Strain identifier

BacDive ID: 10823

Type strain: Yes

Species: Nocardia rhamnosiphila

Strain Designation: 202GMO

Strain history: DSM 45147 <-- P. R. Meyers 202GMO <-- A. E. Cook and M. le Roes.

NCBI tax ID(s): 1223547 (strain), 426716 (species)

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General

@ref: 15418

BacDive-ID: 10823

DSM-Number: 45147

keywords: genome sequence, 16S sequence, Bacteria, spore-forming, mesophilic

description: Nocardia rhamnosiphila 202GMO is a spore-forming, mesophilic bacterium that builds an aerial mycelium and was isolated from suburban compost heap.

NCBI tax id

NCBI tax idMatching level
1223547strain
426716species

strain history

@refhistory
15418<- P. R. Meyers, Univ. Cape Town, South Africa; 202GMO <- A. E. Cook and M. le Roes
67770DSM 45147 <-- P. R. Meyers 202GMO <-- A. E. Cook and M. le Roes.

doi: 10.13145/bacdive10823.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Mycobacteriales
  • family: Nocardiaceae
  • genus: Nocardia
  • species: Nocardia rhamnosiphila
  • full scientific name: Nocardia rhamnosiphila Everest et al. 2012

@ref: 15418

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardiaceae

genus: Nocardia

species: Nocardia rhamnosiphila

full scientific name: Nocardia rhamnosiphila Everest et al. 2012 emend. Nouioui et al. 2018

strain designation: 202GMO

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480no90.995
69480100positive

colony morphology

@refcolony colormedium used
69375Daffodil yellow (1007)ISP 6
69375ColourlessISP 3
69375ColourlessISP 4
69375Pastell yellow (1034)ISP 5
69375Pastell yellow (1034)ISP 7
69375Yellow orange (2000)ISP 2
69375Yellow orange (2000)suter with tyrosine
69375Yellow orange (2000)suter without tyrosine

multicellular morphology

@refforms multicellular complexcomplex namecomplex colormedium name
69375yesAerial myceliumCream (9001)ISP 2
69375yesAerial myceliumPure white (9010)ISP 3
69375noAerial myceliumISP 4
69375yesAerial myceliumPure white (9010)ISP 5
69375yesAerial myceliumLight ivory (1015)ISP 6
69375yesAerial myceliumPure white (9010)ISP 7
69375noAerial myceliumsuter with tyrosine
69375yesAerial myceliumCream (9001)suter without tyrosine

pigmentation

@refproductionname
69375noMelanin
69375nosoluble pigment

multimedia

  • @ref: 15418
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_45147.jpg
  • caption: Medium 65 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
15418GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)yeshttps://mediadive.dsmz.de/medium/65Name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) Composition: Agar 18.0 g/l Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l CaCO3 2.0 g/l Distilled water
15418ISP2 MEDIUM (DSMZ Medium 987)yeshttps://mediadive.dsmz.de/medium/987Name: ISP 2 MEDIUM (DSMZ Medium 987) Composition: Agar 20.0 g/l Malt extract 10.0 g/l Dextrose 4.0 g/l Yeast extract 4.0 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
15418positivegrowth28mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

spore formation

  • @ref: 69481
  • spore formation: yes
  • confidence: 99

halophily

  • @ref: 69375
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-5 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6937522599arabinose-growth
6937562968cellulose-growth
6937528757fructose-growth
6937517234glucose+growth
6937517268inositol-growth
6937537684mannose-growth
6937516634raffinose-growth
6937526546rhamnose+/-growth
6937517992sucrose-growth
6937518222xylose-growth
6837917632nitrate+reduction
6837916199urea-hydrolysis
683795291gelatin-hydrolysis
6837917634D-glucose-fermentation
6837916988D-ribose-fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol-fermentation
6837917306maltose-fermentation
6837917716lactose-fermentation
6837917992sucrose-fermentation
6837928087glycogen-fermentation

enzymes

@refvalueactivityec
68379gelatinase-
68379urease-3.5.1.5
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
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)+
68382leucine arylamidase+3.4.11.1
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 coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
69375+--+----+/-----------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
69375++++++/-+/---++----+---

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
15418suburban compost heapCape TownSouth AfricaZAFAfrica
67770Suburban compost heapCape TownSouth AfricaZAFAfrica

isolation source categories

  • Cat1: #Engineered
  • Cat2: #Biodegradation
  • Cat3: #Composting

taxonmaps

  • @ref: 69479
  • File name: preview.99_3551.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_243;97_658;98_2723;99_3551&stattab=map
  • Last taxonomy: Nocardia
  • 16S sequence: EF418604
  • Sequence Identity:
  • Total samples: 11377
  • soil counts: 8278
  • aquatic counts: 469
  • animal counts: 943
  • plant counts: 1687

Safety information

risk assessment

  • @ref: 15418
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Nocardia rhamnosiphila strain NRRL B-24637 16S ribosomal RNA gene, partial sequenceJN041592462ena1223547
15418Nocardia rhamnosiphila 16S ribosomal RNA gene, partial sequenceEF4186041464ena1223547

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nocardia rhamnosiphila NBRC 1089381223547.4wgspatric1223547
66792Nocardia rhamnosiphila NBRC 1089382731957756draftimg1223547
67770Nocardia rhamnosiphila NBRC 108938GCA_001613485contigncbi1223547
67770Nocardia rhamnosiphila NBRC 108938 NRRL B-24637GCA_000720425contigncbi1223547
67770Nocardia rhamnosiphila NBRC 108938 NRRL B-24637GCA_000721005contigncbi1223547

GC content

  • @ref: 67770
  • GC-content: 68.5
  • method: genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes99no
motileno93.409no
gram-positiveyes87.847no
anaerobicno99.163no
aerobicyes91.373no
halophileno88.822no
spore-formingyes71.613no
glucose-utilyes87.935yes
flagellatedno98.018no
thermophileno99.269yes
glucose-fermentno91.564yes

External links

@ref: 15418

culture collection no.: DSM 45147, JCM 18300, NRRL B-24637, NBRC 108938

straininfo link

  • @ref: 80084
  • straininfo: 401844

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny21551327Nocardia grenadensis sp. nov., isolated from sand of the Caribbean Sea.Kampfer P, Lodders N, Grun-Wollny I, Martin K, Busse HJInt J Syst Evol Microbiol10.1099/ijs.0.030684-02011Bacterial Typing Techniques, Benzoquinones/analysis, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Geologic Sediments/*microbiology, Grenada, Molecular Sequence Data, Nocardia/*classification/genetics/*isolation & purification/physiology, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/analysis, Phylogeny, Polyamines/analysis, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Silicon DioxideGenetics
Phylogeny21596508Nocardia rhamnosiphila sp. nov., isolated from soil.Everest GJ, Cook AE, le Roes-Hill M, Meyers PRSyst Appl Microbiol10.1016/j.syapm.2011.03.0062011Bacterial Typing Techniques, Base Sequence, DNA Gyrase/genetics, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genes, Bacterial, Genes, rRNA, Genotype, Microbial Sensitivity Tests, Molecular Sequence Data, Nocardia/chemistry/*classification/genetics/*isolation & purification/physiology, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil Microbiology, Species SpecificityGenetics
Phylogeny26547854Nocardia zapadnayensis sp. nov., isolated from soil.Ozdemir-Kocak F, Saygin H, Saricaoglu S, Cetin D, Potter G, Sproer C, Guven K, Isik K, Klenk HP, Sahin NAntonie Van Leeuwenhoek10.1007/s10482-015-0612-22015Bacterial Typing Techniques, Base Sequence, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Diaminopimelic Acid/analysis/chemistry, Fatty Acids/analysis, Microscopy, Electron, Scanning, Molecular Sequence Data, Nocardia/chemistry/cytology/genetics/*isolation & purification, Nucleic Acid Hybridization, Phospholipids/analysis/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil, *Soil MicrobiologyGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
15418Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45147)https://www.dsmz.de/collection/catalogue/details/culture/DSM-45147
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
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/
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
69375Wink, J.https://cdn.dsmz.de/wink/DSM%2045147.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
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
80084Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID401844.1StrainInfo: A central database for resolving microbial strain identifiers