Cooperation and competition in microbes: from model systems to the microbiome

Since Darwin, evolutionary biologists have been fascinated by cooperative behaviour. Honeybee workers labour their whole life without reproducing, birds make alarm calls, and humans often help each other. Much less attention has been paid to the microbes. They exist all around us and inside us, and it has become clear that microbes commonly live in densely interacting communities that have major effects on animals and plants. But what determines if microbes are cooperative towards each other and their hosts?  We study this question by combining theory with experimental systems, including pathogenic bacteria, budding yeast and the mammalian microbiome. We find that single-genotype patches naturally emerge in microbial communities, which favours strong cooperation by kin selection. By contrast, interactions between genotypes can be strongly competitive. Bacteria strains are often at war and we find that they can rapidly detect incoming attacks and respond in kind. Microbial interactions then follow the same evolutionary principles that were first understood through the study of animal behavior. However, one unusual and fascinating property of microbes is that an entire ecosystem can lie within another evolving organism: a host. This raises the possibility that hosts will act as ecosystem engineers that change the rules of microbial interaction for their own benefit.