How should one handle polyphyletic taxa in Greengenes2 in publications (for example, there are Firmicutes_A, ...B, and so on)? Keep them like this, or combine as Firmicutes?
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They're phylogenetically distinct, so lumping them together is (sort of) similar to lumping Proteobacteria and Bacteroidetes together. More information on the justification from GTDB can be found here.
Best,
Daniel
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All right, that made it pretty clear 
The link refers to ”alternative evidence that they are monophyletic”. Apologies for my ignorance, but I’m not deeply familiar with GTDB or the current microbial taxonomy work in general. May I ask what is the status of GTDB currently in this field? Compared to e.g. LPSN or SILVA (which still have monophyletic ”Firmicutes”) or NCBI Taxonomy (which has monophyletic ”Bacillota”)? For example, from the practical point of view of nomenclature in a manuscript.
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GTDB is curated by Phil Hugenholtz, who is the original curator for Greengenes, and a well known microbial taxonomist among other roles. It is a phylogenomic taxonomy so it is based on molecular data like SILVA. Unlike SILVA, GTDB is based on whole genome phylogeny. SILVA if I recall actually expresses Firmicutes as polyphyletic in its tree, but doesn't differentiate the labels, similar to Greengenes 13_8. NCBI is explicitly not an authoritative taxonomy per their own disclaimer, and LPSN is not curated as far as I know with respect to phylogeny.
Best,
Daniel
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