Table 4.
All taxa included in top five operational taxonomic units by relative abundance of 16S rRNA read counts across all samples analyzed
| Taxon (No. of OTUs) | Identified by Routine Culture |
Not Identified by Routine Culture |
||||||
|---|---|---|---|---|---|---|---|---|
| No. of Samples |
Mean | No. of Samples |
Mean | |||||
| CF | IC | nIC | CF | IC | nIC | |||
| Staphylococcus spp. (2) | 18 | 2 | 1 | 1,788 | 7 | 15 | 18 | 954 |
| Streptococcus spp. (6) | — | 3 | 1 | 440 | 13 | 4 | 15 | 379 |
| Haemophilus sp. (1) | 1 | 1 | 4 | 2,531 | 2 | 4 | 9 | 997 |
| Stenotrophomonas spp. (4) | 11 | — | 1 | 1,566 | 4 | 1 | 3 | 164 |
| Escherichia coli (1) | — | 1 | — | 892 | 5 | 6 | 7 | 213 |
| Prevotella spp. (7)* | 9 | 5 | 6 | 330 | ||||
| Neisseria spp. (2) | 2 | 2 | 8 | 574 | ||||
| Actinobacillus parahaemolyticus (1) | 2 | 3 | 7 | 490 | ||||
| Veillonella dispar (2) | 4 | 3 | 5 | 137 | ||||
| Pseudomonas sp. (1) | 4 | — | — | 1,695 | 2 | 1 | 2 | 772 |
| Enterococcus sp. (1) | 2 | 1 | 5 | 261 | ||||
| Methylobacterium sp. (1) | 2 | 5 | 1 | 240 | ||||
| Fusobacterium sp. (1) | 1 | 3 | 2 | 505 | ||||
| Moraxella sp. (1) | 1 | 2 | 3 | 334 | ||||
| Brevibacillus sp. (1) | 1 | 4 | 1 | 138 | ||||
| Sphingomonas sp. (1) | 2 | 4 | — | 111 | ||||
| Acinetobacter spp. (2) | 1 | 2 | 2 | 800 | ||||
| Delftia sp. (1) | — | — | 1 | 851 | 1 | 1 | 2 | 775 |
| Corynebacterium spp. (3) | 1 | 3 | 1 | 585 | ||||
| Rothia mucilaginosa (1) | 4 | — | 1 | 89 | ||||
| Granulicatella sp. (1) | 2 | — | 2 | 731 | ||||
| Capnocytophaga spp. (2) | — | 1 | 3 | 244 | ||||
| Achromobacter sp. (1) | 1 | — | 1 | 2,049 | — | — | 1 | 1,275 |
| Parvimonas spp. (2) | 2 | 2 | — | 553 | ||||
| Pantoea agglomerans (1) | — | — | 2 | 1,962 | ||||
| Legionella sp. (1) | 1 | 1 | — | 403 | ||||
| Porphyromonas spp. (2) | 1 | — | 1 | 312 | ||||
| Campylobacter sp. (1) | — | 1 | 1 | 293 | ||||
| Aggregatibacter sp. (1) | — | 1 | 1 | 261 | ||||
| WAL_1855D (1) | 2 | — | — | 219 | ||||
| Meiothermus sp. (1) | — | 2 | — | 129 | ||||
| Leptotrichia spp. (2) | 1 | — | 1 | 64 | ||||
| Proteus sp. (1) | 1 | — | — | 2,338 | — | — | 1 | 38 |
| Nocardia spp. (2) | — | 1 | — | 936 | 1 | — | — | 22 |
| Other† | 5 | 5 | 9 | 258 | ||||
| Unidentified‡ | 20 | 21 | 20 | 331 | ||||
Definition of abbreviations: CF = cystic fibrosis; IC = immunocompromised; nIC = nonimmunocompromised; OTU = operational taxonomic unit.
In many cases, multiple OTUs of a single genus were identified, shown here in parentheses. Those that were present in the top five and also isolated in the clinical laboratory are listed under “identified by routine culture,” along with the mean 16S rRNA gene rarefied abundance for each taxon. Numerous taxa that were present in the top five by 16S rRNA abundance were not isolated in the clinical laboratory, listed here with mean abundances, under “not identified by routine culture.”
Table E1 (in the online supplement) is an extended form of this table, with each OTU listed.
The taxon Prevotella spp. includes two OTUs of genus Prevotella that belong to the family Paraprevotellaceae.
There were 19 taxa identified to genus level that were each present in the top five of only one sample.
Twenty-one different OTUs, detected in 61 samples, were not identified to genus level.