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Comparative analysis of the human saliva microbiome from different climate zones: Alaska, Germany, and Africa

BACKGROUND: Although the importance of the human oral microbiome for health and disease is increasingly recognized, variation in the composition of the oral microbiome across different climates and geographic regions is largely unexplored. RESULTS: Here we analyze the saliva microbiome from native A...

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Autores principales: Li, Jing, Quinque, Dominique, Horz, Hans-Peter, Li, Mingkun, Rzhetskaya, Margarita, Raff, Jennifer A, Hayes, M Geoffrey, Stoneking, Mark
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4272767/
https://www.ncbi.nlm.nih.gov/pubmed/25515234
http://dx.doi.org/10.1186/s12866-014-0316-1
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author Li, Jing
Quinque, Dominique
Horz, Hans-Peter
Li, Mingkun
Rzhetskaya, Margarita
Raff, Jennifer A
Hayes, M Geoffrey
Stoneking, Mark
author_facet Li, Jing
Quinque, Dominique
Horz, Hans-Peter
Li, Mingkun
Rzhetskaya, Margarita
Raff, Jennifer A
Hayes, M Geoffrey
Stoneking, Mark
author_sort Li, Jing
collection PubMed
description BACKGROUND: Although the importance of the human oral microbiome for health and disease is increasingly recognized, variation in the composition of the oral microbiome across different climates and geographic regions is largely unexplored. RESULTS: Here we analyze the saliva microbiome from native Alaskans (76 individuals from 4 populations), Germans (10 individuals from 1 population), and Africans (66 individuals from 3 populations) based on next-generation sequencing of partial 16S rRNA gene sequences. After quality filtering, a total of 67,916 analyzed sequences resulted in 5,592 OTUs (defined at ≥97% identity) and 123 genera. The three human groups differed significantly by the degree of diversity between and within individuals (e.g. beta diversity: Africans > Alaskans > Germans; alpha diversity: Germans > Alaskans > Africans). UniFrac, network, ANOSIM, and correlation analyses all indicated more similarities in the saliva microbiome of native Alaskans and Germans than between either group and Africans. The native Alaskans and Germans also had the highest number of shared bacterial interactions. At the level of shared OTUs, only limited support for a core microbiome shared across all three continental regions was provided, although partial correlation analysis did highlight interactions involving several pairs of genera as conserved across all human groups. Subsampling strategies for compensating for the unequal number of individuals per group or unequal sequence reads confirmed the above observations. CONCLUSION: Overall, this study illustrates the distinctiveness of the saliva microbiome of human groups living under very different climatic conditions. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12866-014-0316-1) contains supplementary material, which is available to authorized users.
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spelling pubmed-42727672014-12-22 Comparative analysis of the human saliva microbiome from different climate zones: Alaska, Germany, and Africa Li, Jing Quinque, Dominique Horz, Hans-Peter Li, Mingkun Rzhetskaya, Margarita Raff, Jennifer A Hayes, M Geoffrey Stoneking, Mark BMC Microbiol Research Article BACKGROUND: Although the importance of the human oral microbiome for health and disease is increasingly recognized, variation in the composition of the oral microbiome across different climates and geographic regions is largely unexplored. RESULTS: Here we analyze the saliva microbiome from native Alaskans (76 individuals from 4 populations), Germans (10 individuals from 1 population), and Africans (66 individuals from 3 populations) based on next-generation sequencing of partial 16S rRNA gene sequences. After quality filtering, a total of 67,916 analyzed sequences resulted in 5,592 OTUs (defined at ≥97% identity) and 123 genera. The three human groups differed significantly by the degree of diversity between and within individuals (e.g. beta diversity: Africans > Alaskans > Germans; alpha diversity: Germans > Alaskans > Africans). UniFrac, network, ANOSIM, and correlation analyses all indicated more similarities in the saliva microbiome of native Alaskans and Germans than between either group and Africans. The native Alaskans and Germans also had the highest number of shared bacterial interactions. At the level of shared OTUs, only limited support for a core microbiome shared across all three continental regions was provided, although partial correlation analysis did highlight interactions involving several pairs of genera as conserved across all human groups. Subsampling strategies for compensating for the unequal number of individuals per group or unequal sequence reads confirmed the above observations. CONCLUSION: Overall, this study illustrates the distinctiveness of the saliva microbiome of human groups living under very different climatic conditions. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12866-014-0316-1) contains supplementary material, which is available to authorized users. BioMed Central 2014-12-17 /pmc/articles/PMC4272767/ /pubmed/25515234 http://dx.doi.org/10.1186/s12866-014-0316-1 Text en © Li et al.; licensee BioMed Central Ltd. 2014 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research Article
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
title Comparative analysis of the human saliva microbiome from different climate zones: Alaska, Germany, and Africa
title_full Comparative analysis of the human saliva microbiome from different climate zones: Alaska, Germany, and Africa
title_fullStr Comparative analysis of the human saliva microbiome from different climate zones: Alaska, Germany, and Africa
title_full_unstemmed Comparative analysis of the human saliva microbiome from different climate zones: Alaska, Germany, and Africa
title_short Comparative analysis of the human saliva microbiome from different climate zones: Alaska, Germany, and Africa
title_sort comparative analysis of the human saliva microbiome from different climate zones: alaska, germany, and africa
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4272767/
https://www.ncbi.nlm.nih.gov/pubmed/25515234
http://dx.doi.org/10.1186/s12866-014-0316-1
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