Strain identifier
BacDive ID: 133840
Type strain:
Species: Bacteroides reticulotermitis
Strain Designation: Rs-03
Strain history: M. Ohkuma Rs-03.
NCBI tax ID(s): 1445607 (strain), 1133319 (species)
General
@ref: 42660
BacDive-ID: 133840
DSM-Number: 105720
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-negative, rod-shaped
description: Bacteroides reticulotermitis Rs-03 is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from gut of a subterranean termite.
NCBI tax id
NCBI tax id | Matching level |
---|---|
1445607 | strain |
1133319 | species |
strain history
@ref | history |
---|---|
42660 | <- JCM RIKEN BioResource Center, Tsukuba, Japan; JCM 10512 <- M. Ohkuma; Rs-03 |
67770 | M. Ohkuma Rs-03. |
doi: 10.13145/bacdive133840.20230509.8.1
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 reticulotermitis
- full scientific name: Bacteroides reticulotermitis Sakamoto and Ohkuma 2013
@ref: 42660
domain: Bacteria
phylum: Bacteroidetes
class: Bacteroidia
order: Bacteroidales
family: Bacteroidaceae
genus: Bacteroides
species: Bacteroides reticulotermitis
full scientific name: Bacteroides reticulotermitis Sakamoto and Ohkuma 2013
strain designation: Rs-03
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
30643 | negative | 2.1 µm | 0.8 µm | rod-shaped | no | |
69480 | no | 91.973 | ||||
69480 | negative | 99.999 |
pigmentation
- @ref: 30643
- production: yes
Culture and growth conditions
culture medium
- @ref: 42660
- name: PYG MEDIUM (MODIFIED) (DSMZ Medium 104)
- growth: yes
- link: https://mediadive.dsmz.de/medium/104
- composition: 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
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
42660 | positive | growth | 37 | mesophilic |
30643 | positive | growth | 25-40 | |
30643 | positive | optimum | 37 | mesophilic |
67770 | positive | growth | 37 | mesophilic |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance | confidence |
---|---|---|
30643 | anaerobe | |
69480 | anaerobe | 98.68 |
spore formation
@ref | spore formation | confidence |
---|---|---|
30643 | no | |
69481 | no | 100 |
69480 | no | 99.998 |
observation
- @ref: 67770
- observation: quinones: MK-9, MK-10
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
30643 | 22599 | arabinose | + | carbon source |
30643 | 17057 | cellobiose | + | carbon source |
30643 | 17234 | glucose | + | carbon source |
30643 | 17716 | lactose | + | carbon source |
30643 | 17306 | maltose | + | carbon source |
30643 | 37684 | mannose | + | carbon source |
30643 | 16634 | raffinose | + | carbon source |
30643 | 26546 | rhamnose | + | carbon source |
30643 | 17814 | salicin | + | carbon source |
30643 | 17992 | sucrose | + | carbon source |
30643 | 18222 | xylose | + | carbon source |
30643 | 4853 | esculin | + | hydrolysis |
enzymes
@ref | value | activity | ec |
---|---|---|---|
30643 | alkaline phosphatase | + | 3.1.3.1 |
30643 | alpha-galactosidase | + | 3.2.1.22 |
Isolation, sampling and environmental information
isolation
@ref | sample type | host species | geographic location | country | origin.country | continent |
---|---|---|---|---|---|---|
30643 | gut of a subterranean termite | |||||
42660 | termite gut Reticulitermes speratus | Reticulitermes speratus | Saitama Prefecture | Japan | JPN | Asia |
67770 | Gut of the subterranean termite Reticulitermes speratus | Reticulitermes speratus |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Host | #Arthropoda | #Insecta |
#Host Body-Site | #Gastrointestinal tract | #Stomach |
taxonmaps
- @ref: 69479
- File name: preview.99_6766.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_21;96_3195;97_3920;98_4990;99_6766&stattab=map
- Last taxonomy: Bacteroides reticulotermitis subclade
- 16S sequence: AB692943
- Sequence Identity:
- Total samples: 16994
- soil counts: 518
- aquatic counts: 1807
- animal counts: 14462
- plant counts: 207
Safety information
risk assessment
- @ref: 42660
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 30643
- description: Bacteroides reticulotermitis gene for 16S ribosomal RNA, partial sequence
- accession: AB692943
- length: 1419
- database: nuccore
- NCBI tax ID: 1445607
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Bacteroides reticulotermitis DSM 105720 | GCA_014196955 | scaffold | ncbi | 1133319 |
66792 | Bacteroides reticulotermitis JCM 10512 | 1445607.3 | wgs | patric | 1445607 |
66792 | Bacteroides reticulotermitis strain DSM 105720 | 1133319.4 | wgs | patric | 1133319 |
66792 | Bacteroides reticulotermitis DSM 105720 | 2830041218 | draft | img | 1133319 |
66792 | Bacteroides reticulotermitis JCM 10512 | 2609459943 | draft | img | 1445607 |
67770 | Bacteroides reticulotermitis JCM 10512 | GCA_000517545 | contig | ncbi | 1445607 |
GC content
@ref | GC-content | method |
---|---|---|
30643 | 44.9 | |
67770 | 44.9 | high performance liquid chromatography (HPLC) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | no | 91.175 | yes |
gram-positive | no | 97.72 | yes |
anaerobic | yes | 94.291 | no |
halophile | no | 92.803 | no |
spore-forming | no | 93.972 | yes |
glucose-util | yes | 90.294 | yes |
thermophile | no | 99.066 | yes |
aerobic | no | 96.333 | yes |
flagellated | no | 96.743 | yes |
glucose-ferment | yes | 70.6 | no |
External links
@ref: 42660
culture collection no.: JCM 10512, CCUG 62153, DSM 105720
straininfo link
- @ref: 91616
- straininfo: 400491
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 22544795 | Bacteroides reticulotermitis sp. nov., isolated from the gut of a subterranean termite (Reticulitermes speratus). | Sakamoto M, Ohkuma M | Int J Syst Evol Microbiol | 10.1099/ijs.0.040931-0 | 2012 | Animals, Bacterial Typing Techniques, Bacteroides/*classification/genetics/isolation & purification, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Gastrointestinal Tract/*microbiology, Isoptera/*microbiology, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analysis | Genetics |
Genetics | 24526645 | Draft Genome Sequence of Bacteroides reticulotermitis Strain JCM 10512T, Isolated from the Gut of a Termite. | Yuki M, Oshima K, Suda W, Sakamoto M, Iida T, Hattori M, Ohkuma M | Genome Announc | 10.1128/genomeA.00072-14 | 2014 | Phylogeny |
Reference
@id | authors | title | doi/url | ID_cross_reference | pubmed | catalogue | journal |
---|---|---|---|---|---|---|---|
20215 | Parte, 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 DSMZ | 10.1099/ijsem.0.004332 | ||||
30643 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 10.1128/mSphere.00237-17 | 26974 | 28776041 | ||
42660 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-105720 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 105720) | ||||
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | ||||
66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | 10.1093/nar/gkaa1025 | 33211880 | Nucleic Acids Res. 49: D498-D508 2020 | ||
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | |||||
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. | MicrobeAtlas 1.0 beta | https://microbeatlas.org/ | ||||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Predictions 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 | ||||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | Predictions based on the model GenomeNet Sporulation v. 1 | 10.21203/rs.3.rs-2527258/v1 | ||||
91616 | Reimer, 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 identifiers | 10.60712/SI-ID400491.1 |