s_Xanthomonas cissicola reclassificaiton


This is a fantastic resource and thank you for creating it. I wanted to alert you to a small misclassification.

Xanthomonas citri is an import plant pathogen in agriculture but doesn’t appear to be in GTDB. The closest I can find is Xanthomonas cissicola, which was once Pseudomonas cissicola, has over 200 genomes in GTDB, and has recently been proposed to be reclassified into X. citri (see Phylo-Taxonogenomics Supports Revision of Taxonomic Status of 20 Xanthomonas Pathovars to Xanthomonas citri | Phytopathology®). ANI is 98.2% between X. citri and X. cissicola type strains. Xanthomonas citri is the name commonly used in the literature as Xanthomonas citri returns hundreds of results in PudMed search and Pseudomonas|Xanthomonas cissicola returns less than 10.

Thank you again for creating GTDB, it has been very useful for my work.



Dear Daniel

Thank you for your kind words, and we are glad to hear that you find our resource to be useful for your work!

I had a look at both the reference you sent and our species clusters.
Unfortunately, that paper does not follow any official nomenclature regulations. Taxonomically speaking, authors proposed to unite X.citri with other species, but described the transfer of pathovars as new combinations for some reasons (!).

Please note that ‘pathovar’ is not regulated by the Prokaryotic code as it is outside of the recognised standard ranks. This is a term which is used for practical purposes in pathology. Therefore, the nomenclature consequences proposed in that paper cannot be implemented or validated. One needs to consider the priority of specific names when species are merged together. Unfortunately, sometimes the species name with priority might be not the preferable choice for microbiologists but this is how it is.
Authors need to propose a proper formal reclassification of all those species and then submit the request to ICSP to state why the name with priority cannot be applied.

In GTDB, we also united X. citri with other species and the choice of name is based on priority of publication. Please note that GTDB is a classification resource and we follow nomenclature rules only to express our taxonomic opinions. We are unable to publish all opinions formally as we believe that this should be a community effort. Still we thrive to provide you with what we believe is the best taxonomic solution given the current knowledge.

Please let me know if you have any other questions! I am always happy to help.

Best wishes,


Thanks for responding Masha. I think I understand your decision. Am I right in thinking that you recognise X. citri as a species but have chosen X. cissicola as the name to represent this group due to a predefined criteria based on priority of publication? Can I ask what that criteria is?

I can understand the difficulties your team face in this task of classifying all organisms considering the changes experienced in taxonomy in the last 3 decades. Xanthomonas taxonomy is one of the worst as it’s gone through quite substantial changes in the molecular era.

I’m sorry if I’m being pushy about this. However, it’s an issue because several pathovars of X. citri are exotic pathogens to Australia and detections of these require a significant outbreak response. False detections and misclassifications can result in delayed responses and significant consequences to agriculture.

An X. citri outbreak occured in Australian citrus crops very recently in 2018 (https://www.outbreak.gov.au/sites/default/files/documents/citrus-canker-response-summary.pdf) and genomics played an important part in the understanding and control of the outbreak. As GTDB is used quite extensively in shotgun metagenomics studies the risk of misidentification from a metagenomic surveillence is quite high.

Once again, I understand your decision on this but I hope you reconsider. Thanks for your time in responding, again this is a great project.