  Sequence differences between the strains of bacteria comprising
host-associated and environmental microbiota may play a role in community
assembly and influence the resilience of microbial communities to disturbances.
Tools for characterizing strain-level variation within microbial communities,
however, are limited in scope, focusing on just single nucleotide
polymorphisms, or relying on reference-based analyses that miss complex
functional and structural variants. Here, we demonstrate the power of assembly
graph analysis to detect and characterize structural variants in almost 1,000
metagenomes generated as part of the Human Microbiome Project. We identify over
nine million variants comprising insertion/deletion events, repeat copy-number
changes, and mobile elements such as plasmids. We highlight some of the
potential functional roles of these genomic changes. Our analysis revealed
striking differences in the rate of variation across body sites, highlighting
niche-specific mechanisms of bacterial adaptation. The structural variants we
detect also include potentially novel prophage integration events, highlighting
the potential use of graph-based analyses for phage discovery.
