Strain identifier

BacDive ID: 1609

Type strain: Yes

Species: Bacteroides intestinalis

Strain Designation: 341

Strain history: M. Kitahara 341 <-- M. Matsumoto 341.

NCBI tax ID(s): 471870 (strain), 329854 (species)

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General

@ref: 6945

BacDive-ID: 1609

DSM-Number: 17393

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

description: Bacteroides intestinalis 341 is an anaerobe, mesophilic, Gram-negative human pathogen that was isolated from human faeces.

NCBI tax id

NCBI tax idMatching level
329854species
471870strain

strain history

@refhistory
6945<- M. Kitahara <- M. Matsumoto
67770M. Kitahara 341 <-- M. Matsumoto 341.

doi: 10.13145/bacdive1609.20230509.8.1

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 intestinalis
  • full scientific name: Bacteroides intestinalis Bakir et al. 2006

@ref: 6945

domain: Bacteria

phylum: Bacteroidetes

class: Bacteroidia

order: Bacteroidales

family: Bacteroidaceae

genus: Bacteroides

species: Bacteroides intestinalis

full scientific name: Bacteroides intestinalis Bakir et al. 2006 emend. Hahnke et al. 2016

strain designation: 341

type strain: yes

Morphology

cell morphology

  • @ref: 31621
  • gram stain: negative
  • cell length: 01-05 µm
  • cell width: 0.8 µm
  • cell shape: rod-shaped
  • motility: no

colony morphology

@reftype of hemolysishemolysis abilityincubation period
6945alpha/beta11-2 days
600582 days

pigmentation

  • @ref: 31621
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6945COLUMBIA 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
6945PYG MEDIUM (MODIFIED) (DSMZ Medium 104)yeshttps://mediadive.dsmz.de/medium/104Name: PYG MEDIUM (modified) (DSMZ Medium 104) Composition: Yeast extract 10.0 g/l Peptone 5.0 g/l Trypticase peptone 5.0 g/l Beef extract 5.0 g/l Glucose 5.0 g/l L-Cysteine HCl x H2O 0.5 g/l NaHCO3 0.4 g/l NaCl 0.08 g/l K2HPO4 0.04 g/l KH2PO4 0.04 g/l MgSO4 x 7 H2O 0.02 g/l CaCl2 x 2 H2O 0.01 g/l Hemin 0.005 g/l Ethanol 0.0038 g/l Resazurin 0.001 g/l Tween 80 Vitamin K1 NaOH Distilled water

culture temp

@refgrowthtypetemperaturerange
6945positivegrowth37mesophilic
31621positivegrowth37mesophilic
31621positiveoptimum37mesophilic
60058positivegrowth37mesophilic
67770positivegrowth37mesophilic

culture pH

@refabilitytypepH
31621positivegrowth7
31621positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
6945anaerobe
31621anaerobe
60058anaerobe

spore formation

  • @ref: 31621
  • spore formation: no

observation

  • @ref: 31621
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3162122599arabinose+carbon source
3162117057cellobiose+carbon source
3162117234glucose+carbon source
3162117716lactose+carbon source
3162117306maltose+carbon source
3162137684mannose+carbon source
3162116634raffinose+carbon source
3162126546rhamnose+carbon source
3162117992sucrose+carbon source
3162118222xylose+carbon source
316214853esculin+hydrolysis
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
6836717754glycerol-builds acid from
683674853esculin+hydrolysis
683675291gelatin-hydrolysis
6836730849L-arabinose+builds acid from
6836765327D-xylose+builds acid from
6836717814salicin-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
6838029985L-glutamate+degradation
6838017632nitrate-reduction
6838027897tryptophan+energy source

metabolite production

@refChebi-IDmetaboliteproduction
3162135581indoleyes
6836735581indoleyes
6838035581indoleyes

metabolite tests

@refChebi-IDmetaboliteindole test
3162135581indole+
6838035581indole+
6836735581indole+

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
68380tryptophan deaminase+4.1.99.1
68380glutamate decarboxylase+4.1.1.15
68380N-acetyl-beta-glucosaminidase+3.2.1.52
68380alpha-arabinosidase+3.2.1.55
68380beta-glucosidase+3.2.1.21
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
6945+-+-+++/--++-+-+/-+-+-+-
6945+-+-+++-++-+-++-+-+-

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
6945--++-+++++++++-++--+----+--+-
6945--++--++-++++--++--+----+--+/--
6945--++-+++-+++++-++--+----+--+/--
6945--++--++-++/--+--++--+----+----

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
6945human faecesJapanJPNAsia
60058Human feces,healthy 32-yr-old female JapaneseJapanJPNAsia
67770Human feces

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_2886.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_21;96_1274;97_1512;98_2233;99_2886&stattab=map
  • Last taxonomy: Bacteroides intestinalis subclade
  • 16S sequence: AB214328
  • Sequence Identity:
  • Total samples: 73416
  • soil counts: 511
  • aquatic counts: 1390
  • animal counts: 71273
  • plant counts: 242

Safety information

risk assessment

  • @ref: 6945
  • pathogenicity human: yes, in single cases
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 6945
  • description: Bacteroides intestinalis gene for 16S rRNA, partial sequence, strain:JCM 13265
  • accession: AB214328
  • length: 1484
  • database: ena
  • NCBI tax ID: 471870

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Bacteroides intestinalis DSM 17393471870.8wgspatric471870
66792Bacteroides intestinalis 341, DSM 17393642791621draftimg471870
67770Bacteroides intestinalis DSM 17393GCA_000172175contigncbi471870

GC content

@refGC-contentmethod
694544
694542.7sequence analysis
6777044high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
gram-positiveno96.847yes
anaerobicyes94.479yes
halophileno93.421no
spore-formingno91.493yes
glucose-utilyes87.923no
aerobicno95.013yes
flagellatedno97.472yes
thermophileno99.212yes
motileno90.622no
glucose-fermentyes70.814no

External links

@ref: 6945

culture collection no.: CCUG 53889, DSM 17393, JCM 13265

straininfo link

  • @ref: 71254
  • straininfo: 289856

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16403880Bacteroides intestinalis sp. nov., isolated from human faeces.Bakir MA, Kitahara M, Sakamoto M, Matsumoto M, Benno YInt J Syst Evol Microbiol10.1099/ijs.0.63914-02006Bacteroides/chemistry/*classification/isolation & purification/physiology, Base Composition, Culture Media, Fatty Acids, Feces/*microbiology, Humans, Molecular Sequence Data, Polyamines, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Homology, Nucleic Acid, Species SpecificityCultivation
Enzymology24463968Two new xylanases with different substrate specificities from the human gut bacterium Bacteroides intestinalis DSM 17393.Hong PY, Iakiviak M, Dodd D, Zhang M, Mackie RI, Cann IAppl Environ Microbiol10.1128/AEM.03176-132014Amino Acid Substitution, Bacteroides/*enzymology/isolation & purification, Catalytic Domain, DNA Mutational Analysis, Gastrointestinal Tract/*microbiology, Humans, Substrate Specificity, Xylans/*metabolism, Xylosidases/chemistry/genetics/*isolation & purification/*metabolismPhylogeny
27681607Bacteroides intestinalis DSM 17393, a member of the human colonic microbiome, upregulates multiple endoxylanases during growth on xylan.Wang K, Pereira GV, Cavalcante JJ, Zhang M, Mackie R, Cann ISci Rep10.1038/srep343602016
Pathogenicity35316064Molecular and Biochemical Analyses of a Novel Trifunctional Endoxylanase/Endoglucanase/Feruloyl Esterase from the Human Colonic Bacterium Bacteroides intestinalis DSM 17393.Zhang R, Lin D, Zhang L, Zhan R, Wang S, Wang KJ Agric Food Chem10.1021/acs.jafc.2c010192022*Bacteroides/enzymology, Carboxylic Ester Hydrolases/chemistry/genetics, *Cellulase, Coumaric Acids, *Endo-1,4-beta Xylanases/genetics, Humans, Xylans/chemistryEnzymology

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
6945Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17393)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17393
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
31621Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2790728776041
60058Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 53889)https://www.ccug.se/strain?id=53889
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/
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
71254Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID289856.1StrainInfo: A central database for resolving microbial strain identifiers