safety

PPRS ARGs VFs PGs Plasmid Prophage IS elements

Probiotic potential risk score

ARGs	VFs	PGs	PPRS
0	28	33	43.28

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	e-value	VF name	VF category	Identity	Coverage	Accession no.
DGIOIDPF_8	9999	10868	rfbA	0.0	Capsule	Immune modulation	100.00	100.00	WP_011681286
DGIOIDPF_8	9406	9999	STER_RS06030	0.0	Capsule	Immune modulation	100.00	100.00	WP_011226149
DGIOIDPF_11	17007	18752	STER_RS07045	0.0	Capsule	Immune modulation	100.00	100.00	WP_011681434
DGIOIDPF_11	18754	20454	STER_RS07050	0.0	Capsule	Immune modulation	100.00	100.00	WP_041827753
DGIOIDPF_11	20472	21674	STER_RS07055	0.0	Capsule	Immune modulation	100.00	100.00	WP_011681436
DGIOIDPF_11	21674	22480	STER_RS07060	0.0	Capsule	Immune modulation	100.00	100.00	WP_011681437
DGIOIDPF_11	22480	23421	STER_RS07065	0.0	Capsule	Immune modulation	100.00	100.00	WP_011681438
DGIOIDPF_11	23418	24566	STER_RS07070	0.0	Capsule	Immune modulation	100.00	100.00	WP_011681439
DGIOIDPF_11	24685	25461	STER_RS07075	0.0	Capsule	Immune modulation	100.00	100.00	WP_011681440
DGIOIDPF_11	25807	26523	STER_RS07085	0.0	Capsule	Immune modulation	100.00	100.00	WP_011681442
DGIOIDPF_11	26524	27492	STER_RS07090	0.0	Capsule	Immune modulation	100.00	100.00	WP_011681443
DGIOIDPF_11	28484	29743	STER_RS07100	0.0	Capsule	Immune modulation	100.00	100.00	WP_011681445
DGIOIDPF_11	27510	28487	STER_RS07095	0.0	Capsule	Immune modulation	99.90	100.00	WP_011681444
DGIOIDPF_8	9406	9999	STR_RS05880	0.0	Capsule	Immune modulation	99.83	100.00	WP_011226149
DGIOIDPF_11	18754	20454	STR_RS06890	0.0	Capsule	Immune modulation	99.71	100.00	WP_041827077
DGIOIDPF_8	9406	9999	STU_RS15260	0.0	Capsule	Immune modulation	99.66	100.00	WP_011226149
DGIOIDPF_5	65617	67275	fbp54	0.0	FBPs	Adherence	99.58	100.00	WP_011227179
DGIOIDPF_1	20790	21629	cbpD	0.0	Autolysin	Exoenzyme	99.52	100.00	WP_011226733
DGIOIDPF_11	21674	22480	STR_RS06900	0.0	Capsule	Immune modulation	99.50	100.00	WP_011227429
DGIOIDPF_27	1117	2260	cshA	0.0	Cell surface hydrophobicity proteins	Adherence	99.48	100.00	-
DGIOIDPF_11	22480	23421	STR_RS06905	0.0	Capsule	Immune modulation	99.47	100.00	WP_011227430
DGIOIDPF_11	20472	21674	STR_RS06895	0.0	Capsule	Immune modulation	99.42	100.00	WP_011227428
DGIOIDPF_11	23418	24566	STR_RS06910	0.0	Capsule	Immune modulation	99.22	100.00	WP_011227431
DGIOIDPF_7	17837	18568	STER_RS05315	0.0	Capsule	Immune modulation	98.50	100.00	WP_011681176
DGIOIDPF_7	17837	18568	STU_RS14645	0.0	Capsule	Immune modulation	98.50	100.00	WP_011226048
DGIOIDPF_7	17837	18568	STR_RS05260	0.0	Capsule	Immune modulation	98.36	100.00	WP_011227248
DGIOIDPF_11	17007	18752	STR_RS06885	0.0	Capsule	Immune modulation	98.22	100.00	WP_011227426
DGIOIDPF_7	18569	20029	STER_RS05320	0.0	Capsule	Immune modulation	97.81	100.00	WP_011681177
DGIOIDPF_8	44770	45531	srtA	0.0	Sortase A	Exoenzyme	97.77	100.00	-
DGIOIDPF_7	18569	20029	STU_RS14650	0.0	Capsule	Immune modulation	97.06	100.21	WP_011226049
DGIOIDPF_7	16386	17126	STU_RS14635	0.0	Capsule	Immune modulation	97.03	100.00	WP_011226046
DGIOIDPF_7	16386	17126	STER_RS05305	0.0	Capsule	Immune modulation	96.90	100.00	WP_011681174
DGIOIDPF_11	29862	30713	rfbD	0.0	Capsule	Immune modulation	96.83	100.00	WP_014621820
DGIOIDPF_7	16391	17126	STR_RS05250	0.0	Capsule	Immune modulation	96.47	98.13	WP_011227246
DGIOIDPF_7	18569	20029	STR_RS05265	0.0	Capsule	Immune modulation	96.23	100.21	WP_041827043
DGIOIDPF_7	14965	16330	STER_RS05300	0.0	Capsule	Immune modulation	95.39	99.85	WP_011681173
DGIOIDPF_7	17136	17828	STR_RS05255	0.0	Capsule	Immune modulation	95.25	99.86	WP_011227247
DGIOIDPF_7	17136	17828	STU_RS14640	0.0	Capsule	Immune modulation	95.25	99.86	WP_011226047
DGIOIDPF_7	14963	16330	STU_RS14630	0.0	Capsule	Immune modulation	94.37	100.00	WP_011226045
DGIOIDPF_7	17136	17828	STER_RS05310	0.0	Capsule	Immune modulation	89.61	100.00	WP_011681175
DGIOIDPF_27	100778	102081	eno	0.0	Streptococcal enolase	Exoenzyme	88.10	99.46	WP_000022832
DGIOIDPF_15	123	1133	plr/gapA	0.0	Streptococcal plasmin receptor/GAPDH	Adherence	86.54	99.41	WP_002986042
DGIOIDPF_11	21674	22480	SGO_RS05020	0.0	Capsule	Immune modulation	82.90	100.00	WP_012000440
DGIOIDPF_24	6383	7666	tig/ropA	0.0	Trigger factor	Stress survival	80.73	99.77	WP_000107753
DGIOIDPF_8	7931	8977	rfbB	0.0	Capsule	Immune modulation	80.61	100.00	WP_009659423
DGIOIDPF_7	5432	6015	SPD_RS01775	1.30e-147	Capsule	Immune modulation	83.11	96.04	WP_001819836
DGIOIDPF_11	20937	21674	SGO_RS05025	0.0	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
DGIOIDPF_27	205159	206232	MntE	0.0	manganese homeostasis	94.41	99.72	ABF32167
DGIOIDPF_8	48218	49201	ldh(Sp_1220)	0.0	L-lactate dehydrogenase	94.21	100.00	AAK75326
DGIOIDPF_27	18539	19507	spr0084	0.0	pathogenitcity related	93.19	98.48	AAK98888
DGIOIDPF_13	57612	59915	pfl2(Sp_0459)	0.0	formate acetyltransferase	92.97	99.22	AAK74619
DGIOIDPF_9	38907	40388	SPD_0310	0.0	UPF0371 protein SPD_0310	92.71	100.00	ABJ54480
DGIOIDPF_28	6177	8423	metE	0.0	methionine biosynthesis enzymes	91.99	100.00	AAK74738
DGIOIDPF_12	11076	12074	recA	0.0	DNA recombination and repair	91.29	85.82	AAL00560
DGIOIDPF_1	4306	5277	prsA2	0.0	ribose-phosphate pyrophosphokinase	90.12	100.00	ABF36968
DGIOIDPF_11	79639	78488	potA	0.0	ABC transporter ATP-binding protein-spermidine/putrescine transport	89.32	99.74	AAL00050
DGIOIDPF_11	43750	41762	uvrB	0.0	excinuclease ABC, B subunit	88.84	100.00	AE014259_2
DGIOIDPF_8	32019	30289	ptsI	0.0	phosphoenolpyruvate-protein phosphotransferase	88.04	100.00	AAK34199
DGIOIDPF_7	157375	158853	IMPDH	0.0	inosine-5'-monophosphate dehydrogenase	87.63	100.00	ADE32434
DGIOIDPF_27	100778	102079	Eno	0.0	enolase	86.21	99.77	ABP90468
DGIOIDPF_7	172113	174005	gidA	0.0	tRNA uridine 5-carboxymethylaminomethyl modification enzyme	85.74	98.90	ABP91129
DGIOIDPF_28	11348	9639	PGM	0.0	phosphoglucomutase	84.06	99.65	ACH87041
DGIOIDPF_16	22397	23407	pdh	0.0	pyruvate dehydrogenase	82.79	99.70	ABP91006
DGIOIDPF_5	92252	90891	mnmE	0.0	central tRNA-modifying GTPase	82.24	99.56	ABP90420
DGIOIDPF_16	72715	70823	PepO	0.0	endopeptidase	80.03	100.00	ABF32980
DGIOIDPF_27	86343	87233	bglB	1.57e-179	putative phospho--glucosidase	88.89	99.66	AAK33487
DGIOIDPF_5	11841	10906	SP_0676	4.67e-169	transcription facot	81.73	96.89	AAK74821
DGIOIDPF_28	8615	9472	metF	1.40e-166	methionine biosynthesis enzymes	86.36	99.31	AAK74739
DGIOIDPF_7	56829	56125	covR	5.18e-132	responder protein	85.53	100.00	AAK71319
DGIOIDPF_9	10803	10132	rr01	8.38e-126	response regulator	83.93	99.56	CAB54566
DGIOIDPF_7	56829	56125	walR	2.18e-122	DNA-binding response regulator	82.13	100.00	ANC99504
DGIOIDPF_28	15302	15970	CiaR	4.18e-121	two-component response regulator	84.75	99.55	AAK74935
DGIOIDPF_25	73607	74293	CovR	6.59e-119	serves to repress GAS virulence factor-encoding genes	80.79	100.00	ACE75886
DGIOIDPF_28	15302	15973	ciaR	8.25e-119	two component system response regulator	82.59	99.12	AIK75708
DGIOIDPF_12	12350	12724	SpxA2	7.97e-72	transcriptional regulator	91.20	94.70	ERL21461
DGIOIDPF_5	103717	104118	SpxA1	2.39e-67	transcriptional regulator	80.60	100.00	ERL19273
DGIOIDPF_25	95991	96278	spr0479	9.30e-49	essential gene	86.46	98.97	AAK99283
DGIOIDPF_26	126308	126562	spr1327	1.56e-44	essential gene	94.12	100.00	AAL00131
DGIOIDPF_7	205761	205498	spr0175	8.46e-42	pathogenitcity related	84.09	100.00	AAK98979
DGIOIDPF_7	204934	204668	spr0177	1.85e-33	essential gene	84.27	88.12	AAK98981
DGIOIDPF_24	7824	8324	RopE (M5005_Spy_1611)	2.27e-76	probable DNA-directed RNA polymerase subunit delta	81.44	87.43	AAK34603
DGIOIDPF_13	57612	59909	PFL (B9H01_RS01125)	0.0	formate C-acetyltransferase	82.94	98.08	MYN69560
DGIOIDPF_16	58261	57242	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.
DGIOIDPF_22	378	1328	rep37	954 / 948	87.21	AF177168

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

PlasmidHunter

Query ID	Prediction	Chromosome	Plasmid
DGIOIDPF_1	0.0	1.0	0.0
DGIOIDPF_2	0.0	1.0	0.0
DGIOIDPF_3	1.0	0.0	1.0
DGIOIDPF_4	1.0	0.0	1.0
DGIOIDPF_5	0.0	1.0	0.0
DGIOIDPF_6	0.0	1.0	0.0
DGIOIDPF_7	0.0	1.0	0.0
DGIOIDPF_8	0.0	1.0	0.0
DGIOIDPF_9	0.0	1.0	0.0
DGIOIDPF_10	0.0	1.0	0.0
DGIOIDPF_11	0.0	1.0	0.0
DGIOIDPF_12	0.0	1.0	0.0
DGIOIDPF_13	0.0	1.0	0.0
DGIOIDPF_14	0.0	1.0	0.0
DGIOIDPF_15	0.0	1.0	0.0
DGIOIDPF_16	0.0	1.0	0.0
DGIOIDPF_17	1.0	0.0	1.0
DGIOIDPF_18	1.0	0.0	1.0
DGIOIDPF_19	0.0	1.0	0.0
DGIOIDPF_20	1.0	0.0	1.0
DGIOIDPF_22	1.0	0.0	1.0
DGIOIDPF_23	0.0	1.0	0.0
DGIOIDPF_24	0.0	1.0	0.0
DGIOIDPF_25	0.0	1.0	0.0
DGIOIDPF_26	0.0	1.0	0.0
DGIOIDPF_27	0.0	1.0	0.0
DGIOIDPF_28	0.0	1.0	0.0
DGIOIDPF_29	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