Strain identifier
BacDive ID: 132488
Type strain:
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)
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
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
43670 | negative | 0.92 µm | 0.47 µm | rod-shaped | no | |
69480 | no | 91.021 | ||||
69480 | negative | 99.806 |
colony morphology
@ref | colony size | colony color | colony shape | incubation period |
---|---|---|---|---|
43670 | 0.1-0.4 mm | slightly opaque, dry | circular | |
54897 | 5 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
@ref | growth | type | temperature | range |
---|---|---|---|---|
43670 | positive | optimum | 35-37 | mesophilic |
24277 | positive | growth | 37 | mesophilic |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance | confidence |
---|---|---|
43670 | obligate anaerobe | |
54897 | anaerobe | |
69480 | anaerobe | 98.261 |
spore formation
@ref | spore formation | confidence |
---|---|---|
43670 | no | |
69481 | no | 92 |
69480 | no | 99.998 |
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
@ref | value | activity | ec |
---|---|---|---|
43670 | esterase (C 4) | + | |
43670 | esterase Lipase (C 8) | + | |
43670 | phenylalanine arylamidase | + | |
43670 | proline-arylamidase | + | 3.4.11.5 |
43670 | tyrosine arylamidase | + | |
43670 | acid phosphatase | - | 3.1.3.2 |
43670 | alkaline phosphatase | - | 3.1.3.1 |
43670 | lipase (C 14) | - | |
43670 | lysine decarboxylase | - | 4.1.1.18 |
43670 | valine arylamidase | - | |
43670 | cystine arylamidase | - | 3.4.11.3 |
43670 | alpha-chymotrypsin | - | 3.4.21.1 |
43670 | trypsin | - | 3.4.21.4 |
43670 | naphthol-AS-BI-phosphohydrolase | - | |
43670 | alpha-galactosidase | - | 3.2.1.22 |
43670 | beta-galactosidase | - | 3.2.1.23 |
43670 | alpha-glucosidase | - | 3.2.1.20 |
43670 | beta-glucosidase | - | 3.2.1.21 |
43670 | beta-glucuronidase | - | 3.2.1.31 |
43670 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
43670 | alpha-mannosidase | - | 3.2.1.24 |
43670 | alpha-fucosidase | - | 3.2.1.51 |
43670 | cytochrome oxidase | - | 1.9.3.1 |
43670 | catalase | - | 1.11.1.6 |
fatty acid profile
fatty acids
@ref fatty acid percentage ECL 54897 C12:0 0.2 12 54897 C14:0 0.9 14 54897 C15:0 0.3 15 54897 C16:0 22.3 16 54897 C17:0 0.8 17 54897 C18:0 22.5 18 54897 C19:0 0.2 19 54897 C20:0 0.5 20 54897 C16:0 iso 0.2 15.626 54897 C16:1 ω7c 1.3 15.819 54897 C16:1 ω9c 0.3 15.774 54897 C17:0 anteiso 0.3 16.722 54897 C17:1 ISO I/C16:0 DMA 1.3 16.481 54897 C17:1 ω8c 0.4 16.792 54897 C18:0 3OH 0.4 19.551 54897 C18:0 ISO 0.3 17.632 54897 C18:1 ω9c 15.1 17.769 54897 C18:2 ω6,9c/C18:0 ANTE 30 17.724 54897 C19:1 ISO I 0.3 18.473 54897 C20:1 ω9c 0.3 19.77 54897 C20:2 ω6,9c 0.3 19.735 54897 C20:4 ω6,9,12,15c 0.6 19.395 54897 Unidentified 0.2 10.732 54897 Unidentified 0.2 14.95 54897 Unidentified 0.2 16.109 54897 Unidentified 0.2 17.199 54897 Unidentified 0.5 18.219 54897 Unidentified 0.2 18.281 - type of FA analysis: whole cell analysis
- method/protocol: CCUG
Isolation, sampling and environmental information
isolation
@ref | sample type | host species | country | origin.country | continent | geographic location | sampling date |
---|---|---|---|---|---|---|---|
24277 | mandibular lymph node abscess in a guinea pig (Cavia porcellus) | Cavia porcellus | Sweden | SWE | Europe | ||
43670 | A mandibular lymph node abscess in a guinea pig (Cavia porcellus) | Sweden | SWE | Europe | Sweden | ||
54897 | Guinea pig mandibular lymph node | Sweden | SWE | Europe | Uppsala | 1998-08-01 |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#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
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Caviibacter abscessus CCUG 39713 | GCA_001517835 | contig | ncbi | 1766719 |
66792 | Caviibacter abscessus strain CCUG 39713 | 1766719.4 | wgs | patric | 1766719 |
66792 | Caviibacter abscessus CCUG 39713 | 2788499922 | draft | img | 1766719 |
GC content
- @ref: 24277
- GC-content: 26.5
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 92 | no |
motile | no | 93.479 | yes |
gram-positive | no | 70.437 | yes |
anaerobic | yes | 65.873 | no |
aerobic | no | 98.631 | yes |
halophile | yes | 65.827 | no |
spore-forming | no | 97.686 | yes |
glucose-util | yes | 81.487 | no |
flagellated | no | 98.314 | yes |
thermophile | no | 87.697 | yes |
glucose-ferment | yes | 73.728 | no |
External links
@ref: 24277
culture collection no.: DSM 101949, CCUG 39713
straininfo link
- @ref: 90818
- straininfo: 108836
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 26813893 | Caviibacter 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 P | Int J Syst Evol Microbiol | 10.1099/ijsem.0.000922 | 2016 | Animals, 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, DNA | Genetics |
Phylogeny | 27031261 | Oceanivirga 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 R | Int J Syst Evol Microbiol | 10.1099/ijsem.0.001050 | 2016 | Animals, 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, DNA | Transcriptome |
Reference
@id | authors | title | doi/url | catalogue | journal | pubmed |
---|---|---|---|---|---|---|
20215 | Parte, 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 DSMZ | 10.1099/ijsem.0.004332 | |||
24277 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-101949 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 101949) | |||
43670 | Tobias Eisenberg, Stefanie P. Glaeser, Christa Ewers, Torsten Semmler, Birgit Drescher, Peter Kämpfer | Caviibacter abscessus gen. nov., sp. nov., a member of the family Leptotrichiaceae isolated from guinea pigs (Cavia porcellus) | 10.1099/ijsem.0.000922 | IJSEM 66: 1652-1659 2016 | 26813893 | |
54897 | Curators of the CCUG | https://www.ccug.se/strain?id=39713 | Culture Collection University of Gothenburg (CCUG) (CCUG 39713) | |||
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Predictions 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 | |||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | Predictions based on the model GenomeNet Sporulation v. 1 | 10.21203/rs.3.rs-2527258/v1 | |||
90818 | Reimer, 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 identifiers | 10.60712/SI-ID108836.1 |