Diversity and prevalence of sulfate- and sulfite-reducing microorganisms in the human gut microbiome

Microorganisms capable of producing hydrogen sulfide have been associated with inflammatory diseases within the human gastrointestinal tract. Using a weighted protein homology search followed by phylogenetic fragment insertion, we sought to characterize the diversity and prevalence of microbial dissimilatory sulfite reduction genes (dsrAB) from over 70,000 human gut samples from publicly available metagenomic sequencing data. We found over 1,700 unique dsrAB sequences that were predominantly within two clades of sulfate- and sulfite-reducing microorganisms (SSRM): the well-studied Desulfovibrionaceae family and the Firmicutes group sensu lato (s.l.). We detected SSRM in over a third of adults, but very few children. Bilophila wadsworthia was the most prevalent SSRM, and along with other members of Desulfovibrionaceae, constituted the majority of SSRM found. About one fifth of people with SSRM contained members of the Firmicutes group s.l. Our study characterizes the overall diversity of SSRM in the human gut from different global populations while highlighting the potential importance of SSRM from the Firmicutes group, which have commonly been overlooked as contributors to microbial hydrogen sulfide production in the human gut.