Over evolutionary time many infectious bacteria have decided to join rather than keep on fighting. Via genetic pickup and adaptation, they learned new skills that allowed them to contribute to a host rather than harm it. In the process, bacteria inactivate and then eliminate genes that no longer serve them.
Obligate host-associated bacteria often have reduced genome sizes in comparison to related bacteria that are known to engage in free-living or opportunistic lifestyles. ~ American biologist Adam Clayton et al
For energetic efficiency emergent endosymbionts streamline their gene inventory to one compatible with their new lifestyle. Their pathogenic past is shed, but their knowledge of how to evade host immune system destruction is retained until a truce is obtained. How this perceptive shift is achieved is not known.
For their hosts, commensal microbes provide adaptation opportunities, though mutually beneficial relationships take time to develop. Plants have been most successful in cultivating partnerships with other organisms, both microbial and macrobial.
Many herbivorous insects harbor microbial symbionts that provide essential nutrients and that help protect against parasites and predators by priming the immune system.
Gut bacteria may allow a host to expand its range of edible vegetation: detoxifying plant metabolites and manipulating plant defense responses to render them ineffective.
Western corn rootworms’ gut flora suppress defensive gene expression in maize roots, allowing their host to feast. Colorado potato beetle larvae chew potato and tomato plant leaves thanks to bacterial symbionts that defuse plant defenses.
The microbiome can affect speciation. Microbes reduce the viability of animal hybrids, even of those otherwise closely related. This arises from self-interest. The microbiome seeks an accommodating environment for itself. It rejects an uncomfortable habitat.
Hybrids can create irregularities that microbes find intolerable. This is especially true for gut bacteria, which are very community oriented. Gut flora incompatibility causes lethality in certain interspecific hybrids. Hence, the microbiome vectors host evolution by genetic contribution and by veto. Internal environmental pressures can be as significant as those in the external environment. The envirotype is both within and without.