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Interspecies hydrogen transfer in the mammalian gut: how interactions between fermenters and hydrogenotrophs influence colonic homeostasis

Periodic Reporting for period 1 - H2Gut (Interspecies hydrogen transfer in the mammalian gut: how interactions between fermenters and hydrogenotrophs influence colonic homeostasis)

Reporting period: 2018-09-01 to 2020-08-31

Hydrogen gas is an important metabolite formed in our gut solely by microorganisms when indigestible components of our diet such as fibre (polysaccharides) are broken down and fermented. Hydrogen that is produced in the human gut builds up to relatively high levels after a meal (0.5-3% by volume) and must be disposed of very efficiently because the buildup of this gas strongly inhibits fermentation and overall function of the gut. Four different groups of anaerobic organisms exist in the gut that can consume this hydrogen and prevent its harmful accumulation: bacteria that produce sulfide (sulfidogens), archaea that produce methane (methanogens), bacteria that produce acetate when they breathe carbon dioxide (acetogens), and bacteria that breathe fumarate. Although we know that microbial hydrogen gas metabolism in the gut has a strong influence on our gut health, we do not know which organisms produce or consume this gas in our gut. We have only limited knowledge of which organisms have the potential to metabolize this important gas in the human gut and only rudimentary knowledge of which organisms actively metabolize hydrogen in the human gut.

Understanding hydrogen gas formation and consumption in the human gut by our microflora is important because it allows us to understand how the presence of various microbes and how different diets may influence our health. For example, eating a high fibre diet may result in high hydrogen production in the human gut which could stimulate hydrogen-consuming bacteria to produce more acetate – a metabolite that plays an important role in prevention/treatment of metabolic syndromes, bowel cancer, and bowel disorders. On the other hand, some pathogens like Salmonella take advantage of hydrogen produced during fibre breakdown to infect and grow in the gut. Characterizing which microbes actively produce and consume hydrogen in the human gut will allow us to better understand how our microbiome, our diet, and incoming pathogens influence our health.

The overall objectives of this project are to: 1) identify which microbes and pathways might contribute to hydrogen production and consumption in the gut, 2) assess which pathways and which microbes express their hydrogenases, 3) to determine which microbes are active hydrogen utilizers, and 4) to integrate the new results into a hypothesis about which organisms are the most important hydrogen metabolizers in the human gut.
Using the most recent and complete collection of gut microbe genomes, we identified and annotated which specific hydrogenases are encoded in these genomes. This survey revealed which specific gut microorganisms have the potential to either produce or consume hydrogen, depending the type and group of hydrogenase we found. Once we identified which gut microorganisms have the potential to metabolize hydrogen and which do not, we quantified the abundance of all these organisms in DNA extracted from 1,076 human fecal samples. This showed which organisms were the must abundant in the human gut community, since the collection of genomes does not represent the actual abundance of those organisms in the human gut. Using RNA extracted from the sane 1,076 human fecal samples, we then quantified the organisms and hydrogenases that were the most abundant in RNA. This analysis allowed us to assign which organisms were actively expressing hydrogen metabolizing genes and may be actively producing or using hydrogen in the human gut, as many organisms that encode hydrogenases in their genome may use them at a very low level or not at all.
To identify which microorganisms in the human gut actively metabolize hydrogen, we incubated fresh human fecal samples from 7 donors in the presence of hydrogen gas and sorted out individual cells that were active in the incubations. This single-cell approach enabled us to quickly and efficiently sort and identify which microorganisms were the most active hydrogen utilizers in human fecal samples. We compared the active hydrogen utilizers that we recovered in the incubations with the microorganisms that were expressing hydrogenases and used this data to construct transcript maps (maps of gene expression) for the organisms that were active and contributed to hydrogenase expression. We analyzed the transcript maps of these keystone hydrogen metabolizing organisms to characterize the metabolic pathways they use for fermentation and/or hydrogen utilization.
The work performed in this project shows which organisms facilitate gut function and fermentation by consuming hydrogen gas. The work demonstrates not only which organisms are the most important to hydrogen formation and consumption in the gut but may also enable a better understanding of how diet influences colonic hydrogen production and how we can inhibit opportunistic pathogens that take advantage of high colonic hydrogen levels by either supplementing our diet with probiotic organisms that keep hydrogen levels low or prebiotics that stimulate hydrogen consuming microorganisms.