safety

PPRS ARGs VFs PGs Plasmid Prophage IS elements

Probiotic potential risk score

ARGs	VFs	PGs	PPRS
0	35	29	45.45

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.
HOMHAHLN_1	1126286	1127155	rfbA	Capsule	Immune modulation	100.00	100.00	WP_011681286
HOMHAHLN_1	980328	981743	STER_RS05250	Capsule	Immune modulation	100.00	100.00	WP_011681165
HOMHAHLN_1	982944	983924	STER_RS05260	Capsule	Immune modulation	100.00	100.00	WP_011681166
HOMHAHLN_1	983917	985101	STER_RS05265	Capsule	Immune modulation	100.00	100.00	WP_011681167
HOMHAHLN_1	985118	986170	STER_RS05270	Capsule	Immune modulation	100.00	100.00	WP_011681168
HOMHAHLN_1	986185	987093	STER_RS05275	Capsule	Immune modulation	100.00	100.00	WP_011681169
HOMHAHLN_1	987114	988175	STER_RS05280	Capsule	Immune modulation	100.00	100.00	WP_202964935
HOMHAHLN_1	988212	988703	STER_RS05285	Capsule	Immune modulation	100.00	100.00	WP_011681171
HOMHAHLN_1	988715	989191	STER_RS05290	Capsule	Immune modulation	100.00	100.00	WP_011681172
HOMHAHLN_1	989947	991314	STER_RS05300	Capsule	Immune modulation	100.00	100.00	WP_011681173
HOMHAHLN_1	991371	992111	STER_RS05305	Capsule	Immune modulation	100.00	100.00	WP_011681174
HOMHAHLN_1	992121	992813	STER_RS05310	Capsule	Immune modulation	100.00	100.00	WP_011681175
HOMHAHLN_1	992822	993553	STER_RS05315	Capsule	Immune modulation	100.00	100.00	WP_011681176
HOMHAHLN_1	993554	995014	STER_RS05320	Capsule	Immune modulation	100.00	100.00	WP_011681177
HOMHAHLN_1	1125693	1126286	STER_RS06030	Capsule	Immune modulation	100.00	100.00	WP_011226149
HOMHAHLN_1	1339353	1341098	STER_RS07045	Capsule	Immune modulation	100.00	100.00	WP_011681434
HOMHAHLN_1	1341100	1342800	STER_RS07050	Capsule	Immune modulation	100.00	100.00	WP_041827753
HOMHAHLN_1	1342818	1344020	STER_RS07055	Capsule	Immune modulation	100.00	100.00	WP_011681436
HOMHAHLN_1	1344020	1344826	STER_RS07060	Capsule	Immune modulation	100.00	100.00	WP_011681437
HOMHAHLN_1	1344826	1345767	STER_RS07065	Capsule	Immune modulation	100.00	100.00	WP_011681438
HOMHAHLN_1	1345764	1346912	STER_RS07070	Capsule	Immune modulation	100.00	100.00	WP_011681439
HOMHAHLN_1	1347031	1347807	STER_RS07075	Capsule	Immune modulation	100.00	100.00	WP_011681440
HOMHAHLN_1	1348153	1348869	STER_RS07085	Capsule	Immune modulation	100.00	100.00	WP_011681442
HOMHAHLN_1	1348870	1349838	STER_RS07090	Capsule	Immune modulation	100.00	100.00	WP_011681443
HOMHAHLN_1	1349856	1350833	STER_RS07095	Capsule	Immune modulation	100.00	100.00	WP_011681444
HOMHAHLN_1	1350830	1352089	STER_RS07100	Capsule	Immune modulation	100.00	100.00	WP_011681445
HOMHAHLN_1	1125693	1126286	STR_RS05880	Capsule	Immune modulation	99.83	100.00	WP_011226149
HOMHAHLN_1	1341100	1342800	STR_RS06890	Capsule	Immune modulation	99.71	100.00	WP_041827077
HOMHAHLN_1	1125693	1126286	STU_RS15260	Capsule	Immune modulation	99.66	100.00	WP_011226149
HOMHAHLN_1	887224	888882	fbp54	FBPs	Adherence	99.64	100.00	WP_011227179
HOMHAHLN_1	45089	45928	cbpD	Autolysin	Exoenzyme	99.52	100.00	WP_011226733
HOMHAHLN_1	1344020	1344826	STR_RS06900	Capsule	Immune modulation	99.50	100.00	WP_011227429
HOMHAHLN_1	1344826	1345767	STR_RS06905	Capsule	Immune modulation	99.47	100.00	WP_011227430
HOMHAHLN_1	1342818	1344020	STR_RS06895	Capsule	Immune modulation	99.42	100.00	WP_011227428
HOMHAHLN_1	1345764	1346912	STR_RS06910	Capsule	Immune modulation	99.22	100.00	WP_011227431
HOMHAHLN_1	1068145	1068935	cshA	Cell surface hydrophobicity proteins	Adherence	98.74	100.00	-
HOMHAHLN_1	991376	992111	STR_RS05250	Capsule	Immune modulation	98.50	98.13	WP_011227246
HOMHAHLN_1	991371	992111	STU_RS14635	Capsule	Immune modulation	98.25	100.00	WP_011226046
HOMHAHLN_1	992822	993553	STR_RS05260	Capsule	Immune modulation	98.22	100.00	WP_011227248
HOMHAHLN_1	1339353	1341098	STR_RS06885	Capsule	Immune modulation	98.22	100.00	WP_011227426
HOMHAHLN_1	992822	993553	STU_RS14645	Capsule	Immune modulation	98.09	100.00	WP_011226048
HOMHAHLN_1	1161055	1161816	srtA	Sortase A	Exoenzyme	97.64	100.00	-
HOMHAHLN_1	993554	995014	STU_RS14650	Capsule	Immune modulation	97.47	100.21	WP_011226049
HOMHAHLN_1	993554	995014	STR_RS05265	Capsule	Immune modulation	96.92	100.21	WP_041827043
HOMHAHLN_1	1352208	1353059	rfbD	Capsule	Immune modulation	96.83	100.00	WP_014621820
HOMHAHLN_1	989951	991314	STU_RS14630	Capsule	Immune modulation	94.94	99.71	WP_011226045
HOMHAHLN_1	992121	992813	STU_RS14640	Capsule	Immune modulation	89.90	100.00	WP_011226047
HOMHAHLN_1	992121	992813	STR_RS05255	Capsule	Immune modulation	89.61	100.00	WP_011227247
HOMHAHLN_1	620012	621315	eno	Streptococcal enolase	Exoenzyme	88.10	99.46	WP_000022832
HOMHAHLN_1	1647043	1648053	plr/gapA	Streptococcal plasmin receptor/GAPDH	Adherence	86.54	99.41	WP_002986042
HOMHAHLN_1	1344020	1344826	SGO_RS05020	Capsule	Immune modulation	82.90	100.00	WP_012000440
HOMHAHLN_1	157096	158379	tig/ropA	Trigger factor	Stress survival	80.73	99.77	WP_000107753
HOMHAHLN_1	1124218	1125264	rfbB	Capsule	Immune modulation	80.61	100.00	WP_009659423
HOMHAHLN_1	1343283	1344020	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
HOMHAHLN_1	1164503	1165486	ldh(Sp_1220)	0.0	L-lactate dehydrogenase	94.82	100.00	AAK75326
HOMHAHLN_1	725315	726388	MntE	0.0	manganese homeostasis	94.41	99.72	ABF32167
HOMHAHLN_1	1517883	1520186	pfl2(Sp_0459)	0.0	formate acetyltransferase	92.97	99.22	AAK74619
HOMHAHLN_1	534956	535924	spr0084	0.0	pathogenitcity related	92.88	98.48	AAK98888
HOMHAHLN_1	1241258	1242739	SPD_0310	0.0	UPF0371 protein SPD_0310	92.51	100.00	ABJ54480
HOMHAHLN_1	757225	759471	metE	0.0	methionine biosynthesis enzymes	91.99	100.00	AAK74738
HOMHAHLN_1	64720	65718	recA	0.0	DNA recombination and repair	91.29	85.82	AAL00560
HOMHAHLN_1	28605	29576	prsA2	0.0	ribose-phosphate pyrophosphokinase	90.12	100.00	ABF36968
HOMHAHLN_1	1401196	1400045	potA	0.0	ABC transporter ATP-binding protein-spermidine/putrescine transport	89.32	99.74	AAL00050
HOMHAHLN_1	1366098	1364110	uvrB	0.0	excinuclease ABC, B subunit	89.14	100.00	AE014259_2
HOMHAHLN_1	1148304	1146574	ptsI	0.0	phosphoenolpyruvate-protein phosphotransferase	87.87	100.00	AAK34199
HOMHAHLN_1	1845391	1843913	IMPDH	0.0	inosine-5'-monophosphate dehydrogenase	87.63	100.00	ADE32434
HOMHAHLN_1	620012	621313	Eno	0.0	enolase	86.21	99.77	ABP90468
HOMHAHLN_1	1830656	1828764	gidA	0.0	tRNA uridine 5-carboxymethylaminomethyl modification enzyme	85.74	98.90	ABP91129
HOMHAHLN_1	762396	760687	PGM	0.0	phosphoglucomutase	84.06	99.65	ACH87041
HOMHAHLN_1	1690036	1691046	pdh	0.0	pyruvate dehydrogenase	83.09	99.70	ABP91006
HOMHAHLN_1	913317	911956	mnmE	0.0	central tRNA-modifying GTPase	82.24	99.56	ABP90420
HOMHAHLN_1	1741769	1739877	PepO	0.0	endopeptidase	80.19	100.00	ABF32980
HOMHAHLN_1	605576	606466	bglB	5.26e-178	putative phospho--glucosidase	88.55	99.66	AAK33487
HOMHAHLN_1	833678	832740	SP_0676	8.23e-168	transcription facot	81.47	97.20	AAK74821
HOMHAHLN_1	759663	760520	metF	1.53e-164	methionine biosynthesis enzymes	86.36	99.31	AAK74739
HOMHAHLN_1	1031836	1031132	covR	4.39e-131	responder protein	85.53	100.00	AAK71319
HOMHAHLN_1	1216652	1215981	rr01	3.01e-124	response regulator	83.93	99.56	CAB54566
HOMHAHLN_1	1031836	1031132	walR	1.85e-121	DNA-binding response regulator	82.13	100.00	ANC99504
HOMHAHLN_1	766351	767019	CiaR	2.02e-117	two-component response regulator	84.31	99.55	AAK74935
HOMHAHLN_1	310055	310741	CovR	5.07e-117	serves to repress GAS virulence factor-encoding genes	80.35	100.00	ACE75886
HOMHAHLN_1	766351	767022	ciaR	1.99e-115	two component system response regulator	82.14	99.12	AIK75708
HOMHAHLN_1	65994	66368	SpxA2	1.16e-69	transcriptional regulator	91.20	94.70	ERL21461
HOMHAHLN_1	924680	925081	SpxA1	3.77e-66	transcriptional regulator	80.60	100.00	ERL19273
HOMHAHLN_1	158537	159037	RopE (M5005_Spy_1611)	4.93e-75	probable DNA-directed RNA polymerase subunit delta	81.44	87.43	AAK34603
HOMHAHLN_1	1517883	1520180	PFL (B9H01_RS01125)	0.0	formate C-acetyltransferase	82.94	98.08	MYN69560
HOMHAHLN_1	1725897	1724878	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.
HOMHAHLN_3	2200	3144	rep37	945 / 945	100.00	HM050421

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

PlasmidHunter

Query ID	Prediction	Chromosome	Plasmid
HOMHAHLN_1	0.0	1.0	0.0
HOMHAHLN_2	1.0	0.0	1.0
HOMHAHLN_3	1.0	0.0	1.0

PlasmidHunter v 1.4.5 (Database: May. 2024 release)

Prophage

Phigaro

Query ID	Begin	End	Transposable	Taxonomy	pVOGs
No hit found