Strain identifier

BacDive ID: 11356

Type strain: Yes

Species: Herbaspirillum rubrisubalbicans

Strain Designation: B579

Variant: Isotype of BacDive ID 11357

Strain history: CIP <- 1996, LMG <- 1981, NCPPB <- 1961, A. Hayward: strain B579

NCBI tax ID(s): 1223495 (strain), 80842 (species)

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General

@ref: 3573

BacDive-ID: 11356

DSM-Number: 9440

keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, mesophilic, motile, plant pathogen

description: Herbaspirillum rubrisubalbicans B579 is an obligate aerobe, mesophilic, motile plant pathogen that was isolated from Saccharum officinarum.

NCBI tax id

NCBI tax idMatching level
1223495strain
80842species

strain history

@refhistory
3573<- LMG
67770IAM 14976 <-- DSM 11543 <-- ATCC 19308 <-- NCPPB 1027 <-- A. C. Hayward 5A.
122291CIP <- 1996, LMG <- 1981, NCPPB <- 1961, A. Hayward: strain B579

doi: 10.13145/bacdive11356.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Burkholderiales
  • family: Oxalobacteraceae
  • genus: Herbaspirillum
  • species: Herbaspirillum rubrisubalbicans
  • full scientific name: Herbaspirillum rubrisubalbicans (Christopher and Edgerton 1930) Baldani et al. 1996

  • synonyms

    @refsynonym
    20215Phytomonas rubrisubalbicans
    20215Pseudomonas rubrisubalbicans

@ref: 3573

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Oxalobacteraceae

genus: Herbaspirillum

species: Herbaspirillum rubrisubalbicans

full scientific name: Herbaspirillum rubrisubalbicans (Christopher and Edgerton 1930) Baldani et al. 1996

strain designation: B579

variant: Isotype of BacDive ID 11357

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes96.599
6948099.991negative
122291yesnegativerod-shaped

pigmentation

  • @ref: 122291
  • production: no
  • name: Pyocyanin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
3573R2A 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
3573NUTRIENT AGAR (OXOID CM3) WITH PHOSPHATE (DSMZ Medium 605a)yeshttps://mediadive.dsmz.de/medium/605aName: NUTRIENT AGAR (OXOID CM3) WITH PHOSPHATE (DSMZ Medium 605a) Composition: Agar 15.0 g/l Peptone 5.0 g/l NaCl 5.0 g/l Na2HPO4 x 12 H2O 2.39 g/l Yeast extract 2.0 g/l Lab-Lemco beef extract 1.0 g/l KH2PO4 0.45 g/l Distilled water
41431MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
122291CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3
122291CIP Medium 212yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=212
122291CIP Medium 203yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=203
122291CIP Medium 9yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=9

culture temp

@refgrowthtypetemperaturerange
3573positivegrowth25mesophilic
41431positivegrowth30mesophilic
67770positivegrowth25mesophilic
122291positivegrowth25-41
122291nogrowth5psychrophilic
122291nogrowth10psychrophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 122291
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481no100
69480no100

halophily

@refsaltgrowthtested relationconcentration
122291NaClpositivegrowth0-2 %
122291NaClnogrowth4 %
122291NaClnogrowth6 %
122291NaClnogrowth8 %
122291NaClnogrowth10 %

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371gluconate-builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371turanose-builds acid from32528
68371gentiobiose-builds acid from28066
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose-builds acid from27082
68371sucrose-builds acid from17992
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371maltose-builds acid from17306
68371cellobiose-builds acid from17057
68371salicin-builds acid from17814
68371esculin-builds acid from4853
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
68371N-acetylglucosamine-builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol-builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371D-mannose-builds acid from16024
68371D-fructose-builds acid from15824
68371D-glucose-builds acid from17634
68371D-galactose-builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose-builds acid from65327
68371D-ribose-builds acid from16988
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754
122291citrate+carbon source16947
122291esculin-hydrolysis4853
122291nitrate+reduction17632
122291nitrite-reduction16301
122291phenol-degradation15882
122291nitrate-respiration17632

antibiotic resistance

  • @ref: 122291
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 122291
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
122291oxidase+
122291beta-galactosidase+3.2.1.23
122291alcohol dehydrogenase-1.1.1.1
122291gelatinase-
122291amylase-
122291DNase-
122291caseinase-3.4.21.50
122291catalase-1.11.1.6
122291tween esterase-
122291lecithinase-
122291lipase-
122291lysine decarboxylase-4.1.1.18
122291ornithine decarboxylase-4.1.1.17
122291protease-
122291tryptophan deaminase-
122291urease-3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)-
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase-
68382cystine arylamidase+3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase-3.2.1.20
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
122291-++--+-+--++--------

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
122291-------------------------------------------------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
122291+++-+-------++-----+++--+-+++--+-+--++-++--+---+++++++++++--+++++--+-----+-+++-++-+-+--+++++-++-++-

Isolation, sampling and environmental information

isolation

@refsample typehost speciescountryorigin.countrycontinent
3573Saccharum officinarumSaccharum officinarumUSAUSANorth America
67770Saccharum officinalisSaccharum officinalisUSAUSANorth America
122291Saccharum officinarumUnited States of AmericaUSANorth America

isolation source categories

  • Cat1: #Host
  • Cat2: #Plants
  • Cat3: #Herbaceous plants (Grass,Crops)

taxonmaps

  • @ref: 69479
  • File name: preview.99_632.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_12;96_128;97_137;98_154;99_632&stattab=map
  • Last taxonomy: Herbaspirillum
  • 16S sequence: AF137508
  • Sequence Identity:
  • Total samples: 5208
  • soil counts: 646
  • aquatic counts: 1120
  • animal counts: 1886
  • plant counts: 1556

Safety information

risk assessment

@refpathogenicity plantbiosafety levelbiosafety level comment
3573yes1Risk group (German classification)
1222911Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Herbaspirillum rubrisubalbicans gene for 16S rRNA, strain: ATCC 19308TAB0214241451ena80842
20218Herbaspirillum rubrisubalbicans gene for 16S rRNA, partial sequence, strain: NBRC 102523AB6818571458ena80842
3573Herbaspirillum rubrisubalbicans 16S ribosomal RNA gene, partial sequenceAF1375081485ena80842

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Herbaspirillum rubrisubalbicans DSM 11543GCA_003719195completencbi80842
66792Herbaspirillum rubrisubalbicans NBRC 1025231223495.3wgspatric1223495
66792Herbaspirillum rubrisubalbicans strain DSM 1154380842.11completepatric80842
66792Herbaspirillum rubrisubalbicans NBRC 1025232681812979draftimg1223495
67770Herbaspirillum rubrisubalbicans NBRC 102523GCA_001591225contigncbi1223495

GC content

  • @ref: 67770
  • GC-content: 62.5
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes89.455no
flagellatedyes54.296no
gram-positiveno99.129no
anaerobicno98.931no
aerobicyes83.024no
halophileno95.879no
spore-formingno93.607no
thermophileno99.129no
glucose-utilyes87.081no
glucose-fermentno89.513no

External links

@ref: 3573

culture collection no.: DSM 9440, ATCC 19308, DSM 11543, LMG 2286, NCPPB 1027, JCM 21447, BCRC 15833, CCUG 17392, CCUG 17679, CFBP 1202, CIP 105019, IAM 14976, ICMP 5777, KACC 12181, NBRC 102523, PDDCC 5777

straininfo link

  • @ref: 80588
  • straininfo: 4234

literature

  • topic: Phylogeny
  • Pubmed-ID: 8782693
  • title: Emended description of Herbaspirillum; inclusion of [Pseudomonas] rubrisubalbicans, a milk plant pathogen, as Herbaspirillum rubrisubalbicans comb. nov.; and classification of a group of clinical isolates (EF group 1) as Herbaspirillum species 3.
  • authors: Baldani JI, Pot B, Kirchhof G, Falsen E, Baldani VL, Olivares FL, Hoste B, Kersters K, Hartmann A, Gillis M, Dobereiner J
  • journal: Int J Syst Bacteriol
  • DOI: 10.1099/00207713-46-3-802
  • year: 1996
  • mesh: Base Sequence, DNA Probes, Edible Grain/*microbiology, Gram-Negative Aerobic Bacteria/*classification/isolation & purification, Molecular Sequence Data, Phylogeny, Pseudomonas/classification/isolation & purification
  • topic2: Enzymology

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
3573Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 9440)https://www.dsmz.de/collection/catalogue/details/culture/DSM-9440
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
41431Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16992
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68371Automatically annotated from API 50CH acid
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
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
80588Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID4234.1StrainInfo: A central database for resolving microbial strain identifiers
122291Curators of the CIPCollection of Institut Pasteur (CIP 105019)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105019