroup had more diversity of species in the microbiome than did the other two subgroups. It was noted that the subgroup with more diversity lived a hunter-gatherer life while the other two subgroups lived an agrarian lifestyle (Li et al. 2014). This suggests that diet and lifestyle may play a role in different microbiomes in different populations; however, this evidence is weakened since it was not consistent among all the groups studied. In this study of saliva microbiomes, another environmental factor suggested that causes distinction in microbiomes of different populations is temperature. The study states that Enterobacteriacae are more prevalent in the saliva microbiome of Africans because this microbe takes well to the warm temperatures (Li et al. 2014). The saliva microbiomes of Alaskans and Germans may be less diverse because these regions are subject to rapid temperature changes which cause the death to some of the microbes present in the microbiome (Li et al 2014).

Continuing Debate Between Genetics and Environment


The reasoning behind the differences in the composition of the microbiome of distinct populations is a very recent topic. As a result the studies on this topic have not come to a common consensus. One study comparing different animal species looked at the importance of a bacterial genus Blautia which is known to live in the gut and help to assimilate nutrients (Murat Eren et al. 2014). This study found that cats, dogs, and humans had the most Blautia compared to chicken, pigs, cows, and deer (Murat Eren et al. 2014). The types of Blautia microbes in each animal species was very distinct from the other animal species tested (Murat Eren et al. 2014). In a few of the species such as cat and deer there was an outlying sample that aligned more closely with another species (Murat Eren et al. 2014). These outliers may be a result of a strange one time addition to the diet of the animal which provided this sample. In addition to evidence of environmental influences on the differences in the composition of the microbiome, this study also contained evidence of possible genetic influences on the microbiome. In addition to sampling human fecal matter from Brazilians, this study tested the sewage from this area which contained fecal matter from over 1 million people (Murat Eren et al. 2014). It was discovered that sewage and the samples from individuals contained almost the same types of microbes (Murat Eren et al. 2014). Sewage samples from a completely different area, Milwaukee, also contained similar types of Blautia microbe types as the samples from Brazil (Murat Eren et al. 2014). This demonstrates that the presence of Blautia extends beyond geographical location and diet/lifestyle. The reasons for this may partly relate to the DNA of humans having more similarities to each other than to other animal’s DNA. One area of evidence for the intersection of the environment and genetics in determining the make-up of the microbiome is differences found between the microbiomes of obese and lean individuals. A study of samples of Columbian gut microbiome found that samples of people with a higher BMI had less Firmicutes in their samples; samples of European gut microbiome did not show decreased Furmicutes, however (Escobar et al. 2014). The differences in microbiome between individuals of different BMIs seem to indicate a genetic influence on the species present in the microbiome due to the tendency toward a higher BMI. It may also indicate an environmental influence due to differences in diet of those with a higher BMI. Furthermore, the fact that these same differences do not occur in different populations shows a blatant inconsistency in the data making it even more difficult to draw conclusions about whether environmental or genetic influences are more important.

Conclusion


The current literature on this topic does show that there are environmental and genetic influences on the differences in the microbiomes of different animal species and different populations of human species. With the current research, however, it is unclear what the specific factors creating these differences are. This is because diet, lifestyle, and geographic location are hard to separate completely from influences present in the genetics of the animal species. Further research on this topic should focus on other human traits that might cause differences in the microbiome. These traits should be ones which are more distinctly caused by genetic or environmental influences so that the reasons for the changes in the microbiome are clearer. Obesity, for example, is a very complicated topic that is intertwined with many other factors still being discovered. Studies should perhaps look at how a specific macronutrient affects the composition of the microbiome or how the levels of a specific hormone affect which microbiotic species are present.

References

[Eren, A. Murat; Sogin, Mitchell L.; Morrison, Hilary G.; Vineis, Joseph H;.Fisher, Jenny C.; Newton, Ryan J.; McLellan, Sandra L. A single genus in the gut microbiome reflects host preference and specificity. 2015. International Society for Microbial Ecology. 9: 90-100.] [Li, Jing; Quinque, Dominique; Horz, Hans-Peter; Li, Mingkun; Rzhetskaya, Margarita; Raff, Jennifer A.; Hayes, M. Geoffrey; Stoneking, Mark. Comparative Analysis of the Human Saliva Microbiome from Different Climate Zones: Alaska, Germany, and Africa. 2014. BMC Microbiology. 14:1-13.] [Li, J.; Ni, J.; Li, J.; Wang, C.; Li, X.; Wu, S.; Zhang, T.; Yu, Y.; Yan, Q. Comparative study on gastrointestinal microbiota of eight fish species with different feeding habits. 2014. Journal of Applied Microbiology. 117(6): 1750-1760.] [Escobar, Juan S.; Klotz, Bernadette; Valdes, Beatriz E.; Agudelo, Gloria M. The Gut Microbiota of Colombians Differs from that of Americans, Europeans and Asians. 2014. BMC Microbiolgy. 14(311): 1-14.] [Kohl, Kevin D.; Amaya, James; Passaent, Celeste A.; Dearing, M. Denise; McCue, Marshall D. Unique and Shared Responses of the Gut Microbiota to Prolonged Fasting: A Comparative Study across Five Classes of Vertebrate Hosts. Federation of European Microbiological Societies Microbiology Ecology. 2014. 90:883-894.] [Goodrich, Julia K.; Waters, Jillian L.; Poole, Angela C.; Sutter, Jessica L.; Koren, Omry; Blekhman, Ran; Beaumont, Michelle; Van Treuren, William; Knight, Rob; Bell, Jordana T.; Spector, Tim D.; Clark, Andrew G.; Ley, Ruth E. Human Genetics Shape the Gut Microbiome. Cell. 2014. 159:789-799.]


Edited by Christina Timko, a student of Suzanne Kern in BIOL168L (Microbiology) in The Keck Science Department of the Claremont Colleges Spring 2015.

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