I recently ran some 16S sequencing data using the DADA2 pipeline using the silva database (silva_nr_v132_train_set.fa) for taxonomic assignment. Strangely, the genus Polaromonas sp. is being identified as belonging to Burkholderiaceae instead of Comamonadaceae. Any ideas or suggestions? Please let me know if any additional information may be useful in determining what is going on. Thank you in advance for any clues.
No, it is not a misidentification. SILVA now bases its database on the Genome Taxonomy Database (GTDB). In GTDB taxonomy, Polaromonas now belongs to the Burkholderiaceae; see here https://gtdb.ecogenomic.org/searches?q=%25Polaromonas%25&s=al or you can search for yourself on the GTDB homepage. To read more about this new standardized bacterial taxonomy that is based on genome phylogeny, please check out this paper: https://www.nature.com/articles/nbt.4229
Thanks for the message. I was in contact with the SILVA staff this morning and it appears that the GTDB assignment was assigning bacteria in the order Burkholderiales to the family Burkholderiaceae (including Comamonadaceae, Oxalobacteraceae, Alcaligenaceae, etc). The new SILVA database reflects the new SSU taxonomy (r138) where this had been corrected. Message from SILVA staff attached.
Ok thanks for the update. In this case, it may be better to quickly clarify this also from the folks at GTDB. In my personal experience, they are quite responsive.
- Badges
- Science topic
- Similar topics
- Biological Science
- Microbiology
- Microorganisms
- Bacteria