Strain identifier

BacDive ID: 6560

Type strain: Yes

Species: Lactobacillus johnsonii

Strain history: CIP <- 1992, F. Gasser, Inst. Pasteur, Paris, France, Lactobacillus acidophilus, group B2 <- J.L. Johnson, Blacksburg, USA : strain VPI 7960 <- D.W. Lambe, USA

NCBI tax ID(s): 525330 (strain), 33959 (species)

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General

@ref: 3968

BacDive-ID: 6560

DSM-Number: 10533

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-positive

description: Lactobacillus johnsonii DSM 10533 is an anaerobe, mesophilic, Gram-positive bacterium that was isolated from human blood.

NCBI tax id

NCBI tax idMatching level
33959species
525330strain

strain history

@refhistory
3968<- NCFB <- J.L. Johnson, VPI 7960
67770ATCC 33200 <-- VPI 7960 <-- D. W. Lambe, Jr..
67771<- CCUG <- JCM <- ATCC 33200 <- VPI 7960 <- DW Lambe, Jr.
120360CIP <- 1992, F. Gasser, Inst. Pasteur, Paris, France, Lactobacillus acidophilus, group B2 <- J.L. Johnson, Blacksburg, USA : strain VPI 7960 <- D.W. Lambe, USA

doi: 10.13145/bacdive6560.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Lactobacillales
  • family: Lactobacillaceae
  • genus: Lactobacillus
  • species: Lactobacillus johnsonii
  • full scientific name: Lactobacillus johnsonii Fujisawa et al. 1992

@ref: 3968

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Lactobacillaceae

genus: Lactobacillus

species: Lactobacillus johnsonii

full scientific name: Lactobacillus johnsonii Fujisawa et al. 1992

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotility
67771positive
120360positiverod-shapedno

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
3968MRS MEDIUM (DSMZ Medium 11)yeshttps://mediadive.dsmz.de/medium/11Name: MRS MEDIUM (DSMZ Medium 11) Composition: Glucose 20.0 g/l Casein peptone 10.0 g/l Meat extract 10.0 g/l Na-acetate 5.0 g/l Yeast extract 5.0 g/l (NH4)3 citrate 2.0 g/l K2HPO4 2.0 g/l Tween 80 1.0 g/l MgSO4 x 7 H2O 0.2 g/l MnSO4 x H2O 0.05 g/l Distilled water
34023MEDIUM 40- for Lactobacillus and LeuconostocyesDistilled water make up to (1000.000 ml);Man Rogosa Sharp agar (68.000 g)
120360CIP Medium 40yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=40

culture temp

@refgrowthtypetemperaturerange
3968positivegrowth37mesophilic
34023positivegrowth37mesophilic
50246positivegrowth37mesophilic
67770positivegrowth37mesophilic
67771positivegrowth37mesophilic
120360positivegrowth37-45
120360nogrowth15psychrophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
50246anaerobe
67771anaerobe
120360facultative anaerobe

murein

  • @ref: 3968
  • murein short key: A11.31
  • type: A4alpha L-Lys-D-Asp

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371gluconate-builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-lyxose-builds acid from62318
68371turanose-builds acid from32528
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371raffinose+builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose-builds acid from27082
68371sucrose+builds acid from17992
68371melibiose-builds acid from28053
68371cellobiose-builds acid from17057
68371salicin-builds acid from17814
68371esculin+builds acid from4853
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
68371N-acetylglucosamine+builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol-builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371D-fructose+builds acid from15824
68371D-glucose+builds acid from17634
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose-builds acid from65327
68371D-ribose-builds acid from16988
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754
120360nitrate-reduction17632
120360nitrite-reduction16301

antibiotic resistance

  • @ref: 120360
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite tests

  • @ref: 120360
  • Chebi-ID: 15688
  • metabolite: acetoin
  • voges-proskauer-test: -

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase+3.2.1.21
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase+3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382leucine arylamidase-3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)-
68382esterase (C 4)-
68382alkaline phosphatase+3.1.3.1
120360oxidase-
120360alcohol dehydrogenase-1.1.1.1
120360catalase-1.11.1.6
120360lysine decarboxylase-4.1.1.18
120360ornithine decarboxylase-4.1.1.17

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
120360-+--------++-+-++---

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
3968----------++++--------+--+--++-+---+---+----------
3968----------+/-+++/---------+--+--++-+---++--+--+/--------
3968----------+++---------+--+--+--+---+--------------
3968----------+/-+++--------+--+--+--+---++/---+/-----------
120360----------+++--------+--+-----+---+---+----------

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentgeographic locationisolation date
3968human bloodBelgiumBELEurope
67771From human bloodBelgiumBELEurope
50246Human blood
67770Human blood
120360Human, BloodUnited States of AmericaUSANorth AmericaAtlanta, Georgia1970

isolation source categories

Cat1Cat2Cat3
#Host#Human
#Host Body Product#Fluids#Blood

taxonmaps

  • @ref: 69479
  • File name: preview.99_840.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_46;96_506;97_581;98_668;99_840&stattab=map
  • Last taxonomy: Lactobacillus
  • 16S sequence: LC071811
  • Sequence Identity:
  • Total samples: 185237
  • soil counts: 4782
  • aquatic counts: 5652
  • animal counts: 173268
  • plant counts: 1535

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
39681Risk group (German classification)
1203601Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Lactobacillus johnsonii 16S-23S rRNA intergenic spacer regionAF074860215ena33959
20218Lactobacillus johnsonii 16S rRNA geneAJ0025151487ena33959
20218Lactobacillus johnsonii partial 16S rRNA gene, type strain CIP 103620THE5739151543ena33959
20218Lactobacillus johnsonii strain DSM 10533 16S ribosomal RNA gene, partial sequenceEF468091411ena33959
20218Lactobacillus johnsonii gene for 16S rRNA, partial sequence, strain: JCM 2012AB289175658ena33959
67771Lactobacillus johnsonii gene for 16S ribosomal RNA, partial sequence, strain: JCM 2012LC0718111470ena33959

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Lactobacillus johnsonii ATCC 33200525330.7wgspatric525330
66792Lactobacillus johnsonii ATCC 33200525330.3wgspatric525330
66792Lactobacillus johnsonii ATCC 332002657245008draftimg525330
66792Lactobacillus johnsonii ATCC 33200643886046draftimg525330
67770Lactobacillus johnsonii ATCC 33200GCA_000159355scaffoldncbi525330
67771Lactobacillus johnsonii ATCC 33200GCA_001433975contigncbi525330

GC content

@refGC-contentmethod
396833.0thermal denaturation, midpoint method (Tm)
6777034.4genome sequence analysis
6777033thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
gram-positiveyes95.136yes
anaerobicno62.458no
halophileyes86.457no
spore-formingno95.515no
glucose-utilyes91.164no
thermophileno99.752yes
aerobicno97.733no
motileno95.631no
flagellatedno97.993no
glucose-fermentyes92.755no

External links

@ref: 3968

culture collection no.: DSM 10533, ATCC 33200, NCFB 2241, CCUG 30725, JCM 2012, KCTC 3801, VPI 7960, CCM 4384, CGMCC 1.3348, CGMCC 1.3397, CIP 103620, KCTC 5085

straininfo link

@refstraininfo
760313189
76032312266

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny1503977Taxonomic study of the Lactobacillus acidophilus group, with recognition of Lactobacillus gallinarum sp. nov. and Lactobacillus johnsonii sp. nov. and synonymy of Lactobacillus acidophilus group A3 (Johnson et al. 1980) with the type strain of Lactobacillus amylovorus (Nakamura 1981).Fujisawa T, Benno Y, Yaeshima T, Mitsuoka TInt J Syst Bacteriol10.1099/00207713-42-3-4871992DNA, Bacterial/chemistry, Lactobacillus/*classification/genetics/physiology, Lactobacillus acidophilus/*classification, Nucleic Acid Hybridization, Phenotype, Sequence Homology, Nucleic AcidPhenotype
Enzymology8953716Functional analysis of the gene encoding immunity to lactacin F, lafI, and its use as a Lactobacillus-specific, food-grade genetic marker.Allison GE, Klaenhammer TRAppl Environ Microbiol10.1128/aem.62.12.4450-4460.19961996Amino Acid Sequence, Bacteriocins/biosynthesis/*genetics, Cloning, Molecular, *Genetic Markers, Lactobacillus/*genetics/immunology, Molecular Sequence Data, Mutation, Open Reading Frames, Transformation, BacterialGenetics
Genetics18223069Identification of genes associated with the long-gut-persistence phenotype of the probiotic Lactobacillus johnsonii strain NCC533 using a combination of genomics and transcriptome analysis.Denou E, Pridmore RD, Berger B, Panoff JM, Arigoni F, Brussow HJ Bacteriol10.1128/JB.01637-072008Animals, Chromosome Mapping, Gene Deletion, Gene Expression Profiling, *Genes, Bacterial, Genomics, Jejunum/*microbiology, Lactobacillus/*genetics, Mice, Mice, Inbred Strains, Phenotype, Polysaccharides, Bacterial/biosynthesis/*genetics, *ProbioticsPhenotype
Phylogeny20849602Characterization of a novel Lactobacillus species closely related to Lactobacillus johnsonii using a combination of molecular and comparative genomics methods.Sarmiento-Rubiano LA, Berger B, Moine D, Zuniga M, Perez-Martinez G, Yebra MJBMC Genomics10.1186/1471-2164-11-5042010Animals, Bacterial Proteins/genetics/metabolism, Comparative Genomic Hybridization/*methods, Conserved Sequence/genetics, DNA, Bacterial/genetics, Electrophoresis, Polyacrylamide Gel, Gene Expression Regulation, Bacterial, Genetic Loci/genetics, Genome, Bacterial/*genetics, Genomics/*methods, Lactobacillus/*genetics/isolation & purification, Nucleic Acid Hybridization, Oligonucleotide Array Sequence Analysis, Phenotype, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rats, Reproducibility of Results, Sequence Analysis, DNA, Species SpecificityGenetics
Phylogeny24478214Lactobacillus rodentium sp. nov., from the digestive tract of wild rodents.Killer J, Havlik J, Vlkova E, Rada V, Pechar R, Benada O, Kopecny J, Kofronova O, Sechovcova HInt J Syst Evol Microbiol10.1099/ijs.0.054924-02014Animals, Bacterial Typing Techniques, Base Composition, Czech Republic, DNA, Bacterial/genetics, Fatty Acids/chemistry, Fermentation, Genes, Bacterial, Intestine, Small/*microbiology, Lactobacillus/*classification/genetics/isolation & purification, Mice/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rectum/microbiology, Sequence Analysis, DNAGenetics
Enzymology25519527Effects of the probiotic Enterococcus faecium NCIMB 10415 on selected lactic acid bacteria and enterobacteria in co-culture.Starke IC, Zentek J, Vahjen WBenef Microbes10.3920/BM2014.00522015Animals, Coculture Techniques, Enterococcus/chemistry/genetics/*growth & development, Enterococcus faecium/chemistry/genetics/*growth & development, Gastrointestinal Tract/microbiology, Kinetics, Lactobacillus/chemistry/genetics/*growth & development, Probiotics/*chemistry, Swine
Metabolism25771812A highly acid-resistant novel strain of Lactobacillus johnsonii No. 1088 has antibacterial activity, including that against Helicobacter pylori, and inhibits gastrin-mediated acid production in mice.Aiba Y, Nakano Y, Koga Y, Takahashi K, Komatsu YMicrobiologyopen10.1002/mbo3.2522015Animals, *Antibiosis, Disease Models, Animal, Gastric Acid/*metabolism, Gastrins/blood/*metabolism, Gastrointestinal Microbiome, Helicobacter Infections/metabolism/microbiology, Helicobacter pylori/*physiology, Humans, Lactobacillus/isolation & purification/*physiology, Mice, Proton Pump Inhibitors/pharmacologyPathogenicity
Pathogenicity28683582Extending viability of Lactobacillus plantarum and Lactobacillus johnsonii by microencapsulation in alginate microgels.Tiani KA, Yeung TW, McClements DJ, Sela DAInt J Food Sci Nutr10.1080/09637486.2017.13432852017Alginates/*chemistry/ultrastructure, Cells, Immobilized/ultrastructure, *Digestion, Fermented Foods/microbiology, Food Additives/*chemistry, Food Storage, Gels, Glucuronic Acid/chemistry, Hexuronic Acids/chemistry, Humans, Lactobacillus johnsonii/*growth & development/ultrastructure, Lactobacillus plantarum/*growth & development/ultrastructure, Microbial Viability, Microscopy, Electron, Scanning, Microspheres, *Models, Biological, Nephelometry and Turbidimetry, Particle Size, *Probiotics/chemistry, Refrigeration, Species Specificity, Surface PropertiesPhylogeny

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
3968Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 10533)https://www.dsmz.de/collection/catalogue/details/culture/DSM-10533
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
34023Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/15438
50246Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 30725)https://www.ccug.se/strain?id=30725
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
68371Automatically annotated from API 50CH acid
68382Automatically annotated from API zym
69479João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.https://microbeatlas.org/MicrobeAtlas 1.0 beta
76031Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID3189.1StrainInfo: A central database for resolving microbial strain identifiers
76032Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID312266.1StrainInfo: A central database for resolving microbial strain identifiers
120360Curators of the CIPCollection of Institut Pasteur (CIP 103620)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103620