Strain Bacteroides thetaiotaomicron TSDC19.1-1.1 was isolated from the fecal microbiota of a USA female at day 0 (bacterial isolates were sequenced from this donor on day 0 and 47). The species name was assigned as the most abundant genus/species associated with a given cluster of genomes (with a cluster containing all strains with a coverage score >0.50). The genome was sequenced with paired-end 101bp reads on an Illumina HiSeq 2000. Genome length is 6558732. Coverage is 13.3x. N50 contig size is 31839.