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Metagenomic data-mining reveals contrasting microbial populations responsible for trimethylamine formation in human gut and marine ecosystems
Existing metagenome datasets from many different environments contain untapped potential for understanding metabolic pathways and their biological impact. Our interest lies in the formation of trimethylamine (TMA), a key metabolite in both human health and climate change. Here, we focus on bacterial...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Microbiology Society
2016
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5537630/ https://www.ncbi.nlm.nih.gov/pubmed/28785417 http://dx.doi.org/10.1099/mgen.0.000080 |
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author | Jameson, Eleanor Doxey, Andrew C. Airs, Ruth Purdy, Kevin J. Murrell, J. Colin Chen, Yin |
author_facet | Jameson, Eleanor Doxey, Andrew C. Airs, Ruth Purdy, Kevin J. Murrell, J. Colin Chen, Yin |
author_sort | Jameson, Eleanor |
collection | PubMed |
description | Existing metagenome datasets from many different environments contain untapped potential for understanding metabolic pathways and their biological impact. Our interest lies in the formation of trimethylamine (TMA), a key metabolite in both human health and climate change. Here, we focus on bacterial degradation pathways for choline, carnitine, glycine betaine and trimethylamine N-oxide (TMAO) to TMA in human gut and marine metagenomes. We found the TMAO reductase pathway was the most prevalent pathway in both environments. Proteobacteria were found to contribute the majority of the TMAO reductase pathway sequences, except in the stressed gut, where Actinobacteria dominated. Interestingly, in the human gut metagenomes, a high proportion of the Proteobacteria hits were accounted for by the genera Klebsiella and Escherichia. Furthermore Klebsiella and Escherichia harboured three of the four potential TMA-production pathways (choline, carnitine and TMAO), suggesting they have a key role in TMA cycling in the human gut. In addition to the intensive TMAO–TMA cycling in the marine environment, our data suggest that carnitine-to-TMA transformation plays an overlooked role in aerobic marine surface waters, whereas choline-to-TMA transformation is important in anaerobic marine sediments. Our study provides new insights into the potential key microbes and metabolic pathways for TMA formation in two contrasting environments. |
format | Online Article Text |
id | pubmed-5537630 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
publisher | Microbiology Society |
record_format | MEDLINE/PubMed |
spelling | pubmed-55376302017-08-07 Metagenomic data-mining reveals contrasting microbial populations responsible for trimethylamine formation in human gut and marine ecosystems Jameson, Eleanor Doxey, Andrew C. Airs, Ruth Purdy, Kevin J. Murrell, J. Colin Chen, Yin Microb Genom Short Paper Existing metagenome datasets from many different environments contain untapped potential for understanding metabolic pathways and their biological impact. Our interest lies in the formation of trimethylamine (TMA), a key metabolite in both human health and climate change. Here, we focus on bacterial degradation pathways for choline, carnitine, glycine betaine and trimethylamine N-oxide (TMAO) to TMA in human gut and marine metagenomes. We found the TMAO reductase pathway was the most prevalent pathway in both environments. Proteobacteria were found to contribute the majority of the TMAO reductase pathway sequences, except in the stressed gut, where Actinobacteria dominated. Interestingly, in the human gut metagenomes, a high proportion of the Proteobacteria hits were accounted for by the genera Klebsiella and Escherichia. Furthermore Klebsiella and Escherichia harboured three of the four potential TMA-production pathways (choline, carnitine and TMAO), suggesting they have a key role in TMA cycling in the human gut. In addition to the intensive TMAO–TMA cycling in the marine environment, our data suggest that carnitine-to-TMA transformation plays an overlooked role in aerobic marine surface waters, whereas choline-to-TMA transformation is important in anaerobic marine sediments. Our study provides new insights into the potential key microbes and metabolic pathways for TMA formation in two contrasting environments. Microbiology Society 2016-09-20 /pmc/articles/PMC5537630/ /pubmed/28785417 http://dx.doi.org/10.1099/mgen.0.000080 Text en © 2016 The Authors http://creativecommons.org/licenses/by/4.0/http://creativecommons.org/licenses/by/4.0/ This is an open access article under the terms of the Creative Commons Attribution 4.04.0 International License (http://creativecommons.org/licenses/by/4.0/http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution and reproduction in any medium, provided the original author and source are credited. |
spellingShingle | Short Paper Jameson, Eleanor Doxey, Andrew C. Airs, Ruth Purdy, Kevin J. Murrell, J. Colin Chen, Yin Metagenomic data-mining reveals contrasting microbial populations responsible for trimethylamine formation in human gut and marine ecosystems |
title | Metagenomic data-mining reveals contrasting microbial populations responsible for trimethylamine formation in human gut and marine ecosystems |
title_full | Metagenomic data-mining reveals contrasting microbial populations responsible for trimethylamine formation in human gut and marine ecosystems |
title_fullStr | Metagenomic data-mining reveals contrasting microbial populations responsible for trimethylamine formation in human gut and marine ecosystems |
title_full_unstemmed | Metagenomic data-mining reveals contrasting microbial populations responsible for trimethylamine formation in human gut and marine ecosystems |
title_short | Metagenomic data-mining reveals contrasting microbial populations responsible for trimethylamine formation in human gut and marine ecosystems |
title_sort | metagenomic data-mining reveals contrasting microbial populations responsible for trimethylamine formation in human gut and marine ecosystems |
topic | Short Paper |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5537630/ https://www.ncbi.nlm.nih.gov/pubmed/28785417 http://dx.doi.org/10.1099/mgen.0.000080 |
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