Subsistence strategies in traditional societies distinguish gut microbiomes

Recent studies suggest that gut microbiomes of urban-industrialized societies are different from those of traditional peoples. Here we examine the relationship between lifeways and gut microbiota through taxonomic and functional potential characterization of faecal samples from hunter-gatherer and traditional agriculturalist communities in Peru and an urban-industrialized community from the US. We find that in addition to taxonomic and metabolic differences between urban and traditional lifestyles, hunter-gatherers form a distinct sub-group among traditional peoples. As observed in previous studies, we find that Treponema are characteristic of traditional gut microbiomes. Moreover, through genome reconstruction (2.2–2.5 MB, coverage depth × 26–513) and functional potential characterization, we discover these Treponema are diverse, fall outside of pathogenic clades and are similar to Treponema succinifaciens, a known carbohydrate metabolizer in swine. Gut Treponema are found in non-human primates and all traditional peoples studied to date, suggesting they are symbionts lost in urban-industrialized societies.

[1]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[2]  B. Israel,et al.  Review of community-based research: assessing partnership approaches to improve public health. , 1998, Annual review of public health.

[3]  U. Göbel,et al.  Treponema brennaborense sp. nov., a novel spirochaete isolated from a dairy cow suffering from digital dermatitis. , 1999, International journal of systematic bacteriology.

[4]  David W. Fleck,et al.  Matses Indian rainforest habitat classification and mammalian diversity in Amazonian Peru , 2000 .

[5]  Amos Bairoch,et al.  The ENZYME database in 2000 , 2000, Nucleic Acids Res..

[6]  Leo Breiman,et al.  Random Forests , 2001, Machine Learning.

[7]  Jared R. Leadbetter,et al.  Description of Treponema azotonutricium sp. nov. and Treponema primitia sp. nov., the First Spirochetes Isolated from Termite Guts , 2004, Applied and Environmental Microbiology.

[8]  Tao Cai,et al.  Automated genome annotation and pathway identification using the KEGG Orthology (KO) as a controlled vocabulary , 2005, Bioinform..

[9]  David L. Wheeler,et al.  GenBank , 2015, Nucleic Acids Res..

[10]  Eoin L. Brodie,et al.  Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB , 2006, Applied and Environmental Microbiology.

[11]  R. Knight,et al.  Evolution of Mammals and Their Gut Microbes , 2008, Science.

[12]  F. Bushman,et al.  The Macaque Gut Microbiome in Health, Lentiviral Infection, and Chronic Enterocolitis , 2008, PLoS pathogens.

[13]  Geoff Holmes,et al.  Propositionalisation of Profile Hidden Markov Models for Biological Sequence Analysis , 2008, Australasian Conference on Artificial Intelligence.

[14]  Ning Ma,et al.  BLAST+: architecture and applications , 2009, BMC Bioinformatics.

[15]  Lu Wang,et al.  The NIH Human Microbiome Project. , 2009, Genome research.

[16]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[17]  Haixu Tang,et al.  FragGeneScan: predicting genes in short and error-prone reads , 2010, Nucleic acids research.

[18]  William A. Walters,et al.  QIIME allows analysis of high-throughput community sequencing data , 2010, Nature Methods.

[19]  S. Massart,et al.  Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa , 2010, Proceedings of the National Academy of Sciences.

[20]  P. Hugenholtz,et al.  Evolutionary Relationships of Wild Hominids Recapitulated by Gut Microbial Communities , 2010, PLoS biology.

[21]  Robert C. Edgar,et al.  BIOINFORMATICS APPLICATIONS NOTE , 2001 .

[22]  Lynne A. Goodwin,et al.  Complete genome sequence of Treponema succinifaciens type strain (6091T) , 2011, Standards in genomic sciences.

[23]  R. Knight,et al.  UniFrac: an effective distance metric for microbial community comparison , 2011, The ISME Journal.

[24]  R. Knight,et al.  Supervised classification of human microbiota. , 2011, FEMS microbiology reviews.

[25]  Ruth Ley,et al.  Unravelling the effects of the environment and host genotype on the gut microbiome , 2011, Nature Reviews Microbiology.

[26]  Rob Knight,et al.  Bayesian community-wide culture-independent microbial source tracking , 2011, Nature Methods.

[27]  Andreas Wilke,et al.  The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome , 2012, GigaScience.

[28]  William A. Walters,et al.  Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms , 2012, The ISME Journal.

[29]  Peter Williams,et al.  IMG: the integrated microbial genomes database and comparative analysis system , 2011, Nucleic Acids Res..

[30]  J. Clemente,et al.  Human gut microbiome viewed across age and geography , 2012, Nature.

[31]  M. Kanehisa,et al.  Evaluation method for the potential functionome harbored in the genome and metagenome , 2012, BMC Genomics.

[32]  Steven L Salzberg,et al.  Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.

[33]  F. Raymond,et al.  which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Ray Meta: scalable de novo metagenome assembly and profiling , 2012 .

[34]  Rob Knight,et al.  Insights from Characterizing Extinct Human Gut Microbiomes , 2012, PloS one.

[35]  M. Berriman,et al.  REAPR: a universal tool for genome assembly evaluation , 2013, Genome Biology.

[36]  Torsten Seemann,et al.  Prokka: rapid prokaryotic genome annotation , 2014, Bioinform..

[37]  R Core Team,et al.  R: A language and environment for statistical computing. , 2014 .

[38]  Amanda G. Henry,et al.  Gut microbiome of the Hadza hunter-gatherers , 2014, Nature Communications.

[39]  Holly M. Bik,et al.  PhyloSift: phylogenetic analysis of genomes and metagenomes , 2014, PeerJ.

[40]  Susumu Goto,et al.  Data, information, knowledge and principle: back to metabolism in KEGG , 2013, Nucleic Acids Res..