Strain identifier

BacDive ID: 139989

Type strain: Yes

Species: Bacteroides nordii

Strain history: CCUG 48943 <-- Y. L. Song WAL 11050.

NCBI tax ID(s): 1203608 (strain), 291645 (species)

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General

@ref: 42597

BacDive-ID: 139989

DSM-Number: 18764

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

description: Bacteroides nordii DSM 18764 is an anaerobe, mesophilic bacterium that was isolated from human peritoneal fluid.

NCBI tax id

NCBI tax idMatching level
1203608strain
291645species

strain history

@refhistory
42597<- T. Maier, Bruker; CCUG 48943 <- CCUG; CCUG 48943 <- Y. Song; WAL11050
67770CCUG 48943 <-- Y. L. Song WAL 11050.

doi: 10.13145/bacdive139989.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Bacteroidia
  • order: Bacteroidales
  • family: Bacteroidaceae
  • genus: Bacteroides
  • species: Bacteroides nordii
  • full scientific name: Bacteroides nordii Song et al. 2005

@ref: 42597

domain: Bacteria

phylum: Bacteroidetes

class: Bacteroidia

order: Bacteroidales

family: Bacteroidaceae

genus: Bacteroides

species: Bacteroides nordii

full scientific name: Bacteroides nordii Song et al. 2005

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480no93.107
6948099.996negative

colony morphology

  • @ref: 58397
  • incubation period: 1 day

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
42597COLUMBIA 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
42597FASTIDIOUS 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

@refgrowthtypetemperaturerange
42597positivegrowth37mesophilic
58397positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
58397anaerobe
69480anaerobe99.998

spore formation

@refspore formationconfidence
69481no100
69480no99.993

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836727082trehalose-builds acid from
6836730911sorbitol-builds acid from
6836716634raffinose+builds acid from
683676731melezitose-builds acid from
6836716024D-mannose+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
6838029985L-glutamate+degradation

metabolite production

  • @ref: 68367
  • Chebi-ID: 35581
  • metabolite: indole
  • production: yes

metabolite tests

  • @ref: 68367
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: +

enzymes

@refvalueactivityec
68380serine 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
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
68380urease-3.5.1.5
68367beta-glucosidase+3.2.1.21
68367gelatinase+
68367urease-3.5.1.5

fatty acid profile

  • fatty acids

    @reffatty acidpercentageECL
    58397C15:07.315
    58397C16:02.816
    58397C17:00.417
    58397C18:01.518
    58397C13:0 ANTEISO0.312.701
    58397C13:0 iso0.412.612
    58397C15:0 3OH2.116.504
    58397C15:0 ANTEISO27.114.711
    58397C15:0 ISO19.214.621
    58397C15:0 ISO 3OH0.516.135
    58397C16:0 3OH1.417.52
    58397C16:0 iso115.626
    58397C16:0 iso 3OH0.517.145
    58397C17:0 2OH0.918.249
    58397C17:0 3OH1.318.535
    58397C17:0 anteiso0.816.722
    58397C17:0 iso1.416.629
    58397C17:0 iso 3OH19.818.161
    58397C18:1 ω9c217.769
    58397C18:2 ω6,9c/C18:0 ANTE4.217.724
    58397unknown 13.5664.713.566
    58397unknown 16.5800.616.58
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG

API 20A

@refINDUREGLUMANLACSACMALSALXYLARAGELESCGLYCELMNEMLZRAFSORRHATRE
42597+-+-+++-++++++/-+-+-+/--

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
42597---+-++--+--+--+/-+--+----+--+/--
42597--++-++--++++---+--+----+--+-
42597-+++-++--++++-+/-++--+----+--+-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitudesampling date
42597human peritoneal fluidLos AngelesUSAUSANorth America34.0522-118.244
58397Human peritoneal fluidLos AngelesUSAUSANorth America1993
67770Human peritoneal fluid

isolation source categories

Cat1Cat2Cat3
#Infection#Patient
#Host#Human
#Host Body Product#Fluids
#Host Body-Site#Other#Abdomen

Safety information

risk assessment

  • @ref: 42597
  • biosafety level: 2
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
42597Bacteroides sp. WAL 11050 16S ribosomal RNA gene, partial sequenceAY6086971413ena1203608
67770Bacteroides nordii gene for 16S ribosomal RNA, partial sequence, strain: JCM 12987AB5107041473ena1203608

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Bacteroides nordii WAL 11050 = JCM 12987GCA_000613465contigncbi1203608
66792Bacteroides nordii JCM 129871235818.3wgspatric1203608
66792Bacteroides nordii strain FDAARGOS_1461291645.80completepatric291645
66792Bacteroides nordii JCM 129872585427864draftimg1203608
66792Bacteroides nordii strain FDAARGOS_1461291645.82completepatric291645
66792Bacteroides nordii strain FDAARGOS_1461291645.83completepatric291645
66792Bacteroides nordii strain FDAARGOS_1461291645.81completepatric291645

GC content

@refGC-contentmethod
4259741.4
6777041.4high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveno97.992no
anaerobicyes94.651yes
halophileno92.352no
spore-formingno93.483no
glucose-utilyes89.622no
motileno90.383no
flagellatedno96.446no
aerobicno96.248yes
thermophileno99.585yes
glucose-fermentyes70.246no

External links

@ref: 42597

culture collection no.: DSM 18764, ATCC BAA 998, CCUG 48943, JCM 12987, WAL 11050

straininfo link

  • @ref: 96420
  • straininfo: 138973

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15583282"Bacteroides nordii" sp. nov. and "Bacteroides salyersae" sp. nov. isolated from clinical specimens of human intestinal origin.Song YL, Liu CX, McTeague M, Finegold SMJ Clin Microbiol10.1128/JCM.42.12.5565-5570.20042004Bacterial Typing Techniques, Bacteroides/*classification/genetics/*isolation & purification/metabolism, Bacteroides Infections/*microbiology, Fatty Acids/analysis, Humans, Intestines/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAPathogenicity
Metabolism28751127Isolation of six novel 7-oxo- or urso-type secondary bile acid-producing bacteria from rat cecal contents.Tawthep S, Fukiya S, Lee JY, Hagio M, Ogura Y, Hayashi T, Yokota AJ Biosci Bioeng10.1016/j.jbiosc.2017.06.0022017Animals, Bacteria/*isolation & purification/*metabolism, Bacteroides/isolation & purification/metabolism, Bile Acids and Salts/*biosynthesis, Cecum/*microbiology, Chenodeoxycholic Acid/metabolism, Cholic Acid/metabolism, Cholic Acids/metabolism, Clostridium/isolation & purification/metabolism, Deoxycholic Acid/metabolism, Male, RatsPhylogeny

Reference

@idauthorstitledoi/urlcatalogue
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
42597Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-18764Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18764)
58397Curators of the CCUGhttps://www.ccug.se/strain?id=48943Culture Collection University of Gothenburg (CCUG) (CCUG 48943)
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68367Automatically annotated from API 20A
68380Automatically annotated from API rID32A
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
96420Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID138973.1