safety

PPRS ARGs VFs PGs Plasmid Prophage IS elements

Probiotic potential risk score

ARGs	VFs	PGs	PPRS
0	29	33	43.93

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.
FLPLINNB_5	88347	89216	rfbA	0.0	Capsule	Immune modulation	100.00	100.00	WP_011681286
FLPLINNB_5	87754	88347	STER_RS06030	0.0	Capsule	Immune modulation	100.00	100.00	WP_011226149
FLPLINNB_1	156613	158358	STER_RS07045	0.0	Capsule	Immune modulation	100.00	100.00	WP_011681434
FLPLINNB_1	160078	161280	STER_RS07055	0.0	Capsule	Immune modulation	100.00	100.00	WP_011681436
FLPLINNB_1	161280	162086	STER_RS07060	0.0	Capsule	Immune modulation	100.00	100.00	WP_011681437
FLPLINNB_1	162086	163027	STER_RS07065	0.0	Capsule	Immune modulation	100.00	100.00	WP_011681438
FLPLINNB_1	164291	165067	STER_RS07075	0.0	Capsule	Immune modulation	100.00	100.00	WP_011681440
FLPLINNB_1	165413	166129	STER_RS07085	0.0	Capsule	Immune modulation	100.00	100.00	WP_011681442
FLPLINNB_1	166130	167098	STER_RS07090	0.0	Capsule	Immune modulation	100.00	100.00	WP_011681443
FLPLINNB_1	167116	168093	STER_RS07095	0.0	Capsule	Immune modulation	100.00	100.00	WP_011681444
FLPLINNB_1	168090	169349	STER_RS07100	0.0	Capsule	Immune modulation	100.00	100.00	WP_011681445
FLPLINNB_1	158360	160060	STER_RS07050	0.0	Capsule	Immune modulation	99.94	100.00	WP_041827753
FLPLINNB_1	163024	164172	STER_RS07070	0.0	Capsule	Immune modulation	99.91	100.00	WP_011681439
FLPLINNB_5	87754	88347	STR_RS05880	0.0	Capsule	Immune modulation	99.83	100.00	WP_011226149
FLPLINNB_1	158360	160060	STR_RS06890	0.0	Capsule	Immune modulation	99.77	100.00	WP_041827077
FLPLINNB_10	11421	12113	STU_RS14640	0.0	Capsule	Immune modulation	99.71	100.00	WP_011226047
FLPLINNB_5	87754	88347	STU_RS15260	0.0	Capsule	Immune modulation	99.66	100.00	WP_011226149
FLPLINNB_4	12996	14654	fbp54	0.0	FBPs	Adherence	99.64	100.00	WP_011227179
FLPLINNB_20	646	1485	cbpD	0.0	Autolysin	Exoenzyme	99.52	100.00	WP_011226733
FLPLINNB_1	161280	162086	STR_RS06900	0.0	Capsule	Immune modulation	99.50	100.00	WP_011227429
FLPLINNB_1	162086	163027	STR_RS06905	0.0	Capsule	Immune modulation	99.47	100.00	WP_011227430
FLPLINNB_1	160078	161280	STR_RS06895	0.0	Capsule	Immune modulation	99.42	100.00	WP_011227428
FLPLINNB_1	163024	164172	STR_RS06910	0.0	Capsule	Immune modulation	99.30	100.00	WP_011227431
FLPLINNB_10	12854	14314	STER_RS05320	0.0	Capsule	Immune modulation	99.25	100.00	WP_011681177
FLPLINNB_10	11421	12113	STR_RS05255	0.0	Capsule	Immune modulation	99.13	100.00	WP_011227247
FLPLINNB_10	7564	8013	STU_RS14620	0.0	Capsule	Immune modulation	99.11	100.00	WP_011226042
FLPLINNB_5	32851	33641	cshA	0.0	Cell surface hydrophobicity proteins	Adherence	98.61	100.00	-
FLPLINNB_1	156613	158358	STR_RS06885	0.0	Capsule	Immune modulation	98.22	100.00	WP_011227426
FLPLINNB_14	14601	15362	srtA	0.0	Sortase A	Exoenzyme	97.77	100.00	-
FLPLINNB_10	12122	12853	STER_RS05315	0.0	Capsule	Immune modulation	97.54	100.00	WP_011681176
FLPLINNB_10	12122	12853	STU_RS14645	0.0	Capsule	Immune modulation	97.54	100.00	WP_011226048
FLPLINNB_10	12122	12853	STR_RS05260	0.0	Capsule	Immune modulation	97.40	100.00	WP_011227248
FLPLINNB_1	169468	170319	rfbD	0.0	Capsule	Immune modulation	97.30	100.00	WP_014621820
FLPLINNB_10	12854	14314	STU_RS14650	0.0	Capsule	Immune modulation	97.26	100.21	WP_011226049
FLPLINNB_10	10671	11411	STU_RS14635	0.0	Capsule	Immune modulation	97.17	100.00	WP_011226046
FLPLINNB_10	8022	9018	STU_RS14625*	0.0	Capsule	Immune modulation	96.89	100.00	-
FLPLINNB_10	10671	11411	STER_RS05305	0.0	Capsule	Immune modulation	96.76	100.00	WP_011681174
FLPLINNB_10	9251	10614	STER_RS05300	0.0	Capsule	Immune modulation	96.63	99.71	WP_011681173
FLPLINNB_10	12854	14314	STR_RS05265	0.0	Capsule	Immune modulation	96.44	100.21	WP_041827043
FLPLINNB_10	10676	11411	STR_RS05250	0.0	Capsule	Immune modulation	95.79	98.13	WP_011227246
FLPLINNB_10	9247	10614	STU_RS14630	0.0	Capsule	Immune modulation	94.44	100.00	WP_011226045
FLPLINNB_10	11421	12113	STER_RS05310	0.0	Capsule	Immune modulation	89.61	100.00	WP_011681175
FLPLINNB_2	72987	74290	eno	0.0	Streptococcal enolase	Exoenzyme	88.10	99.46	WP_000022832
FLPLINNB_22	79	1089	plr/gapA	0.0	Streptococcal plasmin receptor/GAPDH	Adherence	86.54	99.41	WP_002986042
FLPLINNB_1	161280	162086	SGO_RS05020	0.0	Capsule	Immune modulation	82.90	100.00	WP_012000440
FLPLINNB_9	59429	60712	tig/ropA	0.0	Trigger factor	Stress survival	80.73	99.77	WP_000107753
FLPLINNB_5	86279	87325	rfbB	0.0	Capsule	Immune modulation	80.61	100.00	WP_009659423
FLPLINNB_1	160543	161280	SGO_RS05025	0.0	Capsule	Immune modulation	84.96	60.29	WP_012000441
FLPLINNB_10	7242	7564	STU_RS14615	3.36e-123	Capsule	Immune modulation	91.64	66.46	WP_011226041

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
FLPLINNB_14	18049	19032	ldh(Sp_1220)	0.0	L-lactate dehydrogenase	94.82	100.00	AAK75326
FLPLINNB_13	15167	14094	MntE	0.0	manganese homeostasis	94.41	99.72	ABF32167
FLPLINNB_2	156587	155619	spr0084	0.0	pathogenitcity related	93.19	98.48	AAK98888
FLPLINNB_1	325789	328092	pfl2(Sp_0459)	0.0	formate acetyltransferase	92.97	99.22	AAK74619
FLPLINNB_1	60518	61999	SPD_0310	0.0	UPF0371 protein SPD_0310	92.51	100.00	ABJ54480
FLPLINNB_16	13862	16108	metE	0.0	methionine biosynthesis enzymes	91.99	100.00	AAK74738
FLPLINNB_20	20277	21275	recA	0.0	DNA recombination and repair	91.29	85.82	AAL00560
FLPLINNB_23	15342	14371	prsA2	0.0	ribose-phosphate pyrophosphokinase	90.12	100.00	ABF36968
FLPLINNB_1	211781	210630	potA	0.0	ABC transporter ATP-binding protein-spermidine/putrescine transport	89.32	99.74	AAL00050
FLPLINNB_1	183388	181400	uvrB	0.0	excinuclease ABC, B subunit	88.99	100.00	AE014259_2
FLPLINNB_14	1851	121	ptsI	0.0	phosphoenolpyruvate-protein phosphotransferase	88.04	100.00	AAK34199
FLPLINNB_6	27647	29125	IMPDH	0.0	inosine-5'-monophosphate dehydrogenase	87.63	100.00	ADE32434
FLPLINNB_2	74290	72989	Eno	0.0	enolase	86.21	99.77	ABP90468
FLPLINNB_6	42837	44729	gidA	0.0	tRNA uridine 5-carboxymethylaminomethyl modification enzyme	86.05	98.90	ABP91129
FLPLINNB_16	19032	17323	PGM	0.0	phosphoglucomutase	84.06	99.65	ACH87041
FLPLINNB_8	22699	23709	pdh	0.0	pyruvate dehydrogenase	83.09	99.70	ABP91006
FLPLINNB_4	36507	35146	mnmE	0.0	central tRNA-modifying GTPase	82.24	99.56	ABP90420
FLPLINNB_8	73045	71153	PepO	0.0	endopeptidase	80.19	100.00	ABF32980
FLPLINNB_2	88729	87839	bglB	1.21e-179	putative phospho--glucosidase	88.89	99.66	AAK33487
FLPLINNB_11	40801	41739	SP_0676	6.59e-169	transcription facot	81.15	97.20	AAK74821
FLPLINNB_16	16300	17157	metF	3.15e-166	methionine biosynthesis enzymes	86.36	99.31	AAK74739
FLPLINNB_10	51137	50433	covR	1.28e-132	responder protein	85.53	100.00	AAK71319
FLPLINNB_1	28366	27695	rr01	6.56e-125	response regulator	83.93	99.56	CAB54566
FLPLINNB_10	51137	50433	walR	5.41e-123	DNA-binding response regulator	82.13	100.00	ANC99504
FLPLINNB_16	22986	23654	CiaR	4.18e-119	two-component response regulator	84.31	99.55	AAK74935
FLPLINNB_7	73561	74247	CovR	4.50e-119	serves to repress GAS virulence factor-encoding genes	80.79	100.00	ACE75886
FLPLINNB_16	22986	23657	ciaR	4.11e-117	two component system response regulator	82.14	99.12	AIK75708
FLPLINNB_20	21551	21925	SpxA2	1.37e-71	transcriptional regulator	91.20	94.70	ERL21461
FLPLINNB_4	47870	48271	SpxA1	2.36e-67	transcriptional regulator	80.60	100.00	ERL19273
FLPLINNB_15	25574	25287	spr0479	2.99e-49	essential gene	86.46	98.97	AAK99283
FLPLINNB_3	37494	37240	spr1327	2.36e-45	essential gene	95.29	100.00	AAL00131
FLPLINNB_6	76462	76199	spr0175	3.48e-42	pathogenitcity related	84.09	100.00	AAK98979
FLPLINNB_6	75635	75369	spr0177	7.60e-34	essential gene	84.27	88.12	AAK98981
FLPLINNB_9	59271	58771	RopE (M5005_Spy_1611)	1.66e-76	probable DNA-directed RNA polymerase subunit delta	81.44	87.43	AAK34603
FLPLINNB_1	325789	328086	PFL (B9H01_RS01125)	0.0	formate C-acetyltransferase	82.94	98.08	MYN69560
FLPLINNB_8	58584	57565	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
FLPLINNB_1	0.0	1.0	0.0
FLPLINNB_2	0.0	1.0	0.0
FLPLINNB_3	0.0	1.0	0.0
FLPLINNB_4	0.0	1.0	0.0
FLPLINNB_5	0.0	1.0	0.0
FLPLINNB_6	0.0	1.0	0.0
FLPLINNB_7	0.0	1.0	0.0
FLPLINNB_8	0.0	1.0	0.0
FLPLINNB_9	0.0	1.0	0.0
FLPLINNB_10	0.0	1.0	0.0
FLPLINNB_11	0.0	1.0	0.0
FLPLINNB_12	0.0	1.0	0.0
FLPLINNB_13	0.0	1.0	0.0
FLPLINNB_14	0.0	1.0	0.0
FLPLINNB_15	0.0	1.0	0.0
FLPLINNB_16	0.0	1.0	0.0
FLPLINNB_17	0.0	1.0	0.0
FLPLINNB_18	0.0	1.0	0.0
FLPLINNB_19	0.0	1.0	0.0
FLPLINNB_20	0.0	1.0	0.0
FLPLINNB_21	0.0	1.0	0.0
FLPLINNB_22	0.0	1.0	0.0
FLPLINNB_23	0.0	1.0	0.0
FLPLINNB_24	1.0	0.0	1.0
FLPLINNB_25	0.0	1.0	0.0
FLPLINNB_26	1.0	0.0	1.0
FLPLINNB_28	0.0	1.0	0.0
FLPLINNB_29	0.0	1.0	0.0
FLPLINNB_30	0.0	1.0	0.0
FLPLINNB_31	1.0	0.0	1.0
FLPLINNB_32	0.0	1.0	0.0
FLPLINNB_33	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