Table 2.
Abundant and prevalent bacterial OTUs in male D. melanogaster. The OTUs listed are present in at least 50% of individuals or contribute to at least 2% of the reads averaged across all individuals. To obtain the nearest named isolate, the representative sequence for each OTU was compared to the GreenGenes database [66] and its taxonomic classification was generated with the Ribosomal Database Project (RDP) Classifier [67]. OTU IDs refer to Supplementary Dataset 1c
| OTU ID | Mean relative abundance (sd) | % of individuals | Nearest named isolates (identity)a | Taxonomic classification (confidence) |
|---|---|---|---|---|
| 161 | 12.1 (13.8) | 100 | Acetobacter fabarum (100%) | Acetobacteraceae (100%), Acetobacter (96%) |
| Acetobacter lovaniensis (100%) | ||||
| 10 | 11.0 (23.3) | 72 | Enterococcus termitis (99%) | Enterococcaceae (100%), Enterococcus (60%) |
| 49 | 9.7 (16.9) | 81 | Gluconobacter sp. (100%) | Acetobacteraceae (100%) |
| 124 | 6.4 (7.8) | 97 | Gluconobacter oxydans (100%) | Acetobacteraceae (100%), Gluconobacter (100%) |
| Gluconobacter frateurii (100%) | ||||
| Gluconobacter cerinus (100%) | ||||
| 235 | 5.0 (14.3) | 51 | Gluconobacter sp. (97%) | Acetobacteraceae (100%) |
| 167 | 4.8 (10.0) | 76 | Pantoea punctata (100%)b | Enterobacteriaceae (100%), Tatumella (98%) |
| 231c | 4.3 (8.6) | 68 | Enterobacterium str. (90%) | Orbaceae (85%) |
| 61 | 4.2 (8.3) | 59 | Providencia sneebia (100%) | Enterobacteriaceae (100%), Providencia (100%) |
| 111 | 3.8 (5.0) | 91 | Leuconostoc mesenteroides (100%) | Leuconostocaceae (100%), Leuconostoc (100%) |
| Leuconostoc pseudomesenteroides (100%) | ||||
| 64 | 3.6 (9.9) | 30 | Lactobacillus mali (100%) | Lactobacillaceae (100%), Lactobacillus (100%) |
| 242 | 3.1 (12.8) | 25 | Pseudomonas tuomuerensis (93%) | Pseudomonadaceae (100%) |
| 179 | 3.0 (9.7) | 81 | Pantoea agglomerans (99%) | Enterobacteriaceae (100%), Pantoea (98%) |
| Pantoea vagens (99%) | ||||
| 15 | 2.6 (4.7) | 61 | Stenotrophomonas maltophilia (100%) | Xanthomonadaceae (100%), Stenotrophomonas (100%) |
| Xanthomonas sp. (100%) | ||||
| Pseudomonas geniculate (100%) | ||||
| Pseudomonas hibiscicola (100%) | ||||
| 32 | 2.5 (3.4) | 95 | Gluconobacter oxydans (100%) | Acetobacteraceae (100%), Gluconobacter (100%) |
| Gluconobacter krungthepensis (100%) | ||||
| 96 | 1.1 (1.5) | 76 | Leuconostoc citreum (100%) | Leuconostocaceae (100%), Leuconostoc (100%) |
| Leuconostoc mesenteroides (100%) | ||||
| 101 | 0.9 (1.6) | 66 | Acetobacter syzygii (98%) | Acetobacteraceae (100%), Acetobacter (95%) |
| Acetobacter fabarum (98%) | ||||
| Acetobacter lovaniensis (98%) | ||||
| 142 | 0.9 (1.3) | 70 | Acetobacter indonesiensis (99%) | Acetobacteraceae (100%), Acetobacter (100%) |
| Acetobacter cibinongensis (99%) | ||||
| 108 | 0.8 (2.2) | 63 | Kluyvera intermedia (98%) | Enterobacteriaceae (100%) |
| 222 | 0.2 (0.3) | 62 | Gluconobacter cerinus (98%) | Acetobacteraceae (100%), Gluconobacter (82%) |
aSome OTUs had the same sequence identity to multiple named isolates, and all the isolates are shown
bThese species have been assigned to the genus Tatumella [65]
cThe taxonomy of this OTU is not settled. It is assigned to family Enterobacteriaceae (of order Enterobacteriales) by Greengenes (see Table), order Pasteurellales by QIIME, and the family Orbaceae (of order Orbales) by RDP