What this entity is
Canonical name: Klebsiella oxytoca. 1
Known alias: Koxy, the study label used for this organism. 1
Stable external identifier: No stable external identifier was provided in the source document. 1
Key facts from cofitness and co-inheritance analysis
Klebsiella oxytoca was one of 11 species initially targeted for analysis, and it contributed data to the primary analysis. 1
Its dataset contained 399 genomes, 4,942 pangenome clusters, and 423,936 co-fitness pairs. 1
Among 162,160 co-fitness pairs evaluated for co-occurrence, the mean phi coefficient was 0.041 for co-fit pairs versus 0.038 for prevalence-matched random pairs, giving a delta phi of +0.003 with p=3.3e-2. 1
Across organisms, Klebsiella oxytoca showed a small positive pairwise co-occurrence effect, consistent with the broader result that pairwise co-fitness only weakly predicts pangenome co-occurrence. 1
Its ICA (independent component analysis) module results included 44 modules, of which 14 (32%) were significant; the mean within-module phi was 0.079 versus a null mean of 0.040. 1
The analysis mapped co-fitness pairs to pangenome cluster pairs using fb_pangenome_link.tsv, deduplicated the mappings, and evaluated binary genome-by-cluster presence vectors with phi coefficients. 1
Ten prevalence-matched random pairs were generated per co-fitness pair, with each cluster’s prevalence matched independently within a tolerance of +/-5%. 1
The study used Klebsiella oxytoca to examine how laboratory co-fitness measured in the kescience-fitnessbrowser relates to gene co-occurrence in bacterial pangenomes, contributing to cofitness-network-architecture and pangenome-integration. 1
Essential dark-gene prioritization
The newer functional-dark-matter analysis refines this organism’s role beyond co-fitness and pangenome co-inheritance by listing Klebsiella oxytoca BWI76_RS08540 among its highest-ranked essential dark-gene candidates. The candidate received a score of 0.865 and had OmpA/TIGR02802 domain predictions. 2
Because essential genes lack viable transposon mutants and therefore standard fitness magnitudes, the report recommends crispri knockdown followed by growth measurements under standard and stress conditions as the experimental strategy for such candidates. 2 This provides a testable extension of the existing co-fitness evidence rather than contradicting its finding that pairwise co-fitness only weakly predicts pangenome co-occurrence. 2
Source
- Co-fitness and Co-inheritance in Bacterial Pangenomes — co-fitness and co-inheritance analysis across bacterial pangenomes. 1
- Functional Dark Matter — Experimentally Prioritized Novel Genetic Systems — experimentally prioritized dark genes and essential-gene follow-up strategies. 2