Whole-genome sequences of fermentative and spoilage-associated lactic acid bacteria, Lysinibacillus capsici and a Serratia marcescens isolated from commercial cucumber fermentations

ABSTRACT

We report the annotated, whole-genome sequences of 16 bacteria isolated from commercial cucumber fermentations. The collection consists of nine fermentative and two spoilage-associated lactic acid bacteria, four Lysinibacillus strains, and a Serratia marcescens. Half the genome assemblies have fewer than 10 contigs, and the remainder have fewer than 30.

ANNOUNCEMENT

We document genome sequences of Bacilli and a Serratia marcensens isolated from commercial cucumber or sauerkraut fermentations between 1985 and 2015 to augment understanding of the genetics, diversity, and functions hosted in such habitats. Table 1 describes the collection site and year of isolation for the pertaining bacterial cultures. The genome sequences described for Lactococcus lactis 1.8.12, Lactiplantibacillus pentosus MU045, Lactiplantibacillus plantarum 3.2.8, and Pediococcus ethanolidurans 7.8.34 are higher quality versions of previous submissions (1). Additional genome sequences include those for a Lactiplantibacillus paraplantarum, strain 1049, isolated from sauerkraut fermentation by Plengvidhya et al. (2), a Lentilactobacillus buchneri, strain LA1147, isolated from a spoiled commercial cucumber fermentation by Franco et al. (3), and five isolates from commercial cucumber fermentations obtained by Pérez-Díaz et al. (4). S. marcensens was associated with fermented cucumber bloater defect (5) and was isolated from a commercial cucumber fermentation by Pérez-Díaz et al. (6). The four genome sequences derived from Lysinibacillus are relevant to the instability of cucumber fermentation (7).

TABLE 1.

Accession numbers, assembly size, number of contigs, estimated coverage, read pairs, GC content, N50, and site of collection for the genome sequences described in this announcement^a

Strain IDs	NCBI accession number	SRA accession number	Assembly Size (bp)	Contigs	Estimated coverage (x)	Reads	Average raw read length	GC %	N50 (bp)	Collection site	Year of isolation
Lactiplantibacillus pentosus MU045b	JAGYHB000000000	SRR30004943	3,918,757	15	343.29	206,977	6,599.9	45.87	743,007	Mount Olive, NC	1985
Lactiplantibacillus paraplantarum 1049	JBFQYK000000000	SRR30005391	3,381,196	18	288.41	208,150	6,747.6	43.77	401,827	Raleigh, NC	2007
Lactiplantibacillus plantarum 3.2.8b	JAGYGQ000000000	SRR30005648	3,474,346	19	307.15	161,957	6,654.4	44.22	538,455	Mount Olive, NC	2009
Lactiplantibacillus plantarum 7.2.2	JBFRXW000000000	SRR30005937	3,386,939	20	499.998	248,256	6,862.1	44.35	703,285	Mount Olive, NC	2009
Lactococcus lactis 1.8.12b	JAGXCF000000000	SRR30004724	2,638,785	6	288.43	142,637	7,065	34.89	669,663	Mount Olive, NC	2009
Pediococcus pentosaceus 7.2.5	JBFRXV000000000	SRR30006351	1,901,884	15	658.8	214,163	7,048.7	37.2	294,304	Chaska, MN	2009
Weissella cibaria 7.8.34b	JBFWFW000000000	SRR30004637	2,499,177	7	430.154	192,976	5,587.6	44.81	778,684	Chaska, MN	2009
Weissella cibaria 7.8.48	JBFSEU000000000	SRR30006352	2,465,329	9	525.509	211,757	7,375.2	44.85	627,387	Chaska, MN	2009
Weissella paramesenteroides 3.8.13	JBFSEV000000000	SRR30151572	1,946,180	9	576.422	164,515	7,055.6	38.16	573,469	Mount Olive, NC	2009
Lentilactobacillus buchneri LA1147	JBFYGS000000000	SRR30151571	2,712,685	29	405.195	194,664	6,397.1	44.07	334,936	Mount Olive, NC	2010
Lentilactobacillus buchneri 90.8.10	JBFPKA000000000	SRR29918579	2,760,920	17	288.37	113,900	7,051.1	43.92	716,767	Mount Olive, NC	2009
Lysinibacillus capsici Lys06	JBFRXU000000000	SRR30006354	4,676,048	6	304.616	209,238	6,811.7	37.56	1,387,322	Mount Olive, NC	2015
Lysinibacillus capsici Lys16	JBGGIA010000000	SRR30005219	4,639,468	8	340.349	221,361	7,156.5	37.53	1,191,594	Mount Olive, NC	2015
Lysinibacillus capsici Lys19	JBFRXT000000000	SRR30006353	4,644,541	6	444.197	299,160	6,906.2	37.54	4,316,120	Mount Olive, NC	2015
Lysinibacillus capsici Lys21	JBFRYD000000000	SRR30151570	4,709,305	11	323.559	212,901	7,175.9	37.35	1,054,235	Mount Olive, NC	2015
Serratia marcescens 1.8.3	CP163407	SRR30151569	5,241,778	1	295.691	226,499	6,848	59.4	5,241,778	Mount Olive, NC	2009

^a Sites of sample collection are abbreviated as NC and MN for North Carolina and Minnesota, USA, respectively.

^b An asterisk (*) after the strain identification on the first column identifies isolates with previously published genome sequences of lower quality (1).

Pure cultures were transferred from frozen stocks to Lactobacilli deMan, Rogosa, and Sharpe (MRS) broth to obtain a pellet for DNA extraction, while the Lysinibacillus and S. marcensens were transferred to brain heart infusion (BHI) broth. Lysinibacillus was incubated with shaking at 23°C for 48 h. All other cultures were incubated without shaking and aerobically at 30°C in the media described above for 48 h. The Promega Wizard Genomic DNA Extraction Kit (Madison, WI) was used to lyse cells. The cell lysates were treated with 25:24:1 phenol:chloroform:isoamyl alcohol followed by ethanol precipitation (8). A second protein precipitation was performed as needed using the kit described above. The extracted DNA was used for sequencing performed as previously described (9). Briefly, the genomic DNA was sheared using Covaris G-tubes (Woburn, MA) targeting 10 kb fragments. Sheared DNA was prepared for PacBio sequencing using the SMRTbell Prep Kit 3.0 (PacBio, Menlo Park, CA). Samples were barcoded, and libraries were size selected with AMpure PB beads (Pacific Biosciences, Menlo Park, CA) to remove fragments less than 3 kb. Sequencing was performed on a Revio System (Pacific Biosciences, Menlo Park, CA) using the corresponding Polymerase Kit, Sequencing Reagents, and SMRTcell. To target HiFi reads, the library was sequenced using a 30 h movie time using Instrument Control Software Version 13. Raw subreads were converted to HiFi data by processing with circular consensus sequences (CCS) to call a single high-quality consensus sequence for each molecule, using a 99.5% consensus accuracy cutoff. De novo assembly was performed in BV-BRC v. 330.19a (10) via Metaflye v. 2.9.1-b1780 (11) with a minimum contig cut-off of 300 nucleotides. Quality assessment of assemblies was performed with QUAST version 5.0.2 (12), and SamTools version 13 (13). The closest reference genomes were identified with minhash search by Mash (14) using the PATRIC database (15) within BV-BRC. Upon submission to GenBank (Bioproject PRJNA674638), assemblies were reannotated using the NCBI Prokaryotic Genome Annotation Pipeline v. 6.7 (16). Default parameters were used for all software, unless otherwise specified.

DATA AVAILABILITY

Table 1 describes strain identification and accession numbers for each genome annotation and sequence read archive entry.