Predicted Metabolic Potential of Citrobacter farmeri and Enterobacter cloacae from Unhatched Chelonia mydas Eggs: A Genome-Scale Extension

Background/Objectives: Citrobacter farmeri and Enterobacter cloacae are opportunistic Enterobacteriaceae recovered from unhatched Chelonia mydas eggs, but their secondary metabolite and metabolic potential remain unresolved. This study examines which predicted differences between one isolate of each taxon are specific to the isolates and which are shared with public genomes of the same species. Methods: antiSMASH v7.1.0, KofamScan/KEGG-Decoder module profiling (178 modules) with BLASTP verification, and curated CarveMe v1.6.6 genome-scale metabolic modeling were applied to the draft genomes of both isolates. In addition, 18 public genomes (nine C. farmeri; nine labelled E. cloacae, six of them the isolate’s species by average nucleotide identity) were screened with tblastn and uniformly built models. Results: Both isolates carried an enterobactin cluster; E. cloacae also carried an aerobactin cluster and C. farmeri a lower-confidence homoserine lactone synthase. Fourteen of 178 modules differed, notably a cytochrome bc1 complex with c-type cytochromes in C. farmeri versus a Na+-translocating NADH:quinone oxidoreductase (Na+-NQR) operon in E. cloacae. Modeled biosynthetic capacities differed by at most 9.1%. Every presence/absence difference was reproduced in the public genomes (bc1 in 9/9 C. farmeri and 0/9 E. cloacae-labelled genomes; Na+-NQR, pga and iucABCD in 9/9 E. cloacae-labelled and 0/9 C. farmeri genomes); only the Type II secretion cluster varied (absent in 1/9 E. cloacae-labelled genomes). Modeled differences between the isolates matched those among genomes of the same species. Conclusions: The differences are lineage-level features, not isolate-specific traits, and the data do not link them to the turtle-egg niche; all findings are computational predictions requiring phenotypic confirmation.