Desulfovibrio diazotrophica sp. nov., a sulphate reducing bacterium from the human gut capable of nitrogen fixation

Sulphate-reducing bacteria (SRB) are widespread in human guts, yet their expansion has been linked to colonic diseases. We report the isolation, genome sequencing, and physiological characterisation of a novel SRB species belonging to the class Deltaproteobacteria (QI0027T). Phylogenomic analysis revealed that the QI0027T strain belongs to the genus Desulfovibrio with its closest relative being Desulfovibrio legallii. Metagenomic sequencing of stool samples from 45 individuals, as well as comparison with 1690 Desulfovibrionaceae metagenome-assembled genomes, revealed the presence of QI0027T in at least 22 further individuals. QI0027T encoded nitrogen fixation genes and based on the acetylene reduction assay, actively fixed nitrogen. Transcriptomics revealed that QI0027T overexpressed 45 genes in nitrogen limiting conditions as compared to cultures supplemented with ammonia, including nitrogenases, an urea uptake system and the urease enzyme complex. To the best of our knowledge, this is the first Desulfovibrio human isolate for which nitrogen fixation has been demonstrated. This isolate was named Desulfovibrio diazotrophica sp. nov., referring to its ability to fix nitrogen (‘diazotroph’).ImportanceAnimals are often nitrogen limited and have evolved diverse strategies to capture biologically active nitrogen. These strategies range from amino acid transporters to stable associations with beneficial microbes that can provide fixed nitrogen. Although frequently thought as a nutrient-rich environment, nitrogen fixation can occur in the human gut of some populations, but so far it has been attributed mainly to Clostridia and Klebsiella based on sequencing. We have cultivated a novel Desulfovibrio from human gut origin which encoded, expressed and actively used nitrogen fixation genes, suggesting that some sulphate reducing bacteria could also play a role in the availability of nitrogen in the gut.