Strain identifier

BacDive ID: 17502

Type strain: Yes

Species: Pseudoxanthomonas broegbernensis

Strain Designation: B 1616/1, B1616/1

Strain history: CIP <- 2001, A. Lipski, Osnabrück Univ., Osnabrück, Germany: strain B1616/1 -> B. Bendinger

NCBI tax ID(s): 83619 (species)

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General

@ref: 4678

BacDive-ID: 17502

DSM-Number: 12573

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, motile

description: Pseudoxanthomonas broegbernensis B 1616/1 is an aerobe, mesophilic, motile bacterium that was isolated from experimental biofilter.

NCBI tax id

  • NCBI tax id: 83619
  • Matching level: species

strain history

@refhistory
4678<- A. Lipski; B 1616/1
117048CIP <- 2001, A. Lipski, Osnabrück Univ., Osnabrück, Germany: strain B1616/1 -> B. Bendinger

doi: 10.13145/bacdive17502.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Lysobacterales
  • family: Lysobacteraceae
  • genus: Pseudoxanthomonas
  • species: Pseudoxanthomonas broegbernensis
  • full scientific name: Pseudoxanthomonas broegbernensis Finkmann et al. 2000

@ref: 4678

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Xanthomonadales

family: Lysobacteraceae

genus: Pseudoxanthomonas

species: Pseudoxanthomonas broegbernensis

full scientific name: Pseudoxanthomonas broegbernensis Finkmann et al. 2000 emend. Thierry et al. 2004

strain designation: B 1616/1, B1616/1

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes90.537
6948099.992negative
117048yesnegativerod-shaped

pigmentation

  • @ref: 117048
  • production: no
  • name: Pyocyanin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
4678REACTIVATION WITH LIQUID MEDIUM 1 (DSMZ Medium 1a)yeshttps://mediadive.dsmz.de/medium/1aName: REACTIVATION WITH LIQUID MEDIUM 1 (DSMZ Medium 1a) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
33706MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
117048CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
4678positivegrowth30mesophilic
33706positivegrowth30mesophilic
57386positivegrowth30-37mesophilic
117048positivegrowth25-37mesophilic
117048nogrowth10psychrophilic
117048nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
57386aerobe
117048obligate aerobe

spore formation

@refspore formationconfidence
69481no98
69480no99.989

halophily

  • @ref: 117048
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
11704816947citrate-carbon source
1170484853esculin+hydrolysis
11704817632nitrate-reduction
11704816301nitrite+reduction
11704817632nitrate-respiration

antibiotic resistance

  • @ref: 117048
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 117048
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
117048oxidase+
117048beta-galactosidase+3.2.1.23
117048alcohol dehydrogenase-1.1.1.1
117048gelatinase-
117048amylase-
117048DNase-
117048caseinase-3.4.21.50
117048catalase+1.11.1.6
117048tween esterase-
117048lecithinase-
117048lipase-
117048lysine decarboxylase-4.1.1.18
117048ornithine decarboxylase-4.1.1.17
117048protease-
117048tryptophan deaminase-
117048urease-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
117048-+++-++-+-++-+-++---

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
117048+++++-++++++++-++++-+++-----------++---+-+-----------+-----+--------------------------+----++++-+--

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
4678experimental biofilterBrögbern/LingenGermanyDEUEurope
57386Biofilter,experimentalBrögbern/LingenGermanyDEUEurope
117048Experimental biofilterBrögbern, LingenGermanyDEUEurope

isolation source categories

  • Cat1: #Engineered
  • Cat2: #Bioremediation
  • Cat3: #Biofilter

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
46781Risk group (German classification)
1170481Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Pseudoxanthomonas broegbernensis 16S rRNA gene, strain B1616/1AJ0122311522ena83619
20218Pseudoxanthomonas broegbernensis gene for 16S rRNA, partial sequence, strain: NBRC 101013AB6813291470ena83619

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pseudoxanthomonas broegbernensis DSM 12573GCA_014202435scaffoldncbi83619
66792Pseudoxanthomonas broegbernensis DSM 12573GCA_010093165contigncbi83619
66792Pseudoxanthomonas broegbernensis strain DSM 1257383619.3wgspatric83619
66792Pseudoxanthomonas broegbernensis strain DSM 1257383619.4wgspatric83619
66792Pseudoxanthomonas broegbernensis DSM 125732861528275draftimg83619

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno98no
flagellatedno80.747no
gram-positiveno98.735no
anaerobicno98.969no
aerobicyes91.651yes
halophileno94.689no
spore-formingno95.313no
glucose-utilyes92.017no
thermophileno95.736no
motileyes88.662no
glucose-fermentno87.235no

External links

@ref: 4678

culture collection no.: DSM 12573, ATCC BAA 10, CCUG 46890, CIP 107227, CCM 7337, NBRC 101013

straininfo link

  • @ref: 86499
  • straininfo: 44251

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny10826814Characterization of N2O-producing Xanthomonas-like isolates from biofilters as Stenotrophomonas nitritireducens sp. nov., Luteimonas mephitis gen. nov., sp. nov. and Pseudoxanthomonas broegbernensis gen. nov., sp. nov.Finkmann W, Altendorf K, Stackebrandt E, Lipski AInt J Syst Evol Microbiol10.1099/00207713-50-1-2732000DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/analysis, Filtration/*instrumentation, Gammaproteobacteria/*classification/physiology, Gases, Industrial Waste, Molecular Sequence Data, Nitrites/metabolism, Nitrous Oxide/*metabolism, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Stenotrophomonas/*classification/physiology, Xanthomonas/chemistry/*classification/genetics/physiologyGenetics
Phylogeny15545466Pseudoxanthomonas mexicana sp. nov. and Pseudoxanthomonas japonensis sp. nov., isolated from diverse environments, and emended descriptions of the genus Pseudoxanthomonas Finkmann et al. 2000 and of its type species.Thierry S, Macarie H, Iizuka T, Geissdorfer W, Assih EA, Spanevello M, Verhe F, Thomas P, Fudou R, Monroy O, Labat M, Ouattara ASInt J Syst Evol Microbiol10.1099/ijs.0.02810-02004Aerobiosis, Anti-Bacterial Agents/pharmacology, Bacterial Typing Techniques, Base Composition, Bioreactors/*microbiology, Carbohydrate Metabolism, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, Fatty Acids/analysis/isolation & purification, Flagella, Genes, rRNA, Gentian Violet, Humans, Molecular Sequence Data, Movement, Nitrites/metabolism, Nucleic Acid Hybridization, Oxygen/metabolism, Phenazines, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Spores, Bacterial/cytology, Stenotrophomonas/genetics, Ubiquinone/analysis/isolation & purification, Urine/*microbiology, Xanthomonadaceae/*classification/cytology/*isolation & purification/physiology, Xanthomonas/geneticsEnzymology
Phylogeny15774663Pseudoxanthomonas koreensis sp. nov. and Pseudoxanthomonas daejeonensis sp. nov.Yang DC, Im WT, Kim MK, Lee STInt J Syst Evol Microbiol10.1099/ijs.0.63210-02005Bacterial Typing Techniques, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, Korea, Molecular Sequence Data, Panax/growth & development, Phenotype, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Species Specificity, Xanthomonadaceae/chemistry/*classification/genetics/isolation & purificationGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
4678Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 12573)https://www.dsmz.de/collection/catalogue/details/culture/DSM-12573
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
33706Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/4640
57386Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 46890)https://www.ccug.se/strain?id=46890
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)
68382Automatically annotated from API zym
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
86499Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID44251.1StrainInfo: A central database for resolving microbial strain identifiers
117048Curators of the CIPCollection of Institut Pasteur (CIP 107227)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107227