Strain identifier

BacDive ID: 12521

Type strain: Yes

Species: Odoribacter laneus

Strain history: Y. Watanabe B164 (=YIT 12061).

NCBI tax ID(s): 742817 (strain), 626933 (species)

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General

@ref: 16357

BacDive-ID: 12521

DSM-Number: 22474

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

description: Odoribacter laneus DSM 22474 is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from human faeces of healthy Japanese adult.

NCBI tax id

NCBI tax idMatching level
626933species
742817strain

strain history

@refhistory
16357<- Y. Watanabe, Yakult Central Inst. Microbiol. Res., Kunitachi, Japan <- F. Nagai and M. Morotomi; YIT 12061
67770Y. Watanabe B164 (=YIT 12061).

doi: 10.13145/bacdive12521.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Bacteroidia
  • order: Bacteroidales
  • family: Odoribacteraceae
  • genus: Odoribacter
  • species: Odoribacter laneus
  • full scientific name: Odoribacter laneus Nagai et al. 2010

@ref: 16357

domain: Bacteria

phylum: Bacteroidetes

class: Bacteroidia

order: Bacteroidales

family: Odoribacteraceae

genus: Odoribacter

species: Odoribacter laneus

full scientific name: Odoribacter laneus Nagai et al. 2010 emend. Hahnke et al. 2016

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
29508negative9.2 µm1.15 µmrod-shapedno
125439negative97.9

pigmentation

  • @ref: 29508
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
16357FASTIDIOUS 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
16357PYG 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
16357COLUMBIA 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

culture temp

@refgrowthtypetemperature
16357positivegrowth37
67770positivegrowth37

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
16357anaerobe
29508anaerobe

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6838027897tryptophan+energy source
6838029985L-glutamate-degradation
6838016634raffinose-fermentation
6838017632nitrate-reduction
6838016024D-mannose-fermentation
6838029016arginine-hydrolysis
6838016199urea-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
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

@refChebi-IDmetaboliteproduction
2950835581indoleyes
6838035581indoleyes
6836735581indoleyes

metabolite tests

@refChebi-IDmetaboliteindole test
2950835581indole+
6838035581indole+
6836735581indole+

enzymes

@refvalueactivityec
29508acid phosphatase+3.1.3.2
29508alkaline phosphatase+3.1.3.1
29508alpha-galactosidase+3.2.1.22
29508gelatinase+
68380tyrosine arylamidase-
68380proline-arylamidase-3.4.11.5
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
68380pyrrolidonyl arylamidase-3.4.19.3
68380phenylalanine arylamidase-
68380leucyl glycin arylamidase+3.4.11.1
68380tryptophan deaminase+4.1.99.1
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+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
16357+---------+---------

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
16357--+++/-+---+---+/--+++/--+-+/---+----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
16357human faeces of healthy Japanese adultTokyoJapanJPNAsia
67770Human feces

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_4392.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_463;96_2199;97_2661;98_3298;99_4392&stattab=map
  • Last taxonomy: Odoribacter laneus subclade
  • 16S sequence: AB547648
  • Sequence Identity:
  • Total samples: 22620
  • soil counts: 190
  • aquatic counts: 1394
  • animal counts: 21002
  • plant counts: 34

Safety information

risk assessment

  • @ref: 16357
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Odoribacter laneus gene for 16S ribosomal RNA, partial sequence, strain: JCM 16069AB5476481487nuccore742817
16357Odoribacter laneus YIT 12061 gene for 16S rRNA, partial sequenceAB4908051478nuccore742817

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Odoribacter laneus YIT 12061GCA_000243215scaffoldncbi742817
66792Odoribacter laneus YIT 12061742817.3wgspatric742817
66792Odoribacter laneus YIT 120612513237280draftimg742817

GC content

@refGC-contentmethod
1635742.4high performance liquid chromatography (HPLC)
2950842.4
1635740.5sequence analysis

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingno87.304no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)yes79.887yes
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no79.704yes
125438spore-formingspore-formingAbility to form endo- or exosporesno87.655no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno94.093yes
125438motile2+flagellatedAbility to perform flagellated movementno86yes
125439BacteriaNetspore_formationAbility to form endo- or exosporesno66.8
125439BacteriaNetmotilityAbility to perform movementno53
125439BacteriaNetgram_stainReaction to gram-stainingnegative97.9
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthanaerobe86.9

External links

@ref: 16357

culture collection no.: DSM 22474, JCM 16069, YIT 12061, KCTC 15133

straininfo link

  • @ref: 81740
  • straininfo: 397108

literature

  • topic: Phylogeny
  • Pubmed-ID: 19667375
  • title: Alistipes indistinctus sp. nov. and Odoribacter laneus sp. nov., common members of the human intestinal microbiota isolated from faeces.
  • authors: Nagai F, Morotomi M, Watanabe Y, Sakon H, Tanaka R
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.014571-0
  • year: 2009
  • mesh: Adult, Bacteroidetes/classification/genetics/*isolation & purification/metabolism, Catalase/metabolism, Fatty Acids/analysis, Feces/*microbiology, Humans, Male, Middle Aged, Molecular Sequence Data, Phylogeny
  • topic2: Metabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
16357Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22474)https://www.dsmz.de/collection/catalogue/details/culture/DSM-22474
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
29508Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604125907
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
81740Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID397108.1StrainInfo: A central database for resolving microbial strain identifiers
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1