safety

PPRS ARGs VFs PGs Plasmid Prophage IS elements

Probiotic potential risk score

ARGs	VFs	PGs	PPRS
0	25	29	38.29

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.
NMMGEMII_1	43688	44527	cbpD	Autolysin	Exoenzyme	100.00	100.00	WP_011226733
NMMGEMII_1	1084415	1085284	rfbA	Capsule	Immune modulation	100.00	100.00	WP_011681286
NMMGEMII_1	1083822	1084415	STER_RS06030	Capsule	Immune modulation	100.00	100.00	WP_011226149
NMMGEMII_1	1288306	1289115	STU_RS16245	Capsule	Immune modulation	99.88	100.00	WP_002948020
NMMGEMII_1	1083822	1084415	STR_RS05880	Capsule	Immune modulation	99.83	100.00	WP_011226149
NMMGEMII_1	1289099	1290055	STU_RS16250	Capsule	Immune modulation	99.79	100.00	WP_011226328
NMMGEMII_1	1290052	1291200	STU_RS16255	Capsule	Immune modulation	99.74	100.00	WP_041828290
NMMGEMII_1	1083822	1084415	STU_RS15260	Capsule	Immune modulation	99.66	100.00	WP_011226149
NMMGEMII_1	1294696	1295547	rfbD	Capsule	Immune modulation	99.65	100.00	WP_014621820
NMMGEMII_1	853091	854749	fbp54	FBPs	Adherence	99.58	100.00	WP_011227179
NMMGEMII_1	1287101	1288306	STU_RS16240	Capsule	Immune modulation	99.58	100.00	WP_011226326
NMMGEMII_1	1284245	1286029	STU_RS16230	Capsule	Immune modulation	99.50	100.00	WP_011226325
NMMGEMII_1	1291309	1292319	STU_RS16260	Capsule	Immune modulation	99.50	100.00	WP_011226330
NMMGEMII_1	1286026	1287081	STU_RS16235	Capsule	Immune modulation	99.43	100.00	WP_002948022
NMMGEMII_1	1120628	1121389	srtA	Sortase A	Exoenzyme	99.21	100.00	-
NMMGEMII_1	948616	950031	STER_RS05250	Capsule	Immune modulation	98.52	100.00	WP_011681165
NMMGEMII_1	961023	961754	STU_RS14645	Capsule	Immune modulation	98.36	100.00	WP_011226048
NMMGEMII_1	1027702	1028490	cshA	Cell surface hydrophobicity proteins	Adherence	98.36	99.75	-
NMMGEMII_1	961023	961754	STER_RS05315	Capsule	Immune modulation	98.09	100.00	WP_011681176
NMMGEMII_1	961023	961754	STR_RS05260	Capsule	Immune modulation	97.68	100.00	WP_011227248
NMMGEMII_1	961755	963215	STER_RS05320	Capsule	Immune modulation	97.54	100.00	WP_011681177
NMMGEMII_1	1292322	1293593	STU_RS16265	Capsule	Immune modulation	97.48	99.76	WP_011226331
NMMGEMII_1	959572	960312	STU_RS14635	Capsule	Immune modulation	97.30	100.00	WP_011226046
NMMGEMII_1	959572	960312	STER_RS05305	Capsule	Immune modulation	96.90	100.00	WP_011681174
NMMGEMII_1	959577	960312	STR_RS05250	Capsule	Immune modulation	96.33	98.13	WP_011227246
NMMGEMII_1	961755	963215	STU_RS14650	Capsule	Immune modulation	96.23	100.21	WP_011226049
NMMGEMII_1	961755	963215	STR_RS05265	Capsule	Immune modulation	95.41	100.21	WP_041827043
NMMGEMII_1	960322	961014	STR_RS05255	Capsule	Immune modulation	95.40	99.86	WP_011227247
NMMGEMII_1	960322	961014	STU_RS14640	Capsule	Immune modulation	95.40	99.86	WP_011226047
NMMGEMII_1	958148	959515	STU_RS14630	Capsule	Immune modulation	95.39	100.00	WP_011226045
NMMGEMII_1	958150	959515	STER_RS05300	Capsule	Immune modulation	94.14	99.85	WP_011681173
NMMGEMII_1	960322	961014	STER_RS05310	Capsule	Immune modulation	89.47	100.00	WP_011681175
NMMGEMII_1	604287	605590	eno	Streptococcal enolase	Exoenzyme	88.09	99.54	WP_000022832
NMMGEMII_1	1585178	1586188	plr/gapA	Streptococcal plasmin receptor/GAPDH	Adherence	86.54	99.41	WP_002986042
NMMGEMII_1	149179	150462	tig/ropA	Trigger factor	Stress survival	80.73	99.77	WP_000107753
NMMGEMII_1	1082344	1083393	rfbB	Capsule	Immune modulation	80.48	100.10	WP_009659423

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
NMMGEMII_1	1124076	1125059	ldh(Sp_1220)	0.0	L-lactate dehydrogenase	94.82	100.00	AAK75326
NMMGEMII_1	713077	714150	MntE	0.0	manganese homeostasis	94.41	99.72	ABF32167
NMMGEMII_1	1462215	1464518	pfl2(Sp_0459)	0.0	formate acetyltransferase	92.97	99.22	AAK74619
NMMGEMII_1	517358	518326	spr0084	0.0	pathogenitcity related	92.57	98.48	AAK98888
NMMGEMII_1	735020	737266	metE	0.0	methionine biosynthesis enzymes	91.99	100.00	AAK74738
NMMGEMII_1	1193971	1195452	SPD_0310	0.0	UPF0371 protein SPD_0310	91.50	100.00	ABJ54480
NMMGEMII_1	63317	64309	recA	0.0	DNA recombination and repair	91.24	85.31	AAL00560
NMMGEMII_1	27206	28177	prsA2	0.0	ribose-phosphate pyrophosphokinase	90.12	100.00	ABF36968
NMMGEMII_1	1345505	1344354	potA	0.0	ABC transporter ATP-binding protein-spermidine/putrescine transport	89.32	99.74	AAL00050
NMMGEMII_1	1310537	1308549	uvrB	0.0	excinuclease ABC, B subunit	88.84	100.00	AE014259_2
NMMGEMII_1	1107855	1106125	ptsI	0.0	phosphoenolpyruvate-protein phosphotransferase	87.87	100.00	AAK34199
NMMGEMII_1	1777791	1776313	IMPDH	0.0	inosine-5'-monophosphate dehydrogenase	87.42	100.00	ADE32434
NMMGEMII_1	1762602	1760710	gidA	0.0	tRNA uridine 5-carboxymethylaminomethyl modification enzyme	86.05	98.90	ABP91129
NMMGEMII_1	604287	605588	Eno	0.0	enolase	85.98	99.77	ABP90468
NMMGEMII_1	740191	738482	PGM	0.0	phosphoglucomutase	83.71	99.65	ACH87041
NMMGEMII_1	1628187	1629197	pdh	0.0	pyruvate dehydrogenase	82.79	99.70	ABP91006
NMMGEMII_1	881238	879877	mnmE	0.0	central tRNA-modifying GTPase	81.80	99.56	ABP90420
NMMGEMII_1	1681637	1679745	PepO	0.0	endopeptidase	80.19	100.00	ABF32980
NMMGEMII_1	589861	590751	bglB	3.72e-178	putative phospho--glucosidase	88.55	99.66	AAK33487
NMMGEMII_1	798154	797219	SP_0676	7.13e-168	transcription facot	81.73	96.89	AAK74821
NMMGEMII_1	737458	738315	metF	4.49e-164	methionine biosynthesis enzymes	86.01	99.31	AAK74739
NMMGEMII_1	1000018	999314	covR	3.73e-131	responder protein	85.53	100.00	AAK71319
NMMGEMII_1	1175003	1174332	rr01	5.38e-123	response regulator	83.04	99.56	CAB54566
NMMGEMII_1	1000018	999314	walR	1.65e-121	DNA-binding response regulator	82.13	100.00	ANC99504
NMMGEMII_1	744145	744813	CiaR	9.08e-118	two-component response regulator	84.75	99.55	AAK74935
NMMGEMII_1	305605	306291	CovR	9.90e-118	serves to repress GAS virulence factor-encoding genes	80.79	100.00	ACE75886
NMMGEMII_1	744145	744816	ciaR	9.85e-116	two component system response regulator	82.59	99.12	AIK75708
NMMGEMII_1	64606	65001	SpxA2	3.57e-74	transcriptional regulator	90.91	100.00	ERL21461
NMMGEMII_1	892597	892998	SpxA1	3.63e-66	transcriptional regulator	80.60	100.00	ERL19273
NMMGEMII_1	150620	151120	RopE (M5005_Spy_1611)	4.75e-75	probable DNA-directed RNA polymerase subunit delta	81.44	87.43	AAK34603
NMMGEMII_1	1462215	1464512	PFL (B9H01_RS01125)	0.0	formate C-acetyltransferase	82.94	98.08	MYN69560
NMMGEMII_1	1667162	1666143	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
NMMGEMII_1	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