Strain identifier
BacDive ID: 23522
Type strain:
Species: Actinomyces ruminicola
Strain Designation: B71
Strain history: CIP <- 2006, JCM <- D. An strain: B71
NCBI tax ID(s): 332524 (species)
General
@ref: 20246
BacDive-ID: 23522
DSM-Number: 27982
keywords: genome sequence, 16S sequence, Bacteria, obligate anaerobe, mesophilic, Gram-positive
description: Actinomyces ruminicola B71 is an obligate anaerobe, mesophilic, Gram-positive bacterium that was isolated from cattle rumen, 4-years-old bullock.
NCBI tax id
- NCBI tax id: 332524
- Matching level: species
strain history
@ref | history |
---|---|
20246 | <- JCM <- D. An and X. Dong, Chinese Acad. Sci. (CAS), Beijing; B71 |
67770 | D. An and X. Dong B71. |
122310 | CIP <- 2006, JCM <- D. An strain: B71 |
doi: 10.13145/bacdive23522.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Actinomycetes
- order: Actinomycetales
- family: Actinomycetaceae
- genus: Actinomyces
- species: Actinomyces ruminicola
- full scientific name: Actinomyces ruminicola An et al. 2006
@ref: 20246
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Actinomycetaceae
genus: Actinomyces
species: Actinomyces ruminicola
full scientific name: Actinomyces ruminicola An et al. 2006 emend. Nouioui et al. 2018
strain designation: B71
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: positive
- confidence: 100
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
20246 | BHI MEDIUM (DSMZ Medium 215) | yes | https://mediadive.dsmz.de/medium/215 | Name: BHI MEDIUM (DSMZ Medium 215; with strain-specific modifications) Composition: Rumen fluid 150.0 g/l Brain heart infusion 37.0 g/l Distilled water |
20246 | 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 |
36054 | MEDIUM 20 - for Anaerobic bacteria | yes | Agar (15.000 g);Glucose (5.000 g);Yeast extract (20.000 g);Tryptone (30.000 g);Cysteine hydrochloride (0.500 g);distilled water (1000.000 ml);Hemin solution -M00149 (25.000 ml) | |
122310 | CIP Medium 20 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=20 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
20246 | positive | growth | 37 | mesophilic |
36054 | positive | growth | 45 | thermophilic |
67770 | positive | growth | 46 | thermophilic |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance | confidence |
---|---|---|
20246 | obligate anaerobe | |
69480 | anaerobe | 98.65 |
spore formation
- @ref: 69480
- spore formation: no
- confidence: 99.995
observation
- @ref: 67770
- observation: quinones: MK-10 (70%), MK-9 (30%)
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
68375 | 16199 | urea | - | hydrolysis |
68375 | 29016 | arginine | - | hydrolysis |
68375 | 18257 | ornithine | - | degradation |
68375 | 4853 | esculin | + | hydrolysis |
68375 | 17634 | D-glucose | - | fermentation |
68375 | 15824 | D-fructose | + | fermentation |
68375 | 16024 | D-mannose | + | fermentation |
68375 | 17716 | lactose | - | fermentation |
68375 | 27082 | trehalose | - | fermentation |
68375 | 16899 | D-mannitol | + | fermentation |
68375 | 16634 | raffinose | - | fermentation |
68375 | 16988 | D-ribose | - | fermentation |
68375 | 17057 | cellobiose | - | fermentation |
68375 | 17632 | nitrate | - | reduction |
68375 | 17992 | sucrose | + | fermentation |
68375 | 59640 | N-acetylglucosamine | - | fermentation |
68375 | 32528 | turanose | + | fermentation |
68375 | 22599 | arabinose | - | fermentation |
antibiotic resistance
- @ref: 68375
- ChEBI: 28368
- metabolite: novobiocin
- is antibiotic: yes
- is resistant: yes
- resistance conc.: 1.8 µg
metabolite production
- @ref: 68375
- Chebi-ID: 15688
- metabolite: acetoin
- production: no
metabolite tests
- @ref: 68375
- Chebi-ID: 15688
- metabolite: acetoin
- voges-proskauer-test: -
enzymes
@ref | value | activity | ec |
---|---|---|---|
68375 | beta-glucuronidase | - | 3.2.1.31 |
68375 | pyrrolidonyl arylamidase | - | 3.4.19.3 |
68375 | alkaline phosphatase | + | 3.1.3.1 |
68375 | L-arginine arylamidase | - | |
68375 | beta-galactosidase | - | 3.2.1.23 |
68375 | beta-glucosidase | + | 3.2.1.21 |
68375 | ornithine decarboxylase | - | 4.1.1.17 |
68375 | arginine dihydrolase | - | 3.5.3.6 |
68375 | urease | - | 3.5.1.5 |
API ID32STA
@ref | URE | ADH Arg | ODC | ESC | GLU | FRU | MNE | MAL | LAC | TRE | MAN | RAF | RIB | CEL | NIT | VP | beta GAL | ArgA | PAL | PyrA | NOVO | SAC | NAG | TUR | ARA | beta GUR |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
20246 | - | - | - | + | - | + | + | +/- | - | - | + | - | - | - | - | - | - | - | + | - | + | + | - | + | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | country | origin.country | continent |
---|---|---|---|---|
20246 | cattle rumen, 4-years-old bullock | China | CHN | Asia |
67770 | Cattle rumen | |||
122310 | Animal, Cattle rumen |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Host | #Mammals | #Bovinae (Cow, Cattle) |
#Host Body-Site | #Organ | #Rumen |
taxonmaps
- @ref: 69479
- File name: preview.99_40065.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_124;96_553;97_23201;98_29271;99_40065&stattab=map
- Last taxonomy: Actinomyces ruminicola subclade
- 16S sequence: DQ072005
- Sequence Identity:
- Total samples: 331
- soil counts: 11
- aquatic counts: 3
- animal counts: 299
- plant counts: 18
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
20246 | 1 | Risk group (German classification) |
122310 | 2 | Risk group (French classification) |
Sequence information
16S sequences
- @ref: 20246
- description: Actinomyces ruminicola strain B71 16S ribosomal RNA gene, partial sequence
- accession: DQ072005
- length: 1526
- database: ena
- NCBI tax ID: 332524
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Actinomyces ruminicola strain DSM 27982 | 332524.10 | wgs | patric | 332524 |
66792 | Actinomyces ruminicola DSM 27982 | 2651870319 | draft | img | 332524 |
67770 | Actinomyces ruminicola DSM 27982 | GCA_900103885 | scaffold | ncbi | 332524 |
GC content
- @ref: 20246
- GC-content: 68.06
- method: thermal denaturation, midpoint method (Tm)
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 57 | no |
gram-positive | yes | 96.836 | no |
anaerobic | no | 51.995 | yes |
halophile | no | 87.226 | no |
spore-forming | no | 93.262 | no |
glucose-util | yes | 89.17 | no |
motile | no | 93.85 | no |
flagellated | no | 97.634 | no |
thermophile | no | 92.915 | no |
aerobic | no | 95.542 | no |
glucose-ferment | yes | 76.556 | yes |
External links
@ref: 20246
culture collection no.: DSM 27982, CGMCC 1.5030, JCM 13352, CIP 109388, CGMCC 15030
straininfo link
- @ref: 87628
- straininfo: 297111
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 16957097 | Actinomyces ruminicola sp. nov., isolated from cattle rumen. | An D, Cai S, Dong X | Int J Syst Evol Microbiol | 10.1099/ijs.0.64059-0 | 2006 | Actinomyces/*classification/genetics, Animals, Bacterial Typing Techniques, Base Sequence, Cattle, DNA, Bacterial/analysis, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/*analysis/genetics, Rumen/*microbiology, Sequence Analysis, DNA, Terminology as Topic | Genetics |
Phylogeny | 27613227 | Actinomyces succiniciruminis sp. nov. and Actinomyces glycerinitolerans sp. nov., two novel organic acid-producing bacteria isolated from rumen. | Palakawong N A S, Pristas P, Hrehova L, Javorsky P, Stams AJ, Plugge CM | Syst Appl Microbiol | 10.1016/j.syapm.2016.08.001 | 2016 | *Actinomyces/classification/genetics/isolation & purification, Animals, Bacterial Typing Techniques, Base Composition/genetics, Base Sequence, Cattle/*microbiology, Cell Wall/chemistry, DNA, Bacterial/genetics, Fatty Acids/analysis, Female, Genes, Essential/genetics, Glycerol/metabolism, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, Rumen/*microbiology, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Sheep/*microbiology, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/*veterinary, Succinic Acid/metabolism | Metabolism |
Phylogeny | 29270873 | Characterization of a xylanolytic bacterial strain C10 isolated from the rumen of a red deer (Cervus elaphus) closely related of the recently described species Actinomyces succiniciruminis, A. glycerinitolerans, and A. ruminicola. | Simunek J Jr, Killer J, Sechovcova H, Simunek J, Pechar R, Rada V, Svec P, Sedlacek I | Folia Microbiol (Praha) | 10.1007/s12223-017-0577-9 | 2017 | Actinomyces/classification/genetics/*isolation & purification/*metabolism, Animals, Base Composition, Cellulose/metabolism, DNA, Bacterial/genetics, Deer/*microbiology, Fatty Acids/analysis, Genes, Bacterial/genetics, Peptidoglycan/analysis, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Rumen/*microbiology, Xylans/metabolism | Metabolism |
Phylogeny | 36459234 | Actinomyces ruminis sp. nov., an obligately anaerobic bacterium isolated from the rumen of cattle. | Lanjekar VB, Hivarkar SS, Vasudevan G, Joshi A, Dhakephalkar PK, Dagar SS | Arch Microbiol | 10.1007/s00203-022-03339-1 | 2022 | Cattle, Animals, *Rumen, RNA, Ribosomal, 16S/genetics, Anaerobiosis, Base Composition, Phylogeny, Sequence Analysis, DNA, *Bacteria, Anaerobic, Actinomyces/genetics | Transcriptome |
Reference
@id | authors | title | doi/url | catalogue | journal | pubmed |
---|---|---|---|---|---|---|
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 | |||
20246 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-27982 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 27982) | |||
36054 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/7123 | ||||
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 | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
68375 | Automatically annotated from API ID32STA | |||||
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 | |||
87628 | 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-ID297111.1 | |||
122310 | Curators of the CIP | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109388 | Collection of Institut Pasteur (CIP 109388) |