Identity
Canonical name: Sinorhizobium meliloti. 1
Known alias: Smeli. 1
Stable external identifier: Not reported in this document. 1
Sinorhizobium meliloti was analyzed to test whether laboratory-measured gene co-fitness predicts gene co-occurrence across bacterial pangenomes. 1
Key Facts from cofitness_coinheritance
The analysis included 241 genomes, 6,004 pangenome clusters, and 528,699 co-fitness pairs for Sinorhizobium meliloti. 1
Its pairwise co-fitness comparison had a delta phi of +0.002, with 230,516 co-fitness pairs; the mean phi was 0.029 for co-fitness pairs and 0.026 for prevalence-matched random pairs, with p<1e-17. 1
Sinorhizobium meliloti contributed co-fitness data to the cross-organism analysis, in which 7 of 9 organisms had positive pairwise co-occurrence effects, although inter-organism variance limited the aggregate interpretation. 1
All organisms in the primary analysis were evaluated by mapping co-fitness pairs to pangenome cluster pairs and calculating phi coefficients from binary genome-by-cluster presence vectors; ten prevalence-matched random pairs were generated per co-fitness pair. 1
A phylogenetic tree was available for Sinorhizobium meliloti in the targeted organism set. 1
Metabolic capability and fitness
In a separate seven-organism pilot, Smeli had complete GapMind predictions for all 18 amino-acid biosynthesis pathways (18/18; 100%). 2 This refines the co-fitness analysis by adding computational pathway-completeness evidence for the same organism, but does not establish that those pathways are essential for viability because the comparison used computational calls and rich-media RB-TnSeq essential-gene data. 2
The Smeli result contributes to the pilot’s observation that 17 of 18 amino-acid pathways were present in all 7 analyzed organisms; the study’s limited sample means this supports near-universal, not bacteria-wide universal, completeness. 2 GapMind coverage and pathway calls may miss non-canonical or divergent routes, so the finding remains computational. 2
The metabolic-capability/dependency analysis included Sinorhizobium meliloti among its seven Tier 1 organisms, extending the earlier completeness result by placing pathway predictions alongside RB-TnSeq fitness evidence rather than treating capability as dependency. 3 The broader study classified 161 organism–pathway pairs into Active Dependency, Latent Capability, Incomplete but Important, and Missing categories, but did not report a Smeli-specific category in the available summary. 3
Functional dark-matter prioritization
The functional-dark-matter study included Sinorhizobium meliloti in its proposed 10 organism–condition experiment set, with one carbon-source and one stress experiment. 4 This extends the earlier co-fitness and essential-metabolome evidence by translating organism-level pathway and fitness integration into targeted experiments, rather than adding a new organism-specific phenotype for Smeli. 4
Across that 10-experiment set, the experiments were projected to address 242 of the top 500 dark genes (45.3%); the Smeli experiments were part of this coverage estimate, which is a prioritization result rather than a direct measurement in this organism. 4
These findings contribute to cofitness-network-architecture, which evaluates whether co-fitness relationships predict pangenome co-occurrence, and to pangenome-integration, which addresses integration of fitness and pangenome presence/absence data. 1
The underlying integration used the kescience-fitnessbrowser dataset together with KBase pangenome and phylogenetic data. 1
For the complete study context, see Co-fitness and Co-inheritance in Bacterial Pangenomes, Essential Metabolome: GapMind Pathway Analysis Across Essential-Gene Organisms, Functional Dark Matter — Experimentally Prioritized Novel Genetic Systems, and Metabolic Capability vs Dependency. 1 2 4 3