Strain identifier

BacDive ID: 23522

Type strain: Yes

Species: Actinomyces ruminicola

Strain Designation: B71

Strain history: CIP <- 2006, JCM <- D. An strain: B71

NCBI tax ID(s): 332524 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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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

@refhistory
20246<- JCM <- D. An and X. Dong, Chinese Acad. Sci. (CAS), Beijing; B71
67770D. An and X. Dong B71.
122310CIP <- 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

@refnamegrowthlinkcomposition
20246BHI MEDIUM (DSMZ Medium 215)yeshttps://mediadive.dsmz.de/medium/215Name: 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
20246PYG 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
36054MEDIUM 20 - for Anaerobic bacteriayesAgar (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)
122310CIP Medium 20yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=20

culture temp

@refgrowthtypetemperaturerange
20246positivegrowth37mesophilic
36054positivegrowth45thermophilic
67770positivegrowth46thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
20246obligate anaerobe
69480anaerobe98.65

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.995

observation

  • @ref: 67770
  • observation: quinones: MK-10 (70%), MK-9 (30%)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6837516199urea-hydrolysis
6837529016arginine-hydrolysis
6837518257ornithine-degradation
683754853esculin+hydrolysis
6837517634D-glucose-fermentation
6837515824D-fructose+fermentation
6837516024D-mannose+fermentation
6837517716lactose-fermentation
6837527082trehalose-fermentation
6837516899D-mannitol+fermentation
6837516634raffinose-fermentation
6837516988D-ribose-fermentation
6837517057cellobiose-fermentation
6837517632nitrate-reduction
6837517992sucrose+fermentation
6837559640N-acetylglucosamine-fermentation
6837532528turanose+fermentation
6837522599arabinose-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

@refvalueactivityec
68375beta-glucuronidase-3.2.1.31
68375pyrrolidonyl arylamidase-3.4.19.3
68375alkaline phosphatase+3.1.3.1
68375L-arginine arylamidase-
68375beta-galactosidase-3.2.1.23
68375beta-glucosidase+3.2.1.21
68375ornithine decarboxylase-4.1.1.17
68375arginine dihydrolase-3.5.3.6
68375urease-3.5.1.5

API ID32STA

@refUREADH ArgODCESCGLUFRUMNEMALLACTREMANRAFRIBCELNITVPbeta GALArgAPALPyrANOVOSACNAGTURARAbeta GUR
20246---+-+++/---+-------+-++-+--

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
20246cattle rumen, 4-years-old bullockChinaCHNAsia
67770Cattle rumen
122310Animal, Cattle rumen

isolation source categories

Cat1Cat2Cat3
#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

@refbiosafety levelbiosafety level comment
202461Risk group (German classification)
1223102Risk 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

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Actinomyces ruminicola strain DSM 27982332524.10wgspatric332524
66792Actinomyces ruminicola DSM 279822651870319draftimg332524
67770Actinomyces ruminicola DSM 27982GCA_900103885scaffoldncbi332524

GC content

  • @ref: 20246
  • GC-content: 68.06
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno57no
gram-positiveyes96.836no
anaerobicno51.995yes
halophileno87.226no
spore-formingno93.262no
glucose-utilyes89.17no
motileno93.85no
flagellatedno97.634no
thermophileno92.915no
aerobicno95.542no
glucose-fermentyes76.556yes

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

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16957097Actinomyces ruminicola sp. nov., isolated from cattle rumen.An D, Cai S, Dong XInt J Syst Evol Microbiol10.1099/ijs.0.64059-02006Actinomyces/*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 TopicGenetics
Phylogeny27613227Actinomyces 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 CMSyst Appl Microbiol10.1016/j.syapm.2016.08.0012016*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/metabolismMetabolism
Phylogeny29270873Characterization 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 IFolia Microbiol (Praha)10.1007/s12223-017-0577-92017Actinomyces/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/metabolismMetabolism
Phylogeny36459234Actinomyces ruminis sp. nov., an obligately anaerobic bacterium isolated from the rumen of cattle.Lanjekar VB, Hivarkar SS, Vasudevan G, Joshi A, Dhakephalkar PK, Dagar SSArch Microbiol10.1007/s00203-022-03339-12022Cattle, Animals, *Rumen, RNA, Ribosomal, 16S/genetics, Anaerobiosis, Base Composition, Phylogeny, Sequence Analysis, DNA, *Bacteria, Anaerobic, Actinomyces/geneticsTranscriptome

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
20246Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-27982Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 27982)
36054Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7123
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/
68375Automatically annotated from API ID32STA
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/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions 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
87628Reimer, 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-ID297111.1
122310Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109388Collection of Institut Pasteur (CIP 109388)