Genomic Bacterial Species Identification

Explain why a Kraken species call alone cannot establish the species identity of a cultured Enterobacter isolate.

Compare NCBI Taxonomy, GTDB, and validly published nomenclature for an Enterobacter reference genome and document any naming conflicts.

Interpret pairwise average nucleotide identity (ANI) against accepted species-level guidance, including borderline and multi-match results.

Decide when an ANI result requires confirmation by digital DNA–DNA hybridization (dDDH) or phylogenomic analysis.

Construct a versioned comparison set containing appropriate Enterobacter type-strain genomes and high-quality near-neighbour genomes.

Run Kraken 2 on isolate data and interpret the result as a database-dependent screening signal rather than a definitive species assignment.

Run GTDB-Tk on an Enterobacter assembly and interpret its placement within a standardized genome taxonomy.

Calculate ANI between an isolate and the curated reference set and identify all references that meet or approach the species boundary.

Calculate or retrieve dDDH estimates for the strongest candidate references and interpret them alongside ANI.

Construct a focused core-genome phylogeny containing the isolate, relevant Enterobacter references, and a suitable outgroup.

Reconcile Kraken screening, GTDB-Tk placement, ANI, dDDH, and phylogenetic placement into a confidence-rated taxonomic conclusion.

Produce a reproducible species-identification report that records input provenance, software and database versions, decision thresholds, conflicting evidence, and justified reporting at species or species-complex level.