Strain identifier

BacDive ID: 6273

Type strain: Yes

Species: Ornithinicoccus hortensis

Strain Designation: 2115-028

Strain history: CIP <- 1999, I. Groth, Hans Knöll Inst., Jena, Germany: strain HKI 0125

NCBI tax ID(s): 82346 (species)

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General

@ref: 4700

BacDive-ID: 6273

DSM-Number: 12335

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic

description: Ornithinicoccus hortensis 2115-028 is an aerobe, mesophilic bacterium that was isolated from garden soil.

NCBI tax id

  • NCBI tax id: 82346
  • Matching level: species

strain history

@refhistory
4700<- I. Groth <- Ch. Weigel; 2115-028 (= HKI 0125)
67770I. Groth HKI 0125 <-- Ch. Weigel 2115-028.
119973CIP <- 1999, I. Groth, Hans Knöll Inst., Jena, Germany: strain HKI 0125

doi: 10.13145/bacdive6273.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Intrasporangiaceae
  • genus: Ornithinicoccus
  • species: Ornithinicoccus hortensis
  • full scientific name: Ornithinicoccus hortensis Groth et al. 1999

@ref: 4700

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Intrasporangiaceae

genus: Ornithinicoccus

species: Ornithinicoccus hortensis

full scientific name: Ornithinicoccus hortensis Groth et al. 1999

strain designation: 2115-028

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no93.906
69480100positive
119973nopositivecoccus-shaped

colony morphology

@refcolony colorincubation periodmedium used
18498Beige (1001)10-14 daysISP 2
18498Beige (1001)10-14 daysISP 3
18498Beige (1001)10-14 daysISP 4
18498Beige (1001)10-14 daysISP 5
18498Beige (1001)10-14 daysISP 6
18498Beige (1001)10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
18498noISP 2
18498noISP 3
18498noISP 4
18498noISP 5
18498noISP 6
18498noISP 7

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
18498ISP 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
18498ISP 3yesName: ISP 3; 5315 Composition Dog oat flakes 20.0 g/l Trace element solution (5314) 2.5 ml/l Agar 18.0 g/l Preparation: Oat flakes are cooked for 20 minutes, trace element solution and agar are added (in the case of non rolled oat flakes the suspension has to bee filtrated). Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.8 Usage: Maintenance and taxonomy (e.g. SEM As liquid medium for metabolite production) Organisms: All Actinomycetes Trace element solution 5314 Name: Trace element solution 5314; 5314 Composition CaCl2 x H2O 3.0 g/l Fe-III-citrate 1.0 g/l MnSO4 0.2 g/l ZnCl2 0.1 g/l CuSO4 x 5 H2O 0.025 g/l Sodium tetra borate 0.2 g/l CoCl2 x 6 H2O 0.004 g/l Sodium molybdate 0.01 g/l Preparation: Use double destillated water. Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Trace element solution for different media Organisms:
18498ISP 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
18498ISP 5yesName: ISP 5 (5323) Composition L-Asparagine 1.0 g/l Glycerol 10.0 g/l K2HPO4 1.0 g/l Salt solution (see preparation) 1.0 ml/l Agar 20.0 g/l Preparation: Salt solution 1.0 g FeSO4 x 7 H2O 1.0 g MnCl2 x 4 H2O 1.0 g ZNSO4 x 7 H2O in 100 ml water Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.2 Usage: Maintenance and taxonomy Organisms: All Actinomycetes
18498ISP 6yesName: ISP 6 (5318) Composition Peptone 15.0 g/l Proteose peptose 5.0 g/l Ferric ammonium citrate 0.5 g/l Sodium glycerophosphate 1.0 g/l Sodium thiosulfate 0.08 g/l Yeast extract 1.0 g/l Agar 15.0 g/l Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigments Organisms: All Actinomycetes
18498ISP 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
39506MEDIUM 112 - for JanibacteryesDistilled water make up to (1000.000 ml);Magnesium sulphate heptahydrate (1.000 g);Agar (20.000 g);Yeast extract (5.000 g);Peptone (10.000 g);Tween 80 (50.000 mg);Glycerol (2.000 g);Malt extract (5.000 g);Beef extract (2.000 g);Casamino acids (5.000 g);Ca
4700TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yesName: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled waterhttps://mediadive.dsmz.de/medium/92
119973CIP Medium 112yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=112

culture temp

@refgrowthtypetemperaturerange
18498positiveoptimum28mesophilic
39506positivegrowth28mesophilic
55689positivegrowth28-37mesophilic
67770positivegrowth28mesophilic
4700positivegrowth28mesophilic
119973positivegrowth15-30
119973nogrowth10psychrophilic
119973nogrowth41thermophilic
119973nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
55689aerobe
119973obligate aerobe

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.993

halophily

  • @ref: 119973
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-10 %

murein

  • @ref: 4700
  • murein short key: A21.13
  • type: A4ß L-Orn-Gly2-D-Glu

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1849862968cellulose+
1849816634raffinose+
1849826546rhamnose+
1849828757fructose+
1849829864mannitol+
1849817268myo-inositol+
1849818222xylose+
1849817992sucrose+
1849822599arabinose+
1849817234glucose+
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118287L-fucose-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837128066gentiobiose-builds acid from
6837128087glycogen-builds acid from
6837128017starch-builds acid from
6837116634raffinose-builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837128053melibiose-builds acid from
6837117716lactose-builds acid from
6837117057cellobiose-builds acid from
6837117814salicin-builds acid from
683714853esculin-builds acid from
6837118305arbutin-builds acid from
6837127613amygdalin-builds acid from
6837159640N-acetylglucosamine-builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837143943methyl alpha-D-mannoside-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
6837117634D-glucose-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
6837117113erythritol-builds acid from
683685291gelatin+hydrolysis
6836827897tryptophan-energy source
6836816199urea-hydrolysis
6836816947citrate-assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis
11997316947citrate-carbon source
1199734853esculin-hydrolysis
119973606565hippurate+hydrolysis
11997317632nitrate+reduction
11997316301nitrite-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

@refChebi-IDmetaboliteproduction
6836815688acetoinno
6836835581indoleno
6836816136hydrogen sulfideno
11997335581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole testmethylred-test
6836815688acetoin-
6836835581indole-
11997315688acetoin-
11997317234glucose-

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-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin+3.4.21.1
68382trypsin+3.4.21.4
68382cystine arylamidase+3.4.11.3
68382valine arylamidase+
68382leucine arylamidase+3.4.11.1
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
68368gelatinase+
68368tryptophan deaminase-4.1.99.1
68368urease-3.5.1.5
68368ornithine decarboxylase-4.1.1.17
68368lysine decarboxylase-4.1.1.18
68368arginine dihydrolase-3.5.3.6
68368beta-galactosidase-3.2.1.23
119973oxidase-
119973beta-galactosidase-3.2.1.23
119973alcohol dehydrogenase-1.1.1.1
119973gelatinase+
119973amylase-
119973DNase-
119973caseinase+3.4.21.50
119973catalase+1.11.1.6
119973tween esterase+
119973gamma-glutamyltransferase-2.3.2.2
119973lecithinase+
119973lipase+
119973lysine decarboxylase-4.1.1.18
119973ornithine decarboxylase-4.1.1.17
119973phenylalanine ammonia-lyase+4.3.1.24
119973protease+
119973tryptophan deaminase-
119973urease-3.5.1.5

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
18498--+---+-+-+------+-

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
18498+-+++++++++--+++---
119973+++++++++++---+-----

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
18498----------+

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
119973+/--+/---------+/------+/-+/---------+/---+/-+/------+/--+/-----+/-----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
4700garden soilGermany, GießenGermanyDEUEurope
55689Garden soilGermanyDEUEurope
67770Soil in a gardenGiessenGermanyDEUEurope
119973Environment, Soil, gardenGiessen, HessenGermanyDEUEurope1996

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Soil
#Engineered#Agriculture#Garden

taxonmaps

  • @ref: 69479
  • File name: preview.99_79911.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_8115;97_9764;98_11987;99_79911&stattab=map
  • Last taxonomy: Ornithinicoccus hortensis subclade
  • 16S sequence: Y17869
  • Sequence Identity:
  • Total samples: 344
  • soil counts: 19
  • aquatic counts: 27
  • animal counts: 223
  • plant counts: 75

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
184981
47001Risk group (German classification)
1199731Risk group (French classification)

Sequence information

16S sequences

  • @ref: 4700
  • description: Ornithinicoccus hortensis 16S rRNA gene, partial
  • accession: Y17869
  • length: 1492
  • database: ena
  • NCBI tax ID: 82346

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Ornithinicoccus hortensis strain DSM 1233582346.3wgspatric82346
66792Ornithinicoccus hortensis strain HKI012582346.4wgspatric82346
66792Ornithinicoccus hortensis DSM 123352814123446draftimg82346
67770Ornithinicoccus hortensis DSM 12335GCA_006716185contigncbi82346
67770Ornithinicoccus hortensis HKI0125GCA_009602515scaffoldncbi82346

GC content

@refGC-contentmethod
470072.1high performance liquid chromatography (HPLC)
6777072high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes73no
motileno90.039no
flagellatedno98.444no
gram-positiveyes91.794no
anaerobicno99.009yes
halophileno87.207no
spore-formingno90.553no
thermophileno92.408yes
glucose-utilyes90.074yes
aerobicyes94.063yes
glucose-fermentno91.424yes

External links

@ref: 4700

culture collection no.: DSM 12335, ATCC BAA 9, IFO 16434, NBRC 16434, CCUG 43142, HKI 0125, JCM 11538, CIP 106364, IAM 14900, NCIMB 13613

straininfo link

  • @ref: 75750
  • straininfo: 46267

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny10555353Ornithinicoccus hortensis gen. nov., sp. nov., a soil actinomycete which contains L-ornithine.Groth I, Schumann P, Martin K, Schuetze B, Augsten K, Kramer I, Stackebrandt EInt J Syst Bacteriol10.1099/00207713-49-4-17171999Actinomycetales/*chemistry/*classification/metabolism, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Lipids/analysis, Molecular Sequence Data, Ornithine/*analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil MicrobiologyGenetics
Phylogeny26868220Ornithinicoccus halotolerans sp. nov., and emended description of the genus Ornithinicoccus.Zhang YG, Wang HF, Yang LL, Guo JW, Xiao M, Huang MJ, Nabil Hozzein W, Li WJInt J Syst Evol Microbiol10.1099/ijsem.0.0009642016Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Desert Climate, Fatty Acids/chemistry, Glycolipids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryGenetics
Phylogeny31958054Ornithinicoccus soli sp. nov., isolated from farmland soil.Jiang WK, Gao QQ, Zhang L, Sun GJ, Zhang ML, Liu XA, Wang H, Zhou YD, Ke ZJ, Hong QInt J Syst Evol Microbiol10.1099/ijsem.0.0039722020Actinobacteria/*classification/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, *Farms, Fatty Acids/chemistry, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
4700Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 12335)https://www.dsmz.de/collection/catalogue/details/culture/DSM-12335
18498Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM12335.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
39506Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/18486
55689Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 43142)https://www.ccug.se/strain?id=43142
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68368Automatically annotated from API 20E
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)
75750Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID46267.1StrainInfo: A central database for resolving microbial strain identifiers
119973Curators of the CIPCollection of Institut Pasteur (CIP 106364)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106364