Strain identifier
BacDive ID: 12521
Type strain:
Species: Odoribacter laneus
Strain history: Y. Watanabe B164 (=YIT 12061).
NCBI tax ID(s): 742817 (strain), 626933 (species)
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 id | Matching level |
---|---|
742817 | strain |
626933 | species |
strain history
@ref | history |
---|---|
16357 | <- Y. Watanabe, Yakult Central Inst. Microbiol. Res., Kunitachi, Japan <- F. Nagai and M. Morotomi; YIT 12061 |
67770 | Y. Watanabe B164 (=YIT 12061). |
doi: 10.13145/bacdive12521.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacteroidota
- domain: Bacteria
- phylum: Bacteroidota
- class: Bacteroidia
- order: Bacteroidales
- family: 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
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
29508 | negative | 9.2 µm | 1.15 µm | rod-shaped | no | |
69480 | negative | 99.998 |
pigmentation
- @ref: 29508
- production: yes
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
16357 | FASTIDIOUS ANAEROBE BROTH (DSMZ Medium 1203a) | yes | https://mediadive.dsmz.de/medium/1203a | Name: FASTIDIOUS ANAEROBE BROTH (DSMZ Medium 1203a) Composition: Fastidious Anaerobe Basal Broth 35.4 g/l Distilled water |
16357 | PYG MEDIUM (MODIFIED) (DSMZ Medium 104) | yes | https://mediadive.dsmz.de/medium/104 | Name: 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 |
16357 | COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) | yes | https://mediadive.dsmz.de/medium/693 | Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
16357 | positive | growth | 37 | mesophilic |
67770 | positive | growth | 37 | mesophilic |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance | confidence |
---|---|---|
16357 | anaerobe | |
29508 | anaerobe | |
69480 | anaerobe | 99.598 |
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 93 |
69480 | no | 99.989 |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
68367 | 27082 | trehalose | - | builds acid from |
68367 | 62345 | L-rhamnose | - | builds acid from |
68367 | 30911 | sorbitol | - | builds acid from |
68367 | 16634 | raffinose | - | builds acid from |
68367 | 6731 | melezitose | - | builds acid from |
68367 | 16024 | D-mannose | - | builds acid from |
68367 | 17057 | cellobiose | - | builds acid from |
68367 | 17754 | glycerol | - | builds acid from |
68367 | 4853 | esculin | - | hydrolysis |
68367 | 5291 | gelatin | + | hydrolysis |
68367 | 30849 | L-arabinose | - | builds acid from |
68367 | 65327 | D-xylose | - | builds acid from |
68367 | 17814 | salicin | - | builds acid from |
68367 | 17306 | maltose | - | builds acid from |
68367 | 17992 | sucrose | - | builds acid from |
68367 | 17716 | lactose | - | builds acid from |
68367 | 16899 | D-mannitol | - | builds acid from |
68367 | 17634 | D-glucose | - | builds acid from |
68367 | 16199 | urea | - | hydrolysis |
68367 | 27897 | tryptophan | + | energy source |
68380 | 16199 | urea | - | hydrolysis |
68380 | 29016 | arginine | - | hydrolysis |
68380 | 16024 | D-mannose | - | fermentation |
68380 | 16634 | raffinose | - | fermentation |
68380 | 29985 | L-glutamate | - | degradation |
68380 | 17632 | nitrate | - | reduction |
68380 | 27897 | tryptophan | + | energy source |
metabolite production
@ref | Chebi-ID | metabolite | production |
---|---|---|---|
29508 | 35581 | indole | yes |
68367 | 35581 | indole | yes |
68380 | 35581 | indole | yes |
metabolite tests
@ref | Chebi-ID | metabolite | indole test |
---|---|---|---|
29508 | 35581 | indole | + |
68380 | 35581 | indole | + |
68367 | 35581 | indole | + |
enzymes
@ref | value | activity | ec |
---|---|---|---|
29508 | acid phosphatase | + | 3.1.3.2 |
29508 | alkaline phosphatase | + | 3.1.3.1 |
29508 | alpha-galactosidase | + | 3.2.1.22 |
29508 | gelatinase | + | |
68380 | serine arylamidase | - | |
68380 | glutamyl-glutamate arylamidase | - | |
68380 | histidine arylamidase | - | |
68380 | glycin arylamidase | - | |
68380 | alanine arylamidase | + | 3.4.11.2 |
68380 | tyrosine arylamidase | - | |
68380 | pyrrolidonyl arylamidase | - | 3.4.19.3 |
68380 | phenylalanine arylamidase | - | |
68380 | leucyl glycin arylamidase | + | 3.4.11.1 |
68380 | proline-arylamidase | - | 3.4.11.5 |
68380 | alkaline phosphatase | + | 3.1.3.1 |
68380 | tryptophan deaminase | + | 4.1.99.1 |
68380 | glutamate decarboxylase | - | 4.1.1.15 |
68380 | N-acetyl-beta-glucosaminidase | + | 3.2.1.52 |
68380 | beta-glucuronidase | - | 3.2.1.31 |
68380 | alpha-arabinosidase | - | 3.2.1.55 |
68380 | beta-glucosidase | - | 3.2.1.21 |
68380 | alpha-glucosidase | + | 3.2.1.20 |
68380 | beta-galactosidase | + | 3.2.1.23 |
68380 | alpha-galactosidase | + | 3.2.1.22 |
68380 | arginine dihydrolase | - | 3.5.3.6 |
68380 | urease | - | 3.5.1.5 |
68367 | beta-glucosidase | - | 3.2.1.21 |
68367 | gelatinase | + | |
68367 | urease | - | 3.5.1.5 |
API 20A
@ref | IND | URE | GLU | MAN | LAC | SAC | MAL | SAL | XYL | ARA | GEL | ESC | GLY | CEL | MNE | MLZ | RAF | SOR | RHA | TRE |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
16357 | + | - | - | - | - | - | - | - | - | - | + | - | - | - | - | - | - | - | - | - |
API rID32A
@ref | URE | ADH Arg | alpha GAL | beta GAL | beta GP | alpha GLU | beta GLU | alpha ARA | beta GUR | beta NAG | MNE | RAF | GDC | alpha FUC | NIT | IND | PAL | ArgA | ProA | LGA | PheA | LeuA | PyrA | TyrA | AlaA | GlyA | HisA | GGA | SerA |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
16357 | - | - | + | + | +/- | + | - | - | - | + | - | - | - | +/- | - | + | + | +/- | - | + | - | +/- | - | - | + | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
16357 | human faeces of healthy Japanese adult | Tokyo | Japan | JPN | Asia |
67770 | Human feces |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#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
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Odoribacter laneus gene for 16S ribosomal RNA, partial sequence, strain: JCM 16069 | AB547648 | 1487 | ena | 742817 |
16357 | Odoribacter laneus YIT 12061 gene for 16S rRNA, partial sequence | AB490805 | 1478 | ena | 742817 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Odoribacter laneus YIT 12061 | GCA_000243215 | scaffold | ncbi | 742817 |
66792 | Odoribacter laneus YIT 12061 | 742817.3 | wgs | patric | 742817 |
66792 | Odoribacter laneus YIT 12061 | 2513237280 | draft | img | 742817 |
GC content
@ref | GC-content | method |
---|---|---|
16357 | 42.4 | high performance liquid chromatography (HPLC) |
29508 | 42.4 | |
16357 | 40.5 | sequence analysis |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 93 | no |
motile | no | 92.336 | no |
flagellated | no | 97.276 | yes |
gram-positive | no | 96.147 | yes |
anaerobic | yes | 96.201 | yes |
aerobic | no | 93.811 | yes |
halophile | no | 78.756 | no |
spore-forming | no | 95.015 | no |
thermophile | no | 96.385 | no |
glucose-util | yes | 91.72 | no |
glucose-ferment | yes | 58.008 | no |
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
@id | authors | catalogue | doi/url | title | journal | pubmed | ID_cross_reference |
---|---|---|---|---|---|---|---|
16357 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22474) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-22474 | ||||
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | ||||
20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | ||
29508 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 28776041 | 25907 | ||
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | ||||
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | |||||
68367 | Automatically annotated from API 20A | ||||||
68380 | Automatically annotated from API rID32A | ||||||
69479 | João 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 | ||||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | ||||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | ||||
81740 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID397108.1 | StrainInfo: A central database for resolving microbial strain identifiers |