Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 13 | 10 | 7 | 17.83 |
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. |
|---|---|---|---|---|---|---|---|---|
| MDCBHCFC_28 | 1647725 | 1648063 | ykkC | ARO:3003063 | ykkC | 100.00 | 100.00 | AL009126.1 |
| MDCBHCFC_28 | 1647408 | 1647725 | ykkD | ARO:3003064 | ykkD | 99.05 | 100.00 | AL009126.1 |
| MDCBHCFC_28 | 673589 | 674758 | bmr | ARO:3003007 | bmr | 99.49 | 100.00 | M33768.1 |
| MDCBHCFC_28 | 447144 | 448346 | blt | ARO:3003006 | blt | 99.00 | 100.00 | L32599.1 |
| MDCBHCFC_28 | 430326 | 431180 | aadK | ARO:3002627 | aadK | 98.59 | 100.00 | AL009126.1 |
| MDCBHCFC_40 | 421653 | 423299 | vmlR | ARO:3004476 | vmlR | 99.09 | 100.18 | NC_000964.3 |
| MDCBHCFC_42 | 263168 | 265738 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.65 | 100.00 | AL009126.3 |
| MDCBHCFC_40 | 152702 | 153295 | tmrB | ARO:3003059 | tmrB | 97.46 | 100.00 | AL009126.3 |
| MDCBHCFC_40 | 102203 | 103636 | lmrB | ARO:3002813 | lmrB | 99.58 | 100.00 | JYFL01000006.1 |
| MDCBHCFC_40 | 89390 | 90310 | mphK | ARO:3004541 | mphK | 98.37 | 100.00 | CP010314.1 |
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. |
|---|---|---|---|---|---|---|---|
| MDCBHCFC_26 | 103 | 688 | aph(3')-Ia | Neomycin, Kanamycin, Lividomycin, Paromomycin, Ribostamycin, Kanamycin, Neomycin, Kanamycin, Unknown Aminoglycoside | 99.15 | 71.81 | V00359 |
| MDCBHCFC_40 | 89390 | 90310 | mph(K) | Spiramycin, Telithromycin | 99.02 | 100.00 | NC_000964 |
| MDCBHCFC_28 | 430326 | 431180 | aadK | Streptomycin | 98.71 | 100.00 | M26879 |
ResFinder v4.6.0 (Database: resfinder_db, Aug. 2024 release)
AMRFinderPlus
| Query ID | Begin | End | Gene symbol | Sequence name | Method | Identity | Coverage | Accession no. |
|---|---|---|---|---|---|---|---|---|
| MDCBHCFC_40 | 421656 | 423299 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 99.09 | 100.00 | WP_003234144.1 |
| MDCBHCFC_28 | 430326 | 431177 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 98.59 | 100.00 | WP_003229862.1 |
| MDCBHCFC_26 | 103 | 687 | aph(3')-Ia | aminoglycoside O-phosphotransferase APH(3')-Ia | PARTIAL_CONTIG_ENDX | 98.46 | 71.96 | WP_000018329.1 |
| MDCBHCFC_40 | 89390 | 90307 | mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 98.37 | 100.00 | WP_003246254.1 |
| MDCBHCFC_41 | 43554 | 44072 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 93.06 | 100.00 | WP_003242546.1 |
| MDCBHCFC_28 | 968072 | 970669 | rphC | rifamycin-inactivating phosphotransferase RphC | BLASTX | 80.60 | 100.00 | WP_087347987.1 |
AMRFinderPlus v4.0.3 (Database: Oct. 2024 release)
Virulence factors
Virulence Factor Database (VFDB)
| Query ID | qstart | qend | Gene name | e-value | VF name | VF category | Identity | Coverage | Accession no. |
|---|---|---|---|---|---|---|---|---|---|
| MDCBHCFC_36 | 172640 | 173821 | capB | 0.0 | Capsule | Immune modulation | 99.75 | 100.00 | NP_391471 |
| MDCBHCFC_36 | 595402 | 596187 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.75 | 100.00 | NP_391080 |
| MDCBHCFC_28 | 872203 | 872844 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 99.38 | 100.00 | NP_390062 |
| MDCBHCFC_36 | 596213 | 597409 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.33 | 100.00 | NP_391079 |
| MDCBHCFC_28 | 1019584 | 1021347 | dep/capD | 0.0 | Capsule | Immune modulation | 99.15 | 100.00 | NP_389723 |
| MDCBHCFC_36 | 173836 | 174285 | capC | 0.0 | Capsule | Immune modulation | 99.11 | 100.00 | NP_391470 |
| MDCBHCFC_36 | 599085 | 600023 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.83 | 100.00 | NP_391077 |
| MDCBHCFC_36 | 174304 | 175446 | capA | 0.0 | Capsule | Immune modulation | 98.78 | 100.00 | NP_391469 |
| MDCBHCFC_36 | 600043 | 607179 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.71 | 100.00 | NP_391076 |
| MDCBHCFC_36 | 597438 | 599057 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 97.04 | 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 |
|---|---|---|---|---|---|---|---|---|
| MDCBHCFC_53 | 31798 | 32934 | tufA | 0.0 | elongation factor Tu | 84.96 | 95.69 | AHM69299 |
| MDCBHCFC_59 | 11248 | 10379 | pdxS | 1.12e-151 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| MDCBHCFC_28 | 1336317 | 1335541 | CodY | 1.69e-124 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| MDCBHCFC_36 | 331965 | 331396 | ClpP | 4.26e-99 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| MDCBHCFC_28 | 1794705 | 1794313 | spxA1 | 1.33e-69 | redox-responsive transcription factor | 83.97 | 100.00 | AAF21893 |
| MDCBHCFC_28 | 1794705 | 1794313 | spx | 7.93e-68 | essential gene which is a thiol/oxidative stress sensor | 80.15 | 100.00 | BAB57159 |
| MDCBHCFC_55 | 34756 | 34514 | SpoVG | 7.52e-39 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| MDCBHCFC_40 | 374464 | 374661 | CspA | 1.95e-31 | cold shock protein | 90.91 | 100.00 | CAA62903 |
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 |
|---|---|---|---|
| MDCBHCFC_8 | 1.0 | 0.0 | 1.0 |
| MDCBHCFC_28 | 0.0 | 1.0 | 0.0 |
| MDCBHCFC_36 | 0.0 | 1.0 | 0.0 |
| MDCBHCFC_40 | 0.0 | 1.0 | 0.0 |
| MDCBHCFC_41 | 0.0 | 1.0 | 0.0 |
| MDCBHCFC_42 | 0.0 | 1.0 | 0.0 |
| MDCBHCFC_47 | 1.0 | 0.0 | 1.0 |
| MDCBHCFC_53 | 0.0 | 1.0 | 0.0 |
| MDCBHCFC_55 | 0.0 | 1.0 | 0.0 |
| MDCBHCFC_59 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| MDCBHCFC_28 | 473964 | 498083 | False | Myoviridae | VOG0796, VOG10227, VOG4773, VOG4688, VOG4685, VOG0749, VOG4589, VOG4870, VOG10055, VOG3890, VOG3891, VOG3892, VOG6163, VOG4865, VOG4885, VOG3894, VOG4550, VOG4691, VOG4862, VOG7718 |
| MDCBHCFC_28 | 1677577 | 1703889 | False | Myoviridae | VOG0753, VOG4705, VOG7718, VOG4862, VOG4691, VOG4550, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG0749, VOG4685, VOG4773, VOG10227, VOG0796, VOG5447, VOG4861, VOG0189, VOG3490, VOG9667 |
Phigaro v2.4.0 (Database: Jan. 2024 release)