Strain identifier

BacDive ID: 12500

Type strain: Yes

Species: Parabacteroides goldsteinii

Strain history: <- DSM <- JCM <- CCUG <- Y Song, WAL 12034

NCBI tax ID(s): 927665 (strain), 328812 (species)

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General

@ref: 8022

BacDive-ID: 12500

DSM-Number: 19448

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

description: Parabacteroides goldsteinii DSM 19448 is an anaerobe, rod-shaped bacterium that was isolated from human tissue.

NCBI tax id

NCBI tax idMatching level
927665strain
328812species

strain history

@refhistory
8022<- JCM <- CCUG <- Y. Song; WAL 12034
67770CCUG 48944 <-- Y. Song WAL 12034.
67771<- DSM <- JCM <- CCUG <- Y Song, WAL 12034

doi: 10.13145/bacdive12500.20240916.9.1

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 goldsteinii
  • full scientific name: Parabacteroides goldsteinii (Song et al. 2006) Sakamoto and Benno 2006

  • synonyms

    • @ref: 20215
    • synonym: Bacteroides goldsteinii

@ref: 8022

domain: Bacteria

phylum: Bacteroidetes

class: Bacteroidia

order: Bacteroidales

family: Tannerellaceae

genus: Parabacteroides

species: Parabacteroides goldsteinii

full scientific name: Parabacteroides goldsteinii (Song et al. 2006) Sakamoto and Benno 2006

type strain: yes

Morphology

cell morphology

@refcell shapegram stain
67771rod-shaped
67771negative

colony morphology

  • @ref: 58398
  • incubation period: 1 day

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8022COLUMBIA 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
8022FASTIDIOUS ANAEROBE BROTH (DSMZ Medium 1203a)yeshttps://mediadive.dsmz.de/medium/1203aName: FASTIDIOUS ANAEROBE BROTH (DSMZ Medium 1203a) Composition: Fastidious Anaerobe Basal Broth 35.4 g/l Distilled water

culture temp

@refgrowthtypetemperature
8022positivegrowth37
58398positivegrowth37
67770positivegrowth37
67771positivegrowth37

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
8022anaerobe
58398anaerobe
67771anaerobe

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 91.792

observation

@refobservation
67770quinones: MK-9, MK-10
67771quinones: MK-9, MK-10

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836727082trehalose+builds acid from
6836762345L-rhamnose+builds acid from
6836730911sorbitol-builds acid from
6836716634raffinose+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
6838017632nitrate-reduction
6838027897tryptophan-energy source

metabolite production

@refChebi-IDmetaboliteproduction
6836735581indoleno
6838035581indoleno

metabolite tests

@refChebi-IDmetaboliteindole test
6838035581indole-
6836735581indole-

enzymes

@refvalueactivityec
68380glutamyl-glutamate arylamidase+
68380histidine 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
68380N-acetyl-beta-glucosaminidase+3.2.1.52
68380beta-glucuronidase-3.2.1.31
68380alpha-arabinosidase-3.2.1.55
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

@refINDUREGLUMANLACSACMALSALXYLARAGELESCGLYCELMNEMLZRAFSORRHATRECAT
8022--+-+++-+--+--++/-+-+++/-

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
8022--++-+/-+/---++++---++-+++-++++++/-
8022--++-++--+++----++-+++-+++/-++-

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentsampling dategeographic location
8022human tissueUSAUSANorth America
58398Human abdominal fluidUSAUSANorth America1984Los Angeles
67770Human clinical specimens of intestinal origin
67771From human clinical specimens of intestinal origin(human tissue)USAUSANorth America

isolation source categories

Cat1Cat2Cat3
#Host#Human
#Host Body-Site#Other
#Infection#Patient#Specimen

taxonmaps

  • @ref: 69479
  • File name: preview.99_1605.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_126;96_909;97_1059;98_1265;99_1605&stattab=map
  • Last taxonomy: Parabacteroides goldsteinii subclade
  • 16S sequence: AY974070
  • Sequence Identity:
  • Total samples: 141503
  • soil counts: 1445
  • aquatic counts: 3273
  • animal counts: 136228
  • plant counts: 557

Safety information

risk assessment

  • @ref: 8022
  • biosafety level: 2
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Parabacteroides goldsteinii gene for 16S ribosomal RNA, partial sequence, strain: JCM 13446AB5476501476nuccore927665
8022Parabacteroides goldsteinii strain JCM13446 16S ribosomal RNA gene, partial sequenceEU1366972002nuccore927665
67770Parabacteroides goldsteinii strain WAL 12034 16S ribosomal RNA gene, partial sequenceAY9740701396nuccore328812

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Parabacteroides goldsteinii DSM 19448 = WAL 12034 Parabacteroides goldsteinii 82E8GCA_900624825contigncbi927665
66792Parabacteroides goldsteinii DSM 19448 = WAL 12034927665.4wgspatric927665
66792Parabacteroides goldsteinii DSM 19448 = WAL 12034 strain Parabacteroides goldsteinii 81H9927665.27wgspatric927665
66792Parabacteroides goldsteinii DSM 19448 = WAL 12034 strain Parabacteroides goldsteinii 82E8927665.28wgspatric927665
67770Parabacteroides goldsteinii DSM 19448 = WAL 12034GCA_000969835scaffoldncbi927665
67770Parabacteroides goldsteinii DSM 19448 = WAL 12034 NCTC11032GCA_900624735contigncbi927665

GC content

@refGC-contentmethod
802243
6777043high performance liquid chromatography (HPLC)
6777143.0high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69480gram-positivegram-positivePositive reaction to Gram-stainingno89.309no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)yes86.74yes
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no93.268yes
69480spore-formingspore-formingAbility to form endo- or exosporesno91.792no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno94.607yes
69480flagellatedmotile2+Ability to perform flagellated movementno88.095no

External links

@ref: 8022

culture collection no.: DSM 19448, ATCC BAA-1180, CCUG 48944, JCM 13446, KCTC 15612, WAL 12034

straininfo link

  • @ref: 81719
  • straininfo: 290961

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16145101"Bacteroides goldsteinii sp. nov." isolated from clinical specimens of human intestinal origin.Song Y, Liu C, Lee J, Bolanos M, Vaisanen ML, Finegold SMJ Clin Microbiol10.1128/JCM.43.9.4522-4527.20052005Bacterial Typing Techniques, Bacteroides/*classification/genetics/*isolation & purification/physiology, Bacteroides Infections/*microbiology, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Humans, Intestines/*microbiology, Molecular Sequence Data, Phenotype, *Phylogeny, RNA, Ribosomal, 16S/*genetics, Sequence Analysis, DNAPathogenicity
Phylogeny16825636Reclassification of Bacteroides distasonis, Bacteroides goldsteinii and Bacteroides merdae as Parabacteroides distasonis gen. nov., comb. nov., Parabacteroides goldsteinii comb. nov. and Parabacteroides merdae comb. nov.Sakamoto M, Benno YInt J Syst Evol Microbiol10.1099/ijs.0.64192-02006Bacterial Typing Techniques, Bacteroides/chemistry/*classification/genetics/physiology, Bacteroidetes/chemistry/*classification/genetics/metabolism, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis/chemistry, Genes, rRNA/genetics, Molecular Sequence Data, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Vitamin K 2/analysis/chemistryGenetics
Phylogeny19628614Parabacteroides gordonii sp. nov., isolated from human blood cultures.Sakamoto M, Suzuki N, Matsunaga N, Koshihara K, Seki M, Komiya H, Benno YInt J Syst Evol Microbiol10.1099/ijs.0.010611-02009Aged, Bacteroidetes/*classification/genetics/*isolation & purification/metabolism, Blood/*microbiology, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/chemistry/metabolism, Humans, Male, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/geneticsMetabolism
Phylogeny30267315Parabacteroides chongii sp. nov., isolated from blood of a patient with peritonitis.Kim H, Im WT, Kim M, Kim D, Seo YH, Yong D, Jeong SH, Lee KJ Microbiol10.1007/s12275-018-8122-32018Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/isolation & purification, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Gram-Negative Bacterial Infections/*blood, Humans, Male, Middle Aged, Peritonitis/*microbiology, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analysisPathogenicity

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8022Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19448)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19448
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
58398Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 48944)https://www.ccug.se/strain?id=48944
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
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)
81719Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID290961.1StrainInfo: A central database for resolving microbial strain identifiers