31
views
0
recommends
+1 Recommend
0 collections
    0
    shares
      • Record: found
      • Abstract: found
      • Article: found
      Is Open Access

      Marine mammals harbor unique microbiotas shaped by and yet distinct from the sea

      research-article

      Read this article at

      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

          Marine mammals play crucial ecological roles in the oceans, but little is known about their microbiotas. Here we study the bacterial communities in 337 samples from 5 body sites in 48 healthy dolphins and 18 healthy sea lions, as well as those of adjacent seawater and other hosts. The bacterial taxonomic compositions are distinct from those of other mammals, dietary fish and seawater, are highly diverse and vary according to body site and host species. Dolphins harbour 30 bacterial phyla, with 25 of them in the mouth, several abundant but poorly characterized Tenericutes species in gastric fluid and a surprisingly paucity of Bacteroidetes in distal gut. About 70% of near-full length bacterial 16S ribosomal RNA sequences from dolphins are unique. Host habitat, diet and phylogeny all contribute to variation in marine mammal distal gut microbiota composition. Our findings help elucidate the factors structuring marine mammal microbiotas and may enhance monitoring of marine mammal health.

          Abstract

          Little is known about the microbiota of marine mammals, despite the crucial ecological roles played by these animals. Here, Bik et al. describe the bacterial communities associated with various body sites in dolphins and sea lions, as well as the microbiota of their dietary fish and adjacent seawater.

          Related collections

          Most cited references41

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

          Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex.

          We constructed error-correcting DNA barcodes that allow one run of a massively parallel pyrosequencer to process up to 1,544 samples simultaneously. Using these barcodes we processed bacterial 16S rRNA gene sequences representing microbial communities in 286 environmental samples, corrected 92% of sample assignment errors, and thus characterized nearly as many 16S rRNA genes as have been sequenced to date by Sanger sequencing.
            Bookmark
            • Record: found
            • Abstract: found
            • Article: not found

            NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes

            Microbiologists conducting surveys of bacterial and archaeal diversity often require comparative alignments of thousands of 16S rRNA genes collected from a sample. The computational resources and bioinformatics expertise required to construct such an alignment has inhibited high-throughput analysis. It was hypothesized that an online tool could be developed to efficiently align thousands of 16S rRNA genes via the NAST (Nearest Alignment Space Termination) algorithm for creating multiple sequence alignments (MSA). The tool was implemented with a web-interface at . Each user-submitted sequence is compared with Greengenes' ‘Core Set’, comprising ∼10 000 aligned non-chimeric sequences representative of the currently recognized diversity among bacteria and archaea. User sequences are oriented and paired with their closest match in the Core Set to serve as a template for inserting gap characters. Non-16S data (sequence from vector or surrounding genomic regions) are conveniently removed in the returned alignment. From the resulting MSA, distance matrices can be calculated for diversity estimates and organisms can be classified by taxonomy. The ability to align and categorize large sequence sets using a simple interface has enabled researchers with various experience levels to obtain bacterial and archaeal community profiles.
              Bookmark
              • Record: found
              • Abstract: found
              • Article: not found

              Bacterial diversity in the oral cavity of 10 healthy individuals.

              The composition of the oral microbiota from 10 individuals with healthy oral tissues was determined using culture-independent techniques. From each individual, 26 specimens, each from different oral sites at a single point in time, were collected and pooled. An 11th pool was constructed using portions of the subgingival specimens from all 10 individuals. The 16S ribosomal RNA gene was amplified using broad-range bacterial primers, and clone libraries from the individual and subgingival pools were constructed. From a total of 11,368 high-quality, nonchimeric, near full-length sequences, 247 species-level phylotypes (using a 99% sequence identity threshold) and 9 bacterial phyla were identified. At least 15 bacterial genera were conserved among all 10 individuals, with significant interindividual differences at the species and strain level. Comparisons of these oral bacterial sequences with near full-length sequences found previously in the large intestines and feces of other healthy individuals suggest that the mouth and intestinal tract harbor distinct sets of bacteria. Co-occurrence analysis showed significant segregation of taxa when community membership was examined at the level of genus, but not at the level of species, suggesting that ecologically significant, competitive interactions are more apparent at a broader taxonomic level than species. This study is one of the more comprehensive, high-resolution analyses of bacterial diversity within the healthy human mouth to date, and highlights the value of tools from macroecology for enhancing our understanding of bacterial ecology in human health.
                Bookmark

                Author and article information

                Journal
                Nat Commun
                Nat Commun
                Nature Communications
                Nature Publishing Group
                2041-1723
                03 February 2016
                2016
                : 7
                : 10516
                Affiliations
                [1 ]Department of Microbiology and Immunology, Stanford University School of Medicine , Stanford, California 94305, USA
                [2 ]Veterans Affairs Palo Alto Health Care System , Palo Alto, California 94304, USA
                [3 ]Department of Statistics, Stanford University , Stanford, California 94305, USA
                [4 ]Sarasota Dolphin Research Program, Chicago Zoological Society, c/o Mote Marine Laboratory , Sarasota, Florida 34236, USA
                [5 ]Translational Medicine and Research Program, National Marine Mammal Foundation , San Diego, California 92106, USA
                [6 ]Space and Naval Warfare Systems Center Pacific , San Diego, California 92152, USA
                [7 ]Department of Medicine (Infectious Diseases and Geographic Medicine), Stanford University School of Medicine , Stanford, California 94305, USA
                Author notes
                Author information
                http://orcid.org/0000-0001-5477-0324
                http://orcid.org/0000-0001-9793-4181
                Article
                ncomms10516
                10.1038/ncomms10516
                4742810
                26839246
                1c0a077b-78ca-44f7-9d84-7be51e7dfcd1
                Copyright © 2016, Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.

                This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article's Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/

                History
                : 04 August 2015
                : 18 December 2015
                Categories
                Article

                Uncategorized
                Uncategorized

                Comments

                Comment on this article