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Strain identifier

BacDive ID: 10173

Type strain: Yes

Species: Nakamurella multipartita

Strain Designation: Y-104

Strain history: K. Nakamura Y-104.

NCBI tax ID(s): 479431 (strain), 53461 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 11495

BacDive-ID: 10173

DSM-Number: 44233

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

description: Nakamurella multipartita Y-104 is a mesophilic bacterium that was isolated from activated sludge.

NCBI tax id

NCBI tax idMatching level
53461species
479431strain

strain history

doi: 10.13145/bacdive10173.20221219.7.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Nakamurellales
  • family: Nakamurellaceae
  • genus: Nakamurella
  • species: Nakamurella multipartita
  • full scientific name: Nakamurella multipartita (Yoshimi et al. 1996) Tao et al. 2004
  • synonyms

    • @ref: 20215
    • synonym: Microsphaera multipartita

@ref: 11495

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nakamurellaceae

genus: Nakamurella

species: Nakamurella multipartita

full scientific name: Nakamurella multipartita (Yoshimi et al. 1996) Tao et al. 2004 emend. Nouioui et al. 2018

strain designation: Y-104

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: positive
  • confidence: 95.948

colony morphology

@refcolony colorincubation periodmedium used
20027Cream (9001)10-14 days5006
20027Cream (9001)10-14 days5425
20027Cream (9001)10-14 days5428
20027Cream (9001)10-14 days5530
20027Cream (9001)10-14 daysISP 2

multicellular morphology

@refmedium nameforms multicellular complex
20027ISP 2
200275006no
200275425no
200275428no
200275530no

multimedia

  • @ref: 66793
  • multimedia content: EM_DSM_44233_1.jpg
  • caption: electron microscopic image
  • intellectual property rights: © HZI/Manfred Rohde

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11495RICH 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
11495TRYPTICASE 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
20027ISP 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
200275006yesMedium: 5006 Name: Composition (g/l) Sucrose 3,0 Dextrin 15,0 Meat extract 1,0 Yeast extract 2,0 Tryptone soy broth (Oxoid) 5,0 NaCl 0,5 K2HPO4 0,5 MgSO4 x 7 H2O 0,5 FeSO4 x 7 H2O 0,01 Agar 20,0 Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7,3 Usage: Maintenance Organisms: All Actinomycetes
200275425yesName: Brain Heart Infusion (BHI) Agar; 5425 Composition: Calf brain infusion 200.0 g/l Beef heart infusion 250.0 g/l Casein (meat) peptone 10.0 g/l Glucose 2.0 g/l NaCl 5.0 g/l Na2HPO4 2.5 g/l Agar 15.0 g/l Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.4 Usage: Maintenance and revitalization Organisms: Dermatophilus congolensis, Nocardia brasieliensis, N. asteroides, Rhodococcus equi, R. fascians, R. rhodochrous, Streptomyces thermoviol aceus subsp. apingens, Coryneform species
200275428yes
200275530yes
41306MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)

culture temp

@refgrowthtypetemperaturerange
20027positiveoptimum28mesophilic
11495positivegrowth28mesophilic
41306positivegrowth30mesophilic
67770positivegrowth25mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
20027no
69480no76.541

halophily

  • @ref: 69480
  • halophily level: non-halophilic
  • confidence: 92.727

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6837928087glycogen-fermentation
6837917992sucrose+fermentation
6837917716lactose-fermentation
6837917306maltose-fermentation
6837916899D-mannitol-fermentation
6837965327D-xylose-fermentation
6837916988D-ribose-fermentation
6837917634D-glucose-fermentation
683795291gelatin-hydrolysis
6837916199urea-hydrolysis
683794853esculin+hydrolysis
6837917632nitrate-reduction
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816199urea-hydrolysis
6836816947citrate-assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinno
6836835581indoleno
6836816136hydrogen sulfideno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
6836815688acetoin-
6836835581indole-

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase+3.2.1.21
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase-3.2.1.31
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)-
68382esterase (C 4)-
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

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
20027------+-+--------+-

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
20027+---+----+-+--++---

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
20027+----------

Isolation, sampling and environmental information

isolation

@refsample type
11495activated sludge
67770Activated sludge acclimated with sugar-containing synthetic wastewater

isolation source categories

  • Cat1: #Engineered
  • Cat2: #Waste
  • Cat3: #Activated sludge

taxonmaps

  • @ref: 69479
  • File name: preview.99_1362.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_94;96_787;97_916;98_1075;99_1362&stattab=map
  • Last taxonomy: Nakamurella multipartita subclade
  • 16S sequence: Y08541
  • Sequence Identity:
  • Total samples: 2637
  • soil counts: 1210
  • aquatic counts: 805
  • animal counts: 521
  • plant counts: 101

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
114951Risk group (German classification)
200271German classification

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218M.multipartita 16S rRNA geneY085411468ena479431
67770Gram-positive bacterial sp. DNA for 16s rRNA, partial sequenceD500661290ena29566

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nakamurella multipartita DSM 44233 DSM 44233GCA_000024365completencbi479431
66792Nakamurella multipartita DSM 44233479431.6completepatric479431
66792Nakamurella multipartita Y-104, DSM 44233644736393completeimg479431
67770Nakamurella multipartita DSM 44233 chromosome, complete genomeCP001737ena479431
66792uncultured Lachnospiraceae bacterium REFINED_METABAT215_TOP10_CONTIGS_1500_ASSEMBLY_K77_MERGED__Hadza_MoBio_hadza-E-H_K_24_1920.295GCA_934376945contigpatric297314

GC content

@refGC-contentmethod
6777067.5high performance liquid chromatography (HPLC)
6777070.92genome sequence analysis
6777070.2high performance liquid chromatography (HPLC)

External links

@ref: 11495

culture collection no.: DSM 44233, ATCC 700099, CIP 104796, JCM 9543, CCM 4621, FERM P-14709, NBRC 105858

straininfo link

@refpassport
20218http://www.straininfo.net/strains/169342
20218http://www.straininfo.net/strains/125390
20218http://www.straininfo.net/strains/152819
20218http://www.straininfo.net/strains/125391

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17220441Humicoccus flavidus gen. nov., sp. nov., isolated from soil.Yoon JH, Kang SJ, Jung SY, Oh TKInt J Syst Evol Microbiol10.1099/ijs.0.64246-02007Bacterial Typing Techniques, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Gram-Positive Cocci/chemistry/*classification/genetics/isolation & purification, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil MicrobiologyGenetics
Genetics21304699Complete genome sequence of Nakamurella multipartita type strain (Y-104).Tice H, Mayilraj S, Sims D, Lapidus A, Nolan M, Lucas S, Glavina Del Rio T, Copeland A, Cheng JF, Meincke L, Bruce D, Goodwin L, Pitluck S, Ivanova N, Mavromatis K, Ovchinnikova G, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Detter JC, Brettin T, Rohde M, Goker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Chen FStand Genomic Sci10.4056/sigs.7213162010
Phylogeny28820108Nakamurella intestinalis sp. nov., isolated from the faeces of Pseudorhynchus japonicus.Kim SJ, Cho H, Joa JH, Hamada M, Ahn JH, Weon HY, Kwon SWInt J Syst Evol Microbiol10.1099/ijsem.0.0020592017Actinomycetales/*classification/genetics/isolation & purification, Animals, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Feces/*microbiology, Orthoptera/*microbiology, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11495Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44233)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44233
20027Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44233.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
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
41306Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16743
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)
66793Mukherjee et al.10.1038/nbt.3886GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life 35: 676-683 201728604660
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
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)