Gut microbiome 16S rRNA V4 amplicon time series from antibiotic-treated mice colonized with chromosomally barcoded Escherichia coli under spectinomycin selection
This BioProject contains 16S rRNA gene amplicon sequencing of mouse fecalmicrobiota sampled at high temporal resolution during colonization by achromosomally barcoded Escherichia coli MG1655 library under continuousspectinomycin selection.Twelve mice were pretreated for four weeks with a broad-spectrum antibioticcocktail (metronidazole 1 g/L, neomycin 1 g/L, ampicillin 1 g/L, vancomycin0.5 g/L) to deplete the resident microbiota. After a three-day recovery, eightmice were orally gavaged with approximately 10^8 CFU of a barcoded E. coliMG1655 library carrying approximately 10^6 unique heritable chromosomalbarcodes; four control mice received the same antibiotic pretreatment andspectinomycin but no E. coli. The colonized mice were run as two independentcohorts of four at two separate facilities following identical protocols.Fecal pellets were collected at sub-day intervals immediately after gavage(3, 6 and 12 h) and then daily for up to 16 days; control mice were sampleddaily from day 1 to day 10.The dataset provides paired community-composition and within-species lineagedynamics for the same fecal samples, enabling joint analysis of ecologicalsuccession and evolutionary change. In these communities a low-abundancePaenibacillaceae population expanded under spectinomycin pressure and came tocoexist with E. coli, and the data we microbialinteraction networks by dynamic covariance mapping.