With the advance of high-throughput sequencing, the potential to map microbial biodiversity has enabled multiple large-scale microbial surveys such as the Earth Microbiome Project, the Human Microbiome Project, and the European Metagenomics of the Human Intestinal Tract project. Combining reanalyses of these massive datasets with numerical simulation and mathematical analysis of biological models, drawing on insights from statistical physics, machine learning, and theoretical ecology, scientists are sifting for patterns in the ecology of microbial systems, to extract generalizable statements.