Shotgun sequencing of the southern sea otter microbiota: fecal sample
We selected twelve samples for shotgun sequencing from sea otters observed to exhibit the most extreme diet specialization at the prey phylum level (see Watt et al. (2000) for details on observational estimation of diet composition). Sub-samples of feces were collected for DNA extraction by inserting a sterile foam Catch-All sample collection swab into feces and maneuvering the swab such that it came in contact with as much of the fecal material as possible. Care was taken to not collect solid material (e.g., pieces of shell) on swabs. DNA extracts for fecal samples were obtained as described above and used for amplicon sequencing and shotgun sequencing. Libraries for shotgun sequencing were constructed following the purification of DNA using a Zymo Clean and Concentrate Spin Column. Libraries were sequenced in three Illumina HiSeq 2500 lanes. Read quality was assessed using MultiQC (Ewels et al., 2016). This resulted in 439,548,821 pairs of reads, with the number of pairs of reads per sample ranging from 17,968,495 - 103,830,968. The average length of gDNA in the resulting libraries ranged from 236-644 bp. The fecal samples were also sent for 16S rRNA gene amplicon sequencing.