Strain identifier

BacDive ID: 23776

Type strain: Yes

Species: Bacteroides luti

Strain Designation: UasXn-3

Strain history: M. Hatamoto UasXn-3.

NCBI tax ID(s): 1297750 (species)

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General

@ref: 21147

BacDive-ID: 23776

DSM-Number: 26991

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

description: Bacteroides luti UasXn-3 is an anaerobe, mesophilic bacterium that was isolated from anaerobic granular sludge from municipal wastewater.

NCBI tax id

  • NCBI tax id: 1297750
  • Matching level: species

strain history

@refhistory
21147<- M. Hatamoto, Nagaoka Univ. Technology, Japan; UasXn-3 <- K. Masami
67770M. Hatamoto UasXn-3.

doi: 10.13145/bacdive23776.20230509.8.1

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 luti
  • full scientific name: Bacteroides luti Hatamoto et al. 2014

@ref: 21147

domain: Bacteria

phylum: Bacteroidetes

class: Bacteroidia

order: Bacteroidales

family: Bacteroidaceae

genus: Bacteroides

species: Bacteroides luti

full scientific name: Bacteroides luti Hatamoto et al. 2014

strain designation: UasXn-3

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480no91.99
6948099.999negative

colony morphology

  • @ref: 21147
  • incubation period: 2-3 days

Culture and growth conditions

culture medium

  • @ref: 21147
  • name: TREPONEMA SACCHAROPHILUM MEDIUM (DSMZ Medium 323)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/323
  • composition: Name: TREPONEMA SACCHAROPHILUM MEDIUM (DSMZ Medium 323) Composition: Agar 12.0 g/l Na2CO3 2.5 g/l D-Glucose 2.0 g/l Trypticase peptone 2.0 g/l Yeast extract 2.0 g/l L-Cysteine HCl x H2O 1.0 g/l (NH4)2SO4 0.9 g/l NaCl 0.9 g/l KH2PO4 0.45 g/l K2HPO4 0.45 g/l MgSO4 x 7 H2O 0.19 g/l CaCl2 x 2 H2O 0.12 g/l Sodium resazurin 0.0005 g/l n-Butyric acid iso-Butyric acid DL-2-Methylbutyric acid n-Valeric acid iso-Valeric acid Distilled water

culture temp

@refgrowthtypetemperaturerange
21147positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
21147anaerobe
69480anaerobe99.088

spore formation

@refspore formationconfidence
69481no100
69480no99.986

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836727082trehalose-builds acid from
6836730911sorbitol-builds acid from
683676731melezitose-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
6838029985L-glutamate-degradation
6838017632nitrate-reduction

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-
68380glutamyl-glutamate 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
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
21147+-+-+++-++-+-++-+/--+/--

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
21147--+/-+-+++-++--+-+/-+--+----+--+-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
21147anaerobic granular sludge from municipal wastewaterKamitomioka NagaokaJapanJPNAsia
67770Granular sludge of a UASB reactor

isolation source categories

Cat1Cat2Cat3
#Engineered#Waste#Activated sludge
#Condition#Anoxic (anaerobic)

taxonmaps

  • @ref: 69479
  • File name: preview.99_7281.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_21;96_3404;97_4179;98_5340;99_7281&stattab=map
  • Last taxonomy: Bacteroides luti subclade
  • 16S sequence: AB787271
  • Sequence Identity:
  • Total samples: 8287
  • soil counts: 164
  • aquatic counts: 1429
  • animal counts: 6640
  • plant counts: 54

Safety information

risk assessment

  • @ref: 21147
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 21147
  • description: Bacteroides luti gene for 16S ribosomal RNA, partial sequence
  • accession: AB787271
  • length: 1442
  • database: ena
  • NCBI tax ID: 1297750

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Bacteroides luti strain DSM 269911297750.4wgspatric1297750
66792Bacteroides luti DSM 269912695420932draftimg1297750
67770Bacteroides luti DSM 26991GCA_900128905scaffoldncbi1297750

GC content

  • @ref: 21147
  • GC-content: 44.4
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno91.197no
gram-positiveno97.433no
anaerobicyes95.157yes
aerobicno96.651no
halophileno93.14no
spore-formingno93.608no
thermophileno97.953yes
glucose-utilyes90.465no
flagellatedno97.347no
glucose-fermentyes66.731no

External links

@ref: 21147

culture collection no.: DSM 26991, JCM 19020

straininfo link

  • @ref: 87808
  • straininfo: 401156

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny24556634Bacteroides luti sp. nov., an anaerobic, cellulolytic and xylanolytic bacterium isolated from methanogenic sludge.Hatamoto M, Kaneshige M, Nakamura A, Yamaguchi TInt J Syst Evol Microbiol10.1099/ijs.0.056630-02014Bacterial Typing Techniques, Bacteroides/*classification/genetics/isolation & purification, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Japan, Methane/metabolism, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage/*microbiologyGenetics
Phylogeny30141156Bacteroides sedimenti sp. nov., isolated from a chloroethenes-dechlorinating consortium enriched from river sediment.Ismaeil M, Yoshida N, Katayama AJ Microbiol10.1007/s12275-018-8187-z2018Bacteria, Anaerobic/classification/isolation & purification/physiology, Bacterial Typing Techniques, Bacteroides/*classification/genetics/*isolation & purification/physiology, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Genes, Bacterial/genetics, Geologic Sediments/*microbiology, Japan, Phenotype, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rivers/*microbiology, Species SpecificityEnzymology

Reference

@idauthorstitledoi/urlcataloguejournalpubmed
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
21147Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-26991Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 26991)
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
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa1025Nucleic Acids Res. 49: D498-D508 202033211880
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
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
87808Reimer, 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-ID401156.1