The genus Kaistella genus belonging to the family Weeksellaceae was first established by Kim et al. (2004). Since the first report, twenty Kaistella species have been isolated from diverse ecological niches, including soil, aquatic environments and plants root to date (Kim et al., 2004; Kämpfer et al., 2011; Ren et al., 2021; Ai et al., 2024). Members of Kaistella are aerobic, Gram-negative, rod-shaped bacteria that produce yellow pigment and possess genomes ranging from 1.3 Mb to 3.7 Mb. In spite of their noted phenotypic and genotypic characteristics, their roles in the ecosystem have not been extensively studied so far.

Strain 97-N-M2 was isolated from the muscle of a minke whale Balaenoptera acutorostrata collected from Ulsan, South Korea. A 0.1 g of homogenized muscle was serially diluted using phosphate-buffered saline solution (pH7.4, Gibco), and 100 µl of each diluted sample was inoculated onto nutrient agar plates (NA, Difco) and incubated at 25℃ for two days. After the first incubation, colonies were transferred to new NA plates and incubated under the same conditions. Through the second incubation, circular, opaque, slimy, and yellow colonies of strain 97-N-M2 were observed and purely isolated.

The 16S rRNA sequence of the strain showed low similarity compared to the Kaistella jeonii DSM 17048^T (similarity of 97.36%), K. chaponensis DSM 23145^T (97.29%), and Chryseobacterium salivictor NBC122^T (97.29%), which belong to the family Weeksellaceae.

The genomic DNA of strain 97-N-M2 was purified using the MiniBEST Bacteria Genomic DNA Extraction Kit (TaKaRa) and was used for library construction using the Ligation Sequencing Kit (LSK-SQK109, Oxford Nanopore) according to the manufacturer’s instructions. Genomic DNA library was then sequenced by using the MK-1C Nanopore platform (Oxford Nanopore). After sequencing, basecalling and adapter removal were conducted, and sequence reads with the Phred quality score greater than Q7 were assembled using CANU assembler (version 2.0). The library construction and sequencing processes were performed in GENCUBE PLUS (Korea).

Through sequencing and assembly, a single circular genome sequence which was 2,870,393 bp in length (depth of 132×) with 40.5 mol% of the G + C content was obtained and the circular genome map was generated by a browser-based tool Proksee (https://proksee.ca/) (Fig. 1). The complete genome of strain 97-N-M2 was then annotated by NCBI Prokaryotic Genome Annotation Pipeline (PGAP; Tatusova et al., 2016) and a total of 2,687 genes including 2,633 coding sequences (CDSs), 9 ribosomal RNAs (5S, 16S, 23S), 42 transfer RNAs (tRNAs), and 47 pseudogenes were annotated (Table 1).

Table 1

Genome features of Kaistella sp. 97-N-M2 and the close species

Feature	Kaistella sp. 97-N-M2	K. jeonii DSM 17048T	K. chaponensis DSM 23145T	Chryseobacterium salivictor NBC122T
Number of contigs	1	35	34	1
Genome length (bp)	2,870,393	3,261,282	3,043,150	3,139,453
G + C contents (mol%)	40.5	35	35.5	37.5
Total genes	2,687	3,021	2,784	2,875
Total CDS	2,633	2,977	2,742	2,812
rRNAs (5S, 16S, 23S)	3, 3, 3	2, 1, 1	1, 1, 1	4, 4, 4
tRNAs	42	37	36	48
ncRNAs	3	3	3	3
Pseudogenes	47	22	16	21

Data were obtained from NCBI RefSeq.

Fig. 1. Complete genome of Kaistella sp. 97-N-M2. From the inside to the outside: genome label, G + C contents (black), GC skew (green and purple), Reverse CDS, and Forward CDS.

Two CRISPR spacers were detected by CRISPR CasFinder (Couvin et al., 2018) and one incomplete prophage sequence with 56.8 kb region length was found by PHAge Search Tool Enhanced Release (PHASTER; Arndt et al., 2016). A gene cluster involved in biosynthesis of cartenoid pigment was detected by antiSMASH secondary metabolite finder (Blin et al., 2021). Functional annotation of genome was performed by KEGG BlastKOALA (Kanehisa et al., 2016). The genome of strain 97-N-M2 harbored genes encoding endoglucanase (locus tag: L0B70_12260), beta-glucosidase (L0B70_00790), cellobiose 2-epimerase (L0B70_12215), alpha-amylase (amyA, L0B70_09810 and L0B70_03245), glucan 1,4-alpha-glucosidase (SusB, L0B70_09450) and 1,4-alpha-glucan branching enzyme (glgB, L0B70_09650) which are related to the degradation of cellulose and polysaccharide. Also, genes encoding phytoene desaturase (CrtI, L0B70_00710), beta- carotene 3-hydroxylase (CrtZ, L0B70_00725), and glycosyltransferase 2 family protein (L0B70_01845 and L0B70_ 01910) which are involved in carotenoid biosynthesis and, genes encoding peptidoglycan lytic transglycosylase G (mltG, L0B70_09715), peptidoglycan lytic transglycosylase (rlpA, L0B70_09715), N-acetylmuramoyl-L-alanine amidase (amiABC, L0B70_04080), and N-acetylmuramoyl-l-alanine amidase (amiD, L0B70_09610) which degrade bacterial peptidoglycan were annotated. The genome information will provide fundamental knowledge for understanding the ecological roles of Kaistella species in various environments.

Nucleotide sequence accession numbers

Kaistella sp. 97-N-M2 has been deposited in the Korean Collection for Type Cultures with the accession number KCTC 92273 and the complete genome sequence has been deposited in GenBank with the accession number CP090976.

대한민국 울산에서 혼획된 밍크고래의 근육 샘플로부터 분리된 Kaistella sp. 97-N-M2 균주는 2,870,393 bp 길이의 유전체를 가지며, G + C 함량 40.5%로 총 2,687개의 유전자 중 2,633개의 단백질 암호화 서열, 9개 rRNA (5S, 16S, 23S), 42개 tRNA, 그리고 47개의 pseudogene 서열을 포함하는 것으로 확인되었다. 본 연구는 균주의 유전체 내 셀룰로오스와 다당류 분해, 카르테노이드 색소 합성, 세균 펩티도글리칸 분해에 관여하는 다양한 유전자 서열을 확인하여 그동안 자세한 연구가 진행되지 않은 Kaistella 속 세균들의 생태학적 역할을 이해하는데 기초 정보를 제공한다.

This research was supported by National Institute of Fisheries Science grant (R2024053) funded by the Ministry of Oceans and Fisheries.

The authors have no conflict of interest to report.