Strain identifier

BacDive ID: 17860

Type strain: Yes

Species: Leptotrichia buccalis

Strain Designation: C-1013-b

Strain history: CIP <- 1998, CCUG <- R.J. Owen, NCTC, London, UK <- A. Howell, NIH, Maryland, USA: strain C-1013-b

NCBI tax ID(s): 523794 (strain), 40542 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 575

BacDive-ID: 17860

DSM-Number: 1135

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-negative, human pathogen

description: Leptotrichia buccalis C-1013-b is an anaerobe, mesophilic, Gram-negative human pathogen that was isolated from supragingival calculus.

NCBI tax id

NCBI tax idMatching level
523794strain
40542species

strain history

@refhistory
575<- NCTC <- A. Howell, Jr., C-1013-b
67770DSM 1135 <-- NCTC 10249 <-- A. Howell, Jr. C-1013-b.
117066CIP <- 1998, CCUG <- R.J. Owen, NCTC, London, UK <- A. Howell, NIH, Maryland, USA: strain C-1013-b

doi: 10.13145/bacdive17860.20230509.8.1

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 buccalis
  • full scientific name: Leptotrichia buccalis (Robin 1853) Trevisan 1879 (Approved Lists 1980)

  • synonyms

    • @ref: 20215
    • synonym: Leptothrix buccalis

@ref: 575

domain: Bacteria

phylum: Fusobacteria

class: Fusobacteriia

order: Fusobacteriales

family: Leptotrichiaceae

genus: Leptotrichia

species: Leptotrichia buccalis

full scientific name: Leptotrichia buccalis (Robin 1853) Trevisan 1879

strain designation: C-1013-b

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480negative99.806
117066positiverod-shapedno

colony morphology

@refincubation period
5751-2 days
520432 days
117066

multimedia

  • @ref: 66793
  • multimedia content: EM_DSM_1135_1.jpg
  • caption: electron microscopic image
  • intellectual property rights: © HZI/Manfred Rohde

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
575COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)yeshttps://mediadive.dsmz.de/medium/693Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base
575CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110)yeshttps://mediadive.dsmz.de/medium/110Name: CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110) Composition: Ground beef 500.0 g/l Casitone 30.0 g/l Agar 15.0 g/l K2HPO4 5.0 g/l Yeast extract 5.0 g/l D-Glucose 4.0 g/l Starch 1.0 g/l Maltose 1.0 g/l Cellobiose 1.0 g/l L-Cysteine HCl 0.5 g/l Ethanol 0.19 g/l Vitamin K3 0.05 g/l Hemin 0.005 g/l Sodium resazurin 0.0005 g/l Vitamin K1 NaOH Distilled water
575PYG 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
39366MEDIUM 10 - Chocolate medium for Actinobacillus pleuropneumoniae, Capnocytophaga cynodegmi, Haemophilus and NeisseriayesDistilled water make up to (1000.000 ml);Columbia agar (39.000 g);Horseblood (100.000 ml);PolyVitex mischung (10.000 ml)
117066CIP Medium 10yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=10

culture temp

@refgrowthtypetemperaturerange
575positivegrowth37mesophilic
39366positivegrowth37mesophilic
52043positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
575anaerobe
52043anaerobe
52043microaerophile
69480anaerobe98.056
117066anaerobe

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.319

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
117066esculin+hydrolysis4853
117066nitrate-reduction17632
117066nitrite-reduction16301
117066nitrate+respiration17632
68377D-glucose+builds acid from17634
68377D-fructose+builds acid from15824
68377maltose+builds acid from17306
68377ornithine-degradation18257
68377urea-hydrolysis16199
68377tryptophan-energy source27897
68380urea-hydrolysis16199
68380arginine-hydrolysis29016
68380L-glutamate-degradation29985
68380nitrate-reduction17632
68380tryptophan-energy source27897

metabolite production

@refChebi-IDmetaboliteproduction
6837735581indoleno
11706635581indoleno
6838035581indoleno

metabolite tests

@refChebi-IDmetaboliteindole test
6838035581indole-
6837735581indole-

enzymes

@refvalueactivityec
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-galactosidase-3.2.1.23
68380arginine dihydrolase-3.5.3.6
68380urease-3.5.1.5
68377tryptophan deaminase-4.1.99.1
68377beta-galactosidase-3.2.1.23
68377alkaline phosphatase-3.1.3.1
68377lipase-
68377urease-3.5.1.5
68377ornithine decarboxylase-4.1.1.17
117066oxidase-
117066beta-galactosidase-3.2.1.23
117066gelatinase-
117066amylase-
117066DNase-
117066caseinase+3.4.21.50
117066catalase-1.11.1.6
117066tween esterase-
117066lecithinase-
117066lipase-
117066protease-
117066urease-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
117066-+++------++---+----

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
117066+--------++++--------+-+++++++++--+++-++-+----+--

API NH

@refPENGLUFRUMALSACODCURELIPPALbeta GALProAGGTIND
575++++------+/---
575-++++------+/--

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
575--+/--------------+------------
575--+/--+/-++/----+/-+/-----+------------

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
575supragingival calculusUSAUSANorth America
52043Human supragingival calcus
67770Supragingival calculus
117066Human, Supragingival calculus

isolation source categories

  • Cat1: #Host Body-Site
  • Cat2: #Oral cavity and airways

taxonmaps

  • @ref: 69479
  • File name: preview.99_1297.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_108;96_752;97_877;98_1025;99_1297&stattab=map
  • Last taxonomy: Leptotrichia buccalis subclade
  • 16S sequence: AB818949
  • Sequence Identity:
  • Total samples: 29304
  • soil counts: 710
  • aquatic counts: 674
  • animal counts: 27734
  • plant counts: 186

Safety information

risk assessment

@refpathogenicity humanpathogenicity animalbiosafety levelbiosafety level comment
575yesyes2Risk group (German classification)
1170661Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Leptotrichia buccalis gene for 16S ribosomal RNA, partial sequence, strain: JCM 12969AB8189491473ena523794
20218Leptotrichia buccalis strain ATCC 14201 16S ribosomal RNA gene, partial sequence; internal transcribed spacer 1, complete sequence; and 23S ribosomal RNA gene, partial sequenceAF342860716ena523794
67770Leptotrichia buccalis 16S rRNA geneX908311327ena523794

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Leptotrichia buccalis C-1013-b DSM 1135GCA_000023905completencbi523794
66792Leptotrichia buccalis DSM 1135523794.5completepatric523794
66792Leptotrichia buccalis C-1013-b, DSM 1135644736384completeimg523794
66792Leptotrichia buccalis ATCC 142012500645350draftimg523794

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno56no
motileno94.225no
flagellatedno96.818no
gram-positiveno93.276no
anaerobicyes96.216no
aerobicno98.946yes
halophileno74.907no
spore-formingno94.241no
thermophileno96.193yes
glucose-utilyes70.213no
glucose-fermentyes58.5no

External links

@ref: 575

culture collection no.: DSM 1135, ATCC 14201, JCM 12969, NCTC 10249, CCUG 34316, CIP 105792

straininfo link

  • @ref: 86851
  • straininfo: 35996

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Metabolism3864216Oligosaccharides obtained by partial hydrolysis of lipopolysaccharides from Leptotrichia buccalis.Birkeland NK, Hofstad TScand J Dent Res10.1111/j.1600-0722.1985.tb01335.x1985Bacteroidaceae/*metabolism, Chromatography, Gas, Chromatography, Gel, Hydrolysis, Lipopolysaccharides/analysis/*metabolism, Oligosaccharides/*isolation & purificationEnzymology
Enzymology6822410Purification and quantitative chemical analysis of cell wall peptidoglycans of Leptotrichia buccalis.Fukuhara H, Umemoto T, Sagawa H, Kato K, Kotani SInfect Immun10.1128/iai.39.1.132-136.19831983Amino Acids/analysis, Amino Sugars/analysis, Bacteroidaceae/*analysis, Cell Wall/analysis, Peptidoglycan/*isolation & purificationPhylogeny
Phylogeny7148458Chemical composition, ultrastructure and some serological properties of lipopolysaccharides from Leptotrichia buccalis.Birkeland NK, Hofstad TActa Pathol Microbiol Immunol Scand B10.1111/j.1699-0463.1982.tb00127.x1982Amino Sugars, Bacteroidaceae/classification/*immunology, Carbohydrates/analysis, Cross Reactions, Lipopolysaccharides/*analysis/immunology, Microscopy, Electron, Sugar Acids/analysis
Enzymology12351228Purification and some properties of phospho-beta-galactosidase from the Gram-negative oral bacterium Leptotrichia buccalis ATCC 14201.Thompson JFEMS Microbiol Lett10.1111/j.1574-6968.2002.tb11344.x2002Amino Acid Sequence, *Glycoside Hydrolases, Gram-Negative Bacteria/*enzymology/growth & development, Molecular Sequence Data, Molecular Weight, Mouth/*microbiology, beta-Galactosidase/chemistry/genetics/*isolation & purificationGenetics
Genetics21304648Complete genome sequence of Leptotrichia buccalis type strain (C-1013-b).Ivanova N, Gronow S, Lapidus A, Copeland A, Glavina Del Rio T, Nolan M, Lucas S, Chen F, Tice H, Cheng JF, Saunders E, Bruce D, Goodwin L, Brettin T, Detter JC, Han C, Pitluck S, Mikhailova N, Pati A, Mavrommatis K, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Chain P, Rohde C, Goker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HPStand Genomic Sci10.4056/sigs.18542009
Metabolism22230464Metabolism of sugars by genetically diverse species of oral Leptotrichia.Thompson J, Pikis AMol Oral Microbiol10.1111/j.2041-1014.2011.00627.x2011Bacterial Proteins/*genetics, DNA-Binding Proteins/metabolism, Dental Plaque/microbiology, Disaccharidases/*metabolism, Genes, Bacterial, Glycoside Hydrolases/genetics, Isoenzymes, Leptotrichia/*genetics/*metabolism, Monosaccharide Transport Proteins/metabolism, Phosphoenolpyruvate Sugar Phosphotransferase System, Phosphorylation/genetics, Species Specificity, Sucrose/*metabolism, alpha-Glucosidases/geneticsPhylogeny

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
575Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 1135)https://www.dsmz.de/collection/catalogue/details/culture/DSM-1135
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
39366Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17850
52043Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 34316)https://www.ccug.se/strain?id=34316
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)
66793Mukherjee et al.10.1038/nbt.3886GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life 35: 676-683 201728604660
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 updatesNucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68371Automatically annotated from API 50CH acid
68377Automatically annotated from API NH
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)
86851Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID35996.1StrainInfo: A central database for resolving microbial strain identifiers
117066Curators of the CIPCollection of Institut Pasteur (CIP 105792)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105792