Phylogenetic diversity of the carbon monoxide-utilizing prokaryotes and their divergent carbon monoxide metabolisms in the human gut microbiome

Abstract

AbstractAlthough the production of toxic CO within the human body has been detected, only a few CO-utilizing prokaryotes (CO utilizers) have been reported in the human gut, and their phylogenetic and physiological diversity remains unclear. Here, we unveiled more than thousand representative genomes originating from previously unexplored potential CO-utilizing prokaryotes, which contain CO dehydrogenase (CODH) genes. More than half of CODH-bearing prokaryotes possess genes for the autotrophic Wood–Ljungdahl pathway (WLP). However, 95% of these prokaryotes commonly lack a key gene for WLP, which encodes enzyme that synthesizes formate from CO2and H2, suggesting that they share a degenerated WLP. Instead, many were predicted to possess an alternative way of synthesizing formate from pyruvate, which is a product of glycolysis. This suggests that glycolysis may serve as a potential supplier of carbon and reducing power to degenerate WLP, which may no longer function as a complete autotrophic pathway. In addition to degenerated WLP, one of the seven predicted CO metabolic pathways involves CO oxidation, which is linked to nitrate reduction and oxaloacetate synthesis. Our findings reveal the unique and diverse nature of CO metabolism in the human gut microbiome, suggesting its potential contribution to CO consumption and gut homeostasis.Impact statementCarbon monoxide (CO)-utilizing prokaryotes mitigate the toxic impact of CO by consuming it as energy and/or carbon sources. In addition to various environments, CO is also produced via multiple routes, such as heme degradation, in the human body and accumulates in the gut. Revealing CO-utilizing prokaryotes and their CO metabolisms in the human gut would contribute to gaining insight into how microbial community functions are involved in maintaining human gut homeostasis. Nevertheless, the limited number of CO utilizers in the human gut microbiome have been reported. In our study, a significant proportion of human gut microbial genomes belonging to diverse phyla were revealed to be of potential CO-utilizing prokaryotes. Additionally, the majority of CO-utilizing prokaryote genomes in the human gut have potentially remodeled the Wood–Ljungdahl pathway (WLP), one of the most well-known autotrophic pathways, to the degenerated, heterotrophic form. Moreover, we predicted seven other CO-utilizing pathways encoded in the human gut CO-utilizers, including an unpreceded CO metabolism, which is involved in nitrate reduction and/or oxaloacetate synthesis. Our findings would pave the way for future explorations into microbial metabolic adaptations and their implications for human health.Data summaryThe human gut prokaryote genomes were downloaded from HumGut database (Hiseni et al. 2021;https://arken.nmbu.no/~larssn/humgut/). The accession numbers of other genomes containing CODH/ACS available from the NCBI reference sequence (RefSeq) database (http://www.ncbi.nlm.nih.gov/RefSeq/) are listed in Table S3.