Safety assessment of Bifidobacterium longum JDM301 based on complete genome sequences

doi:10.3748/wjg.v18.i5.479

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World Journal of Gastroenterology

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1007-9327

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Baishideng Publishing Group Inc, 7041 Koll Center Parkway, Suite 160, Pleasanton, CA 94566, USA

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World J Gastroenterol. Feb 7, 2012; 18(5): 479-488
Published online Feb 7, 2012. doi: 10.3748/wjg.v18.i5.479

Table 1 Putative antibiotic resistance genes identified in the genome of Bifidobacterium longum JDM301

Antibiotics	Antibiotic resistance genes	Product name
Bacitracin	BLJ_1636	ABC transporter-related protein
	BLJ_0984	ABC transporter-related protein
	BLJ_0923	ABC transporter-related protein
	BLJ_1055	Undecaprenyl pyrophosphate phosphatase
	BLJ_1119	Bacitracin transport ATP-binding protein bcrA
Vancomycin	BLJ_0853	VanU
	BLJ_1764	Dehydrogenase VanH
	BLJ_1084	Sensor protein vanSB
	BLJ_0707	VanSD5
	BLJ_0343	Histidine kinase VanSc3
	BLJ_0287	D-Ala: D-Lac ligase VanD
Multiple drugs	BLJ_1090	ATP-binding protein
	BLJ_1650	Lsa
	BLJ_1437	LmrB
	BLJ_0618	Multidrug export protein MepA
	BLJ_0769	Efflux transporter, RND family, MFP subunit
	BLJ_0181	Multidrug efflux protein QacB
	BLJ_1062	Multidrug export protein MepA
Chloramphenicol	BLJ_1672	Chloramphenicol resistance protein
	BLJ_1322	Chloramphenicol resistance protein
Thiostrepton	BLJ_0885	Thiostrepton-resistance methylase
Penicillin	BLJ_1301	Penicillin binding protein
Kasugamycin	BLJ_2030	S-adenosylmethionine-6-N', N'-adenosyl
Kasugamycin	BLJ_2030	(rRNA) dimethyltransferase
Tetracycline	BLJ_0814	Tetracycline-resistance determinant tetV
	BLJ_1245	TetW
	BLJ_0594	Tetracycline resistance protein
	BLJ_1401	TetQ
Carbomycin	BLJ_1625	Carbomycin resistance protein
Sulfonamide	BLJ_1629	Dihydropteroate synthase
Tetracenomycin C	BLJ_1624	Tetracenomycin C efflux protein
Trimethoprim	BLJ_1657	dihydrofolate reductase
Macrolide	BLJ_0925	Macrolide-efflux protein
	BLJ_1936	Macrolide-efflux protein
	BLJ_0819	Macrolide-efflux protein
	BLJ_0042	Macrolide-efflux protein
	BLJ_1154	Macrolide-efflux protein variant

ABC: ATP-binding cassette; RND: Resistance-nodulation-cell division.

Table 2 Minimum inhibitory concentration values of 16 antibiotics for Bifidobacterium longum JDM301

Antibiotics	Minimum inhibitory concentration (mg/L)
Ciprofloxacin	> 32
Amikacin	> 256
Gentamicin	> 256
Bacitracin	26.67
Streptomycin	170.67
Vancomycin	0.9
Amoxicillin	0.064
Cephalothin	1.33
Chloramphenicol	0.25
Erythromycin	0.04
Ampicillin	0.058
Cefotaxime	0.19
Rifampicin	0.074
Tetracycline	8
Imipenem	0.19
Trimethoprim-sulphamethoxazol	1.83

Table 3 Putative virulence factors identified in the genome of Bifidobacterium longum JDM301

Query	Identity	Subject	Predicted functions
BLJ_1089	24.9	VFG0934	2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase
BLJ_1835	26.36	VFG0934	2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase
BLJ_0323	29.3	VFG0934	2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase
BLJ_1476	22.11	VFG2378	6 kDa early secretory antigenic target esxA
BLJ_0992	32.98	VFG0869	AatC ATB binding protein of ABC transporter
BLJ_1080	34.81	VFG0869	AatC ATB binding protein of ABC transporter
BLJ_1968	37.3	VFG0869	AatC ATB binding protein of ABC transporter
BLJ_0770	37.43	VFG0869	AatC ATB binding protein of ABC transporter
BLJ_0026	35.71	VFG1404	ahpC
BLJ_0136	28.73	VFG2218	ATPase VirB11 homolog
BLJ_0880	24.18	VFG1042	ATP-binding protein FecE
BLJ_0787	47.92	VFG0077	ATP-dependent Clp protease proteolytic subunit
BLJ_0786	53.8	VFG0077	ATP-dependent Clp protease proteolytic subunit
BLJ_0948	37.66	VFG2162	Bile salt hydrolase
BLJ_1243	22.97	VFG2242	Conjugal transfer protein trag
BLJ_0551	26.54	VFG1108	Conserved hypothetical protein
BLJ_1951	29.85	VFG1269	Cyclolysin secretion ATP-binding protein
BLJ_1925	32.31	VFG1269	Cyclolysin secretion ATP-binding protein
BLJ_1863	45.5	VFG0079	Endopeptidase Clp ATP-binding chain C
BLJ_1465	56.77	VFG0079	Endopeptidase Clp ATP-binding chain C
BLJ_0713	30.12	VFG0925	Ferric enterobactin transport ATP-binding protein fepC
BLJ_1872	25.51	VFG2225	GDP-mannose 4,6-dehydratase
BLJ_1324	32.49	VFG1399	glnA1
BLJ_0624	62.11	VFG1399	glnA1
BLJ_1834	29.47	VFG0313	Glucose/galactose transporter
BLJ_1926	30.02	VFG1557	HlyB protein
BLJ_1477	56.12	VFG1855	Hsp60, 60K heat shock protein HtpB
BLJ_0064	26.21	VFG1397	hspX
BLJ_1444	40.85	VFG1563	Hypothetical protein
BLJ_1606	27.78	VFG1593	Hypothetical protein
BLJ_1640	30.81	VFG1593	Hypothetical protein
BLJ_0011	22.16	VFG1604	Hypothetical protein
BLJ_1513	26.3	VFG1604	Hypothetical protein
BLJ_1846	27.67	VFG1604	Hypothetical protein
BLJ_0337	44.25	VFG1630	Hypothetical protein
BLJ_0336	44.38	VFG1630	Hypothetical protein
BLJ_1500	23.53	VFG1963	Hypothetical protein Cj1435c
BLJ_1169	24.64	VFG1390	Hypothetical protein Rv0981
BLJ_0708	36.8	VFG1390	Hypothetical protein Rv0981
BLJ_0802	28.83	VFG1824	Hypothetical protein Rv3133c
BLJ_1357	30.46	VFG1824	Hypothetical protein Rv3133c
BLJ_1113	32.41	VFG1824	Hypothetical protein Rv3133c
BLJ_0835	32.42	VFG1824	Hypothetical protein Rv3133c
BLJ_0859	27.93	VFG1206	Iron(III) ABC transporter, ATP-binding protein
BLJ_0348	28.13	VFG1206	Iron(III) ABC transporter, ATP-binding protein
BLJ_0530	29.29	VFG1206	Iron(III) ABC transporter, ATP-binding protein
BLJ_2016	35.81	VFG1206	Iron(III) ABC transporter, ATP-binding protein
BLJ_1875	36.19	VFG1627	IS100 transposase; transposase ORFA
BLJ_1249	37.55	VFG1627	IS100 transposase; transposase ORFA
BLJ_1252	39.22	VFG1627	IS100 transposase; transposase ORFA
BLJ_0930	42.29	VFG1627	IS100 transposase; transposase ORFA
BLJ_1966	30.68	VFG1485	L7045
BLJ_1850	59.7	VFG1411	leuD
BLJ_0379	39.24	VFG0320	Lipopolysaccharide core biosynthesis protein (kdtB)
BLJ_1549	22.02	VFG1817	mbtA
BLJ_1204	25.8	VFG0574	Mg<up>2+</up> transport protein
BLJ_2010	30.62	VFG0574	Mg<up>2+</up> transport protein
BLJ_1270	28.62	VFG1116	N-acetylglucosamine-6-phosphate deacetylase
BLJ_1832	21.89	VFG1109	N-acetylneuraminate lyase, putative
BLJ_0490	25.95	VFG1109	N-acetylneuraminate lyase, putative
BLJ_0021	26.83	VFG0307	Neutrophil activating protein (bacterioferritin)
BLJ_1889	24.14	VFG2227	O-antigen export system permease protein
BLJ_1251	26.05	VFG1461	ORF A protein
BLJ_0214	30.5	VFG0594	Pathogenicity island encoded protein: SPI3
BLJ_0159	33.25	VFG0594	Pathogenicity island encoded protein: SPI3
BLJ_1474	57.32	VFG1386	phoP
BLJ_1703	25.65	VFG2220	Phosphoglucomutase
BLJ_0497	28.35	VFG2362	Phosphomannomutase
BLJ_1137	25.1	VFG1983	ABC-type amino-acid transporter periplasmic solute-binding protein
BLJ_0508	25.93	VFG1983	ABC-type amino-acid transporter periplasmic solute-binding protein
BLJ_1453	29.27	VFG1983	ABC-type amino-acid transporter periplasmic solute-binding protein
BLJ_0408	38.22	VFG2059	ATP-binding component of ABC transporter
BLJ_0480	27.04	VFG2061	Phosphoprotein phosphatase
BLJ_0805	28.09	VFG1384	proC
BLJ_1396	31.06	VFG1384	proC
BLJ_0584	26.09	VFG1387	purC
BLJ_1772	22.28	VFG0480	Putative amino acid permease
BLJ_0538	25.17	VFG0480	Putative amino acid permease
BLJ_1329	24.42	VFG1965	Putative aminotransferase
BLJ_0025	30.45	VFG2301	Putative carbonic anhydrase
BLJ_0922	23.51	VFG0031	Putative glycosyl transferase
BLJ_1670	38.88	VFG1668	Putative lysil-tRNA synthetase LysU
BLJ_0563	25	VFG1498	Putative periplasmic solute binding protein
BLJ_1171	28.48	VFG0483	Putative regulatory protein, deoR family
BLJ_1517	29.25	VFG0483	Putative regulatory protein, deoR family
BLJ_0344	37.02	VFG1702	Putative response regulator
BLJ_0040	27.91	VFG1746	Putative two-component response regulator
BLJ_0740	29.13	VFG1746	Putative two-component response regulator
BLJ_1105	24.49	VFG0168	Pyochelin biosynthesis protein PchD
BLJ_0409	25.56	VFG0168	Pyochelin biosynthesis protein PchD
BLJ_0720	41.04	VFG0479	Pyruvate kinase I (formerly F), fructose stimulated
BLJ_1163	55.32	VFG1826	relA
BLJ_0995	25.84	VFG1889	Response regulator GacA
BLJ_1679	28.89	VFG1889	Response regulator GacA
BLJ_1083	40.89	VFG0473	Response regulator in two-component regulatory system with BasS
BLJ_1273	26.57	VFG1115	ROK family protein
BLJ_1620	26.62	VFG1115	ROK family protein
BLJ_1622	31.35	VFG1115	ROK family protein
BLJ_1796	27.31	VFG0526	Salmonella iron transporter: fur regulated
BLJ_0662	29.06	VFG0526	Salmonella iron transporter: fur regulated
BLJ_0712	25.4	VFG0528	Salmonella iron transporter: fur regulated
BLJ_1174	51.39	VFG1405	sigA
BLJ_1258	41.15	VFG1412	sigH
BLJ_1342	33.11	VFG2161	Signal peptidase II
BLJ_0906	21.73	VFG2197	Sugar-binding transcriptional regulator, LacI family
BLJ_1923	22.38	VFG2197	Sugar-binding transcriptional regulator, LacI family
BLJ_1360	22.88	VFG2197	Sugar-binding transcriptional regulator, LacI family
BLJ_1421	23.24	VFG2197	Sugar-binding transcriptional regulator, LacI family
BLJ_0611	23.31	VFG2197	Sugar-binding transcriptional regulator, LacI family
BLJ_1836	23.32	VFG2197	Sugar-binding transcriptional regulator, LacI family
BLJ_0459	23.33	VFG2197	Sugar-binding transcriptional regulator, LacI family
BLJ_1278	23.43	VFG2197	Sugar-binding transcriptional regulator, LacI family
BLJ_1998	23.51	VFG2197	Sugar-binding transcriptional regulator, LacI family
BLJ_1522	23.6	VFG2197	Sugar-binding transcriptional regulator, LacI family
BLJ_0109	23.63	VFG2197	Sugar-binding transcriptional regulator, LacI family
BLJ_0418	23.69	VFG2197	Sugar-binding transcriptional regulator, LacI family
BLJ_0118	23.7	VFG2197	Sugar-binding transcriptional regulator, LacI family
BLJ_0520	23.85	VFG2197	Sugar-binding transcriptional regulator, LacI family
BLJ_1976	24.27	VFG2197	Sugar-binding transcriptional regulator, LacI family
BLJ_0099	24.31	VFG2197	Sugar-binding transcriptional regulator, LacI family
BLJ_1605	24.34	VFG2197	Sugar-binding transcriptional regulator, LacI family
BLJ_0132	24.53	VFG2197	Sugar-binding transcriptional regulator, LacI family
BLJ_1912	24.58	VFG2197	Sugar-binding transcriptional regulator, LacI family
BLJ_0912	24.69	VFG2197	Sugar-binding transcriptional regulator, LacI family
BLJ_0318	24.71	VFG2197	Sugar-binding transcriptional regulator, LacI family
BLJ_1515	24.93	VFG2197	Sugar-binding transcriptional regulator, LacI family
BLJ_1933	25	VFG2197	Sugar-binding transcriptional regulator, LacI family
BLJ_1718	25	VFG2197	Sugar-binding transcriptional regulator, LacI family
BLJ_1997	25.36	VFG2197	Sugar-binding transcriptional regulator, LacI family
BLJ_0400	25.37	VFG2197	Sugar-binding transcriptional regulator, LacI family
BLJ_0515	27.08	VFG2197	Sugar-binding transcriptional regulator, LacI family
BLJ_1321	28.21	VFG2197	Sugar-binding transcriptional regulator, LacI family
BLJ_1232	29.83	VFG1028	Tn21 integrase IntI1
BLJ_1160	43.1	VFG2168	Transcriptional regulator, Cro/CI family
BLJ_0747	28.98	VFG1122	Transposase ORFAB, subunit B
BLJ_1180	43.64	VFG1398	trpD
BLJ_1871	39.62	VFG1967	UDP-galactopyranose mutase
BLJ_1644	39	VFG2361	UDP-glucose 4-epimerase
BLJ_1680	54.49	VFG2361	UDP-glucose 4-epimerase
BLJ_1891	52.63	VFG0963	UDP-glucose 6-dehydrogenase
BLJ_0697	46.15	VFG1414	whiB3

MIC: Minimum inhibitory concentration; ABC: ATP-binding cassette.

Table 4 Putative genes associated with adhesion identified in the genome of Bifidobacterium longum JDM301

Locus_tag	Pfam number	Product name
BLJ_1932	pfam01547	Family 1 extracellular solute-binding protein
BLJ_0112	pfam01547	Family 1 extracellular solute-binding protein
BLJ_1284	pfam01547	Family 1 extracellular solute-binding protein
BLJ_1420	pfam01547	Family 1 extracellular solute-binding protein
BLJ_0131	pfam01547	Family 1 extracellular solute-binding protein
BLJ_1604	pfam01547	Family 1 extracellular solute-binding protein
BLJ_1686	pfam01547	Family 1 extracellular solute-binding protein
BLJ_1964	pfam01547	Family 1 extracellular solute-binding protein
BLJ_1994	pfam01547	Family 1 extracellular solute-binding protein
BLJ_1996	pfam01547	Family 1 extracellular solute-binding protein
BLJ_2001	pfam01547	Family 1 extracellular solute-binding protein
BLJ_0288	pfam01547	Family 1 extracellular solute-binding protein
BLJ_0321	pfam01547	Family 1 extracellular solute-binding protein
BLJ_0345	pfam01547	phosphate ABC transporter periplasmic phosphate-binding protein
BLJ_0414	pfam01547	Family 1 extracellular solute-binding protein
BLJ_0522	pfam01547	Family 1 extracellular solute-binding protein
BLJ_0523	pfam01547	Family 1 extracellular solute-binding protein
BLJ_0524	pfam01547	Family 1 extracellular solute-binding protein
BLJ_0012	pfam07174	Hypothetical protein BLJ_0012
BLJ_1801	pfam05738	LPXTG-motif protein cell wall anchor domain-containing protein
BLJ_0140	pfam07811	TadE family protein

Citation: Wei YX, Zhang ZY, Liu C, Malakar PK, Guo XK. Safety assessment of Bifidobacterium longum JDM301 based on complete genome sequences. World J Gastroenterol 2012; 18(5): 479-488
URL: https://www.wjgnet.com/1007-9327/full/v18/i5/479.htm
DOI: https://dx.doi.org/10.3748/wjg.v18.i5.479