Strain identifier

BacDive ID: 6577

Type strain: Yes

Species: Companilactobacillus paralimentarius

Strain Designation: TB 1

Strain history: CIP <- 2000, JCM <- Y. Cai TB1

NCBI tax ID(s): 83526 (species)

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General

@ref: 4978

BacDive-ID: 6577

DSM-Number: 13238

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

description: Companilactobacillus paralimentarius TB 1 is an anaerobe, mesophilic, Gram-positive bacterium that was isolated from sourdough.

NCBI tax id

  • NCBI tax id: 83526
  • Matching level: species

strain history

@refhistory
4978<- JCM <- Y. Cai; TB 1
67770Y. Cai TB1.
121565CIP <- 2000, JCM <- Y. Cai TB1

doi: 10.13145/bacdive6577.20230509.8.1

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 paralimentarius
  • full scientific name: Companilactobacillus paralimentarius (Cai et al. 1999) Zheng et al. 2020

  • synonyms

    • @ref: 20215
    • synonym: Lactobacillus paralimentarius

@ref: 4978

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Lactobacillaceae

genus: Companilactobacillus

species: Companilactobacillus paralimentarius

full scientific name: Companilactobacillus paralimentarius (Cai et al. 1999) Zheng et al. 2020

strain designation: TB 1

type strain: yes

Morphology

cell morphology

  • @ref: 121565
  • gram stain: positive
  • cell shape: rod-shaped
  • motility: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
4978MRS 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
34372MEDIUM 40- for Lactobacillus and LeuconostocyesDistilled water make up to (1000.000 ml);Man Rogosa Sharp agar (68.000 g)
121565CIP Medium 40yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=40

culture temp

@refgrowthtypetemperaturerange
4978positivegrowth30mesophilic
34372positivegrowth30mesophilic
55807positivegrowth37mesophilic
67770positivegrowth30mesophilic
121565positivegrowth15-37
121565nogrowth10psychrophilic
121565nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
55807anaerobe
55807microaerophile

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-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371turanose-builds acid from32528
68371gentiobiose+builds acid from28066
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose+builds acid from27082
68371sucrose+builds acid from17992
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371maltose+builds acid from17306
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-mannose+builds acid from16024
68371D-fructose+builds acid from15824
68371D-glucose+builds acid from17634
68371D-galactose-builds acid from12936
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
121565nitrate-reduction17632
121565nitrite-reduction16301
121565nitrate+respiration17632

antibiotic resistance

  • @ref: 121565
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite tests

  • @ref: 121565
  • 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
121565oxidase-
121565alcohol dehydrogenase-1.1.1.1
121565catalase-1.11.1.6
121565lysine decarboxylase-4.1.1.18
121565ornithine 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
121565--+--+++--++---+++--

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
4978-----+-----+++--------+++++++--++------+----------
4978-----+-----+++--------+++++++--++------+----------
121565----+-----+++--------+++++++--++------+----------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
4978sourdoughJapanJapanJPNAsia
55807Sourdough
67770Sourdough
121565Sourdough

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_2939.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_45;96_954;97_1113;98_2270;99_2939&stattab=map
  • Last taxonomy: Companilactobacillus paralimentarius
  • 16S sequence: LC096230
  • Sequence Identity:
  • Total samples: 738
  • soil counts: 72
  • aquatic counts: 52
  • animal counts: 569
  • plant counts: 45

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
49781Risk group (German classification)
1215651Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Lactobacillus paralimentarius gene for 16S rRNA, partial sequence, strain: JCM 10415AB289234626ena83526
20218Lactobacillus paralimentarius 16S rRNA gene, strain DSM 13238AJ4175001563ena83526
20218Lactobacillus paralimentarius 23S rRNA gene and 16S-23S IGS, strain DSM 13238AJ616014705ena83526
20218Lactobacillus paralimentarius strain DSM 13238 16S-23S ribosomal RNA large intergenic spacer, tRNA-Ile, and tRNA-Ala genes, complete sequenceAY839296437ena83526
20218Lactobacillus paralimentarius strain DSM 13238 16S-23S ribosomal RNA small intergenic spacer, complete sequenceAY839297238ena83526
4978Lactobacillus paralimentarius gene for 16S rRNA, partial sequenceAB0185281476ena83526
67770Lactobacillus paralimentarius gene for 16S ribosomal RNA, partial sequence, strain: JCM 10415LC0962301506ena83526

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Companilactobacillus paralimentarius DSM 13238 = JCM 10415GCA_000615725contigncbi1122151
66792Companilactobacillus paralimentarius DSM 13238GCA_009764345contigncbi83526
66792Lactobacillus paralimentarius DSM 13238 = JCM 104151122151.5wgspatric1122151
66792Lactobacillus paralimentarius DSM 13238 = JCM 104151122151.3wgspatric1122151
66792Lactobacillus paralimentarius strain DSM 1323883526.13wgspatric83526
66792Lactobacillus paralimentarius DSM 132382700989141draftimg1122151
67770Companilactobacillus paralimentarius DSM 13238 = JCM 10415GCA_001434985scaffoldncbi1122151

GC content

@refGC-contentmethod
497837.3high performance liquid chromatography (HPLC)
497837.4high performance liquid chromatography (HPLC)
6777035.1genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno94.388no
flagellatedno97.775no
gram-positiveyes94.876no
anaerobicno82.457no
halophileyes89.691no
spore-formingno93.766no
thermophileno99.721yes
glucose-utilyes91.114no
aerobicno96.945yes
glucose-fermentyes89.399no

External links

@ref: 4978

culture collection no.: DSM 13238, JCM 10415, CCUG 43349, LMG 19152, CIP 106794, NBRC 107152, NCIMB 13723

straininfo link

  • @ref: 76051
  • straininfo: 13090

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny10555326Lactobacillus paralimentarius sp. nov., isolated from sourdough.Cai Y, Okada H, Mori H, Benno Y, Nakase TInt J Syst Bacteriol10.1099/00207713-49-4-14511999Bacterial Typing Techniques, Base Composition, Bread/*microbiology, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fermentation, Lactobacillus/*classification/*genetics/isolation & purification/physiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAGenetics
Phylogeny12710620Lactobacillus versmoldensis sp. nov., isolated from raw fermented sausage.Krockel L, Schillinger U, Franz CMAP, Bantleon A, Ludwig WInt J Syst Evol Microbiol10.1099/ijs.0.02387-02003Fermentation, *Food Microbiology, Lactobacillus/chemistry/*classification/genetics/physiology, Meat/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/*analysis/genetics, Sequence Analysis, DNABiotechnology
Phylogeny22140166Reclassification of Lactobacillus kimchii and Lactobacillus bobalius as later subjective synonyms of Lactobacillus paralimentarius.Pang H, Kitahara M, Tan Z, Wang Y, Qin G, Ohkuma M, Cai YInt J Syst Evol Microbiol10.1099/ijs.0.035329-02011DNA, Bacterial/genetics, Fermentation, Lactobacillus/*classification/genetics/isolation & purification, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Ribotyping, Sequence Analysis, DNA, Silage/*microbiologyGenetics
34991191Lactic acid bacteria strains selected from fermented total mixed rations improve ensiling and in vitro rumen fermentation characteristics of corn stover silage.Huang K, Chen H, Liu Y, Hong Q, Yang B, Wang JAnim Biosci10.5713/ab.21.04612022

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
4978Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 13238)https://www.dsmz.de/collection/catalogue/details/culture/DSM-13238
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
34372Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/18963
55807Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 43349)https://www.ccug.se/strain?id=43349
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
76051Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID13090.1StrainInfo: A central database for resolving microbial strain identifiers
121565Curators of the CIPCollection of Institut Pasteur (CIP 106794)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106794