safety

PPRS ARGs VFs PGs Plasmid Prophage IS elements

Probiotic potential risk score

ARGs	VFs	PGs	PPRS
0	35	32	47.42

PPRS is classified as low-risk (≤4), medium-risk (4-6), and high-risk (≥6).

Antibiotic resistance genes

Comprehensive Antibiotic Resistance Database (CARD)

Query ID	Begin	End	ARO name	ARO accession	CARD name	Identity	Coverage	Accession no.
No hit found

RGI v6.0.3 (Database: CARD Variants v4.0.2, Nov. 2023 release)

ResFinder

Query ID	Begin	End	Resistance gene	Phenotype	Identity	Coverage	Accession no.
No hit found

ResFinder v4.6.0 (Database: resfinder_db, Aug. 2024 release)

AMRFinderPlus

Query ID	Begin	End	Gene symbol	Sequence name	Method	Identity	Coverage	Accession no.
No hit found

AMRFinderPlus v4.0.3 (Database: Oct. 2024 release)

Virulence factors

Virulence Factor Database (VFDB)

Query ID	qstart	qend	Gene name	VF name	VF category	Identity	Coverage	Accession no.
OMOKNICL_4	1069	2212	cshA	Cell surface hydrophobicity proteins	Adherence	100.00	100.00	-
OMOKNICL_11	126611	127480	rfbA	Capsule	Immune modulation	100.00	100.00	WP_011681286
OMOKNICL_54	403	1818	STER_RS05250	Capsule	Immune modulation	100.00	100.00	WP_011681165
OMOKNICL_54	3019	3999	STER_RS05260	Capsule	Immune modulation	100.00	100.00	WP_011681166
OMOKNICL_54	3992	5176	STER_RS05265	Capsule	Immune modulation	100.00	100.00	WP_011681167
OMOKNICL_54	5193	6245	STER_RS05270	Capsule	Immune modulation	100.00	100.00	WP_011681168
OMOKNICL_54	6260	7168	STER_RS05275	Capsule	Immune modulation	100.00	100.00	WP_011681169
OMOKNICL_54	7189	8250	STER_RS05280	Capsule	Immune modulation	100.00	100.00	WP_202964935
OMOKNICL_54	8287	8778	STER_RS05285	Capsule	Immune modulation	100.00	100.00	WP_011681171
OMOKNICL_54	8790	9266	STER_RS05290	Capsule	Immune modulation	100.00	100.00	WP_011681172
OMOKNICL_54	11446	12186	STER_RS05305	Capsule	Immune modulation	100.00	100.00	WP_011681174
OMOKNICL_54	12196	12888	STER_RS05310	Capsule	Immune modulation	100.00	100.00	WP_011681175
OMOKNICL_54	12897	13628	STER_RS05315	Capsule	Immune modulation	100.00	100.00	WP_011681176
OMOKNICL_54	13629	15089	STER_RS05320	Capsule	Immune modulation	100.00	100.00	WP_011681177
OMOKNICL_11	127480	128073	STER_RS06030	Capsule	Immune modulation	100.00	100.00	WP_011226149
OMOKNICL_38	105370	107115	STER_RS07045	Capsule	Immune modulation	100.00	100.00	WP_011681434
OMOKNICL_38	103668	105368	STER_RS07050	Capsule	Immune modulation	100.00	100.00	WP_041827753
OMOKNICL_38	102448	103650	STER_RS07055	Capsule	Immune modulation	100.00	100.00	WP_011681436
OMOKNICL_38	101642	102448	STER_RS07060	Capsule	Immune modulation	100.00	100.00	WP_011681437
OMOKNICL_38	100701	101642	STER_RS07065	Capsule	Immune modulation	100.00	100.00	WP_011681438
OMOKNICL_38	99556	100704	STER_RS07070	Capsule	Immune modulation	100.00	100.00	WP_011681439
OMOKNICL_38	98661	99437	STER_RS07075	Capsule	Immune modulation	100.00	100.00	WP_011681440
OMOKNICL_38	97599	98315	STER_RS07085	Capsule	Immune modulation	100.00	100.00	WP_011681442
OMOKNICL_38	96630	97598	STER_RS07090	Capsule	Immune modulation	100.00	100.00	WP_011681443
OMOKNICL_38	95635	96612	STER_RS07095	Capsule	Immune modulation	100.00	100.00	WP_011681444
OMOKNICL_38	94379	95638	STER_RS07100	Capsule	Immune modulation	100.00	100.00	WP_011681445
OMOKNICL_54	10022	11389	STER_RS05300	Capsule	Immune modulation	99.85	100.00	WP_011681173
OMOKNICL_11	127480	128073	STR_RS05880	Capsule	Immune modulation	99.83	100.00	WP_011226149
OMOKNICL_38	103668	105368	STR_RS06890	Capsule	Immune modulation	99.71	100.00	WP_041827077
OMOKNICL_11	127480	128073	STU_RS15260	Capsule	Immune modulation	99.66	100.00	WP_011226149
OMOKNICL_44	13021	14679	fbp54	FBPs	Adherence	99.64	100.00	WP_011227179
OMOKNICL_12	20641	21480	cbpD	Autolysin	Exoenzyme	99.52	100.00	WP_011226733
OMOKNICL_38	101642	102448	STR_RS06900	Capsule	Immune modulation	99.50	100.00	WP_011227429
OMOKNICL_38	100701	101642	STR_RS06905	Capsule	Immune modulation	99.47	100.00	WP_011227430
OMOKNICL_38	102448	103650	STR_RS06895	Capsule	Immune modulation	99.42	100.00	WP_011227428
OMOKNICL_38	99556	100704	STR_RS06910	Capsule	Immune modulation	99.22	100.00	WP_011227431
OMOKNICL_54	11451	12186	STR_RS05250	Capsule	Immune modulation	98.50	98.13	WP_011227246
OMOKNICL_54	11446	12186	STU_RS14635	Capsule	Immune modulation	98.25	100.00	WP_011226046
OMOKNICL_54	12897	13628	STR_RS05260	Capsule	Immune modulation	98.22	100.00	WP_011227248
OMOKNICL_38	105370	107115	STR_RS06885	Capsule	Immune modulation	98.22	100.00	WP_011227426
OMOKNICL_54	12897	13628	STU_RS14645	Capsule	Immune modulation	98.09	100.00	WP_011226048
OMOKNICL_11	91950	92711	srtA	Sortase A	Exoenzyme	97.64	100.00	-
OMOKNICL_54	13629	15089	STU_RS14650	Capsule	Immune modulation	97.47	100.21	WP_011226049
OMOKNICL_54	13629	15089	STR_RS05265	Capsule	Immune modulation	96.92	100.21	WP_041827043
OMOKNICL_38	93409	94260	rfbD	Capsule	Immune modulation	96.83	100.00	WP_014621820
OMOKNICL_54	10026	11389	STU_RS14630	Capsule	Immune modulation	94.94	99.71	WP_011226045
OMOKNICL_54	12196	12888	STU_RS14640	Capsule	Immune modulation	89.90	100.00	WP_011226047
OMOKNICL_54	12196	12888	STR_RS05255	Capsule	Immune modulation	89.61	100.00	WP_011227247
OMOKNICL_22	75390	76693	eno	Streptococcal enolase	Exoenzyme	88.10	99.46	WP_000022832
OMOKNICL_20	51	1061	plr/gapA	Streptococcal plasmin receptor/GAPDH	Adherence	86.54	99.41	WP_002986042
OMOKNICL_38	101642	102448	SGO_RS05020	Capsule	Immune modulation	82.90	100.00	WP_012000440
OMOKNICL_56	59407	60690	tig/ropA	Trigger factor	Stress survival	80.73	99.77	WP_000107753
OMOKNICL_11	128502	129548	rfbB	Capsule	Immune modulation	80.61	100.00	WP_009659423
OMOKNICL_38	102448	103185	SGO_RS05025	Capsule	Immune modulation	84.96	60.29	WP_012000441

BLASTN v2.16.0 (Database: VFDB, Dec. 2024 release)

VirulenceFinder

Query ID	Begin	End	Database	Virulence factor	Protein function	Identity	Coverage	Accession no.
No hit found

VirulenceFinder v2.0. 4 (Database: virulencefinder_db, Feb . 2024 release)

Pathogenic genes

PHI-base

Query ID	qstart	qend	Gene name	e-value	Function	Identity	Coverage	Gene ID
OMOKNICL_11	89263	88280	ldh(Sp_1220)	0.0	L-lactate dehydrogenase	94.82	100.00	AAK75326
OMOKNICL_55	43400	42327	MntE	0.0	manganese homeostasis	94.41	99.72	ABF32167
OMOKNICL_32	63441	61138	pfl2(Sp_0459)	0.0	formate acetyltransferase	92.97	99.22	AAK74619
OMOKNICL_4	17627	18595	spr0084	0.0	pathogenitcity related	92.88	98.48	AAK98888
OMOKNICL_11	12507	11026	SPD_0310	0.0	UPF0371 protein SPD_0310	92.51	100.00	ABJ54480
OMOKNICL_55	11490	9244	metE	0.0	methionine biosynthesis enzymes	91.99	100.00	AAK74738
OMOKNICL_12	1849	851	recA	0.0	DNA recombination and repair	91.29	85.82	AAL00560
OMOKNICL_12	37964	36993	prsA2	0.0	ribose-phosphate pyrophosphokinase	90.12	100.00	ABF36968
OMOKNICL_38	44939	46090	potA	0.0	ABC transporter ATP-binding protein-spermidine/putrescine transport	89.32	99.74	AAL00050
OMOKNICL_38	80370	82358	uvrB	0.0	excinuclease ABC, B subunit	89.14	100.00	AE014259_2
OMOKNICL_11	105462	107192	ptsI	0.0	phosphoenolpyruvate-protein phosphotransferase	87.87	100.00	AAK34199
OMOKNICL_3	47259	45781	IMPDH	0.0	inosine-5'-monophosphate dehydrogenase	87.63	100.00	ADE32434
OMOKNICL_22	76693	75392	Eno	0.0	enolase	86.21	99.77	ABP90468
OMOKNICL_3	32524	30632	gidA	0.0	tRNA uridine 5-carboxymethylaminomethyl modification enzyme	85.74	98.90	ABP91129
OMOKNICL_55	6319	8028	PGM	0.0	phosphoglucomutase	84.06	99.65	ACH87041
OMOKNICL_1	40149	39139	pdh	0.0	pyruvate dehydrogenase	83.09	99.70	ABP91006
OMOKNICL_44	39114	37753	mnmE	0.0	central tRNA-modifying GTPase	82.24	99.56	ABP90420
OMOKNICL_6	37055	38947	PepO	0.0	endopeptidase	80.19	100.00	ABF32980
OMOKNICL_22	91129	90239	bglB	3.48e-179	putative phospho--glucosidase	88.55	99.66	AAK33487
OMOKNICL_5	11675	10737	SP_0676	2.23e-169	transcription facot	81.47	97.20	AAK74821
OMOKNICL_55	9052	8195	metF	5.82e-166	methionine biosynthesis enzymes	86.36	99.31	AAK74739
OMOKNICL_54	51912	51208	covR	2.12e-132	responder protein	85.53	100.00	AAK71319
OMOKNICL_11	37114	37785	rr01	2.21e-125	response regulator	83.93	99.56	CAB54566
OMOKNICL_54	51912	51208	walR	8.95e-123	DNA-binding response regulator	82.13	100.00	ANC99504
OMOKNICL_48	91205	91891	CovR	5.35e-119	serves to repress GAS virulence factor-encoding genes	80.79	100.00	ACE75886
OMOKNICL_55	2364	1696	CiaR	7.70e-119	two-component response regulator	84.31	99.55	AAK74935
OMOKNICL_55	2364	1693	ciaR	7.58e-117	two component system response regulator	82.14	99.12	AIK75708
OMOKNICL_12	575	201	SpxA2	2.35e-71	transcriptional regulator	91.20	94.70	ERL21461
OMOKNICL_10	25395	25108	spr0479	2.93e-49	essential gene	86.46	98.97	AAK99283
OMOKNICL_9	33675	33929	spr1327	4.16e-45	essential gene	94.12	100.00	AAL00131
OMOKNICL_18	1215	952	spr0175	6.41e-43	pathogenitcity related	84.09	100.00	AAK98979
OMOKNICL_18	388	122	spr0177	1.40e-34	essential gene	84.27	88.12	AAK98981
OMOKNICL_56	59249	58749	RopE (M5005_Spy_1611)	1.74e-76	probable DNA-directed RNA polymerase subunit delta	81.44	87.43	AAK34603
OMOKNICL_32	63441	61144	PFL (B9H01_RS01125)	0.0	formate C-acetyltransferase	82.94	98.08	MYN69560
OMOKNICL_1	4288	5307	ilvC (SPD_0406)	0.0	ketol-acid reductoisomerase (NADP(+))	96.47	100.00	ABJ55451

BLASTX v2.16.0 (Database: PHI base v4.16, May. 2024 release)

Plasmid

PlasmidFinder

Query ID	Begin	End	Plasmid	Query / Template	Identity	Accession no.
No hit found

PlasmidFinder v 2.1.6 (Database: plasmidfinder_db v 2.2.0 , Nov. 2024 release)

PlasmidHunter

Query ID	Prediction	Chromosome	Plasmid
OMOKNICL_1	0.0	1.0	0.0
OMOKNICL_2	0.0	1.0	0.0
OMOKNICL_3	0.0	1.0	0.0
OMOKNICL_4	0.0	1.0	0.0
OMOKNICL_5	0.0	1.0	0.0
OMOKNICL_6	0.0	1.0	0.0
OMOKNICL_7	0.0	1.0	0.0
OMOKNICL_8	0.0	1.0	0.0
OMOKNICL_9	0.0	1.0	0.0
OMOKNICL_10	0.0	1.0	0.0
OMOKNICL_11	0.0	1.0	0.0
OMOKNICL_12	0.0	1.0	0.0
OMOKNICL_13	0.0	1.0	0.0
OMOKNICL_14	0.0	1.0	0.0
OMOKNICL_15	0.0	1.0	0.0
OMOKNICL_16	0.0	1.0	0.0
OMOKNICL_17	0.0	1.0	0.0
OMOKNICL_18	0.0	1.0	0.0
OMOKNICL_19	0.0	1.0	0.0
OMOKNICL_20	0.0	1.0	0.0
OMOKNICL_21	0.0	1.0	0.0
OMOKNICL_22	0.0	1.0	0.0
OMOKNICL_23	0.0	1.0	0.0
OMOKNICL_24	0.0	1.0	0.0
OMOKNICL_25	0.0	1.0	0.0
OMOKNICL_26	0.0	1.0	0.0
OMOKNICL_27	0.0	1.0	0.0
OMOKNICL_28	0.0	1.0	0.0
OMOKNICL_29	0.0	1.0	0.0
OMOKNICL_30	0.0	1.0	0.0
OMOKNICL_31	1.0	0.0	1.0
OMOKNICL_32	0.0	1.0	0.0
OMOKNICL_33	0.0	1.0	0.0
OMOKNICL_34	1.0	0.0	1.0
OMOKNICL_35	0.0	1.0	0.0
OMOKNICL_38	0.0	1.0	0.0
OMOKNICL_44	0.0	1.0	0.0
OMOKNICL_48	0.0	1.0	0.0
OMOKNICL_54	0.0	1.0	0.0
OMOKNICL_55	0.0	1.0	0.0
OMOKNICL_56	0.0	1.0	0.0

PlasmidHunter v 1.4.5 (Database: May. 2024 release)

Prophage

Phigaro

Query ID	Begin	End	Transposable	Taxonomy	pVOGs
No hit found