Strain identifier

BacDive ID: 17801

Type strain: Yes

Species: Ruania albidiflava

Strain Designation: 3-6

Strain history: CIP <- 2007, JCM <- 2006, Y. Huang, Chinese Academy Sciences, Beijing, China: strain 3-6

NCBI tax ID(s): 1123065 (strain), 366586 (species)

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General

@ref: 7254

BacDive-ID: 17801

DSM-Number: 18029

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-positive, coccus-shaped

description: Ruania albidiflava 3-6 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from soil, farmland.

NCBI tax id

NCBI tax idMatching level
1123065strain
366586species

strain history

@refhistory
7254<- Ying Huang <- Qiang Gu, strain 3-6
67770Y. Huang 3-6.
116186CIP <- 2007, JCM <- 2006, Y. Huang, Chinese Academy Sciences, Beijing, China: strain 3-6

doi: 10.13145/bacdive17801.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Ruaniaceae
  • genus: Ruania
  • species: Ruania albidiflava
  • full scientific name: Ruania albidiflava Gu et al. 2007

@ref: 7254

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Ruaniaceae

genus: Ruania

species: Ruania albidiflava

full scientific name: Ruania albidiflava Gu et al. 2007

strain designation: 3-6

type strain: yes

Morphology

cell morphology

@refgram staincell widthcell shapemotilityconfidence
31908positive0.5-0.8 µmcoccus-shapedno
69480no94.403
69480positive100
116186positivecoccus-shapedno

colony morphology

@refcolony colorincubation periodmedium used
21406Cream (9001)10-14 daysISP 2
21406Beige (1001)10-14 daysISP 4

pigmentation

  • @ref: 31908
  • production: yes

multimedia

@refmultimedia contentcaptionintellectual property rights
66793EM_DSM_18029_1.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_18029_2.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_18029_3.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_18029_4.jpgelectron microscopic image© HZI/Manfred Rohde

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7254RICH MEDIUM (DSMZ Medium 736)yeshttps://mediadive.dsmz.de/medium/736Name: RICH MEDIUM (DSMZ Medium 736) Composition: Agar 20.0 g/l Bacto peptone 10.0 g/l Yeast extract 5.0 g/l Malt extract 5.0 g/l Casamino acids 5.0 g/l Glycerol 2.0 g/l Meat extract 2.0 g/l MgSO4 x 7 H2O 1.0 g/l Tween 80 0.05 g/l Distilled water
21406ISP 2yesName: ISP 2 / Yeast Malt Agar (5265); 5265 Composition Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l Agar 15.0 g/l Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.0 Usage: Maintenance and Taxonomy Organisms: All Actinomycetes
21406ISP 4yesName: ISP 4; DSM 547 Solution I: Difco soluble starch, 10.0 g. Make a paste of the starch with a small amount of cold distilled water and bring to a volume of 500 ml. Solution II: CaCO3 2.0 g K2HPO4 (anhydrous) 1.0 g MgSO4 x 7 H2O 1.0 g NaCl 1.0 g (NH4)2SO4 2.0 g Distilled water 500.0 ml Trace salt solution (see below) 1.0 ml The pH should be between 7.0 and 7.4. Do not adjust if it is within this range. Mix solutions I and II together. Add 20.0 g agar. Liquify agar by steaming at 100°C for 10 to 20 min. Trace element solution: FeSO4 x 7 H2O 0.1 g MnCl2 x 4 H2O 0.1 g ZnSO4 x 7 H2O 0.1 g Distilled water 100.0 ml
36057MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
116186CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72
116186CIP Medium 112yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=112

culture temp

@refgrowthtypetemperaturerange
7254positivegrowth28mesophilic
31908positivegrowth20-37
31908positiveoptimum28mesophilic
36057positivegrowth30mesophilic
67770positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
31908positivegrowth5.5-12.5alkaliphile
31908positiveoptimum6.5-10.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31908aerobe
116186facultative anaerobe

spore formation

@refspore formationconfidence
31908no
69481no100
69480no99.987

halophily

@refsaltgrowthtested relationconcentration
31908NaClpositivegrowth0-10 %
31908NaClpositiveoptimum5 %

observation

  • @ref: 67770
  • observation: quinones: MK-8(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3190830089acetate+carbon source
3190816449alanine+carbon source
3190829016arginine+carbon source
3190828757fructose+carbon source
3190833984fucose+carbon source
3190817234glucose+carbon source
3190829987glutamate+carbon source
3190817754glycerol+carbon source
3190817716lactose+carbon source
3190817306maltose+carbon source
3190837657methyl D-glucoside+carbon source
3190826271proline+carbon source
3190833942ribose+carbon source
3190830911sorbitol+carbon source
3190817992sucrose+carbon source
3190827082trehalose+carbon source
3190817632nitrate+reduction
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate-builds acid from
6837118403L-arabitol-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837118305arbutin-builds acid from
6837127613amygdalin-builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol-builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837117266L-sorbose-builds acid from
6837165328L-xylose-builds acid from
6837117113erythritol-builds acid from
11618617632nitrate+reduction
11618616301nitrite-reduction

metabolite production

  • @ref: 116186
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
31908catalase+1.11.1.6
116186oxidase+
116186catalase+1.11.1.6
116186urease-3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
68382cystine arylamidase+3.4.11.3
68382trypsin+3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase+3.2.1.22
68382beta-galactosidase+3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382beta-glucosidase+3.2.1.21
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382alpha-mannosidase+3.2.1.24
68382alpha-fucosidase+3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
116186-+++-++++-++++-+++++

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
116186+/--+/-+/-+/-+/--+/-+/-+/-+/-+/-+/--+/-------+/---+/-+/-+/-+/-+/-+/-+/-+/---+/-+/-+/-+/-+/-+/-+/---+/-+/-----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
7254soil, farmlandShandong ProvinceChinaCHNAsia
67770Farmland soilShandong ProvinceChinaCHNAsia
116186Environment, Soil, farmlandShandongChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Agriculture
#Environmental#Terrestrial#Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_7756.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_3602;97_4425;98_5672;99_7756&stattab=map
  • Last taxonomy: Ruania albidiflava subclade
  • 16S sequence: DQ343153
  • Sequence Identity:
  • Total samples: 1463
  • soil counts: 409
  • aquatic counts: 113
  • animal counts: 842
  • plant counts: 99

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
72541Risk group (German classification)
1161861Risk group (French classification)

Sequence information

16S sequences

  • @ref: 7254
  • description: Ruania albidiflava strain AS 4.3142 16S ribosomal RNA gene, partial sequence
  • accession: DQ343153
  • length: 1454
  • database: ena
  • NCBI tax ID: 366586

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Ruania albidiflava DSM 180291123065.3wgspatric1123065
66792Ruania albidiflava DSM 180292524614511draftimg1123065
67770Ruania albidiflava DSM 18029GCA_000421225contigncbi1123065

GC content

@refGC-contentmethod
725469.8
6777069.8thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno90.74yes
flagellatedno98.714yes
gram-positiveyes87.459yes
anaerobicno99.109yes
aerobicyes85.471no
halophileno79.645no
spore-formingno89.131yes
thermophileno93.783yes
glucose-utilyes85.718yes
glucose-fermentno80.768no

External links

@ref: 7254

culture collection no.: DSM 18029, CGMCC 4.3142, JCM 13910, PCM 2644, NBRC 106322, CIP 109565

straininfo link

  • @ref: 86793
  • straininfo: 302773

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17392211Ruania albidiflava gen. nov., sp. nov., a novel member of the suborder Micrococcineae.Gu Q, Pasciak M, Luo H, Gamian A, Liu Z, Huang YInt J Syst Evol Microbiol10.1099/ijs.0.64635-02007Actinomycetales/*classification/cytology/isolation & purification/physiology, Base Composition, Cell Wall/chemistry, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Molecular Sequence Data, Peptidoglycan/chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil MicrobiologyGenetics
Phylogeny34388085Identification of Haloactinobacterium kanbiaonis sp. nov. and Ruania zhangjianzhongii sp. nov., two novel species of the family Ruaniaceae isolated from faeces of bats (Hipposideros spp.).Xu M, Dai Y, Huang Y, Yang J, Lai XH, Jin D, Lu S, Zhou J, Zhang S, Bai Y, Jiao Y, Qiao L, Jiang Y, Xu JInt J Syst Evol Microbiol10.1099/ijsem.0.0049532021Actinobacteria/*classification/isolation & purification, Animals, Bacterial Typing Techniques, Base Composition, *Chiroptera/microbiology, DNA, Bacterial/genetics, Fatty Acids/chemistry, Feces/microbiology, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny34542394Ruania rhizosphaerae sp. nov., a novel actinobacterium isolated from rhizosphere of Suaeda aralocaspica.Lu WN, Xu YZ, Xie YG, Gao R, Song JQ, Liu DF, Xiao M, Wang HF, Li QL, Li WJInt J Syst Evol Microbiol10.1099/ijsem.0.0050072021Actinobacteria, Bacterial Typing Techniques, Base Composition, *Chenopodiaceae, DNA, Bacterial/genetics, Fatty Acids/chemistry, Phospholipids, Phylogeny, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Sequence Analysis, DNA, Soil MicrobiologyTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
7254Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18029)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18029
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
21406Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM18029.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
31908Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2816528776041
36057Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7322
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)
66793Mukherjee et al.10.1038/nbt.3886GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life28604660 35: 676-683 2017
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68371Automatically annotated from API 50CH acid
68382Automatically annotated from API zym
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
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
86793Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID302773.1StrainInfo: A central database for resolving microbial strain identifiers
116186Curators of the CIPCollection of Institut Pasteur (CIP 109565)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109565