At the Wolbachia meeting, Matt Chung (Ph.D. candidate in the Dunning Hotopp group) presented on our analysis of using whole genome nucleotide alignments and sequence identity matrices to recapitulate classically defined bacterial taxa, as described in “Using Core Genome Alignments to Assign Bacterial Species” by Chung, Munro, and Dunning Hotopp (doi: https://doi.org/10.1101/328021). This manuscript includes an analysis of Wolbachia strains and their supergroup designations that largely supports the ANI-based and DDH-based analyses by Ramirez-Puebla et al. in 2015, although illustrates how nucleotide identity thresholds need to be coupled with a phylogenetic-based approach to ensure the accuracy of the taxonomic assignment. The whole genome alignment based method used is readily amenable to both a combined percentage identity and phylogenetic approach; we would recommend its use, but are open to alternatives. Given these results and a lengthy discussion it seemed like there was broad support for defining Wolbachia species through a working group approach.
Subsequent discussions have led us to proposing a 5-pronged approach:
- Formalize a draft method for assigning Wolbachia species as determined by Wolbachia researchers working in a small working group. This could be ANI, dDDH, phylogeny, and/or whole genome alignment. Regardless there should be a workflow and specific recommendations. It should clarify the criteria for creating a new name, but also criteria for when an existing name is applied to a strain and when Wolbachia sp. is used. The latter two of which would not necessarily require whole genome sequencing but could rely on MLST, keeping in mind that new MLST schemes may be warranted that are more species-specific.
- Take contributed genomes and apply the method to these genomes.
- Formalize a final method for assigning Wolbachia species by this small working group.
- Develop a manuscript to circulate the results of this small working group and identify community supported species names, possibly using BioRXiv to distribute the manuscript to facilitate community engagement. The recommendation that seemed to be supported at the meeting was to avoid the names of living scientists actively working in the Wolbachia field as was suggested previously. However, please see the survey questions below.
- Apply the names, submitting the publication. I would suggest using a consortium as an author for the publication and then listing individual authors as is frequently done in genomics papers. There could be recognition of the small working group members as well, through the author contributions section. I would suggest including as many people as possible as authors, in order to demonstrate the strong community support for the proposal/study/analyses.
If you would like to be either in the small working group or an author on the final paper, please e-mail WolbachiaTaxonomy@gmail.com. To expression your anonymous thoughts about Wolbachia taxonomy to inform decisions to be made, please respond to the survey at: https://www.surveymonkey.com/r/5FKVJ67.