Complete genome sequence of Weissella soli strain 3-88 isolated from Kaldá river in Iceland

TL;DR

This paper presents the full genome sequence of a Weissella soli strain from Iceland's Kaldá river, using advanced sequencing technology.

Contribution

The study provides a new genome sequence and classification of a Weissella soli strain from a unique geographical location.

Findings

The genome of Weissella soli strain 3-88 was sequenced using Oxford Nanopore technology.

Average nucleotide identity values were calculated to classify the strain within W. soli.

Abstract

Here, we report the genome sequence of Weissella soli 3-88 isolated from Kaldá river in Iceland, using Oxford Nanopore sequencing. We classified the strain within W. soli by calculating and reporting its average nucleotide identity values compared to other W. soli strains.

Figures

Heatmap of pairwise ANI values among Weissella soli strains and type strains of various Weissella species, including one freshwater isolate from this study and 26 strains obtained from GenBank. The dendrogram at the top illustrates hierarchical clustering of ANI values based on the Euclidean-distance method.

Tables

TABLE 1. Sampling location description and genome characteristics for Weissella soli 3-88

Characteristic	Value
Description of location
Location	Kaldá river, Iceland, near Eldborg crater
Time	30 August 2024
Type	River water
Geographic coordinates	64°46′43.2″N 22°18′06.1″W
Genome statistics
Assembly size (bp)	1,678,388
Number of circular contigs	1
Contig N50 (bp)	1,678,388
Contig L50	1
GC (%)	43.9
Genome coverage	87 ×
Number of 5S rRNA	6
Number of 16S rRNA	6
Number of 23S rRNA	6
Number of tRNAs	65
Total number of genes	1678
Total number of CDS	1592
Total number of pseudogenes	7
TYGS taxonomy	Weissella soli
GTDB taxonomy	Weissella soli
EPS	eps cluster
Data accession
BioProject	PRJNA1238846
BioSample	SAMN47485272
SRA	SRS24439780
Genome assembly	CP186084

Full text

ANNOUNCEMENT

Weissella soli, found in soil and foods, has technological potential as a producer of exopolysaccharides (EPS) and lactic acid (1–3). A W. soli isolate was obtained from the Kaldá river in Iceland (Table 1) by incubating an unfiltered, undiluted surface water sample in all-purpose Tween (APT) broth (Difco, Sparks, MD) under microaerophilic conditions, using a candlelight, at uncontrolled room temperature for 7 days, before transfer to APT agar (1.35%; Merck, Darmstadt) and anaerobic incubation at 25°C. Gram-positive, catalase-negative lactic acid bacterial colonies were re-streaked and cultured in APT broth for genomic analysis.

Genomic DNA was extracted using the Bead-Beat Micro AX Gravity kit (A&A Biotechnology, Gdynia, Poland), which combined with the Native Barcoding Kit (SQK-NBD114.96, Oxford, UK), ensures isolation of high molecular weight DNA and generation of raw reads with an N50 of approximately 10 kb. DNA concentration was measured with a Qubit 4 fluorometer (Thermo Fisher, Waltham, USA). The final library with ligated motor protein was washed with Long Fragment Buffer to enrich for DNA fragments larger than 3 kb. DNA sequencing was conducted on a PromethION 2 Solo platform using R10.4.1 flow cell (FLO-PRO114M). Basecalling was conducted using the dna_r10.4.1_e8.2_400bps_sup@v5.0.0 basecalling model, and demultiplexing and adapter trimming were performed with Dorado v0.8.1 (https://github.com/nanoporetech/dorado). Bedtools v2.30.0 (4) and seqkit v2.1.0 (5) were utilized to convert the obtained bam files to FASTQ format and to remove duplicated reads, respectively.

Genome assembly and circularization were conducted using Hybracter v0.9.0 (6) using the flye --nano-hq model (7) and the Plassembler (8) plsdb_2023_11_03_v2 database. Reads were filtered at a minimum length of 1,000 bp and a quality score of 16, and the subsample depth value was set at 110×. After filtering, a total of 19,966 reads with an N50 of 9,799 bp were used for the assembly. Chromosome size was estimated automatically with the --auto flag. Polishing with medaka was omitted due to its potential to reduce accuracy (9). The genome was reoriented to start at DnaA using dnaapler v0.8.1 (10).

The complete genome was classified with the Type strain Genome Server (TYGS) v391 (11) and GTDBtk v. 2.3.2 against the Genome Taxonomy Database (release 214) (12). Annotation was conducted using the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) (13–15). The average nucleotide identity (ANI) values between strain 3-88 and other Weissella spp. genomes were calculated by Orthologous ANI tool (16) and visualized using Chiplot (https://www.chiplot.online/) (Fig. 1).

Heatmap of pairwise ANI values among Weissella soli strains and type strains of various Weissella species, including one freshwater isolate from this study and 26 strains obtained from GenBank. The dendrogram at the top illustrates hierarchical clustering of ANI values based on the Euclidean-distance method.

The genome sequence contained genes (bp 1377492–1391637) corresponding to the eps cluster for EPS production via the Wzx-Wzy pathway, the most common pathway for heterosaccharide EPS biosynthesis in lactic acid bacteria, yet understudied in Weisella (17). The regulatory genes cpsBC were detected by homology with those of Lactococcus lactis KLDS 4.0325 using Protein Basic Local Alignment Tool (BLASTP) (18). The Wzx and Wzy flippase and polymerase functions were inferred based on transmembrane domain similarity to KLDS 4.0325, with domains predicted using DeepTMHMM v1.0 (19). Finally, BLASTP analysis resulted in no significant hits against the well-established glucansucrase of Weisella confusa LBAE C39-2 (18, 20).