What this entity is
Canonical name: Mycobacteriaceae. 1
Mycobacteriaceae is a bacterial family analyzed in the Gene Function Ecological Agora project as a focal clade for mycolic-acid gene-function innovation. 1
Known aliases: No aliases were reported in this project document. 1
Stable external identifier: No stable external identifier was reported in this project document. 1
Findings from the Gene Function Ecological Agora
At family rank, the Mycobacteriaceae × mycolic-acid hypothesis was supported, with producer Cohen’s d = +0.31 and consumer Cohen’s d = −0.19. 1
At order rank, the corresponding mycolic-acid result had producer d = +0.288 and consumer d = −0.285. 1
The family-rank Innovator-Isolated subset contained 67 of 582 tuples, or 11.51%, compared with 5.85% across the full atlas. 1
Mycobacteriaceae mycolic-acid gains comprised 53,916 events, of which 79.87% were recent, 16.72% older-recent, 3.41% mid, 0.00% older, and 0.00% ancient. 1
The Mycobacteriaceae gain profile was more recent-weighted than the all-mycolic-acid reference profile, which comprised 48.79% recent, 31.81% older-recent, 9.60% mid, 6.12% older, and 3.68% ancient events. 1
The mean leaf_consistency value for the Mycobacteriaceae mycolic-acid result was 0.15, below the atlas reference of 0.20, indicating that the family-level result was a mixture of within-family sub-clades rather than a uniform family property. 1
A mycolic-positive sub-clade comprising 10 of 13 genera had producer d = +0.394, compared with family-rank d = +0.309 and mycolic-low sub-clade d = +0.211. 1
Consumer d was +0.006 for the mycolic-positive sub-clade, indicating that the original consumer-side Innovator-Isolated signal was rank-dependent and strongest at family aggregation. 1
Ecology and phenotype
Mycobacteriaceae showed 7.88× host-pathogen enrichment with p < 10⁻⁴⁵, while its soil enrichment was 0.88× with p = 0.87. 1
Among 318 Mycobacteriaceae species represented in the phenotype data, 95% of recorded cell shapes were rod-shaped, 99% were non-motile, and 89.4% were aerobic-leaning. 1
In alph-aearth environmental embeddings, 50 Mycobacteriaceae species were analyzed; 34.0% occurred in a gut+sludge cluster and 20.0% occurred in another gut cluster using k = 10 clustering. 1
These ecology and phenotype results are consistent with the project’s interpretation of Mycobacteriaceae as a host-associated focal clade, but they establish association rather than a causal effect of environment on gene innovation. 1
The Polyhydroxybutyrate Granule Formation Pathways — Distribution Across Clades and Environmental Selection analysis further identified Mycobacteriaceae among families enriched for phaC, the committed PHB synthase gene, in corrected family-level tests. This supports a family-level association with PHB distribution but refines the host-associated interpretation: the PHB result alone does not establish that host association drives PHB prevalence, especially because environmental labels were sparse and “other_unknown” was common. 2
Mobile-genetic-element context
The Mycobacteriaceae mycolic-acid hypothesis set had an MGE-machinery rate of 0.57%, compared with an atlas-wide baseline of 1.37% of KO-bearing gene clusters. 1
The project did not complete large-scale mycolic-acid gene-neighborhood scans because Spark and pandas joins exceeded memory limits, so the non-phage-borne interpretation relies on per-cluster MGE-machinery rates and literature context rather than complete cargo-neighborhood scans. 1
Related topics
The family-level result contributes to gene-function-acquisition-depth, which synthesizes Sankoff-derived acquisition depth and within-clade consistency. 1
It also contributes to ecotype-environment-gene-content through the relationship between clade-specific gene-function patterns, environmental enrichment, phenotype data, and within-clade structure. 1
The focal pathway discussed here is mycolic acid. 1
The phenotype evidence was drawn from bacdive, and the environmental clustering used alph-aearth. 1
The PHB finding also feeds phb-granule-ecology as family-level evidence for uneven pathway distribution across clades. 2