Understanding Competition and Cooperation within the Mammalian Gut Microbiome

Abstract

The mammalian gut harbors a vast community of microorganisms -termed the microbiotawhose composition and dynamics are considered to be critical drivers of host health. These factors depend, in part, upon the manner in which microbes interact with one another. Microbes are known to engage in a myriad of different ways, ranging from unprovoked aggression to actively feeding each other. However, the relative extent to which these different interactions occur between microbes within the gut is unclear. In this minireview we assess our current knowledge of microbe-microbe interactions within the mammalian gut microbiota, and the array of methods used to uncover them. In particular, we highlight the discrepancies between different methodologies: some studies have revealed rich networks of cross-feeding interactions between microbes, whereas others suggest that microbes are more typically locked in conflict and actively cooperate only rarely. We argue that to reconcile these contradictions we must recognize that interactions between members of the microbiota can vary across condition, space, and time -and that only through embracing this dynamism will we be able to comprehensively understand the ecology of our gut communities. example, by introducing a new species) and determining how members of the resident microbial community respond (top right); or, tracking an individual's microbiota composition over time or across different conditions, and then using statistical tools to infer likely interactions between microbial taxa (bottom right).Coyte and Rakoff-Nahoum

The key to complexity in interacting systems with multiple strains

“…Studying this equation and its epidemiological consequences in detail, here we find that there is a critical ratio that tunes asymmetry and dynamic regimes in such multi-strain interacting system: namely the ratio of single to co-colonization. This ratio µ, given by the inverse of the product of basic reproduction number and mean permissiveness to co-colonization µ = 1/((R 0 − 1)k), increases or decreases the importance of asymmetry in interaction between strains as they encounter each-other epidemiologically in resident-co-colonizer combinations, and lends support to the context-dependence (Coyte and Rakoff-Nahoum, 2019) of relative fitnesses in a coupled microbial community. In our epidemiological system, individual strain frequency evolution over long times depends on how that strain interacts with other strains, but also on the total net interaction between extant strains.…”

“…Theoretically, a crucial question has been to study stability and coexistence patterns in such Lotka-Volterra multi-species communities, analyzing both structured ecological networks and random networks (Serván et al, 2018). Modeling efforts seek to understand organizing principles for species composition, such as the balance between competition and cooperation (Mougi and Kondoh, 2012), which many are increasingly arguing that should be studied together in integrated and context-dependent frameworks (Bascompte, 2019;Coyte and Rakoff-Nahoum, 2019). Overall, analysis of such models with arbitrarily high dimensionality has been and continues to remain difficult.…”

Alterations of the Gut Microbiome Composition and Lipid Metabolic Profile in Radiation Enteritis

“…In 2017, Ming Cui et al reported that faecal microbiota transplantation could be employed as a therapeutic to ameliorate radiation-induced toxicity and improve the prognosis of patients after radiotherapy (Cui et al, 2017). Obviously, based on current trends, understanding how the enteric microbiota affects health and disease requires a paradigm shift from focusing on individual pathogens to an ecological approach that considers the community as a whole (Coyte and Rakoff-Nahoum, 2019). Therefore, we used high-throughput 16S rDNA sequencing to examine the alterations of the gut microbiome composition after radiation exposure.…”

Changes in Microbiota and Metabolites Are Associated With Effects of Bile Acid Sequestrant on Icteric Primary Biliary Cholangitis

“…The human intestine harbours a huge number of microbes interacting intricately with each other. Previous studies have suggested that microbial interactions are not only essential for maintaining healthy ecology, but also implicated in disease-associated states [35][36][37][38][39] . In this regard, the differential microbial networks in SR and IR group may help explain the variable adaptation to the BA uctuation.…”