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Strain identifier

BacDive ID: 12497

Type strain: Yes

Species: Parabacteroides distasonis

Strain history: ATCC 8503 <-- A. H. Eggerth.

NCBI tax ID(s): 435591 (strain), 823 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 8779

BacDive-ID: 12497

DSM-Number: 20701

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic

description: Parabacteroides distasonis CIP 104284 is an anaerobe, mesophilic bacterium that was isolated from Human feces.

NCBI tax id

NCBI tax idMatching level
435591strain
823species

strain history

doi: 10.13145/bacdive12497.20221219.7.1

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 distasonis
  • full scientific name: Parabacteroides distasonis (Eggerth and Gagnon 1933) Sakamoto and Benno 2006
  • synonyms

    • @ref: 20215
    • synonym: Bacteroides distasonis

@ref: 8779

domain: Bacteria

phylum: Bacteroidetes

class: Bacteroidia

order: Bacteroidales

family: Tannerellaceae

genus: Parabacteroides

species: Parabacteroides distasonis

full scientific name: Parabacteroides distasonis (Eggerth and Gagnon 1933) Sakamoto and Benno 2006 emend. Hahnke et al. 2016

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: negative
  • confidence: 99.346

colony morphology

  • @ref: 8779
  • incubation period: 1-2 days

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8779COLUMBIA 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
8779FASTIDIOUS 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
8779CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110)yeshttps://mediadive.dsmz.de/medium/110Name: CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110) Composition: Ground beef 500.0 g/l Casitone 30.0 g/l Agar 15.0 g/l K2HPO4 5.0 g/l Yeast extract 5.0 g/l D-Glucose 4.0 g/l Starch 1.0 g/l Maltose 1.0 g/l Cellobiose 1.0 g/l L-Cysteine HCl 0.5 g/l Ethanol 0.19 g/l Vitamin K3 0.05 g/l Hemin 0.005 g/l Sodium resazurin 0.0005 g/l Vitamin K1 NaOH Distilled water
41097MEDIUM 20 - for Anaerobic bacteriayesAgar (15.000 g);Glucose (5.000 g);Yeast extract (20.000 g);Tryptone (30.000 g);Cysteine hydrochloride (0.500 g);distilled water (1000.000 ml);Hemin solution -M00149 (25.000 ml)

culture temp

@refgrowthtypetemperaturerange
8779positivegrowth37mesophilic
41097positivegrowth37mesophilic
44811positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
8779anaerobe
44811anaerobe
69480anaerobe96.922

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 96.102

compound production

@refcompound
8779catalase
8779superoxide dismutase

halophily

  • @ref: 69480
  • halophily level: non-halophilic
  • confidence: 99.239

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6838027897tryptophan-energy source
6838017632nitrate-reduction
6838029985L-glutamate+degradation
6838016024D-mannose+fermentation
6838029016arginine-hydrolysis
6838016199urea-hydrolysis

metabolite production

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

metabolite tests

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

enzymes

@refvalueactivityec
68380glutamyl-glutamate arylamidase+
68380glycin arylamidase+
68380alanine arylamidase+3.4.11.2
68380leucine arylamidase+3.4.11.1
68380leucyl glycin arylamidase+3.4.11.1
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
68380beta-glucosidase+3.2.1.21
68380alpha-glucosidase+3.2.1.20
68380beta-galactosidase+3.2.1.23
68380alpha-galactosidase+3.2.1.22
68380arginine dihydrolase-3.5.3.6
68380urease-3.5.1.5
67770catalase1.11.1.6
67770superoxide dismutase1.15.1.1

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
8779--++-+++-++++---+++/-+++++++++-
8779--++-++--++-+---++-+++++/-++++-
8779--++-+++-++++---++-+-+--++-+-
8779--++-+++-++++---++-+++++++++-
8779--++++++-++++---++-++++++++++/-

Isolation, sampling and environmental information

isolation

@refsample type
44811Human feces
67770Human feces

isolation source categories

Cat1Cat2Cat3
#Host#Human
#Host Body Product#Gastrointestinal tract#Feces (Stool)

Safety information

risk assessment

  • @ref: 8779
  • biosafety level: 2
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Parabacteroides distasonis gene for 16S ribosomal RNA, partial sequence, strain: JCM 5825AB2389221488ena823
20218Bacteroides distasonis 16S-23S rDNA intergenic spacer regionAF176689411ena435591
20218Bacteroides distasonis strain ATCC 8503 16S-23S ribosomal RNA intergenic spacer, partial sequenceAY546490519ena435591
20218Parabacteroides distasonis strain JCM5825 16S ribosomal RNA gene, partial sequenceEU1366811911ena823
20218Parabacteroides distasonis culture-collection DSM:20701 16S ribosomal RNA gene, partial sequenceHQ131775933ena823
20218Bacteroides distasonis 16S ribosomal RNAM866951539ena823
8779Parabacteroides distasonis strain JCM 5825 16S ribosomal RNA, partial sequenceNR_0413421488nuccore823

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Parabacteroides distasonis ATCC 8503 ATCC 8503GCA_000012845completencbi435591
66792Parabacteroides distasonis ATCC 8503 Parabacteroides distasonis 82G9GCA_900683725completencbi435591
66792Parabacteroides distasonis ATCC 8503435591.13completepatric435591
66792Parabacteroides distasonis ATCC 8503 strain Parabacteroides distasonis 82G9435591.48completepatric435591
66792Parabacteroides distasonis strain NCTC11152823.244wgspatric823
66792Parabacteroides distasonis ATCC 8503640753039completeimg435591
66792Parabacteroides distasonis NCTC 111522870967820draftimg823
66792Parabacteroides distasonis ATCC 85032841273300completeimg435591
67770Parabacteroides distasonis ATCC 8503, complete genomeCP000140ena435591
67770Parabacteroides distasonis NCTC11152GCA_900445525contigncbi823
66792Acinetobacter baumannii PR364GCA_002137045contigpatric470
66792Acinetobacter baumannii AB21GCA_003007065scaffoldpatric470
66792Klebsiella pneumoniae BD-12GCA_021136655contigpatric573
66792Listeria monocytogenes 9614-19GCA_026094635contigpatric1639
66792Klebsiella pneumoniae EuSCAPE_ES066GCA_900516405contigpatric573
66792uncultured Lachnospiraceae bacterium RUG13137GCA_902786165scaffoldpatric297314

GC content

@refGC-contentmethod
877944.0
877945.1sequence analysis
6777044thermal denaturation, midpoint method (Tm)

External links

@ref: 8779

culture collection no.: CIP 104284, DSM 20701, ATCC 8503, CCUG 4941, JCM 5825, NCTC 11152

straininfo link

@refpassport
20218http://www.straininfo.net/strains/149184
20218http://www.straininfo.net/strains/94765
20218http://www.straininfo.net/strains/128791
20218http://www.straininfo.net/strains/181659
20218http://www.straininfo.net/strains/94766

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Metabolism845116Production and some properties of catalase and superoxide dismutase from the anaerobe Bacteroides distasonis.Gregory EM, Kowalski JB, Holdeman LVJ Bacteriol10.1128/jb.129.3.1298-1302.19771977Azides/pharmacology, Bacteroides/*enzymology, Catalase/*metabolism, Culture Media, Cyanides/pharmacology, Freezing, Hemin/pharmacology, Molecular Weight, Superoxide Dismutase/*metabolism, Vitamin K 1/pharmacologyCultivation
Cultivation6643389Effect of heme on Bacteroides distasonis catalase and aerotolerance.Gregory EM, Fanning DDJ Bacteriol10.1128/jb.156.3.1012-1018.19831983Bacteroides/drug effects/enzymology/*physiology, Catalase/*metabolism, Chloramphenicol/pharmacology, Culture Media, Heme/*analogs & derivatives, Hemin/*pharmacology, Hydrogen Peroxide/pharmacology, Oxygen/*pharmacology, Rifampin/pharmacologyEnzymology
Pathogenicity12650667Growth inhibition of intestinal bacteria and mutagenicity of 2-, 3-, 4-aminobiphenyls, benzidine, and biphenyl.Chung KT, Adris PToxicol In Vitro10.1016/s0887-2333(02)00131-52003Aminobiphenyl Compounds/*toxicity, Benzidines/*toxicity, Biphenyl Compounds/*toxicity, Gram-Negative Bacteria/drug effects/growth & development, Gram-Positive Bacteria/drug effects/growth & development, Humans, Intestines/*microbiology, Mutagenicity Tests, Mutagens/*toxicity
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
Enzymology21092234Identification and characterization of a novel fumarase gene by metagenome expression cloning from marine microorganisms.Jiang C, Wu LL, Zhao GC, Shen PH, Jin K, Hao ZY, Li SX, Ma GF, Luo FF, Hu GQ, Kang WL, Qin XM, Bi YL, Tang XL, Wu BMicrob Cell Fact10.1186/1475-2859-9-912010Amino Acid Sequence, Aquatic Organisms/enzymology/genetics, Cloning, Molecular, Computational Biology, Fumarate Hydratase/chemistry/classification/*genetics, Fumarates/metabolism, Kinetics, Malates/metabolism, Metagenome, Molecular Sequence Data, Phylogeny, Recombinant Proteins/chemistry/isolation & purification/metabolism, Sequence Alignment, TemperaturePhylogeny
Phylogeny30652964Parabacteroides acidifaciens sp. nov., isolated from human faeces.Wang YJ, Xu XJ, Zhou N, Sun Y, Liu C, Liu SJ, You XInt J Syst Evol Microbiol10.1099/ijsem.0.0032302019Bacterial Typing Techniques, Bacteroidetes/*classification/isolation & purification, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Feces/*microbiology, Fermentation, Humans, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryPathogenicity
Metabolism31177942The 'in vivo lifestyle' of bile acid 7alpha-dehydroxylating bacteria: comparative genomics, metatranscriptomic, and bile acid metabolomics analysis of a defined microbial community in gnotobiotic mice.Ridlon JM, Devendran S, Alves JM, Doden H, Wolf PG, Pereira GV, Ly L, Volland A, Takei H, Nittono H, Murai T, Kurosawa T, Chlipala GE, Green SJ, Hernandez AG, Fields CJ, Wright CL, Kakiyama G, Cann I, Kashyap P, McCracken V, Gaskins HRGut Microbes10.1080/19490976.2019.16181732019Animals, Bacteria, Anaerobic/*genetics/*metabolism, Bacteroides/genetics/metabolism, Bile Acids and Salts/*metabolism, Bilophila/genetics/metabolism, Cecum/*microbiology, Cholic Acids/metabolism, Clostridium/genetics/metabolism, Gene Expression Regulation, Bacterial, Genome, Bacterial, Genomics, Germ-Free Life, Humans, *Metabolome, Mice, Mice, Inbred C57BL, Microbiota, Operon, RNA-Seq, *Transcriptome, Up-RegulationGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8779Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20701)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20701
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
41097Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16175
44811Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 4941)https://www.ccug.se/strain?id=4941
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68380Automatically annotated from API rID32A
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)