RT Journal Article
SR Electronic
T1 Longitudinal linked read sequencing reveals ecological and evolutionary responses of a human gut microbiome during antibiotic treatment
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2019.12.21.886093
DO 10.1101/2019.12.21.886093
A1 Roodgar, Morteza
A1 Good, Benjamin H.
A1 Garud, Nandita R.
A1 Martis, Stephen
A1 Avula, Mohan
A1 Zhou, Wenyu
A1 Lancaster, Samuel
A1 Lee, Hayan
A1 Babveyh, Afshin
A1 Nesamoney, Sophia
A1 Pollard, Katherine S.
A1 Snyder, Michael P.
YR 2019
UL http://biorxiv.org/content/early/2019/12/23/2019.12.21.886093.abstract
AB Gut microbial communities can respond to antibiotic perturbations by rapidly altering their taxonomic and functional composition. However, little is known about the strain-level processes that drive this collective response. Here we characterize the gut microbiome of a single individual at high temporal and genetic resolution through a period of health, disease, antibiotic treatment, and recovery. We used deep, linked-read metagenomic sequencing to track the longitudinal dynamics of thousands of single nucleotide variants within 36 species, which allowed us to contrast these genetic dynamics with the ecological fluctuations at the species level. We find that antibiotics can drive rapid shifts in the genetic composition of individual species, often involving incomplete genome-wide sweeps of pre-existing variants. Interestingly, genetic changes frequently occur in species without obvious changes in relative species abundance, emphasizing the importance of monitoring diversity below the species level. Our results provide new insights into the population genetic forces that shape individual microbiomes on therapeutically relevant timescales, with potential implications for personalized health and disease.