Scientists reveal the gut’s hidden hydrogen engine and how it falters in Crohn’s disease

A global research team has identified the enzyme that powers hydrogen production in healthy intestines and showed how its depletion reconnects microbial energy networks in Crohn’s disease, reshaping our understanding of gut metabolism.

Study: A widespread hydrogenase supports fermentative growth of gut bacteria in healthy humans. Image credit: crystal light / Shutterstock

In a recent study published in the journal Nature Microbiologyan international team of researchers leveraged a multifaceted study combining genomic, transcriptomic, and biochemical analyzes to identify the primary driver of fermentative molecular hydrogen (H2) production in healthy individuals. The molecular cycle of H2 is a vital metabolic process in the human gut, but the specific microbes and enzymes responsible for it remain unresolved.

Background

Decades of research have demonstrated that the human gut microbiome is a bustling metabolic reactor, comprising trillions of microbes that ferment the carbohydrates consumed. This process results in the production of energy, beneficial short-chain fatty acids, and vast amounts of gases, including molecular hydrogen (H2).

Conventionally considered a mere waste product, more recent research has revealed that molecular H2 is a critical food source for other microbes (known as “hydrogenotrophs”), thus making fermentation thermodynamically more favorable.

Dysbiosis, or imbalances in H2 production and consumption, are increasingly linked to serious health problems, from gas to irritable bowel syndrome (IBS) in infections and even in gastrointestinal cancers. In addition, some pathogens, such as Salmonellathey have been observed to “hijack” molecular H2 to fuel their invasion of the gut.

Unfortunately, despite its importance, the microbes and specific enzymes involved in H2 production and metabolism remain unresolved.

About the Study

The present study aims to address this knowledge gap and inform future research and gastrointestinal interventions by leveraging a multifaceted approach to elucidate the microbes and enzymes involved in H2 production from the ecosystem level down to the individual enzyme.

The study involved several sequential steps: First, a large-scale computational analysis of 300 faecal metagenomes and 78 metatranscriptomes was performed to elucidate the full range of hydrogen-related genes present and active in the healthy human gut. These findings were validated using 102 mucosal biopsy-enriched metagenomes from 42 donors. In addition, analyzes were focused on samples from the terminal ileum, cecum, and rectum to confirm consistency across all regions of the gut.

Then, to prove that these genes were functional, the study selected 19 different bacterial species from the human gut and grew them under anaerobic (oxygen-free) conditions to simulate gut conditions. Gas chromatography assays were used to accurately measure the amount of H2 gas produced by each bacterial strain over time.

Finally, biochemical assays (on bacterial cell extracts) were performed to elucidate the relationship between H2 production and pyruvate:ferredoxin oxidoreductase (PFOR) reaction, a key part of fermentation. Specifically, PFOR substrates (pyruvate and CoA) and inhibitors were added to see how H2 levels responded, supported by AlphaFold2 modeling, heterologous expression and spectroscopy/EPR evidence that validated the ferredoxin-like domain and catalytic function of the enzyme.

Study Findings

The findings of the study revealed, for the first time, that group B [FeFe]-The hydrogenase enzyme was, by far, the most dominant gene producing hydrogen in the healthy human gut. Abundance estimates found that group B genes averaged 0.75 ± 0.25 copies per genome, about 7.5 times more abundant than the group A1 enzyme (0.10 ± 0.09 copies), which was previously thought to be the major H2 producer.

Activity assays supported these findings, showing that group B genes were also the most highly transcribed (active) posttranscriptionally. Unexpectedly, however, activity tests were revealed Bacteroidesone of the most common genera in the gut, as a primary user of group B enzymes and therefore a major producer of H2, a previously underrecognized compound.

Analyzes of 19 bacterial isolates confirmed these findings, demonstrating that group B gene-encoding species, including seven different Bacteroides isolates, produced high levels of H2 gas. On the contrary, Bacteroides stercorisa species naturally lacking any hydrogenase genes was observed not to produce H2, consistent with the absence of detectable hydrogenase genes.

The most important is the comparison of healthy subjects with 46 patients with CD revealed that “healthy” group B hydrogenase was significantly depleted (P = 0.0023) and significantly replaced by other enzymes: group A1 hydrogenase increased 2.8-fold (P = 6.6 × 10-7), group 4a formate hydrogenylase (often found in E. coli) increased 5.2-fold (P = 6.8 × 10-6) and the 1d group [NiFe]-Hydrogenase increased 2.6-fold (P = 3.8 x 10-5). Genes for respiratory H2 oxidation, particularly group 1d [NiFe]-hydrogenases, also elevated, supporting a restructured hydrogen economy in his inflamed gut CD patients.

Expression also differed significantly between individuals and the combination [FeFe] subgroups did not differ significantly from each other CD and control samples, highlighting that these associations are correlated and require further mechanistic study. Respiratory hydrotrophs likely dominate gut H2 consumption, based on gene abundance and transcriptome data, although validation at the activity level is still required.

conclusions

The present study improves and consolidates the scientific understanding of a fundamental metabolic process in the human gut by identifying group B [FeFe]-hydrogenase as the main driver of fermentative H2 production in healthy individuals and its elevation Bacteroides gender to key player.

This discovery opens new avenues for understanding, diagnosing and potentially treating complex inflammatory gut disorders by leveraging interventions that target the gut microbiome. It also suggests that respiratory hydrotrophs are the main consumers of H2, highlighting the complexity of microbial energy flow in the gut ecosystem.