Table 1.
Sample statistics determined following high-throughput shotgun sequencing on the Illumina HiSeq platform, sequence processing, taxonomic, and functional assignments. The total sequences before and after host sequence removal are shown, and the following quality checking through MG-RAST (v4.0.3). The sequences assigned to domain Bacteria through RefSeq. High-quality sequences that did not receive a taxonomic identity were listed as “Other Seqs”. Alpha diversity was determined for each sample based on the Shannon and Simpson metrics as implemented through QIIME (v1.9.1) at the species level of taxonomic resolution. The number of sequences assigned to a functional gene through KEGG Orthology (KO) was also listed.
| Sample | Total Seqs | Host-Removed Seqs | QC Seqs | Bacteria | Other Seqs | Shannon | Simpson | KO Functions |
|---|---|---|---|---|---|---|---|---|
| LV.GD1 | 11,179,611 | 1,903,485 | 1,879,183 | 646,758 | 3 | 8.99 | 0.996 | 206,021 |
| LV.GD2 | 12,989,418 | 2,191,267 | 2,162,089 | 747,440 | 4 | 8.99 | 0.996 | 238,974 |
| SP.GD1 | 11,280,351 | 6,232,967 | 6,082,068 | 3,323,484 | 4 | 7.47 | 0.965 | 1,103,493 |
| SP.GD2 | 12,994,228 | 7,169,738 | 6,976,796 | 3,823,945 | 12 | 7.47 | 0.965 | 1,265,954 |