Probiotic potential risk score

ARGs (CARD)	VFs (VFDB)	PGs (PHI-base)	PPRS
10	10	8	16.25

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: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:3003006	blt	99.50	100.00	blt	L32599.1
ARO:3002813	lmrB	99.37	100.42	lmrB	JYFL01000006.1
ARO:3004476	vmlR	99.09	100.00	vmlR	NC_000964.3
ARO:3003064	ykkD	99.05	100.00	ykkD	AL009126.1
ARO:3002627	aadK	98.59	100.00	aadK	AL009126.1
ARO:3003059	tmrB	98.48	100.00	tmrB	AL009126.3
ARO:3004541	mphK	97.71	100.00	mphK	CP010314.1

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

ResFinder

Resistance gene	Identity	Coverage	Phenotype	Accession no.
aadK	98.83	100.00	Aminoglycoside resistance	M26879
mph(K)	97.72	100.00	Warning: gene is missing from Notes file. Please inform curator.	NC_000964

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

AMRFinderPlus

Gene symbol	Sequence name	Method	Identity	Coverage	Accession no.
vmlR	ABC-F type ribosomal protection protein VmlR	BLASTX	99.09	100.00	WP_003234144.1
aadK	aminoglycoside 6-adenylyltransferase AadK	BLASTX	98.59	100.00	WP_003229862.1
mphK	macrolide 2'-phosphotransferase MphK	BLASTX	97.71	100.00	WP_003246254.1
satA	streptothricin N-acetyltransferase SatA	BLASTX	94.80	100.00	WP_003242546.1
rphC	rifamycin-inactivating phosphotransferase RphC	BLASTX	80.41	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.
VFG016299	capB	99.66	100.00	0.0	Capsule	Immune modulation	NP_391471
VFG016234	hlyIII	99.53	100.00	0.0	Hemolysin III	Exotoxin	NP_390062
VFG049999	dhbA	99.49	100.00	0.0	Bacillibactin	Nutritional/Metabolic factor	NP_391080
VFG050010	dhbC	99.17	100.00	0.0	Bacillibactin	Nutritional/Metabolic factor	NP_391079
VFG016303	dep/capD	99.04	100.00	0.0	Capsule	Immune modulation	NP_389723
VFG016291	capA	98.69	100.00	0.0	Capsule	Immune modulation	NP_391469
VFG016295	capC	98.67	100.00	0.0	Capsule	Immune modulation	NP_391470
VFG050032	dhbB	98.62	100.00	0.0	Bacillibactin	Nutritional/Metabolic factor	NP_391077
VFG050043	dhbF	98.53	100.00	0.0	Bacillibactin	Nutritional/Metabolic factor	NP_391076
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	5.55e-148	Nutrient-responsive regulator	ACJ80679
P63786	ClpP	81.05	96.94	1.58e-114	Part of proteolytic complex	BAB94595
Q9RGX0	spxA1	83.97	99.24	8.97e-83	Redox-responsive transcription factor	AAF21893
Q724L7	SpoVG	82.72	78.64	2.31e-47	RNA-Binding Protein	AAT02994
Q92AD0	CspD	80.00	97.01	1.10e-35	Cold shock protein	CAC99957
P0A357	CspB	83.08	97.01	2.91e-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.
No hit found

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

Prophage

Phigaro

Scaffold	Begin	End	Transposable	Taxonomy	pVOGs
UATI01000012.1	143491	166644	False	Myoviridae	VOG4705, VOG7718, VOG0906, VOG4862, VOG4691, VOG4550, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG10055, VOG4870, VOG4589, VOG0749, VOG4685, VOG4688, VOG4773, VOG10227
UATI01000012.1	169055	172150	False	Unknown	VOG4693, VOG0189, VOG11060
UATI01000012.1	511816	533547	False	Siphoviridae	VOG4574, VOG0641, VOG4705, VOG6243, VOG4612, VOG4626, VOG4619, VOG0801, VOG6163, VOG5910, VOG0541, VOG4586, VOG0704, VOG0539, VOG4589, VOG0204, VOG5361, VOG4553, VOG4573, VOG4556, VOG0202, VOG1886, VOG4581, VOG4841
UATI01000003.1	3150	25734	False	Myoviridae	VOG4574, VOG0136, VOG0753, VOG5008, VOG4705, VOG3390, VOG7718, VOG4845, VOG4691, VOG4550, VOG0573, VOG1348, VOG1433, VOG1956, VOG6163, VOG4699, VOG1352, VOG1883, VOG1881, VOG1353, VOG4623, VOG4564, VOG4553, VOG4555, VOG0720
UATI01000004.1	6781	30930	False	Myoviridae	VOG7895, VOG7718, VOG0906, VOG4862, VOG4691, VOG10120, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3891, VOG3890, VOG10055, VOG4870, VOG4589, VOG1581, VOG0749, VOG4685, VOG4688, VOG4773
UATI01000004.1	41516	49589	False	Siphoviridae	VOG0025, VOG3709, VOG11060, VOG1292, VOG1309, VOG0083, VOG1878, VOG3549, VOG8241
UATI01000009.1	48519	75800	False	Myoviridae	VOG4602, VOG9667, VOG3490, VOG0189, VOG4861, VOG5447, VOG0796, VOG10227, VOG4773, VOG4685, VOG0749, VOG3890, VOG3891, VOG3892, VOG6163, VOG4865, VOG4885, VOG3894, VOG4550, VOG4691, VOG4862, VOG7718, VOG4705

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