The human gastrointestinal tract is home to diverse mutualistic microorganisms that perform important metabolic functions supporting gastrointestinal health. Recent metagenomic and metabolomic research has identified a variety of microbial metabolic pathways active in the human gut. A central intermediate in these metabolic processes is hydrogen gas (H2), which is consumed and produced by diverse gastrointestinal microorganisms through the action of hydrogenases. H2 metabolism has been linked to various health issues (such as colorectal cancer and IBD) and H2 is often used as a marker for gut conditions via the H2 breath test. Moreover, pathogens within the orders Enterobacterales, Campylobacterales, and Clostridiales depend on H2 metabolism for pathogenesis. Despite these associations, the enzymes and organisms responsible for H2 cycling have not been systematically investigated and remain largely unresolved.
Here we aimed to uncover the key genetic determinants of microbial hydrogen cycling within the human gastrointestinal tract. We analysed ~1000 gut-isolate genomes obtained from human faecal samples to identify hydrogenase and other metabolic genes involved in H2 cycling. Interestingly, the results revealed that the [FeFe] Group B hydrogenase is the most abundant hydrogenase in the human gut. As the function of this hydrogenase is currently unresolved, this suggests there may be large aspects of hydrogen cycling in the human gut that remain uncharacterised. To assess the function of the [FeFe] Group B hydrogenase in vitro, we ran gas chromatography assays on 10 cultured gut isolates representatives from Bacteroides, Firmicutes, Proteobacteria and Fusobacteria phyla that all encoded this hydrogenase. The results suggested that the [FeFe] Group B hydrogenase acts as a functional H2-evolving hydrogenase during fermentation and is highly likely to be responsible for production of large amounts of H2 gas within the human gut. The novel findings presented here demonstrate that our current understanding of H2 cycling in the human GI tract is incomplete, and further exploration into how this gas is produced and consumed by the gut microbiota may uncover more information regarding its links to human health.