Strain identifier

BacDive ID: 12502

Type strain: Yes

Species: Parabacteroides chartae

Strain Designation: NS31-3

Strain history: H.-Q. Tan NS31-3.

NCBI tax ID(s): 1037355 (species)

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General

@ref: 17811

BacDive-ID: 12502

DSM-Number: 24967

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

description: Parabacteroides chartae NS31-3 is an anaerobe, Gram-negative, rod-shaped bacterium that was isolated from wastewater from paper mill.

NCBI tax id

  • NCBI tax id: 1037355
  • Matching level: species

strain history

@refhistory
17811<- T. Hai-Qin, Zhejiang Univ., Hangzhou, China; NS31-3
67770H.-Q. Tan NS31-3.

doi: 10.13145/bacdive12502.20240916.9.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Bacteroidia
  • order: Bacteroidales
  • family: Tannerellaceae
  • genus: Parabacteroides
  • species: Parabacteroides chartae
  • full scientific name: Parabacteroides chartae Tan et al. 2012

@ref: 17811

domain: Bacteria

phylum: Bacteroidetes

class: Bacteroidia

order: Bacteroidales

family: Tannerellaceae

genus: Parabacteroides

species: Parabacteroides chartae

full scientific name: Parabacteroides chartae Tan et al. 2012

strain designation: NS31-3

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
30522negative1.95 µm0.85 µmrod-shapedno
69480no90

colony morphology

  • @ref: 17811
  • incubation period: 1-2 days

pigmentation

  • @ref: 30522
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
17811CHOPPED MEAT MEDIUM (DSMZ Medium 78)yeshttps://mediadive.dsmz.de/medium/78Name: CHOPPED MEAT MEDIUM (DSMZ Medium 78) Composition: Ground beef 500.0 g/l Casitone 30.0 g/l Agar 15.0 g/l Ethanol 9.5 g/l (optional) K2HPO4 5.0 g/l Yeast extract 5.0 g/l L-Cysteine HCl 0.5 g/l Haemin 0.005 g/l (optional) Resazurin 0.001 g/l Vitamin K3 0.0005 g/l (optional) Vitamin K1 (optional) NaOH (optional) Distilled water
17811COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)yeshttps://mediadive.dsmz.de/medium/693Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base

culture temp

@refgrowthtypetemperature
17811positivegrowth37
30522positivegrowth10-40
30522positiveoptimum36
67770positivegrowth37

culture pH

@refabilitytypepHPH range
30522positivegrowth5.5-8.5alkaliphile
30522positiveoptimum7.25

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
17811anaerobe
30522anaerobe

spore formation

@refspore formationconfidence
30522no
69480no90.982
69481no100

halophily

  • @ref: 30522
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-2 %

observation

  • @ref: 67770
  • observation: quinones: MK-9, MK-10

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3052222599arabinose+carbon source
3052217057cellobiose+carbon source
3052217234glucose+carbon source
3052217716lactose+carbon source
3052217306maltose+carbon source
3052229864mannitol+carbon source
3052237684mannose+carbon source
3052216634raffinose+carbon source
3052217814salicin+carbon source
3052230911sorbitol+carbon source
3052217992sucrose+carbon source
3052227082trehalose+carbon source
3052218222xylose+carbon source
305224853esculin+hydrolysis
6838016199urea-hydrolysis
6838029016arginine-hydrolysis
6838016024D-mannose+fermentation
6838016634raffinose+fermentation
6838029985L-glutamate-degradation
6838017632nitrate-reduction
6838027897tryptophan-energy source

metabolite production

  • @ref: 68380
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 68380
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
30522acid phosphatase+3.1.3.2
30522alkaline phosphatase+3.1.3.1
30522alpha-galactosidase+3.2.1.22
30522gelatinase+
68380serine arylamidase-
68380glutamyl-glutamate arylamidase+
68380histidine arylamidase-
68380glycin arylamidase-
68380alanine arylamidase+3.4.11.2
68380tyrosine arylamidase-
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

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuATyrAAlaAGlyAHisAGGASerA
17811--++-++--+++-+---+-+-+-+--+-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitude
17811wastewater from paper millZhejiang Province, Lingqiao town (30° 15' N 120° 10' E)ChinaCHNAsia30.25120.167
67770Wastewater of a paper mill

isolation source categories

Cat1Cat2Cat3
#Engineered#Industrial#Plant (Factory)
#Engineered#Waste#Wastewater

taxonmaps

  • @ref: 69479
  • File name: preview.99_4592.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_126;96_2290;97_2778;98_3449;99_4592&stattab=map
  • Last taxonomy: Macellibacteroides fermentans
  • 16S sequence: JN029805
  • Sequence Identity:
  • Total samples: 19129
  • soil counts: 798
  • aquatic counts: 8663
  • animal counts: 9468
  • plant counts: 200

Safety information

risk assessment

  • @ref: 17811
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 17811
  • description: Parabacteroides chartae strain NS31-3 16S ribosomal RNA gene, partial sequence
  • accession: JN029805
  • length: 1481
  • database: nuccore
  • NCBI tax ID: 1037355

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Parabacteroides chartae DSM 24967GCA_900168155scaffoldncbi1037355
66792Parabacteroides chartae strain DSM 249671037355.4wgspatric1037355
66792Parabacteroides chartae DSM 249672595698220draftimg1037355

GC content

@refGC-contentmethod
1781137.2high performance liquid chromatography (HPLC)
3052237.2

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesno100no
69480gram-positivegram-positivePositive reaction to Gram-stainingno83.749yes
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)yes83.609yes
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no85.988yes
69480spore-formingspore-formingAbility to form endo- or exosporesno90.982no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno95.249yes
69480flagellatedmotile2+Ability to perform flagellated movementno90no

External links

@ref: 17811

culture collection no.: DSM 24967, JCM 17797

straininfo link

  • @ref: 81721
  • straininfo: 397921

literature

  • topic: Phylogeny
  • Pubmed-ID: 22199215
  • title: Parabacteroides chartae sp. nov., an obligately anaerobic species from wastewater of a paper mill.
  • authors: Tan HQ, Li TT, Zhu C, Zhang XQ, Wu M, Zhu XF
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.038000-0
  • year: 2011
  • mesh: Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/isolation & purification, Base Composition, Carbohydrate Metabolism, DNA, Bacterial/genetics, Fatty Acids/analysis, Fermentation, Molecular Sequence Data, *Paper, *Phylogeny, Quinones/analysis, Sequence Analysis, DNA, Waste Water/*microbiology
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
17811Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 24967)https://www.dsmz.de/collection/catalogue/details/culture/DSM-24967
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
30522Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2685428776041
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/
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
81721Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID397921.1StrainInfo: A central database for resolving microbial strain identifiers