title: Comparative analysis of the human saliva microbiome from different climate zones: Alaska, Germany, and Africa.
abstract: 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.
  
  
  CONCLUSIONS
  Overall, this study illustrates the distinctiveness of the saliva microbiome of human groups living under very different climatic conditions.
authors.affiliation: Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103, Leipzig, Germany. jingli1978@gmail.com.|Max Planck Independent Research Group on Population Genomics, Chinese Academy of Sciences and Max Planck Society (CAS-MPG) Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, 200031, China. jingli1978@gmail.com.
authors.forename: Jing
authors.initials: J
authors.lastname: Li
authors.affiliation: Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103, Leipzig, Germany. dquinque@googlemail.com.|Current address: Department of Genetics, Harvard Medical School, 77 Louis Pasteur Avenue, Boston, MA, 02115, USA. dquinque@googlemail.com.
authors.forename: Dominique
authors.initials: D
authors.lastname: Quinque
authors.affiliation: Division of Virology, Institute of Medical Microbiology, RWTH Aachen University Hospital, Pauwelsstrasse 30, D-52057, Aachen, Germany. jhorz@ukaachen.de.
authors.forename: Hans-Peter
authors.initials: HP
authors.lastname: Horz
authors.affiliation: Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103, Leipzig, Germany. fengzys@gmail.com.
authors.forename: Mingkun
authors.initials: M
authors.lastname: Li
authors.affiliation: Division of Endocrinology, Metabolism, and Molecular Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA. m-rzhetskaya@northwestern.edu.
authors.forename: Margarita
authors.initials: M
authors.lastname: Rzhetskaya
authors.affiliation: Division of Endocrinology, Metabolism, and Molecular Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA. jenniferraff@utexas.edu.|Current address: Department of Anthropology, University of Texas, Austin, TX, 78712, USA. jenniferraff@utexas.edu.
authors.forename: Jennifer A
authors.initials: JA
authors.lastname: Raff
authors.affiliation: Division of Endocrinology, Metabolism, and Molecular Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA. ghayes@northwestern.edu.|Department of Anthropology, Northwestern University, Evanston, IL, 60208, USA. ghayes@northwestern.edu.|Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA. ghayes@northwestern.edu.
authors.forename: M Geoffrey
authors.initials: MG
authors.lastname: Hayes
authors.affiliation: Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103, Leipzig, Germany. stonekg@eva.mpg.de.
authors.forename: Mark
authors.initials: M
authors.lastname: Stoneking
mesh_terms: D000328:Adult; D000349:Africa; D000413:Alaska; D000818:Animals; D001419:Bacteria / Q000145:classification* / Q000235:genetics; D002980:Climate; D016000:Cluster Analysis; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D004275:DNA, Ribosomal / Q000737:chemistry / Q000235:genetics; D005260:Female; D005858:Germany; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D008297:Male; D054892:Metagenome; D064307:Microbiota; D008969:Molecular Sequence Data; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D012463:Saliva / Q000382:microbiology*; D017422:Sequence Analysis, DNA; D055815:Young Adult
chemical_list: D004269:DNA, Bacterial; D004275:DNA, Ribosomal; D012336:RNA, Ribosomal, 16S