Probiotic potential risk score

ARGs (CARD)	VFs (VFDB)	PGs (PHI-base)	PPRS
10	10	9	16.76

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:3002627	aadK	100.00	100.00	aadK	AL009126.1
ARO:3003006	blt	100.00	100.00	blt	L32599.1
ARO:3003059	tmrB	100.00	100.00	tmrB	AL009126.3
ARO:3003063	ykkC	100.00	100.00	ykkC	AL009126.1
ARO:3003064	ykkD	100.00	100.00	ykkD	AL009126.1
ARO:3003324	Bacillus subtilis mprF	100.00	100.00	Bsub_mprF	AL009126.3
ARO:3004476	vmlR	100.00	100.00	vmlR	NC_000964.3
ARO:3004541	mphK	100.00	100.00	mphK	CP010314.1
ARO:3002813	lmrB	99.79	100.42	lmrB	JYFL01000006.1
ARO:3003007	bmr	99.74	100.00	bmr	M33768.1

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

ResFinder

Resistance gene	Identity	Coverage	Phenotype	Accession no.
aadK	100.00	100.00	Aminoglycoside resistance	M26879
mph(K)	100.00	100.00	Warning: gene is missing from Notes file. Please inform curator.	NC_000964
tet(L)	100.00	100.00	Tetracycline resistance	X08034

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

AMRFinderPlus

Gene symbol	Sequence name	Method	Identity	Coverage	Accession no.
aadK	aminoglycoside 6-adenylyltransferase AadK	EXACTX	100.00	100.00	WP_003229862.1
mphK	macrolide 2'-phosphotransferase MphK	EXACTX	100.00	100.00	WP_003246254.1
satA	streptothricin N-acetyltransferase SatA	EXACTX	100.00	100.00	WP_003242546.1
tet(L)	tetracycline efflux MFS transporter Tet(L)	EXACTX	100.00	100.00	WP_003242953.1
vmlR	ABC-F type ribosomal protection protein VmlR	EXACTX	100.00	100.00	WP_003234144.1
rphC	rifamycin-inactivating phosphotransferase RphC	BLASTX	81.15	99.88	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.
VFG016291	capA	100.00	100.00	0.0	Capsule	Immune modulation	NP_391469
VFG016299	capB	100.00	100.00	0.0	Capsule	Immune modulation	NP_391471
VFG016295	capC	100.00	100.00	0.0	Capsule	Immune modulation	NP_391470
VFG016303	dep/capD	100.00	100.00	0.0	Capsule	Immune modulation	NP_389723
VFG049999	dhbA	100.00	100.00	0.0	Bacillibactin	Nutritional/Metabolic factor	NP_391080
VFG050032	dhbB	100.00	100.00	0.0	Bacillibactin	Nutritional/Metabolic factor	NP_391077
VFG050010	dhbC	100.00	100.00	0.0	Bacillibactin	Nutritional/Metabolic factor	NP_391079
VFG050021	dhbE	100.00	100.00	0.0	Bacillibactin	Nutritional/Metabolic factor	NP_391078
VFG050043	dhbF	100.00	100.00	0.0	Bacillibactin	Nutritional/Metabolic factor	NP_391076
VFG016234	hlyIII	100.00	100.00	0.0	Hemolysin III	Exotoxin	NP_390062

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	5.97e-148	Nutrient-responsive regulator	ACJ80679
P63786	ClpP	81.05	96.94	1.69e-114	Part of proteolytic complex	BAB94595
Q9RGX0	spxA1	83.21	99.24	4.34e-82	Redox-responsive transcription factor	AAF21893
Q724L7	SpoVG	82.72	78.64	2.48e-47	RNA-Binding Protein	AAT02994
P0A355	CspA	90.91	98.51	8.19e-40	Cold shock protein	CAA62903
Q92AD0	CspD	81.54	97.01	2.13e-36	Cold shock protein	CAC99957
P0A357	CspB	83.08	97.01	3.14e-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)	88.24	187 / 194	NC015392

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

Prophage

Phigaro

Scaffold	Begin	End	Transposable	Taxonomy	pVOGs
CAJNPN010000001.1	322179	348601	False	Siphoviridae	VOG0044, VOG0198, VOG4841, VOG4581, VOG1886, VOG4556, VOG4568, VOG4553, VOG5361, VOG0204, VOG4589, VOG0539, VOG0704, VOG4586, VOG0541, VOG5910, VOG6163, VOG0801, VOG4619, VOG4660, VOG4612, VOG3390, VOG4705, VOG5008, VOG0641
CAJNPN010000001.1	1687322	1713430	False	Myoviridae	VOG4705, VOG7718, VOG4862, VOG4691, VOG4550, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG0749, VOG4685, VOG4773, VOG10227, VOG0796, VOG5447, VOG4861, VOG0189, VOG3490, VOG9667
CAJNPN010000002.1	773807	778589	False	Siphoviridae	VOG0275, VOG1563, VOG9667
CAJNPN010000002.1	783933	810400	False	Siphoviridae	VOG0044, VOG6581, VOG0198, VOG0275, VOG1837, VOG0531, VOG4841, VOG4581, VOG4544, VOG4556, VOG4568, VOG4553, VOG0204, VOG4589, VOG0539, VOG0704, VOG4586, VOG0541, VOG6163, VOG0801, VOG4619, VOG4660, VOG4612, VOG3390, VOG4705, VOG0641, VOG4707
CAJNPN010000007.1	7865	11507	False	Siphoviridae	VOG1574, VOG0918
CAJNPN010000007.1	30305	56804	False	Siphoviridae	VOG4724, VOG0018, VOG9096, VOG0221, VOG4581, VOG4544, VOG4556, VOG4568, VOG4553, VOG0204, VOG4589, VOG0539, VOG0704, VOG4586, VOG5852, VOG6163, VOG4605, VOG4599, VOG9244, VOG10944, VOG1024
CAJNPN010000011.1	13717	43661	False	Myoviridae	VOG7718, VOG4862, VOG4691, VOG4550, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG10055, VOG4870, VOG4589, VOG0749, VOG4685, VOG4688, VOG4773, VOG10227, VOG0796, VOG4673, VOG9587, VOG4693, VOG0189, VOG11060, VOG1309

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