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Methodological considerations for the identification of choline and carnitine-degrading bacteria in the gut

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Methodological considerations for the identification of choline and carnitine-degrading bacteria in the gut. / Jameson, Eleanor; Quareshy, Mussa; Chen, Yin.
In: Methods (San Diego, Calif.), Vol. 149, 01.10.2018, p. 42-48.

Research output: Contribution to journal › Review article › peer-review

HarvardHarvard

Jameson, E, Quareshy, M & Chen, Y 2018, 'Methodological considerations for the identification of choline and carnitine-degrading bacteria in the gut', Methods (San Diego, Calif.), vol. 149, pp. 42-48. https://doi.org/10.1016/j.ymeth.2018.03.012

APA

Jameson, E., Quareshy, M., & Chen, Y. (2018). Methodological considerations for the identification of choline and carnitine-degrading bacteria in the gut. Methods (San Diego, Calif.), 149, 42-48. https://doi.org/10.1016/j.ymeth.2018.03.012

CBE

Jameson E, Quareshy M, Chen Y. 2018. Methodological considerations for the identification of choline and carnitine-degrading bacteria in the gut. Methods (San Diego, Calif.). 149:42-48. https://doi.org/10.1016/j.ymeth.2018.03.012

MLA

Jameson, Eleanor, Mussa Quareshy and Yin Chen. "Methodological considerations for the identification of choline and carnitine-degrading bacteria in the gut". Methods (San Diego, Calif.). 2018, 149. 42-48. https://doi.org/10.1016/j.ymeth.2018.03.012

VancouverVancouver

Jameson E, Quareshy M, Chen Y. Methodological considerations for the identification of choline and carnitine-degrading bacteria in the gut. Methods (San Diego, Calif.). 2018 Oct 1;149:42-48. Epub 2018 Apr 19. doi: 10.1016/j.ymeth.2018.03.012

Author

Jameson, Eleanor ; Quareshy, Mussa ; Chen, Yin. / Methodological considerations for the identification of choline and carnitine-degrading bacteria in the gut. In: Methods (San Diego, Calif.). 2018 ; Vol. 149. pp. 42-48.

RIS

TY - JOUR

T1 - Methodological considerations for the identification of choline and carnitine-degrading bacteria in the gut

AU - Jameson, Eleanor

AU - Quareshy, Mussa

AU - Chen, Yin

N1 - Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.

PY - 2018/10/1

Y1 - 2018/10/1

N2 - The bacterial formation of trimethylamine (TMA) has been linked to cardiovascular disease. This review focuses on the methods employed to investigate the identity of the bacteria responsible for the formation of TMA from dietary choline and carnitine in the human gut. Recent studies have revealed the metabolic pathways responsible for bacterial TMA production, primarily the anaerobic glycyl radical-containing, choline-TMA lyase, CutC and the aerobic carnitine monooxygenase, CntA. Identification of these enzymes has enabled bioinformatics approaches to screen both human-associated bacterial isolate genomes and whole gut metagenomes to determine which bacteria are responsible for TMA formation in the human gut. We centre on several key methodological aspects for identifying the TMA-producing bacteria and report how these pathways can be identified in human gut microbiota through bioinformatics analysis of available bacterial genomes and gut metagenomes.

AB - The bacterial formation of trimethylamine (TMA) has been linked to cardiovascular disease. This review focuses on the methods employed to investigate the identity of the bacteria responsible for the formation of TMA from dietary choline and carnitine in the human gut. Recent studies have revealed the metabolic pathways responsible for bacterial TMA production, primarily the anaerobic glycyl radical-containing, choline-TMA lyase, CutC and the aerobic carnitine monooxygenase, CntA. Identification of these enzymes has enabled bioinformatics approaches to screen both human-associated bacterial isolate genomes and whole gut metagenomes to determine which bacteria are responsible for TMA formation in the human gut. We centre on several key methodological aspects for identifying the TMA-producing bacteria and report how these pathways can be identified in human gut microbiota through bioinformatics analysis of available bacterial genomes and gut metagenomes.

KW - Amino Acid Sequence

KW - Cardiovascular Diseases/etiology

KW - Carnitine/adverse effects

KW - Choline/adverse effects

KW - Computational Biology/methods

KW - Diet/adverse effects

KW - Gastrointestinal Microbiome/physiology

KW - Humans

KW - Klebsiella pneumoniae/genetics

KW - Methylamines/adverse effects

KW - Proteus mirabilis/genetics

U2 - 10.1016/j.ymeth.2018.03.012

DO - 10.1016/j.ymeth.2018.03.012

M3 - Review article

C2 - 29684641

VL - 149

SP - 42

EP - 48

JO - Methods (San Diego, Calif.)

JF - Methods (San Diego, Calif.)

SN - 1046-2023

ER -