Strain identifier

BacDive ID: 6636

Type strain: Yes

Species: Lapidilactobacillus concavus

Strain Designation: C-5-1

Strain history: CIP <- 2005, X. Dong, Chinese Academy Sciences, Beijing, China: strain C-5-1

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 7172

BacDive-ID: 6636

DSM-Number: 17758

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

description: Lapidilactobacillus concavus C-5-1 is a microaerophile, mesophilic, Gram-positive bacterium that was isolated from distilled pirit-fermenting cellar.

NCBI tax id

NCBI tax idMatching level
287844species
1423735strain

strain history

@refhistory
7172<- X. Dong; C-5-1
67770AS 1.5017 <-- H. Tong C-5-1.
118720CIP <- 2005, X. Dong, Chinese Academy Sciences, Beijing, China: strain C-5-1

doi: 10.13145/bacdive6636.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Lactobacillales
  • family: Lactobacillaceae
  • genus: Lapidilactobacillus
  • species: Lapidilactobacillus concavus
  • full scientific name: Lapidilactobacillus concavus (Tong and Dong 2005) Zheng et al. 2020
  • synonyms

    • @ref: 20215
    • synonym: Lactobacillus concavus

@ref: 7172

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Lactobacillaceae

genus: Lapidilactobacillus

species: Lapidilactobacillus concavus

full scientific name: Lapidilactobacillus concavus (Tong and Dong 2005) Zheng et al. 2020

strain designation: C-5-1

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31423positive2.25 µm0.55 µmrod-shapedno
69480no97.123
69480positive100
118720positiverod-shapedno

pigmentation

  • @ref: 31423
  • production: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7172MRS 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
38373MEDIUM 40- for Lactobacillus and LeuconostocyesDistilled water make up to (1000.000 ml);Man Rogosa Sharp agar (68.000 g)
118720CIP Medium 40yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=40

culture temp

@refgrowthtypetemperaturerange
7172positivegrowth37mesophilic
31423positivegrowth10-42
31423positiveoptimum33.5mesophilic
38373positivegrowth37mesophilic
67770positivegrowth37mesophilic

culture pH

@refabilitytypepHPH range
31423positivegrowth3.8-8.1acidophile
31423positiveoptimum6.2

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
7172microaerophile
31423facultative anaerobe
118720facultative anaerobe

spore formation

@refspore formationconfidence
31423no
69481no100
69480no99.995

observation

  • @ref: 31423
  • observation: aggregates in clumps

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3142317057cellobiose+carbon source
3142328757fructose+carbon source
314235417glucosamine+carbon source
3142317234glucose+carbon source
3142317306maltose+carbon source
3142317814salicin+carbon source
3142327082trehalose+carbon source
314234853esculin+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
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
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
6837116988D-ribose-builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol-builds acid from
11872017632nitrate-reduction
11872016301nitrite-reduction

metabolite production

  • @ref: 118720
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

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
118720oxidase-
118720alcohol dehydrogenase-1.1.1.1
118720catalase-1.11.1.6
118720lysine decarboxylase-4.1.1.18
118720ornithine decarboxylase-4.1.1.17
118720urease-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
118720-----++---++---+----

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
118720---+/--+/-----++/----------++/-+/-++++---+---+--+----------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
7172distilled pirit-fermenting cellarHebei ProvinceChinaCHNAsia
67770Distilled-spirit-fermenting cellar
118720Distilled spirit fermenting cellar wallsHebeiChinaCHNAsia2004

isolation source categories

Cat1Cat2Cat3
#Engineered#Food production#Fermented
#Engineered#Food production#Beverage

taxonmaps

  • @ref: 69479
  • File name: preview.99_3407.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_45;96_1782;97_2132;98_2612;99_3407&stattab=map
  • Last taxonomy: Lapidilactobacillus
  • 16S sequence: LC258135
  • Sequence Identity:
  • Total samples: 3827
  • soil counts: 734
  • aquatic counts: 581
  • animal counts: 2349
  • plant counts: 163

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
71721Risk group (German classification)
1187201Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
7172Lactobacillus concavus strain AS 1.5017 16S ribosomal RNA gene, partial sequenceAY6833221528ena287844
67770Lactobacillus concavus gene for 16S ribosomal RNA, partial sequence, strain: JCM 14153LC2581351515ena287844

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Lactobacillus concavus DSM 177581423735.3wgspatric1423735
66792Lactobacillus concavus strain NBRC 106101287844.3wgspatric287844
66792Lactobacillus concavus DSM 177582671180578draftimg1423735
67770Lapidilactobacillus concavus DSM 17758GCA_001435835scaffoldncbi1423735
67770Lapidilactobacillus concavus NBRC 106101GCA_007989025contigncbi287844

GC content

@refGC-contentmethod
717246.9
3142346.4
6777046.4thermal denaturation, midpoint method (Tm)
6777043.3genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno93.741yes
gram-positiveyes97.086yes
anaerobicno91.697yes
halophileyes89.573no
spore-formingno93.916yes
thermophileno96.241yes
glucose-utilyes92.115yes
aerobicno97.774no
flagellatedno97.832yes
glucose-fermentyes88.005no

External links

@ref: 7172

culture collection no.: DSM 17758, AS 1.5017, LMG 22739, JCM 14153, CGMCC 1.5017, CIP 108991, KACC 12410, NBRC 106101

straininfo link

  • @ref: 76110
  • straininfo: 134034

literature

  • topic: Phylogeny
  • Pubmed-ID: 16166732
  • title: Lactobacillus concavus sp. nov., isolated from the walls of a distilled spirit fermenting cellar in China.
  • authors: Tong H, Dong X
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.63509-0
  • year: 2005
  • mesh: Base Composition, China, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fermentation, Genes, rRNA, Genotype, Geologic Sediments/*microbiology, Lactic Acid/*metabolism, Lactobacillus/classification/genetics/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Wine/*microbiology
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
7172Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17758)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17758
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
31423Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2773028776041
38373Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6681
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updates33211880Nucleic Acids Res. 49: D498-D508 2020
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
76110Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID134034.1StrainInfo: A central database for resolving microbial strain identifiers
118720Curators of the CIPCollection of Institut Pasteur (CIP 108991)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108991