Isolation and characterization of a novel choline degrading Citrobacter amalonaticus strain from the human gut

• Published in: Current research in microbial sciences Vol. 3; p. 100157
• Main Authors: Kashyap, Jyoti, Ringiesn, Jeffery R., Schwab, Nathan, Ferguson, Donald J.
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 01.01.2022; Elsevier
• Subjects: Anaerobic culturing; Choline; Choline trimethylamine lyase; CutC; Glycyl radical enzymes; Gut microbiome; Pyruvate-formate lyase; Quaternary amine; Research Paper; Trimethylamine; Anaerobic culturing; CutC; Trimethylamine; Choline; Glycyl radical enzymes; Quaternary amine; Choline trimethylamine lyase; Gut microbiome; Pyruvate-formate lyase
• ISSN: 2666-5174; 2666-5174
• DOI: 10.1016/j.crmicr.2022.100157

•A novel gut bacterium Citrobacter amalonaticus CJ25 isolated from healthy human fecal sample.•CJ25 grows on choline as the sole carbon and energy source.•CJ25 does not produce the harmful proatherogenic metabolite trimethylamine. Gut microbiota metabolism can have profound effects on human health. Choline, a quaternary amine (QA) highly abundant in our diet, is canonically cleaved by a glycyl radical enzyme, choline trimethylamine lyase (CutC), and its SAM-dependent radical activator, CutD. CutC cleaves choline to form trimethylamine (TMA) and acetaldehyde. TMA is oxidized to TMAO by FMO3 in the liver, which plays a role in causing atherosclerosis. We hypothesized that alternative pathways for choline degradation occur within gut microbes and that certain gut microbiota can anaerobically respire or ferment QAs, such as choline. Based on this prediction we established QA-supplemented enrichment cultures using fecal material from healthy volunteers as the inocula. We have isolated, from a choline-supplemented enrichment of a human fecal sample, a strain of Citrobacter amalonaticus, that we have designated CJ25. This strain is capable of anaerobically utilizing choline as its sole carbon and energy source. Its genome does not contain the cutCD genes or genes encoding any COG5598 methyltransferases. We have confirmed the degradation of choline and production of acetate by the organism during growth of the strain. However, we used multiple analytical methods to confirm that no TMA accumulated in the medium during growth. Hence, strain CJ25 is a unique bacterium that degrades choline without the production of the proatherogenic metabolite TMA. [Display omitted]