Draft Genome Sequences of 18 Streptococcus Strains Isolated from Live Dietary Supplements and Cultured Food Products

ABSTRACT

We present the genome sequences of 18 Streptococcus isolates from 8 different dietary supplements and 9 cultured food products. Strains from this species naturally colonize the human mouth and upper respiratory tract. Studies have shown that S. thermophilus and S. salivarius strains confer oral health benefits to their host with little to no risk of pathogenic infection.

ANNOUNCEMENT

Streptococcus is a Gram-positive, lactic acid bacterium found in dairy products and dietary supplements. S. thermophilus use in fermentation of milk products has been linked to the facilitation of dairy product digestion (1, 2). S. salivarius naturally resides in the mouth and upper respiratory tract and is one of the first beneficial microbes to colonize infants (3). This species is thought to be beneficial in the reduction of dental plaque and periodontal health when administered orally (4, 5). It has proven difficult to distinguish S. thermophilus from S. salivarius using medium plating methods, but genomic sequencing accurately identified them within fecal samples from individuals who had consumed dairy products (6). Dietary supplements containing these strains are becoming more prevalent; thus, the need for high-quality genomic sequences representing commonly used strains is crucial for proper identification. Here, we present the draft genome sequences of 2 S. salivarius and 16 S. thermophilus strains isolated from dietary supplements and cultured food products for classification (Table 1).

TABLE 1.

Streptococcus isolates sequenced in this study

Species	Strain	Source	Sequence platform	SRA no.	BioSample no.	GenBank WGS accession no.	No. of reads	Genome coverage (×)	No. of contigs	No. of predicted genes	Largest contig (bp)	Total length (bp)	N50 (bp)	GC (%)	BUSCO assessment (Benchmarking Universal Single-Copy Orthologs)
															Lineage_dataset	Complete	Missing	Total	%
S. salivarius	DS85_40Ba	Dietary supplementb	NextSeq 500/550	SRR11910125	SAMN15078926	JAIQWT000000000	3,817,804	119	58	2,181	307,204	2,320,947	124,435	39.4	lactobacillales_odb10	400	2	402	99.5
S. salivarius	DS85_40Aa	Dietary supplementb	NextSeq 500/550	SRR11910126	SAMN15078925	JAIQWS000000000	3,984,844	69	84	2,154	176,391	2,290,943	65,821	39.4	lactobacillales_odb10	400	2	402	99.5
S. thermophilus	DS14_14	Dietary supplementc	MiSeq	SRR5310871	SAMN06464115	JAIQWG000000000	3,061,692	392	62	1,836	207,436	1,776,323	73,135	38.9	lactobacillales_odb10	399	3	402	99.3
S. thermophilus	CF2_14	Yogurt product	MiSeq	SRR5310876	SAMN06464117	JAIQWF000000000	814,748	92	76	1,824	194,267	1,742,651	53,094	39.0	lactobacillales_odb10	399	3	402	99.3
S. thermophilus	CF1_14	Kefir product	MiSeq	SRR5310877	SAMN06464116	JAIQWE000000000	4,348,482	238	44	1,814	203,892	1,742,991	124,918	39.0	lactobacillales_odb10	388	14	402	95.5
S. thermophilus	DS76_14	Dietary supplementb	NextSeq 500/550	SRR11910219	SAMN15078890	JAIQWR000000000	6,496,696	202	62	1,822	122,821	1,736,106	63,115	38.9	lactobacillales_odb10	392	10	402	97.5
S. thermophilus	DS51_14	Dietary supplementb	NextSeq 500/550	SRR11910208	SAMN15078775	JAIQXB000000000	9,984,694	20	97	1,759	104,555	1,646,584	41,717	39.2	lactobacillales_odb10	398	4	402	99.0
S. thermophilus	CF5_14	Nondairy yogurt product	NextSeq 500/550	SRR11910326	SAMN15078648	JAIQWM000000000	6,256,254	565	56	1,849	137,000	1,777,217	65,705	38.9	lactobacillales_odb10	399	3	402	99.3
S. thermophilus	DS45_14	Dietary supplementb	NextSeq 500/550	SRR11910242	SAMN15078736	JAIQWP000000000	2,494,996	89	64	1,867	122,822	1,774,216	61,113	38.9	lactobacillales_odb10	398	4	402	99.0
S. thermophilus	DS03_14	Dietary supplementb	MiSeq	SRR11910360	SAMN15078662	JAIQWK000000000	938,788	68	61	1,922	175,129	1,848,774	70,646	38.8	lactobacillales_odb10	399	3	402	99.3
S. thermophilus	DS30_14	Dietary supplementb	NextSeq 500/550	SRR11910418	SAMN15078680	JAIQWH000000000	1,259,266	96	81	1,853	117,608	1,766,804	52,466	39.0	lactobacillales_odb10	399	3	402	99.3
S. thermophilus	CF13_14	Yogurt product	NextSeq 500/550	SRR11910376	SAMN15078605	JAIQWJ000000000	1,669,016	105	46	1,892	174,923	1,808,551	93,887	38.9	lactobacillales_odb10	399	3	402	99.3
S. thermophilus	CF12_14	Nondairy yogurt product	NextSeq 500/550	SRR11910216	SAMN15078601	JAIQWU000000000	9,134,166	484	55	1,925	313,755	1,848,466	100,076	38.8	lactobacillales_odb10	399	3	402	99.3
S. thermophilus	CF3_14	Yogurt product	NextSeq 500/550	SRR11910321	SAMN15078635	JAIQWN000000000	8,713,470	173	52	1,778	204,361	1,704,260	97,302	38.9	lactobacillales_odb10	377	25	402	93.8
S. thermophilus	CF10_14	Cheese product	NextSeq 500/550	SRR11910350	SAMN15078596	JAIQWL000000000	1,720,144	123	59	1,847	145,424	1,759,255	70,976	39.0	lactobacillales_odb10	399	3	402	99.3
S. thermophilus	CF4_14	Kefir product	NextSeq 500/550	SRR11910241	SAMN15078639	JAIQWQ000000000	5,057,426	88	69	1,866	158,655	1,771,462	62,823	38.9	lactobacillales_odb10	399	3	402	99.3
S. thermophilus	DS61_14	Dietary supplementb	MiSeq	SRR11910392	SAMN15078830	JAIQWI000000000	4,364,456	550	49	1,847	162,842	1,778,590	71,039	38.9	lactobacillales_odb10	399	3	402	99.3
S. thermophilus	CF8_14	Yogurt product	NextSeq 500/550	SRR11910258	SAMN15078656	JAIQWO000000000	1,755,666	75	68	1,851	130,762	1,773,459	58,946	38.9	lactobacillales_odb10	399	3	402	99.3

^aTwo different strains from the same dietary supplement (DS85).

^bDietary supplement for general population.

^cDietary supplement for women.

A serving from each product was suspended in 5 mL of saline. Then, 100 μL from serial dilutions was plated on MRS agar plates and incubated at 30°C aerobically and 37°C aerobically, CO₂-enriched, microaerophilic and anaerobic conditions. Colonies were selected based on morphologic differences. DNA extraction from overnight cultures of purified colony isolates was performed with the QIAcube using the DNeasy blood and tissue/Gram-positive bacterium or yeast protocol (Qiagen, Hilden, Germany). A DNA clean and concentrator kit (Zymo Research, Irvine, CA) was used to increase the quality of the DNA by removing potential inhibitors that could affect the sequencing process, as well as to concentrate the sample from 150 μL to a final volume of 6 μL. DNA quality and concentration were determined using a Qubit 3.0 fluorometer (Life Technologies, Burlington, CA). Sequencing libraries were prepared with 1 ng of DNA using the Nextera XT DNA library preparation kit and the Nextera XT index kit v2 set A (Illumina, San Diego, CA) and sequenced on either the Illumina MiSeq system using the MiSeq reagent kit v2 (500 cycles) or the NextSeq system using the NextSeq 500/550 midoutput kit v2.5 (300 cycles). The resulting 250-bp (MiSeq) and 150-bp (NextSeq) paired-end reads were quality controlled using FastQC v0.11.9 (Q > 30) (7), and then the reads were trimmed using Trimmomatic v0.38.1 (8) and de novo assembled using SPAdes v3.8.2 (9). The completeness of assemblies was determined using BUSCO v5.0.0 and Lactobacillales_odb10, with genome assemblies completed from 93.7% to 99.5% (10). Species-level taxonomic identification and abundances were inferred for all samples using our in-house kmer database (k = 30) (11). Default parameters were used for all the analytical tools.

Depth of coverage for the draft genomes ranged from 20 to 565×, with genome sizes ranging from 1,646,854 to 2,320,947 bp. The number of contigs ranged from 44 to 97, while the N₅₀ values ranged from 41,717 to 124,918 bp. The GC content varied from 38.8 to 39.4%. The sequences of these 18 Streptococcus isolates were submitted to GenBank and included two S. salivarius strains and 16 S. thermophilus strains.

Data availability.

This whole-genome shotgun project has been deposited at DDBJ/ENA/GenBank under BioProject number PRJNA336518 and under accession numbers JAIQWE000000000 to JAIQXB000000000. The assemblies described in this paper are the first versions. All annotations were done using the NCBI PGAP pipeline v5.2 (12).