Strain identifier

BacDive ID: 6275

Type strain: Yes

Species: Ornithinimicrobium humiphilum

Strain Designation: 2115-015

Strain history: CIP <- 2000, I. Groth, Hans Knoll Inst., Jena, Germany: strain HKI 0124

NCBI tax ID(s): 125288 (species)

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General

@ref: 4621

BacDive-ID: 6275

DSM-Number: 12362

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

description: Ornithinimicrobium humiphilum 2115-015 is an obligate aerobe, mesophilic, Gram-positive bacterium that was isolated from garden soil.

NCBI tax id

  • NCBI tax id: 125288
  • Matching level: species

strain history

@refhistory
4621<- I. Groth; HKI 0124 <- Ch. Weigel; 2115-015
395512000, I. Groth, HKI, Jena, Germany: strain HKI 0124
67770I. Groth HKI 0124 <-- Ch. Weigel 2115-015.
119988CIP <- 2000, I. Groth, Hans Knoll Inst., Jena, Germany: strain HKI 0124

doi: 10.13145/bacdive6275.20230509.8.1

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 humiphilum
  • full scientific name: Ornithinimicrobium humiphilum Groth et al. 2001

@ref: 4621

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Ornithinimicrobiaceae

genus: Ornithinimicrobium

species: Ornithinimicrobium humiphilum

full scientific name: Ornithinimicrobium humiphilum Groth et al. 2001

strain designation: 2115-015

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480positive100
119988positiverod-shapedno

colony morphology

@refcolony colorincubation periodmedium used
18499Lemon yellow (1012)10-14 daysISP 2
18499Lemon yellow (1012)10-14 daysISP 3
18499Lemon yellow (1012)10-14 daysISP 4
18499Lemon yellow (1012)10-14 daysISP 5
18499Lemon yellow (1012)10-14 daysISP 6
18499Lemon yellow (1012)10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
18499noISP 2
18499noISP 3
18499noISP 4
18499noISP 5
18499noISP 6
18499noISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
4621RICH 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
18499ISP 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
18499ISP 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:
18499ISP 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
18499ISP 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
18499ISP 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
18499ISP 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
39551MEDIUM 29- Brain heart agaryesDistilled water make up to (1000.000 ml);Brain heart infusion agar (52.000 g)
119988CIP Medium 29yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=29

culture temp

@refgrowthtypetemperaturerange
18499positiveoptimum28mesophilic
4621positivegrowth28mesophilic
39551positivegrowth37mesophilic
67770positivegrowth28mesophilic
119988positivegrowth10-45
119988nogrowth5psychrophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 119988
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481no97
69480no99.995

halophily

@refsaltgrowthtested relationconcentration
119988NaClpositivegrowth0-6 %
119988NaClnogrowth8 %
119988NaClnogrowth10 %

murein

  • @ref: 4621
  • murein short key: A21.14
  • type: A4ß L-Orn-L-Ala-Gly-D-Asp

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1849962968cellulose+
1849916634raffinose+
1849926546rhamnose+
1849928757fructose+
1849929864mannitol+
1849917268myo-inositol+
1849918222xylose+
1849917992sucrose+
1849922599arabinose+
1849917234glucose+
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816199urea-hydrolysis
6836816947citrate+assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis
11998816947citrate-carbon source
1199884853esculin-hydrolysis
119988606565hippurate-hydrolysis
11998817632nitrate+reduction
11998816301nitrite-reduction
11998835020tributyrin-hydrolysis
11998817632nitrate-respiration
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

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole testmethylred-test
6836815688acetoin-
6836835581indole-
11998815688acetoin-
11998817234glucose-

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
68382cystine arylamidase+3.4.11.3
68382valine arylamidase+
68382leucine arylamidase+3.4.11.1
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
119988oxidase-
119988beta-galactosidase-3.2.1.23
119988alcohol dehydrogenase-1.1.1.1
119988gelatinase+/-
119988amylase-
119988DNase-
119988caseinase-3.4.21.50
119988catalase+1.11.1.6
119988tween esterase-
119988gamma-glutamyltransferase-2.3.2.2
119988lecithinase-
119988lipase-
119988lysine decarboxylase-4.1.1.18
119988ornithine decarboxylase-4.1.1.17
119988protease-

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
18499--++--+----------+-

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
18499+-+++++++++--+++---
119988+++-+++--++---+-----

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
18499----+------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
119988---------------------------------------------------------------------------------------------------

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentgeographic locationisolation date
4621garden soilGermanyDEUEurope
67770Garden soilGermanyDEUEuropeGiessen
119988Environment, Soil, gardenGermanyDEUEuropeGiessen, Hessen1996

isolation source categories

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

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
184991German classification
46211Risk group (German classification)
1199881Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
4621Ornithinimicrobium humiphilum partial 16S rRNA gene, strain DSM 12362AJ2776501306ena125288
67770Ornithinimicrobium humiphilum gene for 16S rRNA, partial sequenceAB5301391475ena125288

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Ornithinimicrobium humiphilum strain DSM 12362125288.3wgspatric125288
66792Ornithinimicrobium humiphilum DSM 123622818991433draftimg125288
67770Ornithinimicrobium humiphilum DSM 12362GCA_006716885contigncbi125288

GC content

  • @ref: 4621
  • GC-content: 70
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno97no
motileno94.819no
gram-positiveyes88.058no
anaerobicno98.651no
aerobicyes94.162no
halophileno89.139no
spore-formingno93.43no
thermophileno91.699no
glucose-utilyes90.043yes
flagellatedno98.67no
glucose-fermentno91.494yes

External links

@ref: 4621

culture collection no.: DSM 12362, CIP 106634, HKI 0124, JCM 11540, KCTC 19900, KCTC 19901, NBRC 106159, NCIMB 13784

straininfo link

  • @ref: 75752
  • straininfo: 49278

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny11211277Ornithinimicrobium humiphilum gen. nov., sp. nov., a novel soil actinomycete with L-ornithine in the peptidoglycan.Groth I, Schumann P, Weiss N, Schuetze B, Augsten K, Stackebrandt EInt J Syst Evol Microbiol10.1099/00207713-51-1-812001Actinomycetales/chemistry/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Molecular Sequence Data, Ornithine/*analysis, Peptidoglycan/*chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil MicrobiologyGenetics
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
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/urltitlejournalpubmed
4621Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 12362)https://www.dsmz.de/collection/catalogue/details/culture/DSM-12362
18499Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM12362.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
39551Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/18786
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
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
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
75752Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID49278.1StrainInfo: A central database for resolving microbial strain identifiers
119988Curators of the CIPCollection of Institut Pasteur (CIP 106634)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106634