Strain identifier
BacDive ID: 11308
Type strain:
Species: Collimonas fungivorans
Strain history: CIP <- 2005, W. de Boer, Netherlands Inst. Ecol., Heteren, Netherlands: strain Ter6
NCBI tax ID(s): 158899 (species)
General
@ref: 6913
BacDive-ID: 11308
DSM-Number: 17622
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, motile, rod-shaped
description: Collimonas fungivorans CCUG 48868 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from dune soil with Marram grass tussocks.
NCBI tax id
- NCBI tax id: 158899
- Matching level: species
strain history
@ref | history |
---|---|
6913 | <- W. de Boer, Centre for Terrest. Ecology, Heteren; Ter6 |
37445 | 2005, W. de Boer, Netherlands Inst. Ecol., Heteren, Netherlands: strain Ter6 |
67772 | de Boer W, NIOO - KNAW, Centre for Terrestrial Ecology |
119491 | CIP <- 2005, W. de Boer, Netherlands Inst. Ecol., Heteren, Netherlands: strain Ter6 |
doi: 10.13145/bacdive11308.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Betaproteobacteria
- order: Burkholderiales
- family: Oxalobacteraceae
- genus: Collimonas
- species: Collimonas fungivorans
- full scientific name: Collimonas fungivorans De Boer et al. 2004
@ref: 6913
domain: Bacteria
phylum: Proteobacteria
class: Betaproteobacteria
order: Burkholderiales
family: Oxalobacteraceae
genus: Collimonas
species: Collimonas fungivorans
full scientific name: Collimonas fungivorans de Boer et al. 2004
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility |
---|---|---|---|---|---|
30085 | negative | 1.5 µm | 0.4 µm | rod-shaped | yes |
119491 | negative | rod-shaped | no |
pigmentation
- @ref: 30085
- production: no
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
6913 | COLLIMONAS MEDIUM (DSMZ Medium 1035) | yes | https://mediadive.dsmz.de/medium/1035 | Name: COLLIMONAS MEDIUM (DSMZ Medium 1035) Composition: NaCl 5.0 g/l Trypticase soy broth 3.0 g/l KH2PO4 1.0 g/l Distilled water |
37445 | MEDIUM 72- for trypto casein soja agar | yes | Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g) | |
119491 | CIP Medium 72 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
6913 | positive | growth | 28 | mesophilic |
30085 | positive | growth | 20-35 | |
30085 | positive | optimum | 25 | mesophilic |
37445 | positive | growth | 25 | mesophilic |
58367 | positive | growth | 20-30 | |
67772 | positive | optimum | 28 | mesophilic |
119491 | positive | growth | 5-30 | |
119491 | no | growth | 37 | mesophilic |
119491 | no | growth | 41 | thermophilic |
culture pH
- @ref: 30085
- ability: positive
- type: optimum
- pH: 6.5
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
30085 | aerobe |
58367 | aerobe |
119491 | obligate aerobe |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
119491 | NaCl | positive | growth | 0 % |
119491 | NaCl | no | growth | 2 % |
119491 | NaCl | no | growth | 4 % |
119491 | NaCl | no | growth | 6 % |
119491 | NaCl | no | growth | 8 % |
119491 | NaCl | no | growth | 10 % |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
30085 | 17596 | inosine | + | carbon source |
30085 | 25017 | leucine | + | carbon source |
30085 | 27082 | trehalose | + | carbon source |
30085 | 16704 | uridine | + | carbon source |
119491 | 4853 | esculin | - | hydrolysis |
119491 | 17632 | nitrate | - | reduction |
119491 | 16301 | nitrite | - | reduction |
119491 | 17632 | nitrate | - | respiration |
antibiotic resistance
- @ref: 119491
- metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
- is antibiotic: yes
- is sensitive: no
- is resistant: yes
metabolite production
- @ref: 119491
- Chebi-ID: 35581
- metabolite: indole
- production: no
enzymes
@ref | value | activity | ec |
---|---|---|---|
30085 | cytochrome oxidase | + | 1.9.3.1 |
119491 | oxidase | + | |
119491 | beta-galactosidase | + | 3.2.1.23 |
119491 | alcohol dehydrogenase | - | 1.1.1.1 |
119491 | gelatinase | + | |
119491 | amylase | - | |
119491 | DNase | + | |
119491 | caseinase | - | 3.4.21.50 |
119491 | catalase | - | 1.11.1.6 |
119491 | tween esterase | - | |
119491 | lecithinase | - | |
119491 | lipase | - | |
119491 | lysine decarboxylase | - | 4.1.1.18 |
119491 | ornithine decarboxylase | - | 4.1.1.17 |
119491 | protease | + | |
119491 | tryptophan deaminase | - | |
119491 | urease | - | 3.5.1.5 |
68382 | alkaline phosphatase | + | 3.1.3.1 |
68382 | esterase (C 4) | + | |
68382 | esterase lipase (C 8) | + | |
68382 | lipase (C 14) | - | |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | valine arylamidase | - | |
68382 | cystine arylamidase | - | 3.4.11.3 |
68382 | trypsin | - | 3.4.21.4 |
68382 | alpha-chymotrypsin | - | 3.4.21.1 |
68382 | acid phosphatase | + | 3.1.3.2 |
68382 | naphthol-AS-BI-phosphohydrolase | + | |
68382 | alpha-galactosidase | - | 3.2.1.22 |
68382 | beta-galactosidase | + | 3.2.1.23 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | alpha-glucosidase | - | 3.2.1.20 |
68382 | beta-glucosidase | - | 3.2.1.21 |
68382 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | alpha-fucosidase | - | 3.2.1.51 |
API zym
@ref | Control | Alkaline phosphatase | Esterase | Esterase Lipase | Lipase | Leucine arylamidase | Valine arylamidase | Cystine arylamidase | Trypsin | alpha- Chymotrypsin | Acid phosphatase | Naphthol-AS-BI-phosphohydrolase | alpha- Galactosidase | beta- Galactosidase | beta- Glucuronidase | alpha- Glucosidase | beta- Glucosidase | N-acetyl-beta- glucosaminidase | alpha- Mannosidase | alpha- Fucosidase |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
119491 | - | + | + | + | - | + | - | - | - | - | + | + | - | + | - | - | - | - | - | - |
API biotype100
@ref | GLU | FRU | GAL | TRE | MNE | SBE | MEL | SAC | RAF | MTE | MAL | LAC | LTE | MbGa | MaGa | CEL | GEN | MbGu | ESC | RIB | ARA | XYL | PLE | RHA | FUC | MLZ | DARL | LARL | XLT | DUL | TAG | GLY | INO | MAN | MTL | TUR | SOR | ADO | HBG | LYX | ERY | MDG | 3MDG | SAT | MUC | LTAT | DTAT | MTAT | DMLT | LMLT | CATE | TATE | TTE | CIT | GRT | GAT | 2KG | 5KG | TRY | NAG | GNT | PAC | PAT | pOBE | QAT | GTE | mOBE | BAT | PPAT | CMT | TGE | BET | PCE | ABT | HIN | LAT | CAP | CYT | HIS | SUC | FUM | GRE | GYT | AVT | ETN | TTN | GLN | ITA | 3OBU | APT | GTT | PRO | DALA | LALA | SER | MNT | PROP | TYR | 2KT |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
119491 | + | + | + | + | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | + | + | - | - | + | - | + | - | + | - | - | + | + | + | - | - | + | - | - | + | - | - | - | + | + | - | - | - | - | + | + | + | - | + | + | + | - | - | - | + | - | - | + | + | + | - | - | - | - | - | - | + | - | + | - | + | - | - | + | + | + | - | + | - | - | - | + | - | + | + | + | + | - | + | - | - | - | + | + |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent | sampling date | latitude | longitude |
---|---|---|---|---|---|---|---|---|
6913 | dune soil with Marram grass tussocks | Terschelling | Netherlands | NLD | Europe | |||
58367 | Soil,slightly acidic dune soil | Wadden Island Terschelling | Netherlands | NLD | Europe | 1994 | ||
67772 | Dune soil | Wadden Islands | Netherlands | NLD | Europe | 1994 | 53.4 | 5.31667 |
119491 | Environment, Soil, dune | Netherlands | NLD | Europe |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Environmental | #Terrestrial | #Soil |
#Host | #Plants | #Herbaceous plants (Grass,Crops) |
taxonmaps
- @ref: 69479
- File name: preview.99_1512.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_12;96_128;97_1012;98_1195;99_1512&stattab=map
- Last taxonomy: Collimonas
- 16S sequence: AJ310394
- Sequence Identity:
- Total samples: 1345
- soil counts: 741
- aquatic counts: 386
- animal counts: 129
- plant counts: 89
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
6913 | 1 | Risk group (German classification) |
67772 | 1 | |
119491 | 1 | Risk group (French classification) |
Sequence information
16S sequences
- @ref: 6913
- description: Collimonas fungivorans partial 16S rRNA gene, isolate Ter6
- accession: AJ310394
- length: 1453
- database: ena
- NCBI tax ID: 158899
Genome sequences
- @ref: 67772
- description: Collimonas fungivorans Ter6
- accession: GCA_001584145
- assembly level: complete
- database: ncbi
- NCBI tax ID: 158899
GC content
- @ref: 30085
- GC-content: 57.8
External links
@ref: 6913
culture collection no.: CCUG 48868, DSM 17622, LMG 21973, NCCB 100033, TER Ter6, TER 6, UCCCB6, CIP 108645
straininfo link
- @ref: 80541
- straininfo: 100062
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 15143036 | Collimonas fungivorans gen. nov., sp. nov., a chitinolytic soil bacterium with the ability to grow on living fungal hyphae. | de Boer W, Leveau JHJ, Kowalchuk GA, Gunnewiek PJAK, Abeln ECA, Figge MJ, Sjollema K, Janse JD, van Veen JA | Int J Syst Evol Microbiol | 10.1099/ijs.0.02920-0 | 2004 | Base Composition, Chitin/metabolism, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/genetics, Fatty Acids/analysis, Fungi, Microscopy, Electron, Molecular Sequence Data, Netherlands, Oxalobacteraceae/*classification/genetics/growth & development/*metabolism, Phenotype, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Soil Microbiology | Metabolism |
Phylogeny | 20935085 | Glaciimonas immobilis gen. nov., sp. nov., a member of the family Oxalobacteraceae isolated from alpine glacier cryoconite. | Zhang DC, Redzic M, Schinner F, Margesin R | Int J Syst Evol Microbiol | 10.1099/ijs.0.028001-0 | 2010 | Bacterial Typing Techniques, Base Composition, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Ice Cover/*microbiology, Molecular Sequence Data, Oxalobacteraceae/*classification/genetics/*isolation & purification/physiology, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Temperature | Genetics |
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
---|---|---|---|---|---|---|
6913 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17622) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-17622 | |||
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
30085 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 26442 | 28776041 | |
37445 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/6297 | ||||
58367 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 48868) | https://www.ccug.se/strain?id=48868 | |||
67772 | Curators of the UCCCB | https://ucccb.uc.pt/ | ||||
68382 | Automatically annotated from API zym | |||||
69479 | João 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 | |||
80541 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID100062.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
119491 | Curators of the CIP | Collection of Institut Pasteur (CIP 108645) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108645 |