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/bacdive6577.20250331.9.3

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

@refgram staincell shapemotilityconfidence
121565positiverod-shapedno
125438no93
125438positive92.181

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

@refgrowthtypetemperature
4978positivegrowth30
34372positivegrowth30
55807positivegrowth37
67770positivegrowth30
121565positivegrowth15-37
121565nogrowth10
121565nogrowth45

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
55807anaerobe
55807microaerophile
125439obligate aerobe96.5

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
12156517632nitrate-reduction
12156516301nitrite-reduction
12156517632nitrate+respiration
68371Potassium 5-ketogluconate-builds acid from
6837118305arbutin+builds acid from
6837127613amygdalin+builds acid from
68371320061methyl alpha-D-glucopyranoside-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
6837159640N-acetylglucosamine+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

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
68382alpha-glucosidase+3.2.1.20
68382beta-glucosidase+3.2.1.21
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382trypsin-3.4.21.4
68382cystine arylamidase+3.4.11.3
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
68382lipase (C 14)-
68382esterase (C 4)+
68382esterase lipase (C 8)-
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
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1

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 10415AB289234626nuccore83526
20218Lactobacillus paralimentarius 16S rRNA gene, strain DSM 13238AJ4175001563nuccore83526
20218Lactobacillus paralimentarius 23S rRNA gene and 16S-23S IGS, strain DSM 13238AJ616014705nuccore83526
20218Lactobacillus paralimentarius strain DSM 13238 16S-23S ribosomal RNA large intergenic spacer, tRNA-Ile, and tRNA-Ala genes, complete sequenceAY839296437nuccore83526
20218Lactobacillus paralimentarius strain DSM 13238 16S-23S ribosomal RNA small intergenic spacer, complete sequenceAY839297238nuccore83526
4978Lactobacillus paralimentarius gene for 16S rRNA, partial sequenceAB0185281476nuccore83526
67770Lactobacillus paralimentarius gene for 16S ribosomal RNA, partial sequence, strain: JCM 10415LC0962301506nuccore83526
124043Lactobacillus paralimentarius gene for 16S rRNA, partial sequence, strain: NBRC 107152.AB6260661492nuccore83526

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

@refmodeltraitdescriptionpredictionconfidencetraining_data
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe96.5
125439BacteriaNetgram_stainReaction to gram-stainingpositive89.4
125439BacteriaNetmotilityAbility to perform movementno67.2
125439BacteriaNetspore_formationAbility to form endo- or exosporesno82.9
125438gram-positivegram-positivePositive reaction to Gram-stainingyes92.181no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no83.829no
125438spore-formingspore-formingAbility to form endo- or exosporesno87.48no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no94.719yes
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno95yes
125438motile2+flagellatedAbility to perform flagellated movementno93no

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
124043Isabel Schober, Julia KoblitzData extracted from sequence databases, automatically matched based on designation and taxonomy
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1