Strain identifier
BacDive ID: 12492
Type strain:
Species: Byssovorax cruenta
Strain Designation: By c2
Strain history: CIP <- 2005, DSMZ <- H. Reichenbach, GBF, Braunschweig, Germany: strain By C2
NCBI tax ID(s): 1300159 (strain), 293647 (species)
General
@ref: 5294
BacDive-ID: 12492
DSM-Number: 14553
keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, mesophilic, Gram-negative
description: Byssovorax cruenta By c2 is a facultative anaerobe, mesophilic, Gram-negative bacterium that was isolated from soil with rotting plant material.
NCBI tax id
NCBI tax id | Matching level |
---|---|
1300159 | strain |
293647 | species |
strain history
@ref | history |
---|---|
5294 | <- H. Reichenbach; By c2 |
67770 | DSM 14553 <-- H. Reichenbach By c2. |
118792 | CIP <- 2005, DSMZ <- H. Reichenbach, GBF, Braunschweig, Germany: strain By C2 |
doi: 10.13145/bacdive12492.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Deltaproteobacteria
- order: Myxococcales
- family: Polyangiaceae
- genus: Byssovorax
- species: Byssovorax cruenta
- full scientific name: Byssovorax cruenta (ex Thaxter 1897) Reichenbach 2006
synonyms
- @ref: 20215
- synonym: Byssophaga cruenta
@ref: 5294
domain: Bacteria
phylum: Proteobacteria
class: Deltaproteobacteria
order: Myxococcales
family: Polyangiaceae
genus: Byssovorax
species: Byssovorax cruenta
full scientific name: Byssovorax cruenta (ex Thaxter 1897) Reichenbach 2006
strain designation: By c2
type strain: yes
Morphology
cell morphology
@ref | gram stain | confidence | cell shape | motility |
---|---|---|---|---|
69480 | negative | 99.687 | ||
118792 | positive | coccus-shaped | no |
multimedia
- @ref: 5294
- multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_14553.jpg
- caption: swarms on medium 9
- intellectual property rights: © Leibniz-Institut DSMZ
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
5294 | VY/2 AGAR (DSMZ Medium 9) | yes | https://mediadive.dsmz.de/medium/9 | Name: VY/2 AGAR (DSMZ Medium 9; with strain-specific modifications) Composition: Agar 15.0 g/l Baker's yeast 5.0 g/l Maltose 2.0 g/l CaCl2 x 2 H2O 1.36 g/l Vitamin B12 0.0005 g/l Distilled water |
38337 | MEDIUM 657 - for Byssovorax cruenta | yes | Distilled water make up to (1000.000 ml);Calcium chloride dihydrate (1.360g);Agar (15.000 g);Yeast Baker (5.000 g);Vitamin B12 solution - M01085 (100.000 ml);Maltose solution - M01084 (100.000 ml) | |
118792 | CIP Medium 657 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=657 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
5294 | positive | growth | 30 | mesophilic |
38337 | positive | growth | 30 | mesophilic |
67770 | positive | growth | 30 | mesophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 118792
- oxygen tolerance: facultative anaerobe
spore formation
- @ref: 69480
- spore formation: no
- confidence: 99.995
metabolite utilization
@ref | metabolite | utilization activity | kind of utilization tested | Chebi-ID |
---|---|---|---|---|
68371 | Potassium 2-ketogluconate | - | builds acid from | |
68371 | gluconate | - | builds acid from | 24265 |
68371 | L-arabitol | - | builds acid from | 18403 |
68371 | D-arabitol | - | builds acid from | 18333 |
68371 | L-fucose | - | builds acid from | 18287 |
68371 | D-fucose | - | builds acid from | 28847 |
68371 | D-tagatose | - | builds acid from | 16443 |
68371 | D-lyxose | - | builds acid from | 62318 |
68371 | gentiobiose | - | builds acid from | 28066 |
68371 | xylitol | - | builds acid from | 17151 |
68371 | glycogen | - | builds acid from | 28087 |
68371 | starch | - | builds acid from | 28017 |
68371 | raffinose | - | builds acid from | 16634 |
68371 | inulin | - | builds acid from | 15443 |
68371 | trehalose | - | builds acid from | 27082 |
68371 | sucrose | + | builds acid from | 17992 |
68371 | melibiose | - | builds acid from | 28053 |
68371 | lactose | + | builds acid from | 17716 |
68371 | maltose | + | builds acid from | 17306 |
68371 | cellobiose | - | builds acid from | 17057 |
68371 | salicin | - | builds acid from | 17814 |
68371 | esculin | - | builds acid from | 4853 |
68371 | arbutin | - | builds acid from | 18305 |
68371 | amygdalin | - | builds acid from | 27613 |
68371 | methyl alpha-D-glucopyranoside | - | builds acid from | 320061 |
68371 | methyl alpha-D-mannoside | - | builds acid from | 43943 |
68371 | D-sorbitol | - | builds acid from | 17924 |
68371 | D-mannitol | - | builds acid from | 16899 |
68371 | myo-inositol | - | builds acid from | 17268 |
68371 | galactitol | - | builds acid from | 16813 |
68371 | L-rhamnose | - | builds acid from | 62345 |
68371 | L-sorbose | - | builds acid from | 17266 |
68371 | D-mannose | + | builds acid from | 16024 |
68371 | D-fructose | + | builds acid from | 15824 |
68371 | D-glucose | + | builds acid from | 17634 |
68371 | D-galactose | + | builds acid from | 12936 |
68371 | methyl beta-D-xylopyranoside | - | builds acid from | 74863 |
68371 | ribitol | - | builds acid from | 15963 |
68371 | L-xylose | - | builds acid from | 65328 |
68371 | D-xylose | - | builds acid from | 65327 |
68371 | L-arabinose | - | builds acid from | 30849 |
68371 | D-arabinose | - | builds acid from | 17108 |
68371 | erythritol | - | builds acid from | 17113 |
68371 | glycerol | + | builds acid from | 17754 |
118792 | nitrate | + | reduction | 17632 |
118792 | nitrite | - | reduction | 16301 |
metabolite production
- @ref: 118792
- Chebi-ID: 35581
- metabolite: indole
- production: no
enzymes
@ref | value | activity | ec |
---|---|---|---|
118792 | 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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
118792 | - | + | + | - | - | - | - | - | - | - | + | + | - | - | - | - | - | - | - | - |
API 50CHac
@ref | GLY | ERY | DARA | LARA | RIB | DXYL | LXYL | ADO | MDX | GAL | GLU | FRU | MNE | SBE | RHA | DUL | INO | MAN | SOR | MDM | MDG | NAG | AMY | ARB | ESC | SAL | CEL | MAL | LAC | MEL | SAC | TRE | INU | MLZ | RAF | AMD | GLYG | XLT | GEN | TUR | LYX | TAG | DFUC | LFUC | DARL | LARL | GNT | 2KG | 5KG |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
118792 | + | - | - | - | +/- | - | - | - | - | + | + | + | + | - | - | - | - | - | - | - | - | +/- | - | - | - | - | - | + | + | - | + | - | - | +/- | - | - | - | - | - | +/- | - | - | - | - | - | - | - | - | +/- |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent | isolation date |
---|---|---|---|---|---|---|
5294 | soil with rotting plant material | Arizona, Holbrook | USA | USA | North America | |
67770 | Soil with decaying plant material | Holbrook, AZ | USA | USA | North America | |
118792 | Environment, Soil with rotting plant material | Holbrook, Arizona | United States of America | USA | North America | 2001 |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Environmental | #Terrestrial | #Soil |
#Host | #Plants | #Decomposing plant |
taxonmaps
- @ref: 69479
- File name: preview.99_26602.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_400;96_13255;97_16110;98_19961;99_26602&stattab=map
- Last taxonomy: Byssovorax cruenta subclade
- 16S sequence: AJ833647
- Sequence Identity:
- Total samples: 20
- soil counts: 16
- aquatic counts: 3
- animal counts: 1
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
5294 | 1 | Risk group (German classification) |
118792 | 1 | Risk group (French classification) |
Sequence information
16S sequences
- @ref: 5294
- description: Byssophaga cruenta partial 16S rRNA gene, strain DSM 14553T
- accession: AJ833647
- length: 1529
- database: ena
- NCBI tax ID: 293647
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Byssovorax cruenta JCM 12614 | GCA_001312805 | contig | ncbi | 1300159 |
66792 | Byssovorax cruenta JCM 12614 | 1300159.4 | wgs | patric | 1300159 |
66792 | Byssovorax cruenta JCM 12614 | 2734481916 | draft | img | 1300159 |
GC content
- @ref: 67770
- GC-content: 69.9
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 52 | no |
motile | no | 84.722 | no |
gram-positive | no | 86.903 | no |
anaerobic | no | 98.007 | no |
halophile | no | 90.766 | no |
spore-forming | no | 82.772 | no |
thermophile | no | 97.957 | yes |
glucose-util | yes | 91.275 | no |
flagellated | no | 97.585 | no |
aerobic | yes | 92.009 | no |
glucose-ferment | no | 88.22 | no |
External links
@ref: 5294
culture collection no.: DSM 14553, JCM 12614, CIP 108850
straininfo link
- @ref: 81711
- straininfo: 133176
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 17012562 | Byssovorax cruenta gen. nov., sp. nov., nom. rev., a cellulose-degrading myxobacterium: rediscovery of 'Myxococcus cruentus' Thaxter 1897. | Reichenbach H, Lang E, Schumann P, Sproer C | Int J Syst Evol Microbiol | 10.1099/ijs.0.63628-0 | 2006 | Base Composition, Cellulose/metabolism, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Molecular Sequence Data, Myxococcales/*classification/genetics/growth & development/ultrastructure, Myxococcus/*classification, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species Specificity | Genetics |
Phylogeny | 25048208 | Vulgatibacter incomptus gen. nov., sp. nov. and Labilithrix luteola gen. nov., sp. nov., two myxobacteria isolated from soil in Yakushima Island, and the description of Vulgatibacteraceae fam. nov., Labilitrichaceae fam. nov. and Anaeromyxobacteraceae fam. nov. | Yamamoto E, Muramatsu H, Nagai K | Int J Syst Evol Microbiol | 10.1099/ijs.0.063198-0 | 2014 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Forests, Islands, Japan, Molecular Sequence Data, Myxococcales/*classification/genetics/isolation & purification, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistry | Genetics |
Phylogeny | 27046779 | Racemicystis crocea gen. nov., sp. nov., a soil myxobacterium in the family Polyangiaceae. | Awal RP, Garcia R, Muller R | Int J Syst Evol Microbiol | 10.1099/ijsem.0.001045 | 2016 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Myxococcales/*classification/genetics/isolation & purification, Philippines, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology | Transcriptome |
Reference
@id | authors | catalogue | doi/url | title |
---|---|---|---|---|
5294 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 14553) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-14553 | |
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 | |
38337 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/6525 | ||
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||
68371 | Automatically annotated from API 50CH acid | |||
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 | |
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |
81711 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID133176.1 | StrainInfo: A central database for resolving microbial strain identifiers | |
118792 | Curators of the CIP | Collection of Institut Pasteur (CIP 108850) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108850 |