Strain identifier

BacDive ID: 17867

Type strain: Yes

Species: Leptotrichia wadei

Strain Designation: LB 16

Strain history: CIP <- 2003, CCUG <- I. Olsen, Oslo, Norway <- T. Hofstad, Bergen, Norway: strain LB 16

NCBI tax ID(s): 1122174 (strain), 157687 (species)

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General

@ref: 8298

BacDive-ID: 17867

DSM-Number: 19758

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

description: Leptotrichia wadei LB 16 is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from human saliva.

NCBI tax id

NCBI tax idMatching level
1122174strain
157687species

strain history

@refhistory
8298<- CIP <- CCUG <- I. Olsen <- T. Hofstad; LB 16
67770CCUG 47505 <-- I. Olsen LB 16 <-- T. Hofstad.
123897CIP <- 2003, CCUG <- I. Olsen, Oslo, Norway <- T. Hofstad, Bergen, Norway: strain LB 16

doi: 10.13145/bacdive17867.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/fusobacteriota
  • domain: Bacteria
  • phylum: Fusobacteriota
  • class: Fusobacteriia
  • order: Fusobacteriales
  • family: Leptotrichiaceae
  • genus: Leptotrichia
  • species: Leptotrichia wadei
  • full scientific name: Leptotrichia wadei Eribe et al. 2004

@ref: 8298

domain: Bacteria

phylum: Fusobacteria

class: Fusobacteriia

order: Fusobacteriales

family: Leptotrichiaceae

genus: Leptotrichia

species: Leptotrichia wadei

full scientific name: Leptotrichia wadei Eribe et al. 2004

strain designation: LB 16

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
30006negative6.25 µm0.45 µmrod-shapedno
69480negative99.982
123897negativerod-shapedno

colony morphology

  • @ref: 123897

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8298PYG 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
8298COLUMBIA BLOOD AGAR (DSMZ Medium 429)yeshttps://mediadive.dsmz.de/medium/429Name: COLUMBIA BLOOD AGAR (DSMZ Medium 429) Composition: Horse blood 40.0 g/l Columbia agar base
34293MEDIUM 6 - Columbia agar with 10 % horse bloodyesDistilled water make up to (1000.000 ml);Columbia agar (39.000 g);Horseblood (100.000 ml)
123897CIP Medium 6yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=6

culture temp

@refgrowthtypetemperaturerange
8298positivegrowth37mesophilic
30006positiveoptimum37mesophilic
34293positivegrowth37mesophilic
57725positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
8298anaerobe
30006anaerobe
57725anaerobe
69480anaerobe98.918
123897facultative anaerobe

spore formation

@refspore formationconfidence
30006no
69480no99.983

observation

  • @ref: 30006
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
300064853esculin+hydrolysis
12389717108D-arabinose-degradation
12389715824D-fructose+degradation
12389717634D-glucose+degradation
12389765327D-xylose-degradation
12389717057cellobiose+degradation
12389717716lactose-degradation
12389717306maltose+degradation
12389717814salicin-degradation
12389717992sucrose+degradation
1238974853esculin+hydrolysis
12389717632nitrate-reduction
12389716301nitrite-reduction
12389717632nitrate+respiration
6838016199urea-hydrolysis
6838029016arginine-hydrolysis
6838029985L-glutamate-degradation
6838017632nitrate-reduction
6838027897tryptophan-energy source

antibiotic resistance

  • @ref: 123897
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

@refChebi-IDmetaboliteproduction
12389735581indoleno
6838035581indoleno

metabolite tests

  • @ref: 68380
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
30006catalase+1.11.1.6
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-
68380leucyl glycin arylamidase-3.4.11.1
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
123897oxidase-
123897beta-galactosidase-3.2.1.23
123897gelatinase-
123897amylase-
123897DNase-
123897caseinase-3.4.21.50
123897catalase+1.11.1.6
123897tween esterase-
123897lecithinase-
123897lipase-
123897protease-
123897urease-3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase-
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
123897-+++-+----+----+----

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
8298-----++---+/-+/-----+-----+------

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentgeographic location
8298human salivaNorwayNOREurope
57725Human saliva,healthy personNorwayNOREuropeBergen
67770Saliva of a healthy person
123897Human, Saliva

isolation source categories

Cat1Cat2Cat3
#Host#Human
#Host Body Product#Oral cavity and Airways#Saliva

taxonmaps

  • @ref: 69479
  • File name: preview.99_6466.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_108;96_3061;97_3759;98_4771;99_6466&stattab=map
  • Last taxonomy: Leptotrichia wadei subclade
  • 16S sequence: AB588021
  • Sequence Identity:
  • Total samples: 36252
  • soil counts: 667
  • aquatic counts: 971
  • animal counts: 34375
  • plant counts: 239

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
82981Risk group (German classification)
1238971Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
8298Leptotrichia wadeii strain LB16 16S ribosomal RNA gene, partial sequenceAY0298021486ena157687
67770Leptotrichia wadei gene for 16S ribosomal RNA, partial sequence, strain: JCM 16777AB5880211473ena157687

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Leptotrichia wadei JCM16777GCA_007990545completencbi157687
66792Leptotrichia wadei DSM 197581122174.3wgspatric1122174
66792Leptotrichia wadei strain JCM16777157687.179wgspatric157687
66792Leptotrichia wadei DSM 197582515154120draftimg1122174
67770Leptotrichia wadei DSM 19758GCA_000373345scaffoldncbi1122174

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno71no
motileno94.3no
motileno94.3no
flagellatedno96.778yes
flagellatedno96.778yes
gram-positiveno93.988yes
gram-positiveno93.988yes
anaerobicyes97.141yes
anaerobicyes97.141yes
aerobicno98.95yes
aerobicno98.95yes
halophileno71.725no
halophileno71.725no
spore-formingno95.413yes
spore-formingno95.413yes
glucose-utilyes72.54no
glucose-utilyes72.54no
thermophileno93.973yes
thermophileno93.973yes
glucose-fermentyes61.849no
glucose-fermentyes61.849no

External links

@ref: 8298

culture collection no.: DSM 19758, CCUG 47505, CIP 107918, JCM 16777

straininfo link

  • @ref: 86857
  • straininfo: 131424

literature

  • topic: Phylogeny
  • Pubmed-ID: 15023979
  • title: Genetic diversity of Leptotrichia and description of Leptotrichia goodfellowii sp. nov., Leptotrichia hofstadii sp. nov., Leptotrichia shahii sp. nov. and Leptotrichia wadei sp. nov.
  • authors: Eribe ERK, Paster BJ, Caugant DA, Dewhirst FE, Stromberg VK, Lacy GH, Olsen I
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.02819-0
  • year: 2004
  • mesh: Base Sequence, DNA Primers, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, *Genetic Variation, Geography, Leptotrichia/*classification/genetics/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
8298Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19758)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19758
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
30006Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2637028776041
34293Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5482
57725Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 47505)https://www.ccug.se/strain?id=47505
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/
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)
86857Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID131424.1StrainInfo: A central database for resolving microbial strain identifiers
123897Curators of the CIPCollection of Institut Pasteur (CIP 107918)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107918