Strain identifier

BacDive ID: 1976

Type strain: Yes

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)

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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 idMatching level
412963species
882378strain

strain history

@refhistory
7825<- L. P. Partida-Martinez; HKI 454
122215CIP <- 2007, L.P. Partida-Martinez, Hans-Knoell Inst., Jena, Germany: strain HKI 454

doi: 10.13145/bacdive1976.20250331.9.3

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

    @refsynonym
    20215Burkholderia rhizoxina
    20215Paraburkholderia rhizoxinica
    20215Burkholderia 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

@refgram staincell lengthcell widthcell shapemotilityconfidence
31924negative1.6 µm0.9 µmovoid-shapedyes
122215negativerod-shapedno
125439negative97.3
125438negative98.375

colony morphology

  • @ref: 7825
  • incubation period: 3-7 days

pigmentation

  • @ref: 31924
  • production: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7825R2A MEDIUM (DSMZ Medium 830)yeshttps://mediadive.dsmz.de/medium/830Name: 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
37309MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
122215CIP Medium 328yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=328
122215CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72
7825BCYE alpha agar (DSMZ Medium 585a)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium585a.pdf
7825BCYE-AGAR (DSMZ Medium 585)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium585.pdf
7825NUTRIENT AGAR (DSMZ Medium 1)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium1.pdf

culture temp

@refgrowthtypetemperature
7825positivegrowth28
31924positivegrowth16-45
31924positiveoptimum30.5
37309positivegrowth30

culture pH

@refabilitytypepH
31924positivegrowth5.0-7.4
31924positiveoptimum6.25

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
31924aerobe
122215obligate aerobe
125439aerobe91.1

spore formation

  • @ref: 125439
  • spore formation: no
  • confidence: 96.9

compound production

  • @ref: 7825
  • compound: rhizoxin

halophily

@refsaltgrowthtested relationconcentration
31924NaClpositivegrowth0-3 %
31924NaClpositiveoptimum1 %

observation

  • @ref: 31924
  • observation: aggregates in clumps

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3192417754glycerol+carbon source
3192437684mannose+carbon source
12221517632nitrate-reduction
12221516301nitrite-reduction
6836925115malate+assimilation
6836927689decanoate-assimilation
6836917306maltose-assimilation
6836959640N-acetylglucosamine-assimilation
6836916899D-mannitol-assimilation
6836916024D-mannose-assimilation
6836930849L-arabinose-assimilation
6836917634D-glucose-assimilation
683695291gelatin-hydrolysis
683694853esculin-hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate-reduction

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
12221535581indoleno

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
7825catalase+1.11.1.6
7825cytochrome-c oxidase+1.9.3.1
31924catalase+1.11.1.6
31924cytochrome oxidase+1.9.3.1
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase+3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-glucosidase-3.2.1.20
68382beta-glucosidase-3.2.1.21
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-galactosidase-3.2.1.22
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382valine arylamidase+
68382cystine arylamidase-3.4.11.3
68382leucine arylamidase+3.4.11.1
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382esterase (C 4)+
68382alkaline phosphatase-3.1.3.1
122215oxidase+
122215catalase-1.11.1.6
122215urease-3.5.1.5
68369cytochrome oxidase+1.9.3.1
68369gelatinase-
68369beta-glucosidase-3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
122215--++-++---++------+-

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
7825--------------+-++--+
7825-----------------+--
7825-----------------+--

Isolation, sampling and environmental information

isolation

@refsample typehost speciescountryorigin.countrycontinentisolation date
7825fungus Rhizopus microsporus van Tieghem var. chinensis (ATCC 62417)Rhizopus microsporus van Tieghem var. chinensisGermanyDEUEurope
122215Other, Fungus, Rhizopus microsporusJapanJPNAsia2004

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

@refbiosafety levelbiosafety level comment
78251Risk group (German classification)
1222151Risk group (French classification)

Sequence information

16S sequences

  • @ref: 7825
  • description: Burkholderia rhizoxinica 16S rRNA gene, type strain HKI 454T
  • accession: AJ938142
  • length: 1525
  • database: nuccore
  • NCBI tax ID: 882378

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Mycetohabitans rhizoxinica HKI 454GCA_000198775completencbi882378
66792Burkholderia rhizoxinica HKI 454882378.3completepatric882378
66792Paraburkholderia rhizoxinica HKI 454882378.20plasmidpatric882378
66792Paraburkholderia rhizoxinica HKI 454882378.19plasmidpatric882378
66792Mycetohabitans rhizoxinica HKI 454650716014completeimg882378

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingno98.375yes
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no94.697yes
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes77.98no
125438spore-formingspore-formingAbility to form endo- or exosporesno89.659no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno91.771yes
125438motile2+flagellatedAbility to perform flagellated movementno51.826no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno96.9
125439BacteriaNetmotilityAbility to perform movementyes73.7
125439BacteriaNetgram_stainReaction to gram-stainingnegative97.3
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthaerobe91.1

External links

@ref: 7825

culture collection no.: DSM 19002, CIP 109453, HKI 454

straininfo link

  • @ref: 71621
  • straininfo: 319367

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17978222Burkholderia 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 CInt J Syst Evol Microbiol10.1099/ijs.0.64660-02007Bacterial 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, *SymbiosisGenetics
Genetics29540638Comparative 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 HMicrobes Environ10.1264/jsme2.ME171382018Burkholderia/*genetics/physiology, Burkholderiaceae/*genetics/physiology, Comparative Genomic Hybridization, Fungi/*physiology, Genome, Bacterial, Metagenome, Phylogeny, Sequence Analysis, DNA, *SymbiosisPhylogeny

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
7825Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19002)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19002
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
31924Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2818128776041
37309Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7198
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
68369Automatically annotated from API 20NE
68382Automatically annotated from API zym
69479João 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
71621Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID319367.1StrainInfo: A central database for resolving microbial strain identifiers
122215Curators of the CIPCollection of Institut Pasteur (CIP 109453)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109453
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1