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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Bibliographic Details
Published in:Microbial genomics 2016-09, Vol.2 (9), p.e000080-e000080
Main Authors: Jameson, Eleanor, Doxey, Andrew C, Airs, Ruth, Purdy, Kevin J, Murrell, J Colin, Chen, Yin
Format: Article
Language:English
Subjects:
Actinobacteria - enzymology
Actinobacteria - genetics
Data Mining
Ecosystem
Gastrointestinal Microbiome - genetics
Geologic Sediments - microbiology
Humans
Metagenomics
Methylamines - metabolism
Oxidoreductases, N-Demethylating - genetics
Proteobacteria - enzymology
Proteobacteria - genetics
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Summary: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 -oxide (TMAO) to TMA in human gut and marine metagenomes. We found the TMAO reductase pathway was the most prevalent pathway in both environments. were found to contribute the majority of the TMAO reductase pathway sequences, except in the stressed gut, where dominated. Interestingly, in the human gut metagenomes, a high proportion of the hits were accounted for by the genera and Furthermore and 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.
ISSN:2057-5858
2057-5858
DOI:10.1099/mgen.0.000080