Strain identifier

BacDive ID: 17146

Type strain: Yes

Species: Pectinatus haikarae

Strain history: <- R. Juvonen <- VTT

NCBI tax ID(s): 349096 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 9 (current version):
version 8.1:
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 9 (current version)

General

@ref: 6599

BacDive-ID: 17146

DSM-Number: 16980

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

description: Pectinatus haikarae DSM 16980 is an anaerobe, Gram-negative, motile bacterium that was isolated from air, bottling hall in a brewery.

NCBI tax id

  • NCBI tax id: 349096
  • Matching level: species

strain history

  • @ref: 6599
  • history: <- R. Juvonen <- VTT

doi: 10.13145/bacdive17146.20240510.9

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 haikarae
  • full scientific name: Pectinatus haikarae Juvonen and Suihko 2006

@ref: 6599

domain: Bacteria

phylum: Firmicutes

class: Negativicutes

order: Selenomonadales

family: Selenomonadaceae

genus: Pectinatus

species: Pectinatus haikarae

full scientific name: Pectinatus haikarae Juvonen and Suihko 2006

type strain: yes

Morphology

cell morphology

  • @ref: 31505
  • gram stain: negative
  • cell length: 03-50 µm
  • cell width: 0.6-0.8 µm
  • cell shape: rod-shaped
  • motility: yes

colony morphology

  • @ref: 6599
  • type of hemolysis: gamma
  • incubation period: 3-7 days

pigmentation

  • @ref: 31505
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6599MRS pre-reduced (DSMZ Medium 11b)yeshttps://mediadive.dsmz.de/medium/11bName: MRS MEDIUM (pre-reduced) (DSMZ Medium 11b) Composition: Glucose 20.0 g/l Casein peptone 10.0 g/l Meat extract 10.0 g/l Na-acetate 5.0 g/l Yeast extract 5.0 g/l (NH4)3 citrate 2.0 g/l K2HPO4 2.0 g/l Tween 80 1.0 g/l L-Cysteine HCl x H2O 0.5 g/l MgSO4 x 7 H2O 0.2 g/l MnSO4 x H2O 0.05 g/l Resazurin 0.001 g/l Distilled water
6599BIFIDOBACTERIUM MEDIUM (DSMZ Medium 58)yeshttps://mediadive.dsmz.de/medium/58Name: 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
6599positivegrowth30
31505positivegrowth15-30
31505positiveoptimum20-30

culture pH

@refabilitytypepH
31505positivegrowth7
31505positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
6599anaerobe
31505anaerobe

spore formation

  • @ref: 31505
  • spore formation: no

observation

  • @ref: 31505
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3150524265gluconate+carbon source
3150517716lactose+carbon source
3150529864mannitol+carbon source
3150528053melibiose+carbon source
3150517272propionate+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
3150516136hydrogen sulfideyes
6836735581indoleno
6838035581indoleno

metabolite tests

@refChebi-IDmetaboliteindole test
6838035581indole-
6836735581indole-

enzymes

@refvalueactivityec
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
6599--+++---++--+-+--++-
6599--+++---++--+-+--++-

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
6599--++------+------------------
6599--++------+------------------

Isolation, sampling and environmental information

isolation

  • @ref: 6599
  • sample type: air, bottling hall in a brewery
  • country: Finland
  • origin.country: FIN
  • continent: Europe

isolation source categories

Cat1Cat2Cat3
#Engineered#Food production#Fermented
#Environmental#Air#Indoor Air
#Engineered#Food production#Beverage

taxonmaps

  • @ref: 69479
  • File name: preview.99_69742.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_16010;96_4179;97_37765;98_48986;99_69742&stattab=map
  • Last taxonomy: Pectinatus haikarae subclade
  • 16S sequence: DQ223731
  • Sequence Identity:
  • Total samples: 537
  • soil counts: 13
  • aquatic counts: 150
  • animal counts: 371
  • plant counts: 3

Safety information

risk assessment

  • @ref: 6599
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 6599
  • description: Pectinatus haikarae strain VTT E-88329 16S ribosomal RNA gene, partial sequence
  • accession: DQ223731
  • length: 1535
  • database: nuccore
  • NCBI tax ID: 349096

Genome sequences

  • @ref: 66792
  • description: Pectinatus haikarae DSM 16980
  • accession: 2926546190
  • assembly level: draft
  • database: img
  • NCBI tax ID: 349096

GC content

  • @ref: 6599
  • GC-content: 38.8

External links

@ref: 6599

culture collection no.: DSM 16980, VTT E-88329

straininfo link

  • @ref: 86145
  • straininfo: 286033

literature

  • topic: Phylogeny
  • Pubmed-ID: 16585679
  • title: Megasphaera paucivorans sp. nov., Megasphaera sueciensis sp. nov. and Pectinatus haikarae sp. nov., isolated from brewery samples, and emended description of the genus Pectinatus.
  • authors: Juvonen R, Suihko ML
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.63699-0
  • year: 2006
  • mesh: Beer/*microbiology, Megasphaera/*classification/genetics/isolation & purification/*metabolism, Molecular Sequence Data, Nucleic Acid Hybridization, Pectinatus/*classification, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/analysis/genetics
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
6599Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16980)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16980
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
31505Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2780328776041
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)
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
86145Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID286033.1StrainInfo: A central database for resolving microbial strain identifiers