Strain identifier

BacDive ID: 11084

Type strain: Yes

Species: Nocardioides aurantiacus

Strain history: CIP <- 2000, C. Urzi, Messina Univ., Messina, Italy: strain BC 361

NCBI tax ID(s): 86796 (species)

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General

@ref: 4780

BacDive-ID: 11084

DSM-Number: 12652

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

description: Nocardioides aurantiacus DSM 12652 is an obligate aerobe, mesophilic bacterium that was isolated from marble statue.

NCBI tax id

  • NCBI tax id: 86796
  • Matching level: species

strain history

@refhistory
4780<- C. Urcì; BC 361
395662000, C Urzi, Sci. Fac., Messina, Italy: strain BC 361
67770DSM 12652 <-- C. Urzì BC361.
116563CIP <- 2000, C. Urzi, Messina Univ., Messina, Italy: strain BC 361

doi: 10.13145/bacdive11084.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Propionibacteriales
  • family: Nocardioidaceae
  • genus: Nocardioides
  • species: Nocardioides aurantiacus
  • full scientific name: Nocardioides aurantiacus (Urzì et al. 2000) Wang et al. 2023

  • synonyms

    • @ref: 20215
    • synonym: Marmoricola aurantiacus

@ref: 4780

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardioidaceae

genus: Marmoricola

species: Marmoricola aurantiacus

full scientific name: Marmoricola aurantiacus Urzì et al. 2000

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no90.6
69480100positive
116563nopositivecoccus-shaped

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
4780GYM 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
39566MEDIUM 359 - for Marmoricola genusyesDistilled water make up to (1000.000 ml);Sodium chloride (5.000 g);Agar(15.000 g);Glucose (10.000 g);Yeast extract (5.000 g);Malt extract (15.000 g);Starch maize (10.000 g);Calcium carbonate (2.000 g)
4780TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://mediadive.dsmz.de/medium/535Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
116563CIP Medium 359yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=359

culture temp

@refgrowthtypetemperaturerange
4780positivegrowth28mesophilic
39566positivegrowth25mesophilic
67770positivegrowth28mesophilic
116563positivegrowth22-30
116563nogrowth10psychrophilic
116563nogrowth37mesophilic
116563nogrowth41thermophilic
116563nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 116563
  • oxygen tolerance: obligate aerobe

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 90.52

halophily

@refsaltgrowthtested relationconcentration
116563NaClpositivegrowth2-6 %
116563NaClnogrowth0 %
116563NaClnogrowth10 %

murein

  • @ref: 4780
  • murein short key: A41.01
  • type: A3gamma LL-Dpm-Gly

observation

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

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371gluconate-builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371turanose+builds acid from32528
68371gentiobiose-builds acid from28066
68371xylitol-builds acid from17151
68371glycogen+builds acid from28087
68371starch+builds acid from28017
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose-builds acid from27082
68371sucrose+builds acid from17992
68371melibiose-builds acid from28053
68371maltose+builds acid from17306
68371cellobiose+builds acid from17057
68371salicin+builds acid from17814
68371esculin+builds acid from4853
68371amygdalin-builds acid from27613
68371N-acetylglucosamine-builds acid from59640
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol-builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371D-glucose+builds acid from17634
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose+builds acid from65327
68371D-ribose+builds acid from16988
68371L-arabinose+builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754
116563citrate-carbon source16947
116563esculin+hydrolysis4853
116563hippurate+hydrolysis606565
116563nitrate-reduction17632
116563nitrite-reduction16301
116563nitrate-respiration17632

metabolite production

  • @ref: 116563
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11656315688acetoin-
11656317234glucose-

enzymes

@refvalueactivityec
116563oxidase-
116563beta-galactosidase+3.2.1.23
116563alcohol dehydrogenase-1.1.1.1
116563gelatinase+/-
116563amylase+
116563DNase-
116563caseinase+3.4.21.50
116563catalase+1.11.1.6
116563tween esterase-
116563gamma-glutamyltransferase+2.3.2.2
116563lysine decarboxylase-4.1.1.18
116563ornithine decarboxylase-4.1.1.17
116563phenylalanine ammonia-lyase+4.3.1.24
116563tryptophan deaminase-
116563urease-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
116563-+++-++++-++---++---

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
116563---+++---+/-++/-+/--------+/---+/-+++++/--+----++--+---------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
116563+++++--+-++++--++-+-+++---+-+--+-++++------------+------+---+--++----------+---++-----+-+----------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
4780marble statueMünchenGermanyDEUEurope
67770Marble statue (Wagmüller's monument) in the old Nordfriedhof cemeteryMunichGermanyDEUEurope
116563Marble statueMünchenGermanyDEUEurope1991

isolation source categories

  • Cat1: #Engineered

taxonmaps

  • @ref: 69479
  • File name: preview.99_2223.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_142;96_723;97_1424;98_1733;99_2223&stattab=map
  • Last taxonomy: Marmoricola aurantiacus
  • 16S sequence: Y18629
  • Sequence Identity:
  • Total samples: 946
  • soil counts: 215
  • aquatic counts: 77
  • animal counts: 557
  • plant counts: 97

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
47801Risk group (German classification)
1165631Risk group (French classification)

Sequence information

16S sequences

  • @ref: 4780
  • description: Marmoricola aurantiacus 16S rRNA gene, partial
  • accession: Y18629
  • length: 1497
  • database: ena
  • NCBI tax ID: 86796

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Marmoricola aurantiacus strain DSM 1265286796.3wgspatric86796
66792Marmoricola aurantiacus DSM 126522781126051draftimg86796
67770Marmoricola aurantiacus DSM 12652GCA_003752505contigncbi86796

GC content

  • @ref: 4780
  • GC-content: 72
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno50no
motileno96.773no
flagellatedno98.67no
gram-positiveyes94.209no
anaerobicno99.364no
halophileno94.485no
spore-formingno89.678no
thermophileno98.64yes
glucose-utilyes88.337no
aerobicyes94.607no
glucose-fermentno92.537no

External links

@ref: 4780

culture collection no.: DSM 12652, JCM 10917, NBRC 105375, BC 361, CIP 106770, NCIMB 13748

straininfo link

  • @ref: 80333
  • straininfo: 49334

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny10758857Marmoricola aurantiacus gen. nov., sp. nov., a coccoid member of the family Nocardioidaceae isolated from a marble statue.Urzi C, Salamone P, Schumann P, Stackebrandt EInt J Syst Evol Microbiol10.1099/00207713-50-2-5292000Actinomycetales/chemistry/*classification/isolation & purification/physiology, Base Composition, *Calcium Carbonate, Culture Media, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, *Sculpture, Sequence Analysis, DNACultivation
Phylogeny17625163Marmoricola aequoreus sp. nov., a novel actinobacterium isolated from marine sediment.Lee SDInt J Syst Evol Microbiol10.1099/ijs.0.64696-02007Actinomycetales/chemistry/*classification/*isolation & purification/physiology, Aerobiosis, Base Composition, Cell Wall/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Genes, rRNA, Geologic Sediments/*microbiology, Hydrogen-Ion Concentration, Molecular Sequence Data, Phospholipids/analysis, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Temperature, Vitamin K 2/analysisGenetics
Phylogeny18450688Marmoricola bigeumensis sp. nov., a member of the family Nocardioidaceae.Dastager SG, Lee JC, Ju YJ, Park DJ, Kim CJInt J Syst Evol Microbiol10.1099/ijs.0.65576-02008Actinomycetales/*classification/genetics/isolation & purification/physiology, Bacterial Typing Techniques, DNA, Bacterial/analysis, Genes, rRNA, Genotype, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Species SpecificityGenetics
Phylogeny19880634Marmoricola scoriae sp. nov., isolated from volcanic ash.Lee DW, Lee SDInt J Syst Evol Microbiol10.1099/ijs.0.018242-02009Actinomycetales/*classification/genetics/*isolation & purification/metabolism, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/metabolism, Geologic Sediments/*microbiology, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Volcanic Eruptions/*analysisMetabolism
Phylogeny20693360Marmoricola korecus sp. nov.Lee SD, Lee DW, Ko YHInt J Syst Evol Microbiol10.1099/ijs.0.025460-02010Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Lipids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistry, *Volcanic EruptionsGenetics
Phylogeny25754550Marmoricola solisilvae sp. nov. and Marmoricola terrae sp. nov., isolated from soil and emended description of the genus Marmoricola.Kim SJ, Lim JM, Hamada M, Ahn JH, Weon HY, Suzuki KI, Ahn TY, Kwon SWInt J Syst Evol Microbiol10.1099/ijs.0.0001842015Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Forests, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Soil, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryGenetics

Reference

@idauthorscataloguedoi/urltitle
4780Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 12652)https://www.dsmz.de/collection/catalogue/details/culture/DSM-12652
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
39566Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/18937
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
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)
80333Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID49334.1StrainInfo: A central database for resolving microbial strain identifiers
116563Curators of the CIPCollection of Institut Pasteur (CIP 106770)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106770