Probiotic potential risk score

ARGs (CARD)	VFs (VFDB)	PGs (PHI-base)	PPRS
9	10	9	16.19

PPRS is classified as low-risk (≤4), medium-risk (4-6), and high-risk (≥6).

Antibiotic resistance genes

Comprehensive Antibiotic Resistance Database (CARD)

ARO accession	ARO name	Identity	Coverage	CARD name	Accession no.
ARO:3002813	lmrB	100.00	100.00	lmrB	JYFL01000006.1
ARO:3003063	ykkC	100.00	100.00	ykkC	AL009126.1
ARO:3003324	Bacillus subtilis mprF	99.77	100.00	Bsub_mprF	AL009126.3
ARO:3003007	bmr	99.74	100.00	bmr	M33768.1
ARO:3004541	mphK	99.67	100.00	mphK	CP010314.1
ARO:3003059	tmrB	99.49	100.00	tmrB	AL009126.3
ARO:3003006	blt	99.25	100.00	blt	L32599.1
ARO:3003064	ykkD	99.05	100.00	ykkD	AL009126.1
ARO:3004476	vmlR	98.72	100.18	vmlR	NC_000964.3

RGI v6.0.0 (Database: CARD Variants v4.0.0, Jul. 2022 release)

ResFinder

Resistance gene	Identity	Coverage	Phenotype	Accession no.
mph(K)	99.57	100.00	Warning: gene is missing from Notes file. Please inform curator.	NC_000964
tet(L)	98.84	100.00	Tetracycline resistance	D12567

ResFinder v4.0 (Database: resfinder_db, May 2022 release)

AMRFinderPlus

Gene symbol	Sequence name	Method	Identity	Coverage	Accession no.
mphK	macrolide 2'-phosphotransferase MphK	BLASTX	99.67	100.00	WP_003246254.1
tet(L)	tetracycline efflux MFS transporter Tet(L)	BLASTX	98.91	100.00	WP_063856081.1
vmlR	ABC-F type ribosomal protection protein VmlR	BLASTX	98.72	100.00	WP_003234144.1
satA	streptothricin N-acetyltransferase SatA	BLASTX	93.06	100.00	WP_003242546.1
rphC	rifamycin-inactivating phosphotransferase RphC	INTERNAL_STOP	80.25	100.00	WP_087347987.1

AMRFinderPlus v3.10.42 (Database: Oct. 2022 release)

Virulence factors

Virulence Factor Database (VFDB)

Gene ID	Gene name	Identity	Coverage	e-value	VF name	VF category	Accession no.
VFG049999	dhbA	99.75	100.00	0.0	Bacillibactin	Nutritional/Metabolic factor	NP_391080
VFG016295	capC	99.56	100.00	0.0	Capsule	Immune modulation	NP_391470
VFG016299	capB	99.49	100.00	0.0	Capsule	Immune modulation	NP_391471
VFG016234	hlyIII	99.38	100.00	0.0	Hemolysin III	Exotoxin	NP_390062
VFG016291	capA	99.30	100.00	0.0	Capsule	Immune modulation	NP_391469
VFG050032	dhbB	99.25	100.00	0.0	Bacillibactin	Nutritional/Metabolic factor	NP_391077
VFG016303	dep/capD	98.98	100.00	0.0	Capsule	Immune modulation	NP_389723
VFG050043	dhbF	98.70	100.00	0.0	Bacillibactin	Nutritional/Metabolic factor	NP_391076
VFG050010	dhbC	98.58	100.00	0.0	Bacillibactin	Nutritional/Metabolic factor	NP_391079
VFG050021	dhbE	97.53	100.00	0.0	Bacillibactin	Nutritional/Metabolic factor	NP_391078

BLASTN v2.8.1+ (Database: VFDB, Jun. 2022 release)

VirulenceFinder

Database	Virulence factor	Identity	Coverage	Protein function	Accession no.
No hit found

VirulenceFinder v2.0.3 (Database: virulencefinder_db, Dec. 2022 release)

Pathogenic genes

PHI-base

Protein ID	Gene name	Identity	Coverage	e-value	Function	Gene ID
W8TRT9	tufA	85.03	99.24	0.0	Elongation factor Tu	AHM69299
B3GXB6	pdxS	83.79	97.97	0.0	Encodes the putative pyridoxal 5�-phosphate synthase subunit PdxS	ACE61268
B7HLG1	CodY	81.08	99.62	6.05e-148	Nutrient-responsive regulator	ACJ80679
P63786	ClpP	81.05	96.94	1.72e-114	Part of proteolytic complex	BAB94595
Q9RGX0	spxA1	83.97	99.24	9.78e-83	Redox-responsive transcription factor	AAF21893
Q724L7	SpoVG	82.72	78.64	2.52e-47	RNA-Binding Protein	AAT02994
P0A355	CspA	90.91	98.51	8.31e-40	Cold shock protein	CAA62903
Q92AD0	CspD	81.54	97.01	2.16e-36	Cold shock protein	CAC99957
P0A357	CspB	83.08	97.01	3.18e-34	Cold shock protein	CAD00094

BLASTP v2.8.1+ (Database: PHI-base v4.14, Nov. 2022 release)

Plasmid

PlasmidFinder

Plasmid	Identity	Query / Template	Accession no.
Col(SD853)	83.23	161 / 194	NC015392

PlasmidFinder 2.0.1 (Database: plasmidfinder_db, Jan. 2023 release)

Prophage

Phigaro

Scaffold	Begin	End	Transposable	Taxonomy	pVOGs
CP089148.1	164248	189078	False	Siphoviridae	VOG2752, VOG10041, VOG8320, VOG0198, VOG4841, VOG4581, VOG4544, VOG3607, VOG4556, VOG4568, VOG4553, VOG5361, VOG0204, VOG4589, VOG0539, VOG0704, VOG4586, VOG5852, VOG5910, VOG6163, VOG0801, VOG4619, VOG4626, VOG4612, VOG3390, VOG4705, VOG0641
CP089148.1	670127	703701	False	Siphoviridae	VOG1565, VOG0535, VOG1936, VOG4606, VOG7060, VOG2752, VOG10041, VOG7372, VOG0044, VOG8320, VOG0198, VOG9029, VOG4841, VOG0713, VOG4581, VOG1886, VOG3607, VOG4556, VOG4568, VOG4553, VOG5361, VOG0204, VOG9583, VOG0704, VOG4586, VOG0541, VOG5910, VOG0801, VOG4772, VOG4626, VOG3390, VOG4705, VOG4612, VOG3390, VOG7896, VOG0641, VOG4707, VOG4972
CP089148.1	1367253	1392549	False	Myoviridae	VOG4602, VOG9667, VOG3490, VOG0189, VOG4861, VOG5447, VOG0796, VOG10227, VOG4773, VOG4685, VOG0749, VOG3890, VOG3891, VOG3892, VOG6163, VOG4865, VOG4885, VOG3894, VOG4550, VOG4691, VOG4862, VOG7718, VOG3390, VOG7895, VOG0753
CP089148.1	2197303	2202984	False	Myoviridae	VOG5722, VOG5779, VOG5721
CP089148.1	2214362	2231226	False	Siphoviridae	VOG9312, VOG4910, VOG3389, VOG5042, VOG9712, VOG4626, VOG3390, VOG4705, VOG4574, VOG8537
CP089148.1	2685837	2708752	False	Siphoviridae	VOG4707, VOG0641, VOG7896, VOG3390, VOG4612, VOG4705, VOG3390, VOG4626, VOG4772, VOG0801, VOG5910, VOG0541, VOG4586, VOG0704, VOG0539, VOG0204, VOG5361, VOG4553, VOG4568, VOG4556, VOG3607, VOG1886, VOG4581, VOG0713, VOG4841
CP089148.1	2797686	2822436	False	Siphoviridae	VOG4615, VOG0136, VOG5221, VOG7896, VOG3390, VOG4612, VOG4705, VOG3390, VOG4626, VOG4619, VOG0801, VOG6163, VOG5910, VOG0541, VOG4586, VOG0704, VOG0539, VOG4589, VOG0204, VOG5361, VOG4553, VOG4568, VOG4556, VOG1886, VOG4581, VOG4841, VOG0713
CP089148.1	3159234	3181881	False	Myoviridae	VOG4574, VOG0641, VOG4705, VOG3390, VOG7718, VOG4845, VOG4691, VOG4550, VOG0573, VOG1348, VOG1433, VOG1956, VOG6163, VOG4699, VOG1352, VOG1883, VOG1881, VOG1353, VOG4623, VOG4564, VOG4553, VOG4555, VOG0720
CP089148.1	3189578	3193151	False	Unknown	VOG0189, VOG4566, VOG1309, VOG4600

Phigaro v2.3.0 (Database: Aug. 2017 release)