Genome sequence-based identification of Enterobacter strains and description of Enterobacter pasteurii sp. nov

Abstract

Accurate taxonomy is essential for microbial biological resource centers, since the microbial resources are often used to support new discoveries and subsequent research. Here, we used genome sequence data, alongside matrix-assisted laser desorption/ionization time-of-flight mass spectrometer biotyper-based protein profiling, to accurately identify six Enterobacter cloacae complex strains. This approach effectively identified distinct species within the E. cloacae complex, including Enterobacter asburiae, "Enterobacter xiangfangensis," and Enterobacter quasihormaechei. Moreover, the study revealed the existence of a novel species within the Enterobacter genus, for which we proposed the name Enterobacter pasteurii sp. nov. In summary, this study demonstrates the significance of adopting a genome sequence-driven taxonomy approach for the precise identification of bacterial strains in a biological resource center and expands our understanding of the E. cloacae complex.

Keywords: Enterobacter; Enterobacteriaceae; MALDI-TOF MS; phylogenomic; taxonomy.

Fig 1

Phylogenetic tree inferred using the likelihood method in IQ-TREE pipeline using the concatenated alignment of bac120 genes of six E. cloacae complex strains and their closely related taxa. Values shown next to the branches are the percentage of replicate trees with associated taxa clustered together in the bootstrap test (1,000 replicates). The color strips indicate the ANI values.

Fig 2

Phylogenetic tree inferred using the likelihood method in IQ-TREE pipeline using the concatenated sequences of 2,551 core genes identified and extracted from only Enterobacter genome data set (consisting six E. cloacae complex CIP strains, four strains identical to strain A-8^T, and all type strains of Enterobacter species) using Panaroo. Values shown next to the branches are the percentage of replicate trees with associated taxa clustered together in the bootstrap test (1,000 replicates). The color strips indicate the ANI values.

Fig 3

(a) Gram stain image of cells of strain A-8^T under a bright-field microscope at magnification 100×; (b SEM image of cells of strain A-8^T. Arrows indicating the formation of constriction.

Fig 4

Pangenome analysis depicting the shared and unique gene clusters (nos. 14,270) among the members of the genus Enterobacter. The genomes are organized in radial layers such as genus core, genus soft core, species core, and unique singleton gene clusters (Euclidean distance; Ward linkage) which are defined by the gene tree in the center. E. pasteurii sp. nov. is represented by genomes including strain A-8^T and four strains identical to A-8^T, while E. asburiae, E. quasihormaechei, and “E. xiangfangesis” include genomes of strains used in this study along with the type strains, and the remaining species are represented by genomes of their type strains.