Strain identifier

BacDive ID: 2348

Type strain: Yes

Species: Phenylobacterium composti

Strain Designation: 4T-6

Strain history: CIP <- 2010, KACC <- Rural Deveropiment Administration, H.-Y. Weon: strain 4T-6

NCBI tax ID(s): 1122958 (strain), 457173 (species)

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General

@ref: 8099

BacDive-ID: 2348

DSM-Number: 19425

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

description: Phenylobacterium composti 4T-6 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from cotton waste compost.

NCBI tax id

NCBI tax idMatching level
457173species
1122958strain

strain history

@refhistory
360782010, KACC
8099<- S.-W. Kwon, National Institute of Agricultural Biotechnology; 4T-6
118718CIP <- 2010, KACC <- Rural Deveropiment Administration, H.-Y. Weon: strain 4T-6

doi: 10.13145/bacdive2348.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Caulobacterales
  • family: Caulobacteraceae
  • genus: Phenylobacterium
  • species: Phenylobacterium composti
  • full scientific name: Phenylobacterium composti Weon et al. 2008

@ref: 8099

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Caulobacteraceae

genus: Phenylobacterium

species: Phenylobacterium composti

full scientific name: Phenylobacterium composti Weon et al. 2008

strain designation: 4T-6

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
32464negative0.8-1.8 µm0.5 µmrod-shapedyes
118718negativerod-shapedyes

pigmentation

  • @ref: 32464
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8099R2A 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
36078MEDIUM 566- Reasoner's 2A agar for Flavobacterium micromatiyesDistilled water make up to (1000.000 ml);R2A agar (18.200 g)
118718CIP Medium 566yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=566

culture temp

@refgrowthtypetemperaturerange
8099positivegrowth28mesophilic
32464positivegrowth15-45
32464positiveoptimum30mesophilic
36078positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
32464positivegrowth06-09alkaliphile
32464positiveoptimum07-08

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
32464aerobe
118718obligate aerobe

spore formation

  • @ref: 32464
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
32464NaClpositivegrowth0-2 %
32464NaClpositiveoptimum0-1 %

observation

  • @ref: 32464
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
32464370543-hydroxybutyrate+carbon source
3246417128adipate+carbon source
3246428087glycogen+carbon source
3246424996lactate+carbon source
3246428044phenylalanine+carbon source
3246426271proline+carbon source
324649300suberic acid+carbon source
3246431011valerate+carbon source
11871817632nitrate-reduction
11871816301nitrite-reduction

metabolite production

  • @ref: 118718
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
32464catalase+1.11.1.6
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin+3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase+
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase+3.1.3.1
118718oxidase-
118718catalase+1.11.1.6
118718urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
118718-+++-++-+-++---+-+--

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
8099cotton waste compostSuwonRepublic of KoreaKORAsia
118718Environment, Cotton waste compostSuwonRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Agriculture
#Engineered#Biodegradation#Composting
#Engineered#Waste#Solid plant waste
#Host#Plants#Shrub (Scrub)

taxonmaps

  • @ref: 69479
  • File name: preview.99_1635.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_73;96_931;97_1083;98_1292;99_1635&stattab=map
  • Last taxonomy: Phenylobacterium
  • 16S sequence: EU022524
  • Sequence Identity:
  • Total samples: 1721
  • soil counts: 809
  • aquatic counts: 300
  • animal counts: 569
  • plant counts: 43

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
80991Risk group (German classification)
1187181Risk group (French classification)

Sequence information

16S sequences

  • @ref: 8099
  • description: Phenylobacterium composti strain 4T-6 16S ribosomal RNA gene, partial sequence
  • accession: EU022524
  • length: 1396
  • database: ena
  • NCBI tax ID: 1122958

Genome sequences

  • @ref: 66792
  • description: Phenylobacterium composti DSM 19425
  • accession: 2571042909
  • assembly level: draft
  • database: img
  • NCBI tax ID: 1122958

GC content

  • @ref: 32464
  • GC-content: 67.5

External links

@ref: 8099

culture collection no.: DSM 19425, KACC 12597, CIP 110190, NBRC 106419

straininfo link

  • @ref: 71903
  • straininfo: 359527

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny18842845Phenylobacterium composti sp. nov., isolated from cotton waste compost in Korea.Weon HY, Kim BY, Kwon SW, Go SJ, Koo BS, Stackebrandt EInt J Syst Evol Microbiol10.1099/ijs.0.65530-02008Bacterial Typing Techniques, Base Composition, Caulobacteraceae/chemistry/*classification/*genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genes, Bacterial, Genes, rRNA, Gossypium/*microbiology, Korea, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil MicrobiologyGenetics
Phylogeny29536278Phenylobacterium terrae sp. nov., isolated from a soil sample of Khyber-Pakhtun-Khwa, Pakistan.Khan IU, Habib N, Xiao M, Huang X, Khan NU, Im WT, Ahmed I, Zhi XY, Li WJAntonie Van Leeuwenhoek10.1007/s10482-018-1064-22018Alphaproteobacteria/chemistry/*classification/genetics/*isolation & purification, Bacterial Typing Techniques, Molecular Typing, Pakistan, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil MicrobiologyPhenotype

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
8099Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19425)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19425
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
32464Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2868528776041
36078Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/8022
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
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
71903Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID359527.1StrainInfo: A central database for resolving microbial strain identifiers
118718Curators of the CIPCollection of Institut Pasteur (CIP 110190)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110190