Upon going through GTDB articles, FAQs, and taxon history I still couldn’t understand why the family Alteromonadaceae is classified under the parent order Enterobacterales. According to NCBI, WORMS, and LPSN the family Alteromonadaceae is categorized under the order Alteromonadales . I am aware that different databases may use different sets of marker genes, but I don’t understand why only GTDB includes Alteromonadaceae in the parent order Enterobacterales.
Will be a great help if you can clarify this.
Salute to the GTDB team for all the hard work in maintaining this enormous comprehensive prokaryotic classification database.
This classification is based on the relative evolutionary divergence (RED) of the group. The Alteromonadales is too shallow to be classified as an order as is the Enterobacteriales as currently defined in LPSN/NCBI. Together they are form a monophyletic group with a RED in the order-level range (similar to Pseudomonadales). Ultimately, there is no right or wrong, this is the taxonomic opinion of the GTDB team.
Thank you for clarifying that.
@Phil_Hugenholtz @p.hugenholtz It appears that in the 214 release, the familyAlteromonadaceae has been moved to a new classification, specifically o__Enterobacterales_A. The suffix (_A) is consistent with your earlier response. However, the reason why Alteromonadaceae was included in earlier editions in the o__Enterobacterales without a suffix is unclear.
Sorry for the lengthy message. The focus of my current article is f__Alteromonadaceae, which I have labeled as a member of o__Enterobacterales. Will this cause any issues? or should I use NCBI taxonomy instead?
Phil is on holidays at the moment, so I permit myself to reply.
The reason this family is under the Enterobacterales_A in R214 is because the order is not resolved as monophyletic in the current reference tree. Typically this would be caused by endosymbionts with reduced genomes from the family Enterobacteriaceae. This group will then be given a suffix at the family and order level since the type genus of Enterobacteriaceae and its other members (together with other families of Enterobacterales including Alteromonadaceae) will be located in another part of the tree. In R214, all members of the family Enterobacteriacea (including the type genus Enterobacter) are, unfortunately, split from the rest of the order. According to the nomenclature rules, the portion of taxon that contains nomenclature type keeps the name. This is why this time we have family Alteromonadaceae under the suffixed order name. For the purpose of the paper, I will use order name Enterobacterales without a suffix. We still assume that this order is monophyletic but just not resolved as such in the current tree (the are more evidence for it to be so).
Please don’t hesitate to ask any further questions!
@m.chuvochina thank you for your quick and clear response. Yes, I have used Enterobacterales without a suffix in the manuscript. I really appreciate the efforts put forward by you and other members of the GTDB team in maintaining this vast database.