Strain identifier

BacDive ID: 132488

Type strain: Yes

Species: Caviibacter abscessus

Strain history: <- T. Eisenberg, Landesbetrieb Hess. Landeslabor, Giessen, Germany <- CCUG; CCUG 39713 <- V. Baverud, Natl. Veterinary Inst., SVA, Sweden

NCBI tax ID(s): 1766719 (species)

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General

@ref: 24277

BacDive-ID: 132488

DSM-Number: 101949

keywords: genome sequence, Bacteria, obligate anaerobe, mesophilic, Gram-negative, rod-shaped, colony-forming

description: Caviibacter abscessus DSM 101949 is an obligate anaerobe, mesophilic, Gram-negative bacterium that forms circular colonies and was isolated from mandibular lymph node abscess in a guinea pig .

NCBI tax id

  • NCBI tax id: 1766719
  • Matching level: species

strain history

  • @ref: 24277
  • history: <- T. Eisenberg, Landesbetrieb Hess. Landeslabor, Giessen, Germany <- CCUG; CCUG 39713 <- V. Baverud, Natl. Veterinary Inst., SVA, Sweden

doi: 10.13145/bacdive132488.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/fusobacteriota
  • domain: Bacteria
  • phylum: Fusobacteriota
  • class: Fusobacteriia
  • order: Fusobacteriales
  • family: Leptotrichiaceae
  • genus: Caviibacter
  • species: Caviibacter abscessus
  • full scientific name: Caviibacter abscessus Eisenberg et al. 2016

@ref: 24277

domain: Bacteria

phylum: Fusobacteria

class: Fusobacteriia

order: Fusobacteriales

family: Leptotrichiaceae

genus: Caviibacter

species: Caviibacter abscessus

full scientific name: Caviibacter abscessus Eisenberg et al. 2016

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
43670negative0.92 µm0.47 µmrod-shapedno
69480no91.021
69480negative99.806

colony morphology

@refcolony sizecolony colorcolony shapeincubation period
436700.1-0.4 mmslightly opaque, drycircular
548975 days

Culture and growth conditions

culture medium

  • @ref: 24277
  • name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/535
  • composition: Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535; with strain-specific modifications) Composition: Horse serum 200.0 g/l Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
43670positiveoptimum35-37mesophilic
24277positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
43670obligate anaerobe
54897anaerobe
69480anaerobe98.261

spore formation

@refspore formationconfidence
43670no
69481no92
69480no99.998

observation

  • @ref: 43670
  • observation: require blood, serum or ascitic fluid for growth

metabolite utilization

  • @ref: 43670
  • Chebi-ID: 17632
  • metabolite: nitrate
  • utilization activity: -
  • kind of utilization tested: reduction

metabolite production

  • @ref: 43670
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
43670esterase (C 4)+
43670esterase Lipase (C 8)+
43670phenylalanine arylamidase+
43670proline-arylamidase+3.4.11.5
43670tyrosine arylamidase+
43670acid phosphatase-3.1.3.2
43670alkaline phosphatase-3.1.3.1
43670lipase (C 14)-
43670lysine decarboxylase-4.1.1.18
43670valine arylamidase-
43670cystine arylamidase-3.4.11.3
43670alpha-chymotrypsin-3.4.21.1
43670trypsin-3.4.21.4
43670naphthol-AS-BI-phosphohydrolase-
43670alpha-galactosidase-3.2.1.22
43670beta-galactosidase-3.2.1.23
43670alpha-glucosidase-3.2.1.20
43670beta-glucosidase-3.2.1.21
43670beta-glucuronidase-3.2.1.31
43670N-acetyl-beta-glucosaminidase-3.2.1.52
43670alpha-mannosidase-3.2.1.24
43670alpha-fucosidase-3.2.1.51
43670cytochrome oxidase-1.9.3.1
43670catalase-1.11.1.6

fatty acid profile

  • fatty acids

    @reffatty acidpercentageECL
    54897C12:00.212
    54897C14:00.914
    54897C15:00.315
    54897C16:022.316
    54897C17:00.817
    54897C18:022.518
    54897C19:00.219
    54897C20:00.520
    54897C16:0 iso0.215.626
    54897C16:1 ω7c1.315.819
    54897C16:1 ω9c0.315.774
    54897C17:0 anteiso0.316.722
    54897C17:1 ISO I/C16:0 DMA1.316.481
    54897C17:1 ω8c0.416.792
    54897C18:0 3OH0.419.551
    54897C18:0 ISO0.317.632
    54897C18:1 ω9c15.117.769
    54897C18:2 ω6,9c/C18:0 ANTE3017.724
    54897C19:1 ISO I0.318.473
    54897C20:1 ω9c0.319.77
    54897C20:2 ω6,9c0.319.735
    54897C20:4 ω6,9,12,15c0.619.395
    54897Unidentified0.210.732
    54897Unidentified0.214.95
    54897Unidentified0.216.109
    54897Unidentified0.217.199
    54897Unidentified0.518.219
    54897Unidentified0.218.281
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG

Isolation, sampling and environmental information

isolation

@refsample typehost speciescountryorigin.countrycontinentgeographic locationsampling date
24277mandibular lymph node abscess in a guinea pig (Cavia porcellus)Cavia porcellusSwedenSWEEurope
43670A mandibular lymph node abscess in a guinea pig (Cavia porcellus)SwedenSWEEuropeSweden
54897Guinea pig mandibular lymph nodeSwedenSWEEuropeUppsala1998-08-01

isolation source categories

Cat1Cat2Cat3
#Host#Mammals#Rodentia (Other)
#Host Body-Site#Organ#Lymph node
#Host Body-Site#Oral cavity and airways
#Host Body-Site#Other#Abscess
#Host#Mammals#Rodentia (Other)

Sequence information

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Caviibacter abscessus CCUG 39713GCA_001517835contigncbi1766719
66792Caviibacter abscessus strain CCUG 397131766719.4wgspatric1766719
66792Caviibacter abscessus CCUG 397132788499922draftimg1766719

GC content

  • @ref: 24277
  • GC-content: 26.5

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno92no
motileno93.479yes
gram-positiveno70.437yes
anaerobicyes65.873no
aerobicno98.631yes
halophileyes65.827no
spore-formingno97.686yes
glucose-utilyes81.487no
flagellatedno98.314yes
thermophileno87.697yes
glucose-fermentyes73.728no

External links

@ref: 24277

culture collection no.: DSM 101949, CCUG 39713

straininfo link

  • @ref: 90818
  • straininfo: 108836

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny26813893Caviibacter abscessus gen. nov., sp. nov., a member of the family Leptotrichiaceae isolated from guinea pigs (Cavia porcellus).Eisenberg T, Glaeser SP, Ewers C, Semmler T, Drescher B, Kampfer PInt J Syst Evol Microbiol10.1099/ijsem.0.0009222016Animals, Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/chemistry, Fusobacteria/*classification/genetics/isolation & purification, Genes, Bacterial, Germany, Guinea Pigs/*microbiology, Lymph Nodes/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAGenetics
Phylogeny27031261Oceanivirga salmonicida gen. nov., sp. nov., a member of the Leptotrichiaceae isolated from Atlantic salmon (Salmo salar).Eisenberg T, Kampfer P, Ewers C, Semmler T, Glaeser SP, Collins E, Ruttledge M, Palmer RInt J Syst Evol Microbiol10.1099/ijsem.0.0010502016Animals, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Fusobacteria/*classification/genetics/isolation & purification, Genes, Bacterial, Ireland, *Phylogeny, RNA, Ribosomal, 16S/genetics, Salmo salar/*microbiology, Sequence Analysis, DNATranscriptome

Reference

@idauthorstitledoi/urlcataloguejournalpubmed
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
24277Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-101949Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 101949)
43670Tobias Eisenberg, Stefanie P. Glaeser, Christa Ewers, Torsten Semmler, Birgit Drescher, Peter KämpferCaviibacter abscessus gen. nov., sp. nov., a member of the family Leptotrichiaceae isolated from guinea pigs (Cavia porcellus)10.1099/ijsem.0.000922IJSEM 66: 1652-1659 201626813893
54897Curators of the CCUGhttps://www.ccug.se/strain?id=39713Culture Collection University of Gothenburg (CCUG) (CCUG 39713)
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
90818Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID108836.1