Table 2. Simplified overview on the nature of bacterial findings.
| Signals | ||||||
|---|---|---|---|---|---|---|
|
|
||||||
| Independent of: | Not in negative controls‡ | Sample-associated§ | verified meta-genomics‖ | |||
|
|
||||||
| DNA extraction batch* | Date of delivery† | Mode of delivery | ||||
| Capable pathogens | ||||||
| Streptococcus agalactiae | ✔ | ✔ | ✔ | ✔ | ✔ | ✔ |
| Listeria monocytogenes e | ✔ | ✔ | ✔ | ✔ | ✔ | - |
| Vaginal lactobacilli | ||||||
| Lactobacillus crispatus | ✔ | ✔ | - | ~ | ✔ | ~ |
| Lactobacillus iners | ✔ | ✔ | - | ~ | ✔ | - |
| Lactobacillus gasseri | ✔ | ✔ | - | ✔ | ✔ | - |
| Lactobacillus jensenii | ✔ | ✔ | - | ~ | ✔ | - |
| Vaginosis associated bacteria | ||||||
| Gardnerella vaginalis | ✔ | ✔ | - | ~ | ✔ | - |
| Atopobium vaginae | ✔ | ✔ | - | ~ | ✔ | - |
| Ureaplasma genus | ✔ | ✔ | - | ✔ | ✔ | - |
| Prevotella bivia | ✔ | ✔ | - | ~ | ✔ | - |
| Prevotella amnii | ✔ | ✔ | - | ✔ | ✔ | - |
| Prevotella timonensis | ✔ | ✔ | - | ~ | ✔ | - |
| Aerococcus christensenii | ✔ | ✔ | - | ✔ | ✔ | - |
| Streptococcus anginosus | ✔ | ✔ | - | ~ | ✔ | - |
| Sneathia sanguinegens | ✔ | ✔ | - | ✔ | ✔ | - |
| Megasphaera elsdenii | ✔ | ✔ | - | ~ | ✔ | - |
| Faecal associated bacteria | ||||||
| Bacteroides genus | ✔ | ✔ | - | ~ | ✔ | - |
| Faecalibacterium prausnitzii | ✔ | ✔ | - | ~ | ✔ | - |
| Roseburia faeces | - | ✔ | - | ~ | ✔ & - | - |
| Coriobacterium sp. | ✔ | ✔ | - | ~ | ✔ | - |
| Collinsella intestinalis | ✔ | ✔ | - | + | ✔ | - |
| Suspected oral origin | ||||||
| Fusobacterium nucleatum | ✔ | ✔ | ✔ | ~ | ✔ | - |
| Streptococcus mitis | ✔ | ✔ | ✔ | ~ | ✔ | - |
| Streptococcus vestibularis | - | ✔ | ✔ | ~ | ✔ & - | - |
| Genuine reagent contaminants | ||||||
| Acinetobacter baumanii e | - | ✔ | ✔ | ~ | - | ~ |
| Thiohalocapsa halophila | - | ✔ | ✔ | - | - | - |
| Propionibacterium acnes | - | ✔ | ✔ | - | - | - |
| S. maltophilia | - | ✔ | ✔ | - | - | - |
| Bradyrhizobium japonicum | - | ✔ | ✔ | - | - | - |
| Melioribacter roseus | - | ✔ | ✔ | - | - | - |
| Pelomonas genus | - | ✔ | ✔ | - | - | - |
| Methylobacterium genus | - | ✔ | ✔ | - | - | - |
| Aquabacterium genus | - | ✔ | ✔ | - | - | - |
| Sediminibacterium genus | - | ✔ | ✔ | - | - | - |
| Desulfovibrio alkalitolerans | - | ✔ | ✔ | - | - | - |
| Delftia tsuruhatensis | - | ✔ | ✔ | - | - | - |
| Streptococcus pyogenes | - | ✔ | ✔ | ~ | - | - |
| Burkholderia multivorans | - | ✔ | ✔ | - | - | - |
| Caulobacter genus | - | ✔ | ✔ | - | - | - |
| Steroidobacter sp. JC2953 | - | ✔ | ✔ | - | - | - |
| Afipia genus | - | ✔ | ✔ | - | - | - |
| Burkholderia silvatlantica | - | ✔ | ✔ | - | - | - |
| Lysinimicrobium mangrove | - | ✔ | ✔ | - | - | - |
| Bradyrhizobium elkanii | - | ✔ | ✔ | - | - | - |
| Achromobacter xylosoxidans | - | ✔ | ✔ | - | - | - |
| C. tuberculostearicum | - | ✔ | ✔ | - | - | - |
| Rhodococcus fascians | ✔ | - | ✔ | ~ | ✔ | - |
| Sphingobium rhizovicinum | ✔ | - | ✔ | ~ | ✔ | - |
| Methylobac. organophilum | ✔ | - | ✔ | ~ | ✔ | - |
| Deinococcus geothermalis e | ✔ | - | ✔ | ✔ | ✔ | ✔ |
*
Includes batch effects caused by different DNA isolation kits, PCR reagents and MiSeq run.
‡
A ✔ indicates absence, ~ indicates detection (any %) in less than 20% of negative controls.
§
Detection of signal in corresponding Qiagen and Mpbio DNA isolations. “✔ & -” indicates that signals from these OTUs are sample-associated in most 16S runs, but reagent contaminants in others. See Supplementary Table 4 for details.
‖
See Table 1 and Supplementary Table 3. A ~ indicates some level of concordance was detected using a different 16S threshold. Presence or absence of verification should be interpreted with caution, as indicated by examples.