Reviewer's Criticism on Methodology and Phylogenetic Analyses: A Detailed Breakdown

The reviewer criticizes the authors for inadequately describing their methodology, hindering the reproducibility of their analyses. They express concern about the selection of reference sequences and the lack of clarity regarding the parametrization of various software used. Specifically, the reviewer requests detailed information on the alignment and concatenation of marker genes used in the analyses.

The reviewer questions the significance of the authors' 16S rRNA gene analysis, noting that a similar study with a broader set of reference sequences has already been published. They point out inconsistencies between the phylogenies presented by the authors, specifically regarding the placement of 'Steroidobacteraceae' and the lack of discussion on these discrepancies. The reviewer also suggests including reference sequences from Hoffmann et al. (2020) in the figures to facilitate comparison.

Regarding the concatenated protein marker phylogeny, the reviewer seeks clarification on the methodology used and its added value compared to the GTDB phylogeny, particularly if both analyses rely on the same marker genes and a more comprehensive set of taxa in GTDB.