Bile acid oxidation byEggerthella lentastrains C592 and DSM 2243^T

Abstract

Strains of Eggerthella lenta are capable of oxidation-reduction reactions capable of oxidizing and epimerizing bile acid hydroxyl groups. Several genes encoding these enzymes, known as hydroxysteroid dehydrogenases (HSDH) have yet to be identified. It is also uncertain whether the products of E. lenta bile acid metabolism are further metabolized by other members of the gut microbiota. We characterized a novel human fecal isolate identified as E. lenta strain C592. The complete genome of E. lenta strain C592 was sequenced and comparative genomics with the type strain (DSM 2243) revealed high conservation, but some notable differences. E. lenta strain C592 falls into group III, possessing 3α, 3β, 7α, and 12α-hydroxysteroid dehydrogenase (HSDH) activity, as determined by mass spectrometry of thin layer chromatography (TLC) separated metabolites of primary and secondary bile acids. Incubation of E. lenta oxo-bile acid and iso-bile acid metabolites with whole-cells of the high-activity bile acid 7α-dehydroxylating bacterium, Clostridium scindens VPI 12708, resulted in minimal conversion of oxo-derivatives to lithocholic acid (LCA). Further, Iso-chenodeoxycholic acid (iso-CDCA; 3β,7α-dihydroxy-5β-cholan-24-oic acid) was not metabolized by C. scindens. We then located a gene encoding a novel 12α-HSDH in E. lenta DSM 2243, also encoded by strain C592, and the recombinant purified enzyme was characterized and substrate-specificity determined. Genomic analysis revealed genes encoding an Rnf complex (rnfABCDEG), an energy conserving hydrogenase (echABCDEF) complex, as well as what appears to be a complete Wood-Ljungdahl pathway. Our prediction that by changing the gas atmosphere from nitrogen to hydrogen, bile acid oxidation would be inhibited, was confirmed. These results suggest that E. lenta is an important bile acid metabolizing gut microbe and that the gas atmosphere may be an important and overlooked regulator of bile acid metabolism in the gut.

Metabolism of hydrogen gases and bile acids in the gut microbiome

“…We observed genes in both the methyl branch and the carbonyl branch of the Wood-Ljundhal Pathway in the genome of E. lenta DSM 2243. Acetogens require acetyl-CoA synthase/carbon monoxide dehydrogenase, and these genes are located in a gene cluster (Elen_3026-3030) in E. lenta DSM 2243 [75]. We also observed that iso-CDCA is highly resistant to bile acid 7a-dehydroxylation by C. scindens as this bacterium does not have 3b-HSDH.…”

“…The identity of genes encoding 7a-HSDH in E. lenta is still unknown, although reported in other gut bacteria such as C. scindens [56], Escherichia coli, and Bacteroides fragilis [47]. Intriguingly, when the gas atmosphere is replaced with hydrogen, bile acid oxidation is dramatically inhibited [75]. Intriguingly, when the gas atmosphere is replaced with hydrogen, bile acid oxidation is dramatically inhibited [75].…”

“…2). Acetogens require acetyl-CoA synthase/carbon monoxide dehydrogenase, and these genes are located in a gene cluster (Elen_3026-3030) in E. lenta DSM 2243 [75]. We also observe several hydrogenases including NiFe Group 4e energy conserving hydrogenase and NiFe Group 1a [25].…”

“…The Rnf complex is a proton-translocating ferrodoxin : NAD + oxidoreductase which establishes a proton-motive force and conserves energy via H +translocating ATPase under autotrophic conditions, using H 2 as an electron donor and CO 2 as electron acceptor [76]. Moreover, oxo-bile acids are also resistant to bile acid 7a-dehydroxylation [75]. It is typical of acetogens to bifurcate electrons from H 2 through FeFe hydrogenases, and it is not clear whether NiFe hydrogenases could participate in electron bifurcation.…”

“…Under strict anaerobic conditions (nitrogen atmosphere), we observed the complete conversion of primary and secondary bile acids to di-and tri-oxo derivatives, as well as the formation of small amounts of 3b-isomers. Intriguingly, when the gas atmosphere is replaced with hydrogen, bile acid oxidation is dramatically inhibited [75].…”