Human bodies are luxury condominiums for bacteria, populated with billions if not trillions of microbial cells. These microbes have crucial roles in metabolism and protection from pathogens that we are just beginning to appreciate. Next generation DNA sequencing and in particular metagenomics has been instrumental in revealing the previously hidden diversity of microbes in our bodies and characterising their roles in human health and the environment. Until now, most studies of bacterial population genomics have focused on cultured isolates. From these studies we have learned that acquisition of genes via lateral transfer and swapping of alleles via homologous recombination can dramatically alter how microbes interact with the environment and with hosts. This type of fine scale genetic variation in bacterial populations is important, but still poorly understood outside laboratoryculture.

Recent work in my own group and others around the world has led to new molecular tools for resolving the fine-scale genetic structure in wild bacterial populations. Among these are single-cell genome sequencing,single-molecule long read sequencing, and metagenomic Hi-C. These new data types hold great promise to reveal the private lives of microbes,but also pose a major analytical challenge because the data violate common assumptions of existing models and population genetic inference frameworks.