Geography, Ethnicity or Subsistence-Specific Variations in Human Microbiome Composition and Diversity - PubMed (original) (raw)

Review

Geography, Ethnicity or Subsistence-Specific Variations in Human Microbiome Composition and Diversity

Vinod K Gupta et al. Front Microbiol. 2017.

Abstract

One of the fundamental issues in the microbiome research is characterization of the healthy human microbiota. Recent studies have elucidated substantial divergences in the microbiome structure between healthy individuals from different race and ethnicity. This review provides a comprehensive account of such geography, ethnicity or life-style-specific variations in healthy microbiome at five major body habitats-Gut, Oral-cavity, Respiratory Tract, Skin, and Urogenital Tract (UGT). The review focuses on the general trend in the human microbiome evolution-a gradual transition in the gross compositional structure along with a continual decrease in diversity of the microbiome, especially of the gut microbiome, as the human populations passed through three stages of subsistence like foraging, rural farming and industrialized urban western life. In general, gut microbiome of the hunter-gatherer populations is highly abundant with Prevotella, Proteobacteria, Spirochaetes, Clostridiales, Ruminobacter etc., while those of the urban communities are often enriched in Bacteroides, Bifidobacterium, and Firmicutes. The oral and skin microbiome are the next most diverse among different populations, while respiratory tract and UGT microbiome show lesser variations. Higher microbiome diversity is observed for oral-cavity in hunter-gatherer group with higher prevalence of Haemophilus than agricultural group. In case of skin microbiome, rural and urban Chinese populations show variation in abundance of Trabulsiella and Propionibacterium. On the basis of published data, we have characterized the core microbiota-the set of genera commonly found in all populations, irrespective of their geographic locations, ethnicity or mode of subsistence. We have also identified the major factors responsible for geography-based alterations in microbiota; though it is not yet clear which factor plays a dominant role in shaping the microbiome-nature or nurture, host genetics or his environment. Some of the geographical/racial variations in microbiome structure have been attributed to differences in host genetics and innate/adaptive immunity, while in many other cases, cultural/behavioral features like diet, hygiene, parasitic load, environmental exposure etc. overshadow genetics. The ethnicity or population-specific variations in human microbiome composition, as reviewed in this report, question the universality of the microbiome-based therapeutic strategies and recommend for geographically tailored community-scale approaches to microbiome engineering.

Keywords: body habitats; disease susceptibility; host genetics; hunter-gatherers; lifestyle; non-western people; rural community; urban life.

PubMed Disclaimer

Figures

Figure 1

Figure 1

Enriched taxa at various niches of the human body in diverse populations around the world. Box color: body niche; Color in Map: percentage urbanization of countries (

http://www.unicef.org/

); Up arrow: Dominant abundance of Phylum/Genus compared to respective population; Down arrow: Low abundances of Phylum/Genus/family compared to respective population; * and # comparisons between specific countries; Number in respective boxes: Citations.

Figure 2

Figure 2

Gradual transition of the gut microbiota composition with changes in the host subsistence strategies.

Figure 3

Figure 3

Principal Component Analysis based on relative abundances of core microbiota among different countries/populations derived from a specific body niche (population wise data shown in Tables S1–S3): (A) Gut (B) Oral cavity (C) Vagina.

Similar articles

Cited by

References

    1. Adlerberth I., Wold A. E. (2009). Establishment of the gut microbiota in Western infants. Acta Paediatr. 98, 229–238. 10.1111/j.1651-2227.2008.01060.x - DOI - PubMed
    1. Albert A. Y., Chaban B., Wagner E. C., Schellenberg J. J., Links M. G., van Schalkwyk J., et al. . (2015). A study of the vaginal microbiome in healthy canadian women utilizing cpn60-based molecular profiling reveals distinct gardnerella subgroup community state types. PLoS ONE 10:e0135620. 10.1371/journal.pone.0135620 - DOI - PMC - PubMed
    1. Allen E. K., Koeppel A. F., Hendley J. O., Turner S. D., Winther B., Sale M. M. (2014). Characterization of the nasopharyngeal microbiota in health and during rhinovirus challenge. Microbiome 2:22. 10.1186/2049-2618-2-22 - DOI - PMC - PubMed
    1. Anderson C. A., Boucher G., Lees C. W., Franke A., D'Amato M., Taylor K. D., et al. . (2011). Meta-analysis identifies 29 additional ulcerative colitis risk loci, increasing the number of confirmed associations to 47. Nat. Genet. 43, 246–252. 10.1038/ng.764 - DOI - PMC - PubMed
    1. Armougom F., Henry M., Vialettes B., Raccah D., Raoult D. (2009). Monitoring bacterial community of human gut microbiota reveals an increase in Lactobacillus in obese patients and Methanogens in anorexic patients. PLoS ONE 4:e7125. 10.1371/journal.pone.0007125 - DOI - PMC - PubMed

Publication types

LinkOut - more resources