Strain identifier

BacDive ID: 17147

Type strain: Yes

Species: Pectinatus brassicae

Strain Designation: TY

Strain history: W.-W. Zhang strain TY.

NCBI tax ID(s): 862415 (species)

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General

@ref: 17723

BacDive-ID: 17147

DSM-Number: 24661

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

description: Pectinatus brassicae TY is an anaerobe, Gram-negative, motile bacterium that was isolated from salty pickle wastewater.

NCBI tax id

  • NCBI tax id: 862415
  • Matching level: species

strain history

@refhistory
17723<- W.-W. Zhang, Zhejiang Univ., Hangzhou, China; TY
67770W.-W. Zhang strain TY.

doi: 10.13145/bacdive17147.20240916.9.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Negativicutes
  • order: Selenomonadales
  • family: Selenomonadaceae
  • genus: Pectinatus
  • species: Pectinatus brassicae
  • full scientific name: Pectinatus brassicae Zhang et al. 2012

@ref: 17723

domain: Bacteria

phylum: Firmicutes

class: Negativicutes

order: Selenomonadales

family: Selenomonadaceae

genus: Pectinatus

species: Pectinatus brassicae

full scientific name: Pectinatus brassicae Zhang et al. 2012

strain designation: TY

type strain: yes

Morphology

cell morphology

  • @ref: 30270
  • gram stain: negative
  • cell length: 24 µm
  • cell width: 0.75 µm
  • cell shape: rod-shaped
  • motility: yes

colony morphology

  • @ref: 17723
  • type of hemolysis: gamma
  • incubation period: 1-2 days

pigmentation

  • @ref: 30270
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 17723
  • name: BIFIDOBACTERIUM MEDIUM (DSMZ Medium 58)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/58
  • composition: Name: BIFIDOBACTERIUM MEDIUM (DSMZ Medium 58) Composition: Glucose 10.0 g/l Casein peptone 10.0 g/l Bacto Soytone 5.0 g/l Meat extract 5.0 g/l Yeast extract 5.0 g/l L-Cysteine HCl x H2O 0.5 g/l NaHCO3 0.4 g/l NaCl 0.08 g/l MnSO4 x H2O 0.05 g/l KH2PO4 0.04 g/l K2HPO4 0.04 g/l MgSO4 x 7 H2O 0.02 g/l CaCl2 x 2 H2O 0.01 g/l Tween 80 Resazurin Distilled water

culture temp

@refgrowthtypetemperature
17723positivegrowth30
30270positivegrowth10-40
30270positiveoptimum28
67770positivegrowth28

culture pH

@refabilitytypepHPH range
30270positivegrowth3.8-8.5alkaliphile
30270positiveoptimum6.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
17723anaerobe
30270anaerobe

spore formation

@refspore formationconfidence
30270no
69481no100

halophily

@refsaltgrowthtested relationconcentration
30270NaClpositivegrowth0-3 %
30270NaClpositiveoptimum1 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3027017754glycerol+carbon source
3027029864mannitol+carbon source
3027017992sucrose+carbon source
6836727082trehalose-builds acid from
6836762345L-rhamnose+builds acid from
6836730911sorbitol-builds acid from
6836716634raffinose-builds acid from
683676731melezitose-builds acid from
6836716024D-mannose+builds acid from
6836717057cellobiose+builds acid from
6836717754glycerol+builds acid from
683674853esculin-hydrolysis
683675291gelatin-hydrolysis
6836730849L-arabinose+builds acid from
6836765327D-xylose+builds acid from
6836717814salicin+builds acid from
6836717306maltose+builds acid from
6836717992sucrose+builds acid from
6836717716lactose+builds acid from
6836716899D-mannitol+builds acid from
6836717634D-glucose+builds acid from
6836716199urea-hydrolysis
6836727897tryptophan-energy source
6838016199urea-hydrolysis
6838029016arginine-hydrolysis
6838016024D-mannose+fermentation
6838016634raffinose-fermentation
6838029985L-glutamate-degradation
6838017632nitrate-reduction
6838027897tryptophan-energy source

metabolite production

@refChebi-IDmetaboliteproduction
3027016136hydrogen sulfideyes
6836735581indoleno
6838035581indoleno

metabolite tests

@refChebi-IDmetaboliteindole test
6838035581indole-
6836735581indole-

enzymes

@refvalueactivityec
17723catalase-1.11.1.6
17723cytochrome-c oxidase-1.9.3.1
30270acid phosphatase+3.1.3.2
68380serine arylamidase-
68380glutamyl-glutamate arylamidase-
68380histidine arylamidase-
68380glycin arylamidase-
68380alanine arylamidase-3.4.11.2
68380tyrosine arylamidase-
68380pyrrolidonyl arylamidase-3.4.19.3
68380leucine arylamidase-3.4.11.1
68380phenylalanine arylamidase-
68380leucyl glycin arylamidase-3.4.11.1
68380proline-arylamidase-3.4.11.5
68380L-arginine arylamidase-
68380alkaline phosphatase-3.1.3.1
68380tryptophan deaminase-4.1.99.1
68380alpha-fucosidase-3.2.1.51
68380glutamate decarboxylase-4.1.1.15
68380N-acetyl-beta-glucosaminidase-3.2.1.52
68380beta-glucuronidase-3.2.1.31
68380alpha-arabinosidase-3.2.1.55
68380beta-glucosidase-3.2.1.21
68380alpha-glucosidase-3.2.1.20
68380beta-Galactosidase 6-phosphate-
68380beta-galactosidase-3.2.1.23
68380alpha-galactosidase-3.2.1.22
68380arginine dihydrolase-3.5.3.6
68380urease-3.5.1.5
68367beta-glucosidase-3.2.1.21
68367gelatinase-
68367urease-3.5.1.5

API 20A

@refINDUREGLUMANLACSACMALSALXYLARAGELESCGLYCELMNEMLZRAFSORRHATRE
17723--++++++++--+++---+-

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
17723----------+------------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
17723salty pickle wastewaterZhejiang Province, CixiChinaCHNAsia
67770Salty pickle wastewater

isolation source categories

Cat1Cat2Cat3
#Engineered#Waste#Wastewater
#Condition#Saline

taxonmaps

  • @ref: 69479
  • File name: preview.99_158874.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_16010;96_59816;97_77458;98_104595;99_158874&stattab=map
  • Last taxonomy: Pectinatus brassicae subclade
  • 16S sequence: HM212531
  • Sequence Identity:
  • Total samples: 1951
  • soil counts: 91
  • aquatic counts: 1245
  • animal counts: 602
  • plant counts: 13

Safety information

risk assessment

  • @ref: 17723
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 17723
  • description: Pectinatus brassicae strain TY 16S ribosomal RNA gene, partial sequence
  • accession: HM212531
  • length: 1470
  • database: nuccore
  • NCBI tax ID: 862415

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pectinatus brassicae DSM 24661GCA_014201835scaffoldncbi862415
66792Pectinatus brassicae strain DSM 24661862415.3wgspatric862415
66792Pectinatus brassicae strain MB591862415.4wgspatric862415
66792Pectinatus brassicae DSM 246612861266387draftimg862415

GC content

@refGC-contentmethod
1772335.9high performance liquid chromatography (HPLC)
3027035.9

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesno100no
69480gram-positivegram-positivePositive reaction to Gram-stainingno87.441no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)yes81.712yes
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no89.573yes
69480spore-formingspore-formingAbility to form endo- or exosporesno67.692yes
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno84.433no
69480flagellatedmotile2+Ability to perform flagellated movementyes63.87no

External links

@ref: 17723

culture collection no.: DSM 24661, JCM 17499

straininfo link

  • @ref: 86146
  • straininfo: 398906

literature

  • topic: Phylogeny
  • Pubmed-ID: 22058316
  • title: Pectinatus brassicae sp. nov., a Gram-negative, anaerobic bacterium isolated from salty wastewater.
  • authors: Zhang WW, Fang MX, Tan HQ, Zhang XQ, Wu M, Zhu XF
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.032144-0
  • year: 2011
  • mesh: Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/*analysis, Hydrogen-Ion Concentration, Molecular Sequence Data, Pectinatus/*classification/genetics/isolation & purification, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride, Temperature, Waste Water/*microbiology
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
17723Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 24661)https://www.dsmz.de/collection/catalogue/details/culture/DSM-24661
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
30270Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2661128776041
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/
68367Automatically annotated from API 20A
68380Automatically annotated from API rID32A
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
86146Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID398906.1StrainInfo: A central database for resolving microbial strain identifiers