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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...

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Autores principales: Jameson, Eleanor, Doxey, Andrew C., Airs, Ruth, Purdy, Kevin J., Murrell, J. Colin, Chen, Yin
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Microbiology Society 2016
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.
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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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