Strain identifier

BacDive ID: 11366

Type strain: Yes

Species: Herbaspirillum chlorophenolicum

Strain Designation: CPW301

Strain history: CIP <- 2004, KCTC <- S.T. Lee, KAIST, Korea: strain CPW301

NCBI tax ID(s): 1349766 (strain), 211589 (species)

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General

@ref: 7191

BacDive-ID: 11366

DSM-Number: 17796

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, motile, rod-shaped

description: Herbaspirillum chlorophenolicum CPW301 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from soil sediment collected at a stream near an industrial region.

NCBI tax id

NCBI tax idMatching level
211589species
1349766strain

strain history

@refhistory
7191<- S.-T. Lee, KAIST; CPW301 <- H.-S. Bae, Dept. of Biol. Sci., LSU, LA, USA
67770IAM 15024 <-- W.-T. Im CPW301.
67771<- ST Lee, KAIST
67772Lee S.-T., Korea Advanced Institute of Science and Technology; CPW301 < Bae H.-S., Deptartment of Biological Sciences., LSU, LA, USA
118240CIP <- 2004, KCTC <- S.T. Lee, KAIST, Korea: strain CPW301

doi: 10.13145/bacdive11366.20230509.8.1

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 chlorophenolicum
  • full scientific name: Herbaspirillum chlorophenolicum Im et al. 2004

@ref: 7191

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Oxalobacteraceae

genus: Herbaspirillum

species: Herbaspirillum chlorophenolicum

full scientific name: Herbaspirillum chlorophenolicum Im et al. 2004

strain designation: CPW301

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
30000negative2.3 µm0.7 µmrod-shapedyes
67771negative
69480yes94.035
69480negative99.996
118240negativerod-shapedyes

pigmentation

  • @ref: 118240
  • production: no
  • name: Pyocyanin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7191NUTRIENT AGAR (DSMZ Medium 1)yeshttps://mediadive.dsmz.de/medium/1Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
33241MEDIUM 328- for nutrient agaryesDistilled water make up to (1000.000 ml);Agar (15.000 g);Peptone (5.000g);Beef extract (3.000 g)
118240CIP Medium 328yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=328

culture temp

@refgrowthtypetemperaturerange
7191positivegrowth28mesophilic
30000positiveoptimum30mesophilic
33241positivegrowth30mesophilic
59716positivegrowth30mesophilic
67770positivegrowth30mesophilic
67771positivegrowth30mesophilic
67772positiveoptimum28mesophilic
118240positivegrowth5-30
118240nogrowth37mesophilic
118240nogrowth41thermophilic

culture pH

@refabilitytypepH
30000positivegrowth06-08
30000positiveoptimum6.5
67772positivemaximum8.0
67772positiveminimum6.0

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
30000aerobe
59716aerobe
67771aerobe
118240obligate aerobe

spore formation

@refspore formationconfidence
69481no100
69480no100

halophily

@refsaltgrowthtested relationconcentration
118240NaClpositivegrowth0-4 %
118240NaClnogrowth6 %
118240NaClnogrowth8 %
118240NaClnogrowth10 %

observation

@refobservation
67770quinones: Q-8
67771quinones: Q-8

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
30000506227N-acetylglucosamine+carbon source
3000016199urea+carbon source
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837132528turanose-builds acid from
6837128066gentiobiose-builds acid from
6837117151xylitol-builds acid from
6837128087glycogen-builds acid from
6837128017starch-builds acid from
6837116634raffinose-builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837127082trehalose-builds acid from
6837117992sucrose-builds acid from
6837128053melibiose-builds acid from
6837117716lactose-builds acid from
6837117306maltose-builds acid from
6837117057cellobiose-builds acid from
6837117814salicin-builds acid from
683714853esculin-builds acid from
6837118305arbutin-builds acid from
6837127613amygdalin-builds acid from
6837159640N-acetylglucosamine-builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol-builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose-builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose-builds acid from
6837115824D-fructose-builds acid from
6837117634D-glucose-builds acid from
6837112936D-galactose-builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose-builds acid from
6837116988D-ribose-builds acid from
6837130849L-arabinose-builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol-builds acid from
6836925115malate+assimilation
6836917128adipate-assimilation
6836927689decanoate+assimilation
6836924265gluconate+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
11824016947citrate+carbon source
1182404853esculin-hydrolysis
11824017632nitrate-reduction
11824016301nitrite-reduction
11824017632nitrate-respiration

antibiotic resistance

  • @ref: 118240
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
11824035581indoleno

metabolite tests

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

enzymes

@refvalueactivityec
30000catalase+1.11.1.6
30000cytochrome oxidase+1.9.3.1
30000urease+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
118240oxidase-
118240beta-galactosidase-3.2.1.23
118240alcohol dehydrogenase-1.1.1.1
118240gelatinase-
118240amylase-
118240DNase-
118240caseinase-3.4.21.50
118240catalase+1.11.1.6
118240tween esterase+
118240lecithinase-
118240lipase-
118240lysine decarboxylase-4.1.1.18
118240ornithine decarboxylase-4.1.1.17
118240protease-
118240tryptophan deaminase-
118240urease-3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
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
59716-++--+----+---------
118240-+++-++---++--------

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
59716--------++-++-++-++++

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
118240-------------------------------------------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling datelatitudelongitude
7191soil sediment collected at a stream near an industrial regionCheongjuRepublic of KoreaKORAsia
59716Soil sedimentindustrial region of CheongjuRepublic of KoreaKORAsia
67770Industrial stream near Chungju industry complexRepublic of KoreaKORAsia
67771From soilRepublic of KoreaKORAsia
67772Soil sediment collected from a stream near an industrial regionNorth Chungcheong Province, CheongjuRepublic of KoreaKORAsia199736.6333127.483
118240Environment, SoilCheongju, ChungbukRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Industrial
#Environmental#Aquatic
#Environmental#Terrestrial#Sediment
#Environmental#Terrestrial#Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_176.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_12;96_128;97_137;98_154;99_176&stattab=map
  • Last taxonomy: Herbaspirillum
  • 16S sequence: AB681859
  • Sequence Identity:
  • Total samples: 850
  • soil counts: 183
  • aquatic counts: 163
  • animal counts: 75
  • plant counts: 429

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
71911Risk group (German classification)
677721
1182401Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Herbaspirillum chlorophenolicum gene for 16S rRNA, partial sequence, strain: NBRC 102525AB6818591458ena211589
7191Herbaspirillum chlorophenolicum gene for 16S rRNA, partial sequenceAB0944011474ena211589

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Herbaspirillum chlorophenolicum NBRC 1025251349766.3wgspatric1349766
66792Herbaspirillum chlorophenolicum NBRC 1025252731957620draftimg1349766
66792Herbaspirillum chlorophenolicum CPW3012645727693draftimg211589
67770Herbaspirillum chlorophenolicum NBRC 102525GCA_001571165contigncbi1349766
67770Herbaspirillum chlorophenolicum CPW301GCA_001189955contigncbi211589

GC content

@refGC-contentmethod
719161.3high performance liquid chromatography (HPLC)
3000061.3
6777160.0

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes90.477yes
gram-positiveno98.845no
anaerobicno99.353yes
halophileno94.441no
spore-formingno94.971no
glucose-utilyes83.02yes
flagellatedno50no
thermophileno98.984no
aerobicyes87.209yes
glucose-fermentno89.402yes

External links

@ref: 7191

culture collection no.: DSM 17796, IAM 15024, JCM 21487, KCTC 12096, NBRC 102525, CCUG 52898, CIP 108432, UCCCB8

straininfo link

  • @ref: 80597
  • straininfo: 107096

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15143035Herbaspirillum chlorophenolicum sp. nov., a 4-chlorophenol-degrading bacterium.Im WT, Bae HS, Yokota A, Lee STInt J Syst Evol Microbiol10.1099/ijs.0.02812-02004Base Composition, Base Sequence, Biodegradation, Environmental, Chlorophenols/*metabolism, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/genetics, Fatty Acids/analysis, Herbaspirillum/*classification/genetics/*metabolism, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/geneticsMetabolism
Phylogeny29485397Herbaspirillum robiniae sp. nov., isolated from root nodules of Robinia pseudoacacia in a lead-zinc mine.Fan MC, Guo YQ, Zhang LP, Zhu YM, Chen WM, Lin YB, Wei GHInt J Syst Evol Microbiol10.1099/ijsem.0.0026662018Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Herbaspirillum/*cytology/genetics/isolation & purification, Lead, Mining, *Phylogeny, RNA, Ribosomal, 16S/genetics, Robinia/*microbiology, Root Nodules, Plant/*microbiology, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/chemistry, ZincTranscriptome
Phylogeny30303473Herbaspirillum piri sp. nov., isolated from bark of a pear tree.Xu G, Chang J, Xue H, Guo M, Piao CG, Li YInt J Syst Evol Microbiol10.1099/ijsem.0.0030502018Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Herbaspirillum/*classification/genetics/isolation & purification, Phospholipids/chemistry, *Phylogeny, Plant Bark/*microbiology, Pyrus/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Ubiquinone/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
7191Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17796)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17796
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
30000Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604126365
33241Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6054
59716Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 52898)https://www.ccug.se/strain?id=52898
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/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
67772Curators of the UCCCBhttps://ucccb.uc.pt/
68369Automatically annotated from API 20NE
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
80597Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID107096.1StrainInfo: A central database for resolving microbial strain identifiers
118240Curators of the CIPCollection of Institut Pasteur (CIP 108432)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108432