Strain identifier

BacDive ID: 6279

Type strain: Yes

Species: Ornithinimicrobium kibberense

Strain Designation: K22-20

Strain history: CIP <- 2006, JCM <- 2004, MTCC

NCBI tax ID(s): 282060 (species)

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General

@ref: 7128

BacDive-ID: 6279

DSM-Number: 17687

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, rod-shaped

description: Ornithinimicrobium kibberense K22-20 is an aerobe, mesophilic, rod-shaped bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 282060
  • Matching level: species

strain history

@refhistory
7128<- S. Mayilraj; K22-20
67770S. Mayilraj K22-20.
120411CIP <- 2006, JCM <- 2004, MTCC

doi: 10.13145/bacdive6279.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Ornithinimicrobiaceae
  • genus: Ornithinimicrobium
  • species: Ornithinimicrobium kibberense
  • full scientific name: Ornithinimicrobium kibberense Mayilraj et al. 2006

@ref: 7128

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Ornithinimicrobiaceae

genus: Ornithinimicrobium

species: Ornithinimicrobium kibberense

full scientific name: Ornithinimicrobium kibberense Mayilraj et al. 2006

strain designation: K22-20

type strain: yes

Morphology

cell morphology

@refcell shapemotilityconfidencegram stain
31731rod-shapedno
69480no90.344
69480100positive
120411oval-shapednopositive

colony morphology

  • @ref: 19754
  • colony color: Pearl orange (2013)
  • incubation period: 10-14 days
  • medium used: ISP 7

multicellular morphology

  • @ref: 19754
  • forms multicellular complex: no
  • medium name: ISP 7

pigmentation

  • @ref: 31731
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
19754ISP 7yesName: ISP 7 (5322) Composition Glycerol 15.0 g/l L-Tyrosine 0.5 g/l L-Asparagine 1.0 g/l K2HPO4 0.5 g/l NaCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Trace element solution 5343 1.0 ml/l Agar 20.0 Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.3 Usage: Production of melanoid pigments Organisms: All Actinomycetes
33293MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
120411CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72
120411CIP Medium 112yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=112

culture temp

@refgrowthtypetemperaturerange
19754positiveoptimum28mesophilic
31731positivegrowth20-37
31731positiveoptimum28mesophilic
33293positivegrowth25mesophilic
67770positivegrowth25mesophilic

culture pH

@refabilitytypepHPH range
31731positivegrowth9alkaliphile
31731positiveoptimum9

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31731aerobe
120411facultative anaerobe

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.989

halophily

@refsaltgrowthtested relationconcentration
31731NaClpositivegrowth0-7 %
31731NaClpositiveoptimum0-7 %

observation

@refobservation
31731aggregates in chains
67770quinones: MK-8(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3173118403L-arabitol+carbon source
3173117057cellobiose+carbon source
3173128260galactose+carbon source
3173124265gluconate+carbon source
3173128087glycogen+carbon source
3173117632nitrate+reduction
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837132528turanose-builds acid from
6837128066gentiobiose-builds acid from
6837117151xylitol-builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837128053melibiose-builds acid from
6837117716lactose-builds acid from
6837117814salicin-builds acid from
6837118305arbutin-builds acid from
6837127613amygdalin-builds acid from
6837159640N-acetylglucosamine-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
6837162345L-rhamnose-builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose-builds acid from
6837112936D-galactose-builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose-builds acid from
6837116988D-ribose-builds acid from
6837130849L-arabinose-builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol-builds acid from
12041117632nitrate+reduction
12041116301nitrite-reduction
6837917632nitrate-reduction
683794853esculin-hydrolysis
6837916199urea-hydrolysis
683795291gelatin-hydrolysis
6837917634D-glucose-fermentation
6837916988D-ribose-fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol-fermentation
6837917306maltose-fermentation
6837917716lactose-fermentation
6837917992sucrose-fermentation
6837928087glycogen-fermentation

metabolite production

  • @ref: 120411
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-chymotrypsin-3.4.21.1
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382lipase (C 14)-
68382esterase lipase (C 8)-
68382alkaline phosphatase-3.1.3.1
68379gelatinase-
68379urease-3.5.1.5
68379beta-glucosidase-3.2.1.21
68379N-acetyl-beta-glucosaminidase-3.2.1.52
68379alpha-glucosidase+3.2.1.20
68379beta-galactosidase-3.2.1.23
68379beta-glucuronidase-3.2.1.31
68379alkaline phosphatase-3.1.3.1
68379pyrrolidonyl arylamidase-3.4.19.3
68379pyrazinamidase+3.5.1.B15
120411oxidase-
120411catalase+1.11.1.6
120411urease-3.5.1.5

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
19754-+----+------------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
19754----------+---+----
120411-+--+--+-+++--++----

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
120411----------+/-+/---------+/----+/--+/-+/---+/-+/---+/-+/-+/-------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
7128soilThe HimalayasIndiaINDAsia
67770SoilLahaul-Spiti Valley, the Indian HimalayasIndiaINDAsia
120411Cold desertIndian HimalayasIndiaINDAsia

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_15891.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_3098;97_3799;98_4825;99_15891&stattab=map
  • Last taxonomy: Ornithinimicrobium
  • 16S sequence: AY636111
  • Sequence Identity:
  • Total samples: 255
  • soil counts: 37
  • aquatic counts: 62
  • animal counts: 101
  • plant counts: 55

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
71281Risk group (German classification)
197541Risk group (German classification)
1204111Risk group (French classification)

Sequence information

16S sequences

  • @ref: 7128
  • description: Ornithinimicrobium kibberense strain K22-20 16S ribosomal RNA gene, partial sequence
  • accession: AY636111
  • length: 1488
  • database: ena
  • NCBI tax ID: 282060

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Ornithinimicrobium sp. DSM 176872590013.3wgspatric2590013
66792Ornithinimicrobium sp. DSM 176872891388395draftimg2590013
67770Ornithinimicrobium kibberense DSM 17687GCA_006519705scaffoldncbi282060

GC content

@refGC-contentmethod
712871
6777071thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno70no
motileno94.025no
gram-positiveyes87.506no
anaerobicno98.862yes
aerobicyes90.133no
halophileno77.281no
spore-formingno93.614no
glucose-utilyes88.467no
thermophileno95.289yes
flagellatedno98.969yes
glucose-fermentno88.579yes

External links

@ref: 7128

culture collection no.: DSM 17687, JCM 12763, MTCC 6545, CGMCC 1.6491, CIP 109338

straininfo link

  • @ref: 75755
  • straininfo: 297277

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16825645Ornithinimicrobium kibberense sp. nov., isolated from the Indian Himalayas.Mayilraj S, Saha P, Suresh K, Saini HSInt J Syst Evol Microbiol10.1099/ijs.0.64138-02006Actinomycetales/*classification/genetics/*isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, Carbohydrate Metabolism, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis/chemistry, Genes, rRNA, India, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Pigments, Biological/biosynthesis, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, *Soil MicrobiologyGenetics
Phylogeny18175694Ornithinimicrobium pekingense sp. nov., isolated from activated sludge.Liu XY, Wang BJ, Jiang CY, Liu SJInt J Syst Evol Microbiol10.1099/ijs.0.65229-02008Actinomycetales/*classification/genetics/*isolation & purification/physiology, Bacterial Typing Techniques, *Bioreactors, China, DNA, Bacterial/analysis, Genes, rRNA, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage/*microbiology, Species SpecificityGenetics
Phylogeny22888195Ornithinimicrobium murale sp. nov., isolated from an indoor wall colonized by moulds.Kampfer P, Glaeser SP, Schafer J, Lodders N, Martin K, Schumann PInt J Syst Evol Microbiol10.1099/ijs.0.035873-02012Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Environmental Microbiology, Fatty Acids/analysis, Fungi/growth & development, Germany, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/analysis, Phospholipids/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/analysisGenetics
Phylogeny23907216Ornithinimicrobium tianjinense sp. nov., isolated from a recirculating aquaculture system.Liu LZ, Liu Y, Chen Z, Liu HC, Zhou YG, Liu ZPInt J Syst Evol Microbiol10.1099/ijs.0.052514-02013Actinomycetales/*classification/genetics/isolation & purification, *Aquaculture, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Peptidoglycan/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry, *Water MicrobiologyGenetics
Phylogeny26395130Ornithinimicrobium algicola sp. nov., a marine actinobacterium isolated from the green alga of the genus Ulva.Ramaprasad EVV, Sasikala C, Ramana CVInt J Syst Evol Microbiol10.1099/ijsem.0.0006242015Actinobacteria/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, India, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Ulva/*microbiology, Vitamin K 2/analogs & derivatives/chemistryGenetics
Phylogeny30382345Ornithinimicrobium panacihumi sp. nov., Antagonistic Bacteria Against Root Rot Fungal Pathogens, Isolated from Cultivated Ginseng Soil.Huo Y, Kang JP, Ahn JC, Yang DU, Yang DCCurr Microbiol10.1007/s00284-018-1579-92018Antibiosis/*physiology, Bacterial Typing Techniques, Base Composition/genetics, DNA, Bacterial/genetics, Fatty Acids/analysis, Fusarium/*growth & development, Hypocreales/*growth & development, Micrococcaceae/classification/genetics/*isolation & purification/*metabolism, Panax/*microbiology, Plant Roots/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil MicrobiologyTranscriptome
Phylogeny33174834Ornithinimicrobium pratense sp. nov., isolated from meadow soil.Guo Q, Wang B, Zhou Z, Ke X, Zhang L, Chen M, Lin M, Wang W, Zhang W, Li XInt J Syst Evol Microbiol10.1099/ijsem.0.0045572020Actinobacteria/*classification/*isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Grassland, Nucleic Acid Hybridization, Ornithine/chemistry, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny35044904Ornithinimicrobium laminariae sp. nov., isolated from the kelp Laminaria japonica.Cao WR, Yu XR, Sun YY, Jiang MY, Xu XD, Li YJInt J Syst Evol Microbiol10.1099/ijsem.0.0051872022Actinobacteria/*classification/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Kelp/microbiology, *Laminaria/microbiology, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNATranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
7128Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17687)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17687
19754Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM17687.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
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
31731Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2800728776041
33293Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7068
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68371Automatically annotated from API 50CH acid
68379Automatically annotated from API Coryne
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)
75755Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID297277.1StrainInfo: A central database for resolving microbial strain identifiers
120411Curators of the CIPCollection of Institut Pasteur (CIP 109338)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109338