Strain identifier

BacDive ID: 10173

Type strain: Yes

Species: Nakamurella multipartita

Strain Designation: Y-104

Strain history: CIP <- 1996, K. Nakamura, Nat. Inst. of Bioscience and Human Technol., Japan: strain Y-104

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

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General

@ref: 11495

BacDive-ID: 10173

DSM-Number: 44233

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

description: Nakamurella multipartita Y-104 is an obligate aerobe, mesophilic bacterium that was isolated from activated sludge.

NCBI tax id

NCBI tax idMatching level
479431strain
53461species

strain history

@refhistory
11495<- K. Nakamura, Y-104
67770K. Nakamura Y-104.
121173CIP <- 1996, K. Nakamura, Nat. Inst. of Bioscience and Human Technol., Japan: strain Y-104

doi: 10.13145/bacdive10173.20230509.8.1

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

@refmotilityconfidencegram staincell shape
69480no91.125
69480100positive
121173nopositivecoccus-shaped

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
121173

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)
121173CIP Medium 135yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=135
121173CIP Medium 216yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=216
121173CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
20027positiveoptimum28mesophilic
11495positivegrowth28mesophilic
41306positivegrowth30mesophilic
67770positivegrowth25mesophilic
121173positivegrowth22-37
121173nogrowth10psychrophilic
121173nogrowth41thermophilic
121173nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 121173
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
20027no
69481yes99
69480no90.898

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
68371turanose-builds acid from32528
68371gentiobiose-builds acid from28066
68371xylitol-builds acid from17151
68371raffinose+builds acid from16634
68371melezitose+builds acid from6731
68371inulin-builds acid from15443
68371sucrose+builds acid from17992
68371melibiose+builds acid from28053
68371lactose-builds acid from17716
68371cellobiose+builds acid from17057
68371amygdalin-builds acid from27613
68371N-acetylglucosamine-builds acid from59640
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol+builds acid from17924
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371D-mannose+builds acid from16024
68371D-fructose+builds acid from15824
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
68368gelatin-hydrolysis5291
68368tryptophan-energy source27897
68368urea-hydrolysis16199
68368citrate-assimilation16947
68368ornithine-degradation18257
68368lysine-degradation25094
68368arginine-hydrolysis29016
121173hippurate-hydrolysis606565
121173nitrate+reduction17632
121173nitrite-reduction16301
68379nitrate-reduction17632
68379esculin+hydrolysis4853
68379urea-hydrolysis16199
68379gelatin-hydrolysis5291
68379D-glucose-fermentation17634
68379D-ribose-fermentation16988
68379D-xylose-fermentation65327
68379D-mannitol-fermentation16899
68379maltose-fermentation17306
68379lactose-fermentation17716
68379sucrose+fermentation17992
68379glycogen-fermentation28087

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinno
6836835581indoleno
6836816136hydrogen sulfideno
12117335581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
6836815688acetoin-
6836835581indole-
12117315688acetoin-

enzymes

@refvalueactivityec
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
121173oxidase-
121173beta-galactosidase+3.2.1.23
121173alcohol dehydrogenase-1.1.1.1
121173gelatinase-
121173amylase-
121173DNase-
121173caseinase-3.4.21.50
121173catalase+1.11.1.6
121173coagulase-
121173tween esterase+
121173gamma-glutamyltransferase-2.3.2.2
121173lecithinase-
121173lipase-
121173lysine decarboxylase-4.1.1.18
121173ornithine decarboxylase-4.1.1.17
121173protease-
121173tryptophan deaminase-
121173urease+3.5.1.5
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
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
20027------+-+--------+-

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
20027+---+----+-+--++---
121173-++-+----+++--++----

API 20E

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

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
121173+----+---+/-+++---+/-+/-+-+/---+/-+/-+/-++/--+++/--+++/-+/----+/---------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
121173+++++-++++++---++++--++--+-----+-+++---+-------------+--++--+-----------+--+-----+------+------++--

Isolation, sampling and environmental information

isolation

@refsample typeisolation date
11495activated sludge
67770Activated sludge acclimated with sugar-containing synthetic wastewater
121173Environment, Activated sludge1993

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
1211731Risk group (French 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 44233GCA_000024365completencbi479431
66792Nakamurella multipartita DSM 44233479431.6completepatric479431
66792Nakamurella multipartita Y-104, DSM 44233644736393completeimg479431

GC content

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

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes99no
motileno92.956no
flagellatedno98.155no
gram-positiveyes91.679no
anaerobicno98.392no
aerobicyes89.69no
halophileno93.63no
spore-formingno83.274yes
thermophileno98.197no
glucose-utilyes87.748no
glucose-fermentno89.416yes

External links

@ref: 11495

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

straininfo link

  • @ref: 79551
  • straininfo: 46213

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
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)
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
79551Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID46213.1StrainInfo: A central database for resolving microbial strain identifiers
121173Curators of the CIPCollection of Institut Pasteur (CIP 104796)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104796