The strain H. alvei CBA7124 was isolated from a fecal sample of 66-year old Korean female from Geochang, Republic of Korea. The fecal sample was cultured in a brain heart infusion agar (BD) in anaerobic conditions at 37  C for 24 h. The isolate was transferred at least thrice in the same conditions. The cell morphology of the strain was examined using a scanning electron microscope (SEM). The strain was then preserved in 20% (v/v) glycerol at -80  C. The genomic DNA of the isolated strain was extracted using the QuickGene DNA tissue kit S (Kurabo, Japan) and purified using the MG Genomic DNA purification kit (Doctor Protein, Korea). The quality and concentration of the extracted DNA were determined using 1%-agarose gel electrophoresis and a NanoDrop spectrophotometer (Nanodrop Technologies, UK).
Whole genome sequencing was performed using Pacific Biosciences RS II (Pacific Biosciences, Menlo Park, USA) (Additional file 1: Table S1). A 20-kb sequencing library was constructed using SMRTbell  Template Prep Kit and sequenced with P6 polymerase and C4 chemistry. The genome was assembled according to the protocol in the Hierarchical Genome Assembly Process version 2 with PacBio SMRT analysis version 2.3, and polishing was performed with Quiver. Identification of rRNA and tRNA genes was performed with the RNAmmer 1.21 server and the tRNA scan-SE 1.21, respectively. Functional genes were predicted and annotated using the SEED subsystems in the RAST server (rapid annotation using subsystem technology) and the COG (clusters of orthologous groups of proteins) databases. The presence of CRISPRs was detected using the CRISPRfinder server. PathogenFinder was used for predicting pathogenicity towards humans. The ResFinder program was used to screen for antimicrobial resistance genes.
Comparative genomic analysis was performed on 11 Hafnia alvei strains, ATCC 29926, ATCC 13337T, DSM 30099, FB1, HUMV-5920, DSM 30098, LE8, GB001, FDAARGOS_158, bta3-1, and ATCC 51873. The orthologous average nucleotide identity (orthoANI) algorithm was used to measure the phylogenetic distances between these strains. Pan-genome orthologous groups (POGs) were identified using the EzBioCloud Comparative Genomics Database (http://cg.ezbiocloud.net/). The heat map was clustered according to the presence or absence of genes.
Before the genome sequencing, the identity of the H. alvei CBA7124 strain was verified through 16S rRNA gene sequencing and cell morphology analysis (Additional file 1: Figure S1). In addition, the identity of the strain CBA7124 was confirmed through analysis of the 16S rRNA gene obtained after genome sequencing. In addition, we used the orthoANI values with the genome sequence of H. alvei.