Bacillus subtilis is a Firmicutes (Bacillota) bacterium. Strain 168 is described as the best-studied Gram-positive model organism and has well-established RB-TnSeq (random barcode transposon sequencing, a pooled mutant-fitness assay) protocols (Koo et al. 2017). Aliases: B. subtilis, B. subtilis 168. 1
Proposed Fitness Browser library addition
Functional Dark Matter — Experimentally Prioritized Novel Genetic Systems ranks B. subtilis 168 first among proposed RB-TnSeq library additions. The report’s reason is that it would fill the largest phylogenetic gap in kescience-fitnessbrowser and allow Gram-positive versus Gram-negative comparisons for universal dark gene families (DUF484, DUF971, EamA). The existing Fitness Browser Firmicutes strain, BFirm, produced only 5 top-500 genes. The report argues that a purpose-built library with broader condition screening could greatly expand this. 1
The report projects that adding B. subtilis and S. coelicolor would fill the two largest phylogenetic gaps (Firmicutes depth and Actinobacteria absence). Together they would allow cross-phylum testing of the ~100 “universal” dark gene families that currently can only be studied in Proteobacteria. This projection is prospective, not a demonstrated result. It suggests the hypothesis that these families could be tested across phyla once such libraries exist. 1
The report’s own extended covering-set analysis refines this prioritization. That analysis added 25 non-Fitness-Browser organisms to the candidate pool. The conservation-weighted covering set then produced a 50-organism set covering 98.7% of OGs across 6 phyla. At N=5 organisms, coverage reached 57.7%, compared with 38.1% for Fitness-Browser-only candidates. B. subtilis and staphylococcus-aureus were not selected because their OGs are subsets of coverage already provided by Pseudomonadota. The report states that both remain valuable for studying genes in their native Gram-positive genomic context. The two analyses use different criteria: phylogenetic-gap filling and OG coverage. Because of this, the covering-set result qualifies the first-place ranking rather than establishing a conflict with it. How to weigh the two criteria when choosing new libraries remains an open question. 1
In the extended candidate list, B. subtilis 168 is one of six Bacillota organisms. The others are S. aureus USA300, S. pneumoniae TIGR4, C. difficile R20291, E. faecium and L. monocytogenes EGD-e. The list gives tnseq and crispri as the available resources and cites Koo et al. 2017, Bae et al. 2004, van Opijnen et al. 2009 and Dembek et al. 2015. 1
Prophage validation species
Prophage Gene Modules and Terminase-Defined Lineages Across Bacterial Phylogeny and Environmental Gradients used B. subtilis as one of 8 well-characterized prophage-carrying validation species. The other species were E. coli, S. enterica, S. aureus, pseudomonas-aeruginosa, mycobacterium-tuberculosis, V. cholerae and S. pyogenes. 2