Strain identifier

BacDive ID: 6674

Type strain: Yes

Species: Companilactobacillus nodensis

Strain Designation: IZ4B, iz4b-1

Strain history: CIP <- 2009, DSMZ <- T. Kashiwagi, Tokyo Univ. of Science, Chiba, Japan: strain IZ4B

NCBI tax ID(s): 460870 (species)

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General

@ref: 8253

BacDive-ID: 6674

DSM-Number: 19682

keywords: genome sequence, 16S sequence, Bacteria, microaerophile, mesophilic, Gram-positive, rod-shaped

description: Companilactobacillus nodensis IZ4B is a microaerophile, mesophilic, Gram-positive bacterium that was isolated from Japanese pickles.

NCBI tax id

  • NCBI tax id: 460870
  • Matching level: species

strain history

@refhistory
8253<- T. Kashiwagi, Tokyo University of Science;IZ4B
67770T. Kashiwagi iz4b-1.
121322CIP <- 2009, DSMZ <- T. Kashiwagi, Tokyo Univ. of Science, Chiba, Japan: strain IZ4B

doi: 10.13145/bacdive6674.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Lactobacillales
  • family: Lactobacillaceae
  • genus: Companilactobacillus
  • species: Companilactobacillus nodensis
  • full scientific name: Companilactobacillus nodensis (Kashiwagi et al. 2009) Zheng et al. 2020

  • synonyms

    • @ref: 20215
    • synonym: Lactobacillus nodensis

@ref: 8253

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Lactobacillaceae

genus: Companilactobacillus

species: Companilactobacillus nodensis

full scientific name: Companilactobacillus nodensis (Kashiwagi et al. 2009) Zheng et al. 2020

strain designation: IZ4B, iz4b-1

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
32611positive5 µm1.8 µmrod-shapedno
69480no96.423
69480positive100
121322positiverod-shapedno

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8253MRS 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
40607MEDIUM 40- for Lactobacillus and LeuconostocyesDistilled water make up to (1000.000 ml);Man Rogosa Sharp agar (68.000 g)
121322CIP Medium 40yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=40

culture temp

@refgrowthtypetemperaturerange
8253positivegrowth30mesophilic
32611positivegrowth15-37
32611positiveoptimum26mesophilic
40607positivegrowth37mesophilic
67770positivegrowth30mesophilic
121322positivegrowth15-37
121322nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
8253microaerophile
32611anaerobe
121322facultative anaerobe

spore formation

@refspore formationconfidence
32611no
69481no100
69480no99.999

halophily

@refsaltgrowthtested relationconcentration
32611NaClpositivegrowth0-15 %
32611NaClpositiveoptimum7.5 %

murein

  • @ref: 8253
  • murein short key: A11.31
  • type: A4alpha L-Lys-D-Asp

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3261122599arabinose+carbon source
3261128757fructose+carbon source
3261128260galactose+carbon source
3261117234glucose+carbon source
3261137684mannose+carbon source
32611506227N-acetylglucosamine+carbon source
3261133942ribose+carbon source
326114853esculin+hydrolysis
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837132528turanose-builds acid from
6837128066gentiobiose-builds acid from
6837117151xylitol-builds acid from
6837128087glycogen-builds acid from
6837128017starch-builds acid from
6837116634raffinose-builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837127082trehalose-builds acid from
6837117992sucrose-builds acid from
6837128053melibiose-builds acid from
6837117716lactose-builds acid from
6837117306maltose-builds acid from
6837117057cellobiose-builds acid from
6837117814salicin-builds acid from
683714853esculin+builds acid from
6837118305arbutin-builds acid from
6837127613amygdalin-builds acid from
6837159640N-acetylglucosamine+builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol-builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose-builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose+builds acid from
6837115824D-fructose+builds acid from
6837117634D-glucose+builds acid from
6837112936D-galactose+builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose-builds acid from
6837116988D-ribose-builds acid from
6837130849L-arabinose-builds acid from
6837117108D-arabinose+builds acid from
6837117113erythritol-builds acid from
6837117754glycerol-builds acid from
12132217632nitrate-reduction
12132216301nitrite-reduction
12132217632nitrate+respiration

metabolite production

  • @ref: 121322
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 121322
  • 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
121322oxidase-
121322alcohol dehydrogenase+1.1.1.1
121322catalase-1.11.1.6
121322lysine decarboxylase-4.1.1.18
121322ornithine decarboxylase-4.1.1.17
121322urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
121322-+---+----++---++---

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
8253---+------++++--------+--+------------------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
8253Japanese picklesTochigi prefecture, Utsunomiya cityJapanJPNAsia
67770Rice bran
121322Food, Rice bran, Japanse picklesUtsunomiyaJapanJPNAsia

isolation source categories

  • Cat1: #Engineered
  • Cat2: #Food production
  • Cat3: #Food

taxonmaps

  • @ref: 69479
  • File name: preview.99_3365.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_45;96_1756;97_2100;98_2579;99_3365&stattab=map
  • Last taxonomy: Companilactobacillus
  • 16S sequence: LC258158
  • Sequence Identity:
  • Total samples: 357
  • soil counts: 37
  • aquatic counts: 22
  • animal counts: 270
  • plant counts: 28

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
82531Risk group (German classification)
1213221Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
8253Lactobacillus nodensis gene for 16S ribosomal RNA, partial sequenceAB3320241556ena460870
67770Lactobacillus nodensis gene for 16S ribosomal RNA, partial sequence, strain: JCM 14932LC2581581513ena460870

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Lactobacillus nodensis DSM 19682 = JCM 14932 = NBRC 1071601423775.4wgspatric1423775
66792Lactobacillus nodensis DSM 19682 = JCM 14932 = NBRC 1071601423775.5wgspatric1423775
66792Lactobacillus nodensis JCM 149321236953.3wgspatric1423775
66792Lactobacillus nodensis JCM 149322585427881draftimg1423775
66792Lactobacillus nodensis NBRC 1071602681812987draftimg1423775
66792Lactobacillus nodensis DSM 196822690315703draftimg1423775
67770Companilactobacillus nodensis DSM 19682 = JCM 14932 = NBRC 107160GCA_001435555scaffoldncbi1423775
67770Companilactobacillus nodensis DSM 19682 = JCM 14932 = NBRC 107160GCA_000615905contigncbi1423775
67770Companilactobacillus nodensis DSM 19682 = JCM 14932 = NBRC 107160GCA_001592065contigncbi1423775

GC content

@refGC-contentmethod
825340.6
6777037.6genome sequence analysis
6777040.6high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno95.082yes
gram-positiveyes94.104no
anaerobicno90.404no
halophileyes86.03no
spore-formingno94.843yes
glucose-utilyes89.701yes
thermophileno99.216yes
aerobicno97.073no
flagellatedno98.05yes
glucose-fermentyes90.495no

External links

@ref: 8253

culture collection no.: DSM 19682, CIP 109958, JCM 14932, NBRC 107160

straininfo link

  • @ref: 76148
  • straininfo: 360509

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19126729Lactobacillus nodensis sp. nov., isolated from rice bran.Kashiwagi T, Suzuki T, Kamakura TInt J Syst Evol Microbiol10.1099/ijs.0.65772-02009Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis, DNA, Ribosomal/genetics, Fermentation, Genes, rRNA, Japan, Lactobacillus/*classification/genetics/*isolation & purification/physiology, Nucleic Acid Hybridization, Oryza/*microbiology, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species SpecificityTranscriptome
Phylogeny26486967Lactobacillus insicii sp. nov., isolated from fermented raw meat.Ehrmann MA, Krockel L, Lick S, Radmann P, Bantleon A, Vogel RFInt J Syst Evol Microbiol10.1099/ijsem.0.0007052015Animals, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Dipeptides/chemistry, Fatty Acids/chemistry, Fermentation, *Food Microbiology, Lactobacillus/*cytology/genetics/isolation & purification, Meat Products/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, SwineBiotechnology
Phylogeny30010525Lactobacillus terrae sp. nov., a novel species isolated from soil samples in the Republic of Korea.Kim HJ, Lee HJ, Lim B, Kim E, Kim HY, Suh M, Hur MInt J Syst Evol Microbiol10.1099/ijsem.0.0029182018Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Lactobacillus/*classification/genetics/isolation & purification, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
8253Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19682)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19682
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
32611Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2882428776041
40607Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7760
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/
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
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
76148Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID360509.1StrainInfo: A central database for resolving microbial strain identifiers
121322Curators of the CIPCollection of Institut Pasteur (CIP 109958)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109958