Reevaluating human-microbiota symbiosis: Strain-level insights and evolutionary perspectives across animal species

The prevailing consensus in scientific literature underscores the mutualistic bond between the microbiota and the human host, suggesting a finely tuned coevolutionary partnership that enhances the fitness of both parties. This symbiotic relationship has been extensively studied, with certain bacterial attributes being construed as hallmarks of natural selection favoring the benefit of the human host. Some scholars go as far as equating the intricate interplay between humans and their intestinal microbiota to that of endosymbiotic relationships, even conceptualizing microbiota as an integral human organ.

However, amidst the prevailing narrative of bacterial species being categorized as beneficial or detrimental to human health, a critical oversight often emerges – the inherent functional diversity within bacterial strains. Such reductionist perspectives risk oversimplifying the complex dynamics at play within the microbiome. Recent genomic analysis at the strain level is highly limited, which is surprising given that strain information provides critical data about selective pressures in the intestine. These pressures appear to focus more on the well-being of bacteria rather than human health. Connected to this is the extent to which animals depend on metabolic activity from intestinal bacteria, which varies widely across species. While omnivores like humans exhibit lower dependency, certain herbivores rely entirely on bacterial activity and have developed specialized compartments to house these bacteria.