Chromosomal barcode amplicon sequencing of Escherichia coli lineage dynamics in the mouse gut under spectinomycin selection
This BioProject contains chromosomal barcode amplicon sequencing used to trackEscherichia coli lineage dynamics at high temporal resolution during colonizationof the antibiotic-treated mouse gut under continuous spectinomycin selection.Eight mice were pretreated for four weeks with a broad-spectrum antibiotic cocktail(metronidazole 1 g/L, neomycin 1 g/L, ampicillin 1 g/L, vancomycin 0.5 g/L) todeplete the resident microbiota. After a three-day recovery they were orally gavagedwith approximately 10^8 CFU of a chromosomally barcoded Escherichia coli MG1655library carrying approximately 10^6 unique heritable 15-nucleotide barcodes(Jasinska et al. 2020). The mice were run as two independent cohorts of four at twoseparate facilities following identical protocols. Fecal pellets were collected dailyfor up to 16 days; barcode sequencing was performed daily throughout for cohort two,and daily to day 10 and then on days 14 and 16 for cohort one.Genomic DNA was extracted from whole fecal pellets (QIAamp Fast DNA Stool Mini Kit)and used for two parallel workflows: the barcode amplicon libraries deposited hereand 16S rRNA V4 amplicon libraries characterizing community composition (depositedseparately). Barcodes were amplified from fecal community DNA in a two-step PCR thatadded Illumina adaptors and Nextera XT dual indices, and the pooled libraries werespiked with 15 percent PhiX to improve sequence complexity.Because each barcode is heritable and neutral, read counts per barcode per timepointgive frequency trajectories for thousands of individual E. coli lineages within acomplex resident microbiota. The data resolve intraspecific competition duringcolonization, the response of individual lineages to antibiotic selection, and thesubsequent restructuring of the community, and were combined with the matched 16Sprofiles to infer time-varying microbial interaction networks by dynamic covariancemapping.