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

Abstract

Although 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, 79% of these prokaryotes commonly lack a key gene for WLP, which encodes enzyme that synthesizes formate from CO2 and reductants such as 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. In addition to degenerated WLP, seven genes neighboring the CODH gene were found, which may reflect diverse utilization of CO in the human gut. 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, there were seven other genes neighboring CODH in the human gut CO-utilizers, suggesting various CO utilization. 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 CODH/ACS-bearing genomes from environments without host-association (Inoue et al., 2022) are listed in Table S1. Metatranscriptomic datasets were downloaded from the NCBI Sequence Read Archive (SRA) under the Bioproject accession numbers PRJNA354235 and PRJNA707065 and their accession IDs are listed in Table S2.