Changes in the genetic requirements for microbial interactions with increasing community complexity

Microorganisms live almost everywhere on Earth. Whether it is rainforest soil or human skin, each environment hosts a unique community of microbes, referred to as its microbiome. There can be upwards of hundreds of species in a single microbiome, and these species can interact in a variety of ways; some cooperate, others compete, and some can kill other species. Deciphering the nature of these interactions is crucial to knowing how microbiomes work, and how they might be manipulated, for example, to improve human health. Yet studies into these interactions have proven difficult, not least because most of the species involved are difficult to grow in controlled experiments. One environment that is home to a rich community of microbes is the outer surface of cheese, known as the cheese rind. The cheese rind microbiome is a useful system for laboratory experiments, because it is relatively easy to replicate and its microbes can be grown on their own or in combinations with others. To explore the nature of interactions in microbiomes, Morin et al. have now grown a large collection of E. coli mutants as members of simplified microbiomes based on the cheese rind. The mutant bacteria were grown on cheese either alone, paired with one other species, or alongside a community of three species. The aim was to see which mutants grew poorly when other species were present, thus allowing Morin et al. to identify specific genes that are important for interactions within the experimental microbiomes. Even in these simplified microbiomes, the microbes interacted in a variety of ways. Some microbes competed with E. coli for elements like iron and nitrogen; others cooperated by sharing the building blocks needed to make larger molecules. Many of the interactions that happened when E. coli was paired with one species were not seen when more species were added to the community. Similarly, some interactions were only seen when E. coli was grown alongside a community of microbes, and not when it was paired with any of the three species on their own. These findings show that complex interactions are present even in a simplified microbiome. This experimental approach can now be applied to other microbiomes that can be grown in the laboratory to examine whether the patterns of interactions seen are generalizable or specific to the cheese rind system.