Cross-domain interactions: archaea-bacterial syntrophy in digestive health

About This Grant

Abstract While much of the human microbiome research is focused on bacteria, one of the most prevalent yet underappreciated components of the human microbiome is the methanogenic archaea (methanogens). They catalyze the unique methanogenesis metabolism responsible for methane production in the human body. About 1/3 of the healthy adults are breath methane positive, and at least 2/3 are tested positive for fecal methanogens. Although growing evidence has suggested both beneficial and detrimental roles of methanogens in digestive health, the foundational biology supporting these roles remains elusive. Our working hypothesis is that methanogens of the Archaea domain form interdomain syntrophic partnerships (syntrophy) with their surrounding microbiome of the Bacteria domain, specifically defined as methanogen-bacterial syntrophy (MBS) in this application. Normally, MBS is an energy-efficient partnership that benefits food digestion and thus contributes to homeostasis. However, when MBS becomes dysfunctional for reasons yet to be known, growth of methanogens becomes dysregulated, leading to dysbiosis marked by enrichment or depletion of methanogens. The former is already defined by the American College of Gastroenterology as Intestinal Methanogen Overgrowth (IMO) which is strongly associated with constipation suffered by millions of Americans, particularly those with irritable bowel syndrome (IBS). We hypothesize that a shift in redox and dietary environment causes dysfunction in MBS, because 1) methanogens are strict anaerobes that are very sensitive to oxygen, rapidly lose activities in a matter of hours, and require a highly reduced environment for robust growth, and 2) gut microbiome and their functions vary greatly depending on the diet. That is, when the gut microbiome is challenged with oxidative stress, oxidative dysfunction occurs in MBS which leads to depletion of methanogens. When facing reductive stress, reductive dysfunction develops in MBS which contributes to enrichment of methanogens. In terms of diet, we hypothesize that there are multiple yet-to-be-determined subtypes of MBS that drive digestion of glycan, fat, and protein, respectively. Depending on the specific MBS subtype and diet a person has, either enrichment or depletion of methanogens occurs. At least four major technical and knowledge gaps exist in our working hypothesis: 1) What is the technical approach that models both oxidative and reductive stress for microbiome studies? 2) What are the MBS subtypes that drive digestion of various organic matters? 3) What are the potential molecular mechanisms that mediate MBS under different redox and nutrient conditions? 4) What is the impact of MBS on digestive health in vivo? To fill these gaps in this application, PI Lyu (PhD microbiologist) and Co-I Pimentel (MD physician scientist) seek to leverage our Anaerobic Tandem Chamber System (ATCS) platform to model redox stress, combine both cultivation- dependent and -independent approaches to determine MBS subtypes, build in vitro co-culture models for MBS, and test the impact of MBS on digestive health in rats in vivo for IBS-like symptoms. These efforts will help us achieve our shared long-term goal of understanding the role of methanogens in human health. The contribution of the proposed research is significant as it seeks to move away from documenting correlations and move toward investigating functions using live microbes, a necessary step to tap the full potential of microbiome sciences. Another significance is that it aims to develop in vitro and in vivo models to include both archaea and bacteria under various redox and nutrient conditions. This will add more dimensions to digestive and microbiome research. The findings in this proposal will create fundamental knowledge about the biology of human-associated archaea, advance understanding of interdomain interactions between archaea and bacteria, and begin to unravel the interplay between microbiome, redox, and diet in the context of IMO and IBS. This will ultimately benefit efforts in developing microbiome-, redox-, and diet-based diagnostics and therapeutics for IMO and IBS, helping us maximize the benefits and minimize the detriments of microbiome on digestive health.