All of these are iconic examples of cooperation, commonly found in textbooks and wildlife documentaries. And each of them is tinged with conflict, manipulation, and deceit in ways that popular presentations rarely acknowledge. ‘We need to separate important from harmonious. The microbiome is incredibly important but it doesn’t mean that it’s harmonious,’ says evolutionary biologist Toby Kiers at Vrije Universiteit in the Netherlands. A well-functioning partnership could easily be seen as a case of reciprocal exploitation. ‘Both partners may benefit but there’s this inherent tension. Symbiosis is conflict – conflict that can never be totally resolved.’ Such a relationship can, however, be managed and stabilised. Our internal biology has no ideology of ‘good’ and ‘bad’ microbes. We have evolved many solutions to the ever-present conflicts that exist with our microbes, and many ways of enforcing our contracts with them. We can restrict them to certain parts of our bodies by creating physical corrals or creating chemical no-go zones. We can go for the carrot, by nourishing the species we want using dedicated foods. We can beat them with the stick, by using our immune system to keep them in place. We have evolved ways of selecting which species live with us, and of controlling their behaviour so they are more likely to be mutualistic than pathogenic. These means of control reflect the true lesson behind the microbiome: not that nature is inherently harmonious and cooperative, but that all the best relationships take work. - https://aeon.co/essays/there-is-no-such-thing-as-a-good-or-a-bad-microbe