publication . Article . 2018

Latent environment allocation of microbial community data

Higashi, Koichi; Suzuki, Shinya; Kurosawa, Shin; Mori, Hiroshi; Kurokawa, Ken;
Open Access English
  • Published: 01 Jun 2018 Journal: PLoS Computational Biology, volume 14, issue 6 (issn: 1553-734X, eissn: 1553-7358, Copyright policy)
  • Publisher: Public Library of Science
Abstract
As data for microbial community structures found in various environments has increased, studies have examined the relationship between environmental labels given to retrieved microbial samples and their community structures. However, because environments continuously change over time and space, mixed states of some environments and its effects on community formation should be considered, instead of evaluating effects of discrete environmental categories. Here we applied a hierarchical Bayesian model to paired datasets containing more than 30,000 samples of microbial community structures and sample description documents. From the training results, we extracted la...
Subjects
free text keywords: Bodies of Water, Research Article, Earth Sciences, Freshwater Environments, Data Management, Ecology and Environmental Sciences, Taxonomy, Ecology, Marine and Aquatic Sciences, Genetics, Controlled Vocabularies, Genomics, Microbial Taxonomy, Sequence Analysis, Aquatic Environments, Database and Informatics Methods, Rivers, Sequence Databases, Biology and Life Sciences, Computer and Information Sciences, Biological Databases, Hydrology, Community Ecology, Research and Analysis Methods, Microbiology, Microbiome, Microbial Genomics, QH301-705.5, Surface Water, Medical Microbiology, Community Structure, Metagenomics, Bioinformatics, Biology (General)
64 references, page 1 of 5

1 Henschel A, Anwar MZ, Manohar V. Comprehensive Meta-analysis of Ontology Annotated 16S rRNA Profiles Identifies Beta Diversity Clusters of Environmental Bacterial Communities. PLoS Comput Biol. 2015;11: 1–24. doi: 10.1371/journal.pcbi.1004468 26458130 [OpenAIRE] [PubMed]

2 Lozupone CA, Knight R. Global patterns in bacterial diversity. Proc Natl Acad Sci U S A. 2007;104: 11436–11440. doi: 10.1073/pnas.0611525104 17592124 [OpenAIRE] [PubMed]

3 Lozupone CA, Stombaugh J, Gonzalez A, Ackermann G, Wendel D, Vasquez-Baeza Y. Meta-analysis studi es of the human microbiota. Genome Res. 2013;23: 1704–1714. doi: 10.1101/gr.151803.112 23861384 [OpenAIRE] [PubMed]

4 Tamames J, Abellán JJ, Pignatelli M, Camacho A, Moya A. Environmental distribution of prokaryotic taxa. BMC Microbiol. 2010;10: 85 doi: 10.1186/1471-2180-10-85 20307274 [OpenAIRE] [PubMed]

5 Buttigieg PL, Morrison N, Smith B, Mungall CJ, Lewis SE, ENVO Consortium. The environment ontology: contextualising biological and biomedical entities. J Biomed Semantics. 2013;4: 43 doi: 10.1186/2041-1480-4-43 24330602 [OpenAIRE] [PubMed]

6 Buttigieg PL, Pafilis E, Lewis SE, Schildhauer MP, Walls RL, Mungall CJ. The environment ontology in 2016: bridging domains with increased scope, semantic density, and interoperation. J Biomed Semantics. Journal of Biomedical Semantics; 2016;7: 57 doi: 10.1186/s13326-016-0097-6 27664130 [OpenAIRE] [PubMed]

7 Arumugam M, Raes J, Pelletier E, Le P, Yamada T, Mende DR, et al Enterotypes of the human gut microbiome. Nature. 2011;473: 174–180. doi: 10.1038/nature09944 21508958 [OpenAIRE] [PubMed]

8 Zhou X, Brown CJ, Abdo Z, Davis CC, Hansmann MA, Joyce P, et al Differences in the composition of vaginal microbial communities found in healthy Caucasian and black women. ISME J. 2007;1: 121–133. doi: 10.1038/ismej.2007.12 18043622 [PubMed]

9 Ravel J, Gajer P, Abdo Z, Schneider GM, Koenig SSK, McCulle SL, et al Vaginal microbiome of reproductive-age women. Proc Natl Acad Sci. 2011;108: 4680–4687. doi: 10.1073/pnas.1002611107 20534435 [OpenAIRE] [PubMed]

10 Lax S, Smith D, Hampton-marcell J. Longitudinal analysis of microbial interactions between humans and indoor environment. Science (80-). 2014;345: 1048–1052. [OpenAIRE]

11 Herlemann DPR, Labrenz M, Ju K, Bertilsson S, Waniek JJ, Andersson AF. Transitions in bacterial communities along the 2000 km salinity gradient of the Baltic Sea. ISME J. 2011;5: 1571–1579. doi: 10.1038/ismej.2011.41 21472016 [OpenAIRE] [PubMed]

12 David LA, Maurice CF, Carmody RN, Gootenberg DB, Button JE, Wolfe BE, et al Diet rapidly and reproducibly alters the human gut microbiome. Nature. Nature Publishing Group; 2014;505: 559–63. doi: 10.1038/nature12820 24336217 [OpenAIRE] [PubMed]

13 Kato H, Mori H, Maruyama F, Toyoda A, Oshima K, Endo R, et al Time-series metagenomic analysis reveals robustness of soil microbiome against chemical disturbance. DNA Res. 2015;22: 413–424. doi: 10.1093/dnares/dsv023 26428854 [OpenAIRE] [PubMed]

14 Hermans SM, Buckley HL, Case BS, Curran-cournane F, Taylor M. Bacteria as Emerging Indicators of Soil Condition. Appl Environ Microbiol. 2017;83: 1–13.

15 Lau KEM, Washington VJ, Fan V, Neale MW, Lear G, Curran J, et al A novel bacterial community index to assess stream ecological health. Freshw Biol. 2015;60: 1988–2002. doi: 10.1111/fwb.12625

64 references, page 1 of 5
Abstract
As data for microbial community structures found in various environments has increased, studies have examined the relationship between environmental labels given to retrieved microbial samples and their community structures. However, because environments continuously change over time and space, mixed states of some environments and its effects on community formation should be considered, instead of evaluating effects of discrete environmental categories. Here we applied a hierarchical Bayesian model to paired datasets containing more than 30,000 samples of microbial community structures and sample description documents. From the training results, we extracted la...
Subjects
free text keywords: Bodies of Water, Research Article, Earth Sciences, Freshwater Environments, Data Management, Ecology and Environmental Sciences, Taxonomy, Ecology, Marine and Aquatic Sciences, Genetics, Controlled Vocabularies, Genomics, Microbial Taxonomy, Sequence Analysis, Aquatic Environments, Database and Informatics Methods, Rivers, Sequence Databases, Biology and Life Sciences, Computer and Information Sciences, Biological Databases, Hydrology, Community Ecology, Research and Analysis Methods, Microbiology, Microbiome, Microbial Genomics, QH301-705.5, Surface Water, Medical Microbiology, Community Structure, Metagenomics, Bioinformatics, Biology (General)
64 references, page 1 of 5

1 Henschel A, Anwar MZ, Manohar V. Comprehensive Meta-analysis of Ontology Annotated 16S rRNA Profiles Identifies Beta Diversity Clusters of Environmental Bacterial Communities. PLoS Comput Biol. 2015;11: 1–24. doi: 10.1371/journal.pcbi.1004468 26458130 [OpenAIRE] [PubMed]

2 Lozupone CA, Knight R. Global patterns in bacterial diversity. Proc Natl Acad Sci U S A. 2007;104: 11436–11440. doi: 10.1073/pnas.0611525104 17592124 [OpenAIRE] [PubMed]

3 Lozupone CA, Stombaugh J, Gonzalez A, Ackermann G, Wendel D, Vasquez-Baeza Y. Meta-analysis studi es of the human microbiota. Genome Res. 2013;23: 1704–1714. doi: 10.1101/gr.151803.112 23861384 [OpenAIRE] [PubMed]

4 Tamames J, Abellán JJ, Pignatelli M, Camacho A, Moya A. Environmental distribution of prokaryotic taxa. BMC Microbiol. 2010;10: 85 doi: 10.1186/1471-2180-10-85 20307274 [OpenAIRE] [PubMed]

5 Buttigieg PL, Morrison N, Smith B, Mungall CJ, Lewis SE, ENVO Consortium. The environment ontology: contextualising biological and biomedical entities. J Biomed Semantics. 2013;4: 43 doi: 10.1186/2041-1480-4-43 24330602 [OpenAIRE] [PubMed]

6 Buttigieg PL, Pafilis E, Lewis SE, Schildhauer MP, Walls RL, Mungall CJ. The environment ontology in 2016: bridging domains with increased scope, semantic density, and interoperation. J Biomed Semantics. Journal of Biomedical Semantics; 2016;7: 57 doi: 10.1186/s13326-016-0097-6 27664130 [OpenAIRE] [PubMed]

7 Arumugam M, Raes J, Pelletier E, Le P, Yamada T, Mende DR, et al Enterotypes of the human gut microbiome. Nature. 2011;473: 174–180. doi: 10.1038/nature09944 21508958 [OpenAIRE] [PubMed]

8 Zhou X, Brown CJ, Abdo Z, Davis CC, Hansmann MA, Joyce P, et al Differences in the composition of vaginal microbial communities found in healthy Caucasian and black women. ISME J. 2007;1: 121–133. doi: 10.1038/ismej.2007.12 18043622 [PubMed]

9 Ravel J, Gajer P, Abdo Z, Schneider GM, Koenig SSK, McCulle SL, et al Vaginal microbiome of reproductive-age women. Proc Natl Acad Sci. 2011;108: 4680–4687. doi: 10.1073/pnas.1002611107 20534435 [OpenAIRE] [PubMed]

10 Lax S, Smith D, Hampton-marcell J. Longitudinal analysis of microbial interactions between humans and indoor environment. Science (80-). 2014;345: 1048–1052. [OpenAIRE]

11 Herlemann DPR, Labrenz M, Ju K, Bertilsson S, Waniek JJ, Andersson AF. Transitions in bacterial communities along the 2000 km salinity gradient of the Baltic Sea. ISME J. 2011;5: 1571–1579. doi: 10.1038/ismej.2011.41 21472016 [OpenAIRE] [PubMed]

12 David LA, Maurice CF, Carmody RN, Gootenberg DB, Button JE, Wolfe BE, et al Diet rapidly and reproducibly alters the human gut microbiome. Nature. Nature Publishing Group; 2014;505: 559–63. doi: 10.1038/nature12820 24336217 [OpenAIRE] [PubMed]

13 Kato H, Mori H, Maruyama F, Toyoda A, Oshima K, Endo R, et al Time-series metagenomic analysis reveals robustness of soil microbiome against chemical disturbance. DNA Res. 2015;22: 413–424. doi: 10.1093/dnares/dsv023 26428854 [OpenAIRE] [PubMed]

14 Hermans SM, Buckley HL, Case BS, Curran-cournane F, Taylor M. Bacteria as Emerging Indicators of Soil Condition. Appl Environ Microbiol. 2017;83: 1–13.

15 Lau KEM, Washington VJ, Fan V, Neale MW, Lear G, Curran J, et al A novel bacterial community index to assess stream ecological health. Freshw Biol. 2015;60: 1988–2002. doi: 10.1111/fwb.12625

64 references, page 1 of 5
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publication . Article . 2018

Latent environment allocation of microbial community data

Higashi, Koichi; Suzuki, Shinya; Kurosawa, Shin; Mori, Hiroshi; Kurokawa, Ken;