Strain-resolved microbiome sequencing reveals mobile elements that drive bacterial competition on a clinical timescale.
Soumaya ZlitniAlex BisharaEli L MossEkaterina TkachenkoJoyce B KangRebecca N CulverTessa M AndermannZiming WengChristina WoodChristine HandyHanlee P JiSerafim BatzoglouAmi Siddharth BhattPublished in: Genome medicine (2020)
We find read cloud assembly to be useful in identifying key structural genomic strain variants within a metagenomic sample. These strains have fluctuating relative abundance over relatively short time periods in human microbiomes. We also find specific structural genomic variations that are associated with increased antibiotic resistance over the course of clinical treatment.