safety

PPRS ARGs VFs PGs Plasmid Prophage IS elements

Probiotic potential risk score

ARGs	VFs	PGs	PPRS
13	10	4	16.88

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.
CIFHKDKF_1	2696594	2697448	aadK	ARO:3002627	aadK	100.00	100.00	AL009126.1
CIFHKDKF_1	2677889	2679091	blt	ARO:3003006	blt	100.00	100.00	L32599.1
CIFHKDKF_1	2455570	2456739	bmr	ARO:3003007	bmr	99.74	100.00	M33768.1
CIFHKDKF_1	1431182	1431499	ykkD	ARO:3003064	ykkD	100.00	100.00	AL009126.1
CIFHKDKF_1	1430844	1431182	ykkC	ARO:3003063	ykkC	100.00	100.00	AL009126.1
CIFHKDKF_1	971103	973673	Bacillus subtilis mprF	ARO:3003324	Bsub_mprF	100.00	100.00	AL009126.3
CIFHKDKF_1	656973	658616	vmlR	ARO:3004476	vmlR	100.00	100.00	NC_000964.3
CIFHKDKF_1	391394	391987	tmrB	ARO:3003059	tmrB	100.00	100.00	AL009126.3
CIFHKDKF_1	340891	342324	lmrB	ARO:3002813	lmrB	100.00	100.00	JYFL01000006.1

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.
CIFHKDKF_1	2696594	2697448	aadK	Streptomycin	100.00	100.00	M26879
CIFHKDKF_1	4187409	4188785	tet(L)	Doxycycline, Tetracycline, Doxycycline, Tetracycline, Minocycline, Tigecycline	100.00	100.00	X08034
CIFHKDKF_1	328067	328996	mph(K)	Spiramycin, Telithromycin	99.03	100.00	NC_000964

ResFinder v4.6.0 (Database: resfinder_db, Aug. 2024 release)

AMRFinderPlus

Query ID	Begin	End	Gene symbol	Sequence name	Method	Identity	Coverage	Accession no.
CIFHKDKF_1	2696597	2697448	aadK	aminoglycoside 6-adenylyltransferase AadK	EXACTX	100.00	100.00	WP_003229862.1
CIFHKDKF_1	4184891	4185409	satA	streptothricin N-acetyltransferase SatA	EXACTX	100.00	100.00	WP_003242546.1
CIFHKDKF_1	4187412	4188785	tet(L)	tetracycline efflux MFS transporter Tet(L)	EXACTX	100.00	100.00	WP_003242953.1
CIFHKDKF_1	656976	658616	vmlR	ABC-F type ribosomal protection protein VmlR	EXACTX	100.00	100.00	WP_003234144.1
CIFHKDKF_1	2146658	2149252	rphC	rifamycin-inactivating phosphotransferase RphC	BLASTX	81.15	99.88	WP_087347987.1

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.
CIFHKDKF_1	3697550	3698692	capA	Capsule	Immune modulation	100.00	100.00	NP_391469
CIFHKDKF_1	3699175	3700356	capB	Capsule	Immune modulation	100.00	100.00	NP_391471
CIFHKDKF_1	3698711	3699160	capC	Capsule	Immune modulation	100.00	100.00	NP_391470
CIFHKDKF_1	2100000	2101763	dep/capD	Capsule	Immune modulation	100.00	100.00	NP_389723
CIFHKDKF_1	3291215	3292000	dhbA	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391080
CIFHKDKF_1	2256224	2256865	hlyIII	Hemolysin III	Exotoxin	100.00	100.00	NP_390062
CIFHKDKF_1	3280223	3287359	dhbF	Bacillibactin	Nutritional/Metabolic factor	99.99	100.00	NP_391076
CIFHKDKF_1	3287379	3288317	dhbB	Bacillibactin	Nutritional/Metabolic factor	99.89	100.00	NP_391077
CIFHKDKF_1	3289993	3291189	dhbC	Bacillibactin	Nutritional/Metabolic factor	99.67	100.00	NP_391079
CIFHKDKF_1	3288345	3289964	dhbE	Bacillibactin	Nutritional/Metabolic factor	99.57	100.00	NP_391078

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
CIFHKDKF_1	132473	133609	tufA	0.0	elongation factor Tu	84.96	95.69	AHM69299
CIFHKDKF_1	18665	19534	pdxS	3.13e-149	encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS	83.79	98.31	ACE61268
CIFHKDKF_1	1744447	1745223	CodY	3.42e-124	nutrient-responsive regulator	81.08	100.00	ACJ80679
CIFHKDKF_1	3545938	3546507	ClpP	2.54e-98	part of proteolytic complex	81.05	97.44	BAB94595

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
CIFHKDKF_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
CIFHKDKF_1	168222	175512	False	Unknown	VOG9667, VOG9667, VOG8241, VOG3549, VOG1878, VOG0083, VOG1309, VOG1292
CIFHKDKF_1	188322	212119	False	Myoviridae	VOG4773, VOG4688, VOG4685, VOG0749, VOG4589, VOG4870, VOG10055, VOG3890, VOG3891, VOG3892, VOG6163, VOG4865, VOG4885, VOG3894, VOG10120, VOG4691, VOG4862, VOG0906, VOG7718, VOG3390, VOG4705
CIFHKDKF_1	1374897	1401005	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
CIFHKDKF_1	1942322	1970964	False	Siphoviridae	VOG0198, VOG6093, VOG7462, VOG4581, VOG1886, VOG4556, VOG4568, VOG4553, VOG5361, VOG0204, VOG4589, VOG0539, VOG0704, VOG4586, VOG0541, VOG5910, VOG6163, VOG0801, VOG4619, VOG4660, VOG4612, VOG3390, VOG4705, VOG0641, VOG4918
CIFHKDKF_1	2627960	2658204	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, VOG4600
CIFHKDKF_1	2823878	2858604	False	Siphoviridae	VOG4972, VOG4574, VOG0641, VOG5008, VOG4705, VOG3390, VOG4612, VOG4660, VOG4619, VOG0801, VOG4545, VOG5910, VOG5852, VOG4586, VOG0704, VOG0539, VOG4589, VOG0204, VOG5361, VOG4553, VOG4568, VOG4556, VOG3644, VOG4544, VOG4581, VOG8909, VOG0198, VOG4548, VOG0327, VOG4609, VOG0026, VOG1565, VOG0021, VOG1047, VOG7438