Strain identifier
BacDive ID: 1976
Type strain:
Species: Mycetohabitans rhizoxinica
Strain history: CIP <- 2007, L.P. Partida-Martinez, Hans-Knoell Inst., Jena, Germany: strain HKI 454
NCBI tax ID(s): 882378 (strain), 412963 (species)
General
@ref: 7825
BacDive-ID: 1976
DSM-Number: 19002
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, motile, ovoid-shaped
description: Mycetohabitans rhizoxinica DSM 19002 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from fungus Rhizopus microsporus van Tieghem var. chinensis .
NCBI tax id
NCBI tax id | Matching level |
---|---|
882378 | strain |
412963 | species |
strain history
@ref | history |
---|---|
7825 | <- L. P. Partida-Martinez; HKI 454 |
122215 | CIP <- 2007, L.P. Partida-Martinez, Hans-Knoell Inst., Jena, Germany: strain HKI 454 |
doi: 10.13145/bacdive1976.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Betaproteobacteria
- order: Burkholderiales
- family: Burkholderiaceae
- genus: Mycetohabitans
- species: Mycetohabitans rhizoxinica
- full scientific name: Mycetohabitans rhizoxinica (Partida-Martinez et al. 2007) Estrada-de Los Santos et al. 2018
synonyms
@ref synonym 20215 Burkholderia rhizoxinica 20215 Burkholderia rhizoxina 20215 Paraburkholderia rhizoxinica
@ref: 7825
domain: Bacteria
phylum: Proteobacteria
class: Betaproteobacteria
order: Burkholderiales
family: Burkholderiaceae
genus: Mycetohabitans
species: Mycetohabitans rhizoxinica
full scientific name: Mycetohabitans rhizoxinica (Partida-Martinez et al. 2007) Estrada-de Los Santos et al. 2018
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
31924 | negative | 1.6 µm | 0.9 µm | ovoid-shaped | yes | |
69480 | negative | 99.88 | ||||
122215 | negative | rod-shaped | no |
colony morphology
- @ref: 7825
- incubation period: 3-7 days
pigmentation
- @ref: 31924
- production: no
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
7825 | R2A MEDIUM (DSMZ Medium 830) | yes | https://mediadive.dsmz.de/medium/830 | Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water |
37309 | MEDIUM 72- for trypto casein soja agar | yes | Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g) | |
122215 | CIP Medium 328 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=328 | |
122215 | CIP Medium 72 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
7825 | positive | growth | 28 | mesophilic |
31924 | positive | growth | 16-45 | |
31924 | positive | optimum | 30.5 | mesophilic |
37309 | positive | growth | 30 | mesophilic |
culture pH
@ref | ability | type | pH |
---|---|---|---|
31924 | positive | growth | 5.0-7.4 |
31924 | positive | optimum | 6.25 |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
31924 | aerobe |
122215 | obligate aerobe |
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.993 |
compound production
- @ref: 7825
- compound: rhizoxin
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
31924 | NaCl | positive | growth | 0-3 % |
31924 | NaCl | positive | optimum | 1 % |
observation
- @ref: 31924
- observation: aggregates in clumps
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
31924 | 17754 | glycerol | + | carbon source |
31924 | 37684 | mannose | + | carbon source |
68369 | 25115 | malate | + | assimilation |
68369 | 27689 | decanoate | - | assimilation |
68369 | 17306 | maltose | - | assimilation |
68369 | 59640 | N-acetylglucosamine | - | assimilation |
68369 | 16899 | D-mannitol | - | assimilation |
68369 | 16024 | D-mannose | - | assimilation |
68369 | 30849 | L-arabinose | - | assimilation |
68369 | 17634 | D-glucose | - | assimilation |
68369 | 5291 | gelatin | - | hydrolysis |
68369 | 4853 | esculin | - | hydrolysis |
68369 | 16199 | urea | - | hydrolysis |
68369 | 29016 | arginine | - | hydrolysis |
68369 | 17634 | D-glucose | - | fermentation |
68369 | 27897 | tryptophan | - | energy source |
68369 | 17632 | nitrate | - | reduction |
122215 | 17632 | nitrate | - | reduction |
122215 | 16301 | nitrite | - | reduction |
metabolite production
@ref | Chebi-ID | metabolite | production |
---|---|---|---|
68369 | 35581 | indole | no |
122215 | 35581 | indole | no |
metabolite tests
- @ref: 68369
- Chebi-ID: 35581
- metabolite: indole
- indole test: -
enzymes
@ref | value | activity | ec |
---|---|---|---|
7825 | catalase | + | 1.11.1.6 |
7825 | cytochrome-c oxidase | + | 1.9.3.1 |
31924 | catalase | + | 1.11.1.6 |
31924 | cytochrome oxidase | + | 1.9.3.1 |
68382 | alpha-fucosidase | - | 3.2.1.51 |
68382 | alpha-mannosidase | + | 3.2.1.24 |
68382 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68382 | beta-glucosidase | - | 3.2.1.21 |
68382 | alpha-glucosidase | - | 3.2.1.20 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | beta-galactosidase | - | 3.2.1.23 |
68382 | alpha-galactosidase | - | 3.2.1.22 |
68382 | naphthol-AS-BI-phosphohydrolase | + | |
68382 | acid phosphatase | + | 3.1.3.2 |
68382 | alpha-chymotrypsin | - | 3.4.21.1 |
68382 | trypsin | - | 3.4.21.4 |
68382 | cystine arylamidase | - | 3.4.11.3 |
68382 | valine arylamidase | + | |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | lipase (C 14) | - | |
68382 | esterase lipase (C 8) | + | |
68382 | esterase (C 4) | + | |
68382 | alkaline phosphatase | - | 3.1.3.1 |
68369 | cytochrome oxidase | + | 1.9.3.1 |
68369 | gelatinase | - | |
68369 | beta-glucosidase | - | 3.2.1.21 |
68369 | urease | - | 3.5.1.5 |
68369 | arginine dihydrolase | - | 3.5.3.6 |
122215 | oxidase | + | |
122215 | catalase | - | 1.11.1.6 |
122215 | urease | - | 3.5.1.5 |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
122215 | - | - | + | + | - | + | + | - | - | - | + | + | - | - | - | - | - | - | + | - |
API 20NE
@ref | NO3 | TRP | GLU_ Ferm | ADH Arg | URE | ESC | GEL | PNPG | GLU_ Assim | ARA | MNE | MAN | NAG | MAL | GNT | CAP | ADI | MLT | CIT | PAC | OX |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
7825 | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | - | + | + | - | - | + |
7825 | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | - | - | |
7825 | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | host species | country | origin.country | continent | isolation date |
---|---|---|---|---|---|---|
7825 | fungus Rhizopus microsporus van Tieghem var. chinensis (ATCC 62417) | Rhizopus microsporus van Tieghem var. chinensis | Germany | DEU | Europe | |
122215 | Other, Fungus, Rhizopus microsporus | Japan | JPN | Asia | 2004 |
isolation source categories
- Cat1: #Host
- Cat2: #Fungi
taxonmaps
- @ref: 69479
- File name: preview.99_2541.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_12;96_18;97_1623;98_1974;99_2541&stattab=map
- Last taxonomy: Burkholderia
- 16S sequence: AJ938142
- Sequence Identity:
- Total samples: 11924
- soil counts: 4868
- aquatic counts: 1257
- animal counts: 2903
- plant counts: 2896
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
7825 | 1 | Risk group (German classification) |
122215 | 1 | Risk group (French classification) |
Sequence information
16S sequences
- @ref: 7825
- description: Burkholderia rhizoxinica 16S rRNA gene, type strain HKI 454T
- accession: AJ938142
- length: 1525
- database: ena
- NCBI tax ID: 882378
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Mycetohabitans rhizoxinica HKI 454 | GCA_000198775 | complete | ncbi | 882378 |
66792 | Burkholderia rhizoxinica HKI 454 | 882378.3 | complete | patric | 882378 |
66792 | Paraburkholderia rhizoxinica HKI 454 | 882378.20 | plasmid | patric | 882378 |
66792 | Paraburkholderia rhizoxinica HKI 454 | 882378.19 | plasmid | patric | 882378 |
66792 | Mycetohabitans rhizoxinica HKI 454 | 650716014 | complete | img | 882378 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | no | 53.114 | yes |
flagellated | no | 96.288 | no |
gram-positive | no | 98.46 | yes |
anaerobic | no | 98.655 | yes |
aerobic | yes | 85.34 | yes |
halophile | no | 89.634 | yes |
spore-forming | no | 90.186 | no |
thermophile | no | 95.253 | no |
glucose-util | no | 64.39 | yes |
glucose-ferment | no | 90.516 | yes |
External links
@ref: 7825
culture collection no.: DSM 19002, CIP 109453, HKI 454
straininfo link
- @ref: 71621
- straininfo: 319367
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 17978222 | Burkholderia rhizoxinica sp. nov. and Burkholderia endofungorum sp. nov., bacterial endosymbionts of the plant-pathogenic fungus Rhizopus microsporus. | Partida-Martinez LP, Groth I, Schmitt I, Richter W, Roth M, Hertweck C | Int J Syst Evol Microbiol | 10.1099/ijs.0.64660-0 | 2007 | Bacterial Typing Techniques, Burkholderia/chemistry/*classification/genetics/*growth & development, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Freeze Fracturing, Genes, rRNA, Microscopy, Electron, Molecular Sequence Data, Nucleic Acid Hybridization, Oryza/microbiology, Phylogeny, Plant Diseases/*microbiology, RNA, Ribosomal, 16S/genetics, *Rhizopus/growth & development/pathogenicity/ultrastructure, Sequence Analysis, DNA, Species Specificity, *Symbiosis | Genetics |
Genetics | 29540638 | Comparative Genomic Insights into Endofungal Lifestyles of Two Bacterial Endosymbionts, Mycoavidus cysteinexigens and Burkholderia rhizoxinica. | Sharmin D, Guo Y, Nishizawa T, Ohshima S, Sato Y, Takashima Y, Narisawa K, Ohta H | Microbes Environ | 10.1264/jsme2.ME17138 | 2018 | Burkholderia/*genetics/physiology, Burkholderiaceae/*genetics/physiology, Comparative Genomic Hybridization, Fungi/*physiology, Genome, Bacterial, Metagenome, Phylogeny, Sequence Analysis, DNA, *Symbiosis | Phylogeny |
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
---|---|---|---|---|---|---|
7825 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19002) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-19002 | |||
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 | |||
31924 | 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 | 28181 | 28776041 | |
37309 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/7198 | ||||
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) | |||
68369 | Automatically annotated from API 20NE | |||||
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) | |||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |||
71621 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID319367.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
122215 | Curators of the CIP | Collection of Institut Pasteur (CIP 109453) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109453 |