Probiotic potential risk score

ARGs (CARD)	VFs (VFDB)	PGs (PHI-base)	PPRS
5	10	8	13.75

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:3003324	Bacillus subtilis mprF	97.90	100.00	Bsub_mprF	AL009126.3
ARO:3003064	ykkD	97.14	100.00	ykkD	AL009126.1
ARO:3002813	lmrB	97.06	100.00	lmrB	JYFL01000006.1
ARO:3004476	vmlR	93.05	100.00	vmlR	NC_000964.3
ARO:3004541	mphK	88.78	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.
mph(K)	91.77	99.67	Warning: gene is missing from Notes file. Please inform curator.	NC_000964
aadK	90.91	99.88	Aminoglycoside resistance	M26879

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	93.05	100.00	WP_003234144.1
mphK	macrolide 2'-phosphotransferase MphK	BLASTX	88.78	99.02	WP_003246254.1
aadK	aminoglycoside 6-adenylyltransferase AadK	PARTIALX	88.63	73.94	WP_003229862.1
rphC	rifamycin-inactivating phosphotransferase RphC	BLASTX	81.45	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	96.70	100.00	0.0	Capsule	Immune modulation	NP_391471
VFG016295	capC	96.67	100.00	0.0	Capsule	Immune modulation	NP_391470
VFG016291	capA	94.31	100.00	0.0	Capsule	Immune modulation	NP_391469
VFG016303	dep/capD	92.91	100.00	0.0	Capsule	Immune modulation	NP_389723
VFG050032	dhbB	92.23	99.79	0.0	Bacillibactin	Nutritional/Metabolic factor	NP_391077
VFG016234	hlyIII	91.75	100.00	0.0	Hemolysin III	Exotoxin	NP_390062
VFG049999	dhbA	91.35	100.00	0.0	Bacillibactin	Nutritional/Metabolic factor	NP_391080
VFG050043	dhbF	91.08	99.99	0.0	Bacillibactin	Nutritional/Metabolic factor	NP_391076
VFG050021	dhbE	91.05	100.00	0.0	Bacillibactin	Nutritional/Metabolic factor	NP_391078
VFG050010	dhbC	88.56	99.92	0.0	Bacillibactin	Nutritional/Metabolic factor	NP_391079

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	86.04	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	5.70e-148	Nutrient-responsive regulator	ACJ80679
Q9RGX0	spxA1	83.21	99.24	2.15e-82	Redox-responsive transcription factor	AAF21893
Q724L7	SpoVG	82.72	78.64	2.37e-47	RNA-Binding Protein	AAT02994
P0A355	CspA	92.42	98.51	1.93e-40	Cold shock protein	CAA62903
Q92AD0	CspD	81.54	97.01	2.04e-36	Cold shock protein	CAC99957
P0A357	CspB	83.08	97.01	2.99e-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
RPHC01000001.1	142865	168921	False	Siphoviridae	VOG4574, 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, VOG7466
RPHC01000001.1	177295	179721	False	Unknown	VOG0650, VOG4552, VOG6495
RPHC01000001.1	711589	738954	False	Myoviridae	VOG4705, VOG7718, VOG4862, VOG4691, VOG4550, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG0749, VOG4685, VOG4773, VOG10227, VOG0796, VOG5447, VOG0189, VOG3490, VOG9667

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