Strain identifier

BacDive ID: 6677

Type strain: Yes

Species: Ligilactobacillus ceti

Strain Designation: 142-2

Strain history: CIP <- 2006, CECT <- A.I. Vela, Complutense Univ. VISAVET, Madrid, Spain: strain 142-2

NCBI tax ID(s): 1122146 (strain), 395085 (species)

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General

@ref: 16321

BacDive-ID: 6677

DSM-Number: 22408

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

description: Ligilactobacillus ceti 142-2 is an anaerobe, mesophilic, Gram-positive bacterium that was isolated from lungs of a beaked whale .

NCBI tax id

NCBI tax idMatching level
395085species
1122146strain

strain history

@refhistory
16321<- CCUG <- A. I. Vela, Univ. Complutense, Madrid, Spain; 142-2
67770CCUG 53626 <-- A. I. Vela 142-2.
118220CIP <- 2006, CECT <- A.I. Vela, Complutense Univ. VISAVET, Madrid, Spain: strain 142-2

doi: 10.13145/bacdive6677.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Lactobacillales
  • family: Lactobacillaceae
  • genus: Ligilactobacillus
  • species: Ligilactobacillus ceti
  • full scientific name: Ligilactobacillus ceti (Vela et al. 2008) Zheng et al. 2020

  • synonyms

    • @ref: 20215
    • synonym: Lactobacillus ceti

@ref: 16321

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Lactobacillaceae

genus: Ligilactobacillus

species: Ligilactobacillus ceti

full scientific name: Ligilactobacillus ceti (Vela et al. 2008) Zheng et al. 2020

strain designation: 142-2

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
32356positive2.7 µm0.5 µmrod-shapedno
69480no90.367
69480positive100
118220positiverod-shapedno

colony morphology

  • @ref: 59954
  • incubation period: 1-2 days

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
16321PYG MEDIUM (MODIFIED) (DSMZ Medium 104)yeshttps://mediadive.dsmz.de/medium/104Name: PYG MEDIUM (modified) (DSMZ Medium 104) Composition: Yeast extract 10.0 g/l Peptone 5.0 g/l Trypticase peptone 5.0 g/l Beef extract 5.0 g/l Glucose 5.0 g/l L-Cysteine HCl x H2O 0.5 g/l NaHCO3 0.4 g/l NaCl 0.08 g/l K2HPO4 0.04 g/l KH2PO4 0.04 g/l MgSO4 x 7 H2O 0.02 g/l CaCl2 x 2 H2O 0.01 g/l Hemin 0.005 g/l Ethanol 0.0038 g/l Resazurin 0.001 g/l Tween 80 Vitamin K1 NaOH Distilled water
37860MEDIUM 6 - Columbia agar with 10 % horse bloodyesDistilled water make up to (1000.000 ml);Columbia agar (39.000 g);Horseblood (100.000 ml)
118220CIP Medium 45yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=45
118220CIP Medium 6yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=6

culture temp

@refgrowthtypetemperaturerange
16321positivegrowth37mesophilic
32356positivegrowth15-37
37860positivegrowth37mesophilic
59954positivegrowth37mesophilic
67770positivegrowth37mesophilic
118220positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
16321anaerobe
32356facultative anaerobe
59954anaerobe
59954microaerophile
118220facultative anaerobe

spore formation

@refspore formationconfidence
32356no
69481no100
69480no99.97

halophily

  • @ref: 32356
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: <3 %

murein

  • @ref: 16321
  • murein short key: A11.14
  • type: A3alpha L-Lys-L-Ser

observation

  • @ref: 32356
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3235633942ribose+carbon source
68371Potassium 2-ketogluconate-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
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
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
6837130849L-arabinose-builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol-builds acid from
11822017632nitrate-reduction
11822016301nitrite-reduction
11822017632nitrate+respiration
6838016199urea-hydrolysis
6838029016arginine-hydrolysis
6838016024D-mannose+fermentation
6838016634raffinose-fermentation
6838029985L-glutamate-degradation
6838017632nitrate-reduction
6838027897tryptophan-energy source

metabolite production

  • @ref: 68380
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetaboliteindole testvoges-proskauer-test
6838035581indole-
11822015688acetoin-

enzymes

@refvalueactivityec
32356acid phosphatase+3.1.3.2
32356alkaline phosphatase+3.1.3.1
32356gelatinase+
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
68380serine arylamidase+
68380glutamyl-glutamate arylamidase-
68380histidine arylamidase+
68380glycin arylamidase+
68380alanine arylamidase+3.4.11.2
68380tyrosine arylamidase+
68380pyrrolidonyl arylamidase-3.4.19.3
68380leucine arylamidase+3.4.11.1
68380phenylalanine arylamidase+
68380proline-arylamidase-3.4.11.5
68380L-arginine arylamidase+
68380alkaline phosphatase-3.1.3.1
68380tryptophan deaminase-4.1.99.1
68380alpha-fucosidase-3.2.1.51
68380glutamate decarboxylase-4.1.1.15
68380N-acetyl-beta-glucosaminidase-3.2.1.52
68380beta-glucuronidase-3.2.1.31
68380alpha-arabinosidase-3.2.1.55
68380beta-glucosidase-3.2.1.21
68380alpha-glucosidase-3.2.1.20
68380beta-Galactosidase 6-phosphate-
68380beta-galactosidase-3.2.1.23
68380alpha-galactosidase-3.2.1.22
68380arginine dihydrolase-3.5.3.6
68380urease-3.5.1.5
118220oxidase-
118220alcohol dehydrogenase+1.1.1.1
118220catalase-1.11.1.6
118220lysine decarboxylase-4.1.1.18
118220ornithine 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
118220--++-+------++-++---

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
118220----+/-+----+/-+---------------+/-------------------+/--+/-

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
16321----------+------+-+/-++-++++-+

Isolation, sampling and environmental information

isolation

@refsample typehost speciescountryorigin.countrycontinentsampling dategeographic locationisolation date
16321lungs of a beaked whale ( Ziphius cavirostris)Ziphius cavirostrisSpainESPEurope
59954Whale lung (Beaked whale: Ziphius cavirostris)SpainESPEurope2006Madrid
67770Beaked whales (Ziphius cavirostris)Ziphius cavirostris
118220Whale, lungs and liverSpainESPEuropeMadrid2006

isolation source categories

Cat1Cat2Cat3
#Host#Mammals#Aquatic mammal
#Host Body-Site#Oral cavity and airways#Lung

taxonmaps

  • @ref: 69479
  • File name: preview.99_95270.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_45;96_39033;97_49719;98_65387;99_95270&stattab=map
  • Last taxonomy: Ligilactobacillus ceti subclade
  • 16S sequence: LC480806
  • Sequence Identity:
  • Total samples: 1115
  • soil counts: 35
  • aquatic counts: 46
  • animal counts: 976
  • plant counts: 58

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
163211Risk group (German classification)
1182201Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
16321Lactobacillus ceti 16S rRNA gene, type strain 142-2TAM2927991397ena1122146
67770Lactobacillus ceti JCM 15609 gene for 16S ribosomal RNA, partial sequenceLC4808061504ena395085

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Lactobacillus ceti DSM 224081122146.3wgspatric1122146
66792Lactobacillus ceti DSM 224081122146.4wgspatric1122146
66792Ligilactobacillus ceti DSM 224082700989270draftimg1122146
66792Lactobacillus ceti DSM 224082523231024draftimg1122146
67770Ligilactobacillus ceti DSM 22408GCA_000423245scaffoldncbi1122146
67770Ligilactobacillus ceti DSM 22408GCA_001438785scaffoldncbi1122146

GC content

  • @ref: 67770
  • GC-content: 33.7
  • method: genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno95.126no
flagellatedno98.785yes
gram-positiveyes94.359no
anaerobicno83.142no
halophileyes85.095no
spore-formingno96.999yes
thermophileno98.066yes
glucose-utilyes92.146no
aerobicno95.717yes
glucose-fermentyes86.332no

External links

@ref: 16321

culture collection no.: DSM 22408, CCUG 53626, CECT 7185, JCM 15609, CIP 109847, KCTC 5852

straininfo link

  • @ref: 76151
  • straininfo: 343807

literature

  • topic: Phylogeny
  • Pubmed-ID: 18398189
  • title: Lactobacillus ceti sp. nov., isolated from beaked whales (Ziphius cavirostris).
  • authors: Vela AI, Fernandez A, Espinosa de los Monteros A, Goyache J, Herraez P, Tames B, Cruz F, Dominguez L, Fernandez-Garayzabal JF
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.65372-0
  • year: 2008
  • mesh: Animals, Genes, Bacterial, Lactobacillus/*classification/genetics/*isolation & purification/metabolism, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Species Specificity, Whales/*microbiology
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
16321Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22408)https://www.dsmz.de/collection/catalogue/details/culture/DSM-22408
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
32356Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2858528776041
37860Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7638
59954Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 53626)https://www.ccug.se/strain?id=53626
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
68380Automatically annotated from API rID32A
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
76151Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID343807.1StrainInfo: A central database for resolving microbial strain identifiers
118220Curators of the CIPCollection of Institut Pasteur (CIP 109847)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109847