safety

PPRS ARGs VFs PGs Plasmid Prophage IS elements

Probiotic potential risk score

ARGs	VFs	PGs	PPRS
0	26	29	38.95

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.
CHFECOIO_1	43550	44389	cbpD	Autolysin	Exoenzyme	100.00	100.00	WP_011226733
CHFECOIO_1	1131638	1132507	rfbA	Capsule	Immune modulation	100.00	100.00	WP_011681286
CHFECOIO_1	1131045	1131638	STER_RS06030	Capsule	Immune modulation	100.00	100.00	WP_011226149
CHFECOIO_1	1351401	1352210	STU_RS16245	Capsule	Immune modulation	99.88	100.00	WP_002948020
CHFECOIO_1	1131045	1131638	STR_RS05880	Capsule	Immune modulation	99.83	100.00	WP_011226149
CHFECOIO_1	995646	996338	STU_RS14640	Capsule	Immune modulation	99.71	100.00	WP_011226047
CHFECOIO_1	1131045	1131638	STU_RS15260	Capsule	Immune modulation	99.66	100.00	WP_011226149
CHFECOIO_1	885070	886728	fbp54	FBPs	Adherence	99.52	100.00	WP_011227179
CHFECOIO_1	1347340	1349124	STU_RS16230	Capsule	Immune modulation	99.50	100.00	WP_011226325
CHFECOIO_1	1350196	1351401	STU_RS16240	Capsule	Immune modulation	99.25	100.00	WP_011226326
CHFECOIO_1	1352194	1353150	STU_RS16250	Capsule	Immune modulation	99.16	100.00	WP_011226328
CHFECOIO_1	1349121	1350176	STU_RS16235	Capsule	Immune modulation	99.15	100.00	WP_002948022
CHFECOIO_1	995646	996338	STR_RS05255	Capsule	Immune modulation	99.13	100.00	WP_011227247
CHFECOIO_1	1167830	1168591	srtA	Sortase A	Exoenzyme	99.08	100.00	-
CHFECOIO_1	1073553	1074343	cshA	Cell surface hydrophobicity proteins	Adherence	98.74	100.00	-
CHFECOIO_1	1359330	1360181	rfbD	Capsule	Immune modulation	98.71	100.00	WP_014621820
CHFECOIO_1	977523	978938	STER_RS05250	Capsule	Immune modulation	98.66	100.00	WP_011681165
CHFECOIO_1	1355991	1356953	STU_RS16260	Capsule	Immune modulation	98.65	95.25	WP_011226330
CHFECOIO_1	996347	997078	STER_RS05315	Capsule	Immune modulation	98.63	100.00	WP_011681176
CHFECOIO_1	1353147	1354295	STU_RS16255	Capsule	Immune modulation	98.52	100.00	WP_041828290
CHFECOIO_1	996347	997078	STU_RS14645	Capsule	Immune modulation	98.36	100.00	WP_011226048
CHFECOIO_1	996347	997078	STR_RS05260	Capsule	Immune modulation	98.22	100.00	WP_011227248
CHFECOIO_1	997079	998539	STER_RS05320	Capsule	Immune modulation	97.95	100.00	WP_011681177
CHFECOIO_1	1356956	1358227	STU_RS16265	Capsule	Immune modulation	97.41	99.76	WP_011226331
CHFECOIO_1	997079	998539	STU_RS14650	Capsule	Immune modulation	97.19	100.21	WP_011226049
CHFECOIO_1	997079	998539	STR_RS05265	Capsule	Immune modulation	96.37	100.21	WP_041827043
CHFECOIO_1	993454	994821	STU_RS14630	Capsule	Immune modulation	96.13	100.00	WP_011226045
CHFECOIO_1	993456	994821	STER_RS05300	Capsule	Immune modulation	94.88	99.85	WP_011681173
CHFECOIO_1	994878	995636	STER_RS05305	Capsule	Immune modulation	93.54	100.94	WP_011681174
CHFECOIO_1	994878	995636	STU_RS14635	Capsule	Immune modulation	93.15	100.94	WP_011226046
CHFECOIO_1	994883	995636	STR_RS05250	Capsule	Immune modulation	92.84	99.07	WP_011227246
CHFECOIO_1	991720	992711	STU_RS14625*	Capsule	Immune modulation	90.79	99.70	-
CHFECOIO_1	995646	996338	STER_RS05310	Capsule	Immune modulation	89.61	100.00	WP_011681175
CHFECOIO_1	619534	620837	eno	Streptococcal enolase	Exoenzyme	88.02	99.54	WP_000022832
CHFECOIO_1	1658410	1659420	plr/gapA	Streptococcal plasmin receptor/GAPDH	Adherence	87.46	99.80	WP_002986042
CHFECOIO_1	152710	153993	tig/ropA	Trigger factor	Stress survival	80.73	99.77	WP_000107753
CHFECOIO_1	1129570	1130616	rfbB	Capsule	Immune modulation	80.61	100.00	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
CHFECOIO_1	1171278	1172261	ldh(Sp_1220)	0.0	L-lactate dehydrogenase	94.82	100.00	AAK75326
CHFECOIO_1	728415	729488	MntE	0.0	manganese homeostasis	94.41	99.72	ABF32167
CHFECOIO_1	1535582	1537885	pfl2(Sp_0459)	0.0	formate acetyltransferase	92.97	99.22	AAK74619
CHFECOIO_1	536061	537029	spr0084	0.0	pathogenitcity related	92.57	98.48	AAK98888
CHFECOIO_1	750328	752574	metE	0.0	methionine biosynthesis enzymes	91.72	100.00	AAK74738
CHFECOIO_1	1251508	1252989	SPD_0310	0.0	UPF0371 protein SPD_0310	91.50	100.00	ABJ54480
CHFECOIO_1	72094	73086	recA	0.0	DNA recombination and repair	91.24	85.31	AAL00560
CHFECOIO_1	27068	28039	prsA2	0.0	ribose-phosphate pyrophosphokinase	90.12	100.00	ABF36968
CHFECOIO_1	1421707	1420556	potA	0.0	ABC transporter ATP-binding protein-spermidine/putrescine transport	89.32	99.74	AAL00050
CHFECOIO_1	1373354	1371366	uvrB	0.0	excinuclease ABC, B subunit	88.99	100.00	AE014259_2
CHFECOIO_1	1155080	1153350	ptsI	0.0	phosphoenolpyruvate-protein phosphotransferase	88.04	100.00	AAK34199
CHFECOIO_1	1878721	1877243	IMPDH	0.0	inosine-5'-monophosphate dehydrogenase	87.42	100.00	ADE32434
CHFECOIO_1	619534	620835	Eno	0.0	enolase	86.21	99.77	ABP90468
CHFECOIO_1	1863532	1861640	gidA	0.0	tRNA uridine 5-carboxymethylaminomethyl modification enzyme	86.05	98.90	ABP91129
CHFECOIO_1	755499	753790	PGM	0.0	phosphoglucomutase	84.06	99.65	ACH87041
CHFECOIO_1	1701412	1702422	pdh	0.0	pyruvate dehydrogenase	82.79	99.70	ABP91006
CHFECOIO_1	913256	911895	mnmE	0.0	central tRNA-modifying GTPase	81.80	99.56	ABP90420
CHFECOIO_1	1751729	1749837	PepO	0.0	endopeptidase	80.19	100.00	ABF32980
CHFECOIO_1	605095	605985	bglB	1.36e-178	putative phospho--glucosidase	88.89	99.66	AAK33487
CHFECOIO_1	829837	828899	SP_0676	2.40e-167	transcription facot	81.15	97.20	AAK74821
CHFECOIO_1	752766	753623	metF	8.82e-165	methionine biosynthesis enzymes	86.36	99.31	AAK74739
CHFECOIO_1	1035389	1034685	covR	4.47e-131	responder protein	85.53	100.00	AAK71319
CHFECOIO_1	1223108	1222437	rr01	3.06e-124	response regulator	83.93	99.56	CAB54566
CHFECOIO_1	759454	760122	CiaR	8.90e-123	two-component response regulator	86.10	99.55	AAK74935
CHFECOIO_1	1035389	1034685	walR	1.88e-121	DNA-binding response regulator	82.13	100.00	ANC99504
CHFECOIO_1	759454	760125	ciaR	1.21e-120	two component system response regulator	83.93	99.12	AIK75708
CHFECOIO_1	310762	311448	CovR	1.05e-117	serves to repress GAS virulence factor-encoding genes	80.79	100.00	ACE75886
CHFECOIO_1	73383	73778	SpxA2	3.78e-74	transcriptional regulator	90.91	100.00	ERL21461
CHFECOIO_1	924616	925017	SpxA1	3.84e-66	transcriptional regulator	80.60	100.00	ERL19273
CHFECOIO_1	154151	154651	RopE (M5005_Spy_1611)	3.61e-75	probable DNA-directed RNA polymerase subunit delta	82.04	87.43	AAK34603
CHFECOIO_1	1535582	1537879	PFL (B9H01_RS01125)	0.0	formate C-acetyltransferase	82.94	98.08	MYN69560
CHFECOIO_1	1737272	1736253	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
CHFECOIO_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