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BacDive ID 23776
Type strain
Strain Designation UasXn-3
Culture col. no. DSM 26991 JCM 19020 UasXn-3
NCBI tax ID(s) 1297750
Links
For citation purpose refer to the digital object identifier (doi) of the current version.

Archive

version 9.3 (current version):
version 9.3 (current version)

General

@ref: 21147

BacDive-ID: 23776

DSM-Number: 26991

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-negative

description: Bacteroides luti UasXn-3 is an anaerobe, mesophilic, Gram-negative 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/bacdive23776.20250331.9.3

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

@refgram stainconfidence
125438negative94.613
125439negative99.6

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

@refgrowthtypetemperature
21147positivegrowth37
67770positivegrowth37

Physiology and metabolism

oxygen tolerance

  • @ref: 21147
  • oxygen tolerance: anaerobe

spore formation

@refspore formationconfidence
125438no90
125439no98.6

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6838016634raffinose-fermentation
6838029985L-glutamate-degradation
6838016199urea-hydrolysis
6838017632nitrate-reduction
6838016024D-mannose+fermentation
6838029016arginine-hydrolysis
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

metabolite production

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

metabolite tests

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

enzymes

@refvalueactivityec
68380tyrosine arylamidase-
68380pyrrolidonyl arylamidase-3.4.19.3
68380leucine arylamidase-3.4.11.1
68380leucyl glycin arylamidase+3.4.11.1
68380proline-arylamidase-3.4.11.5
68380L-arginine arylamidase-
68380alkaline phosphatase+3.1.3.1
68380glutamate decarboxylase-4.1.1.15
68380serine arylamidase-
68380glutamyl-glutamate arylamidase+
68380histidine arylamidase-
68380glycin arylamidase-
68380alanine arylamidase+3.4.11.2
68380phenylalanine arylamidase-
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-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: nuccore
  • 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

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingno94.613no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)yes76.122yes
125438spore-formingspore-formingAbility to form endo- or exosporesno90no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no85.617no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno95.653yes
125438motile2+flagellatedAbility to perform flagellated movementno89.095no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno98.6
125439BacteriaNetmotilityAbility to perform movementno71.3
125439BacteriaNetgram_stainReaction to gram-stainingnegative99.6
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe79.3

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/
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
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg OvermannPredicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets10.1101/2024.08.12.607695
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardydeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1https://github.com/GenomeNet/deepG

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