Table 2. Difference in the abundance of selected tissue and fecal genera or OTUs in infants for a number of tested comparisons for taxa that were significant with the DESeq2 test.
| Taxon | Sample type | Groups compared | Base mean* | Log2 fold change† | q-value‡ |
|---|---|---|---|---|---|
| Staphylococcus | tissue | NEC/non-NEC | 177.975 | 4.455 | 0.0006 |
| Clostridium sensu stricto | tissue | NEC/non-NEC | 1.552 | 3.226 | 0.0519 |
| Staphylococcus | fecal | NEC/non-NEC | 317.6 | 4.696 | 0.0002 |
| Staphyloocccus.OTU0004 | fecal | NEC/non-NEC | 230.90 | 5.32 | 6.26e-04 |
| Staphyloocccus.OTU0004 | tissue | NEC/non-NEC | 148.7 | 4.703 | 0.001 |
| Actinomyces | tissue | NEC/non-NEC | 1.550 | -3.647 | 0.008 |
| Corynebacterium | tissue | NEC/non-NEC | 1.960 | -1.711 | 0.087 |
| Staphylococcus | tissue | Male/female | 78.701 | -3.699 | 0.012 |
| Actinomyces | fecal | Age (days) | 7.725 | 0.0871 | 0.004 |
| Staphylococcus | tissue | Vancomycin (yes/no) | 78.701 | 3.758 | 0.015 |
* Base means are calculated in the DESeq2 package for each taxon after normalizing read counts for each sample to account for differences in sequencing depth.
† Log2 fold changes are calculated by the DESeq2 package and indicate the magnitude of the difference in abundance for each comparison. For categorical tests, positive values indicate that DESeq2 estimated the taxon was more abundant in the first tested group while negative values indicate that DESeq2 estimated the taxon was more abundant in the second group. When age in days was used as the group to test, a positive value indicates that DESeq2 found that taxon increased in abundance with each age day.
‡ Reported q-values are the result of a Wald test with the Benjamini and Hochberg correction for multiple comparisons.
NEC, necrotizing enterocolit