Blog
About

  • Record: found
  • Abstract: found
  • Article: not found

Human gut microbiome viewed across age and geography

Read this article at

ScienceOpenPublisherPMC
Bookmark
      There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

      Abstract

      Gut microbial communities represent one source of human genetic and metabolic diversity. To examine how gut microbiomes differ between human populations when viewed from the perspective of component microbial lineages, encoded metabolic functions, stage of postnatal development, and environmental exposures, we characterized bacterial species present in fecal samples obtained from 531 individuals representing healthy Amerindians from the Amazonas of Venezuela, residents of rural Malawian communities, and inhabitants of USA metropolitan areas, as well as the gene content of 110 of their microbiomes. This cohort encompassed infants, children, teenagers and adults, parents and offspring, and included mono- and dizygotic twins. Shared features of the functional maturation of the gut microbiome were identified during the first three years of life in all three populations, including age-associated changes in the representation of genes involved in vitamin biosynthesis and metabolism. Pronounced differences in bacterial species assemblages and functional gene repertoires were noted between individuals residing in the USA compared to the other two countries. These distinctive features are evident in early infancy as well as adulthood. In addition, the similarity of fecal microbiomes among family members extends across cultures. These findings underscore the need to consider the microbiome when evaluating human development, nutritional needs, physiological variations, and the impact of Westernization.

      Related collections

      Most cited references 39

      • Record: found
      • Abstract: not found
      • Article: not found

      QIIME allows analysis of high-throughput community sequencing data.

        Bookmark
        • Record: found
        • Abstract: not found
        • Article: not found

        A human gut microbial gene catalogue established by metagenomic sequencing.

        To understand the impact of gut microbes on human health and well-being it is crucial to assess their genetic potential. Here we describe the Illumina-based metagenomic sequencing, assembly and characterization of 3.3 million non-redundant microbial genes, derived from 576.7 gigabases of sequence, from faecal samples of 124 European individuals. The gene set, approximately 150 times larger than the human gene complement, contains an overwhelming majority of the prevalent (more frequent) microbial genes of the cohort and probably includes a large proportion of the prevalent human intestinal microbial genes. The genes are largely shared among individuals of the cohort. Over 99% of the genes are bacterial, indicating that the entire cohort harbours between 1,000 and 1,150 prevalent bacterial species and each individual at least 160 such species, which are also largely shared. We define and describe the minimal gut metagenome and the minimal gut bacterial genome in terms of functions present in all individuals and most bacteria, respectively.
          Bookmark
          • Record: found
          • Abstract: found
          • Article: not found

          UniFrac: a new phylogenetic method for comparing microbial communities.

          We introduce here a new method for computing differences between microbial communities based on phylogenetic information. This method, UniFrac, measures the phylogenetic distance between sets of taxa in a phylogenetic tree as the fraction of the branch length of the tree that leads to descendants from either one environment or the other, but not both. UniFrac can be used to determine whether communities are significantly different, to compare many communities simultaneously using clustering and ordination techniques, and to measure the relative contributions of different factors, such as chemistry and geography, to similarities between samples. We demonstrate the utility of UniFrac by applying it to published 16S rRNA gene libraries from cultured isolates and environmental clones of bacteria in marine sediment, water, and ice. Our results reveal that (i) cultured isolates from ice, water, and sediment resemble each other and environmental clone sequences from sea ice, but not environmental clone sequences from sediment and water; (ii) the geographical location does not correlate strongly with bacterial community differences in ice and sediment from the Arctic and Antarctic; and (iii) bacterial communities differ between terrestrially impacted seawater (whether polar or temperate) and warm oligotrophic seawater, whereas those in individual seawater samples are not more similar to each other than to those in sediment or ice samples. These results illustrate that UniFrac provides a new way of characterizing microbial communities, using the wealth of environmental rRNA sequences, and allows quantitative insight into the factors that underlie the distribution of lineages among environments.
            Bookmark

            Author and article information

            Affiliations
            [1 ]Center for Genome Sciences and Systems Biology, Washington University in St. Louis
            [2 ]Department of Pediatrics, Washington University in St. Louis
            [3 ]Department of Psychiatry, Washington University in St. Louis
            [4 ]Department of Biology, University of Puerto Rico Rio Piedras, Puerto Rico
            [5 ]Venezuelan Institute of Scientific Research (IVIC), Caracas
            [6 ]Venezuela, Amazonic Center for Research and Control of Tropical Diseases (CAICET), Puerto Ayacucho, Amazonas, Venezuela
            [7 ]Department of Pediatrics, University of Pennsylvania
            [8 ]Department of Chemistry and Biochemistry, University of Colorado, Boulder
            [9 ]Howard Hughes Medical Institute, University of Colorado, Boulder
            Author notes
            Address correspondence to: jgordon@ 123456wustl.edu
            [*]

            Current address: Department of Computer Science, Northern Arizona University, Flagstaff, AZ 86011, USA

            Journal
            0410462
            6011
            Nature
            Nature
            Nature
            0028-0836
            1476-4687
            22 March 2012
            09 May 2012
            14 December 2012
            : 486
            : 7402
            : 222-227
            22699611
            3376388
            10.1038/nature11053
            NIHMS365354

            Users may view, print, copy, download and text and data- mine the content in such documents, for the purposes of academic research, subject always to the full Conditions of use: http://www.nature.com/authors/editorial_policies/license.html#terms

            Funding
            Funded by: National Institute of Diabetes and Digestive and Kidney Diseases : NIDDK
            Award ID: P01 DK078669-05 || DK
            Categories
            Article

            Uncategorized

            Comments

            Comment on this article