Thread by @Ge_BoRo

The ICSP voted to include the rank "phylum" into the code of bacterial nomenclature, and NCBI taxonomy followed.

Many people voiced anger for this #taxonomygate bc... twitter. Here some thoughts on the matter... (1/n)

https://twitter.com/watermicrobe/status/1469791937419005959?s=20

There were many complains about nomenclature being worthless or irrelevant. As a microbial ecologist, I understand where this comes from, particularly with bioinformatic tools that require only spaceholders as identifiers. As a microbiologist, I think this is short-sighted. (2)

But #microbialtaxonomy is important for other people too. For example, it is central for diagnostics in #healthcare and #foodsafety and #biotechnology. Many who don't care about ecology or evolution need this.
It might not matter to you, but it matters to others. (3)

Now #bacteriasystematics is particularly problematic because "the sheer diversity" of the microbial world and the lack of a species unit. And recently, the fact that bioinformatics made comparative genomics easier, while genome quality remains hard. (4)

We cannot "simply embrace it". A taxonomy needs to be logical, and we've agreed on making it "natural" by reflecting the evolutionary relationships amongst microbes.
But it also needs to be practical, useful: We'll keep Ecoli separate from Shigella and Citrobacter, it is useful

This also means that taxonomy will keep changing. As someone pointed out to me, it is a model just as phylogenies are hypotheses.
There will always be a trade-off between updating it and keeping it consistent, and we will have to live with it. (6)

So this change affects deep taxonomic ranks. Most didn't even know that phylum wasn't in the #ICNP. imho this was a good change.
Your species, genus and family names will keep changing bc 1. we don't really have a natural bacterial species concept and 2. we keep learning. (7)

This is hard, and considering all the stakeholders' opinions makes it harder.
But the recent revision of genus Lactobacillus, one of the oldest and most studied bacterial groups sets an example of how it can be done minimizing disruption.
doi.org/10.1099/ijsem.… (8)

I welcome the introduction of the "-ota" suffix for phyla, as extesnively explained by Phil Hugenholtz's commentary here:

https://twitter.com/PhilHugenholtz/status/1470225417017511938?s=20

(9)

My (loud?) complain is towards the change of the name of three phyla, which are the oldest, most studied, perhaps most abundant and diverse bacterial phyla almost everywhere. (10)

First, Proteobacteria and Firmicutes represent very broad groupings that appeared much later than the description of their first species. That is we knew they are together much later. (11)

"Proteo" comes from the morphing god "Proteus", grouping what we haven't been able to group.
But we all know what we mean what #Proteobacteria are now, it is a real lineage that is easily identified and has now a meaning by itself. w/o delta and epsilon after the update.
(12)

But going for 'Pseudomonadota doesn't makes any sense, since #Pseudomonas is not a representative of the #Proteobacteria. The name would be misleading and confusing, just imagine talking about "#Acetobacter the Pseudomonadota"... (13)

In the same sense, #Firmicutes refers to the single thick cell wall present in most of its members, while 'Bacillota' implies a bacilli shape way less widespread, or a similarity with Bacillus, which is not the case of many members (just think #Clostridia or #Veillonella) (14)

Finally, Actinomycetota. #Actinobacteria includes organisms that were thought to be fungi. But they are not. Putting that 'mykes' in the very name of the phylum is imho a terrible, misleading mistake. (15)

Anyway, I think most of the discussion stems from a lack of understanding of the opposite arguments. If you don't mind about names, then let people keep the names they want. If you do care deeply about a name for your research, I also think you should be consulted. Cheers. (16)

A thread with a different yet similar view.

https://twitter.com/archaearama/status/1470141668385075200?s=20

This!

https://twitter.com/Joe_E_Weaver/status/1470340970474524672?s=20