Strain identifier

BacDive ID: 12625

Type strain: Yes

Species: Microlunatus phosphovorus

Strain Designation: NM-1

Strain history: CIP <- 1995, K. Nakamura, Nat. Inst. of Bioscience Human Technol., Ibaraki, Japan: strain NM-1

NCBI tax ID(s): 29405 (species)

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

@ref: 3973

BacDive-ID: 12625

DSM-Number: 10555

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

description: Microlunatus phosphovorus NM-1 is an obligate aerobe, mesophilic, Gram-positive bacterium that was isolated from activated sludge.

NCBI tax id

  • NCBI tax id: 29405
  • Matching level: species

strain history

@refhistory
3973<- JCM <- K. Nakamura, NM-1
67770K. Nakamura NM-1.
121810CIP <- 1995, K. Nakamura, Nat. Inst. of Bioscience Human Technol., Ibaraki, Japan: strain NM-1

doi: 10.13145/bacdive12625.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Propionibacteriales
  • family: Propionibacteriaceae
  • genus: Microlunatus
  • species: Microlunatus phosphovorus
  • full scientific name: Microlunatus phosphovorus Nakamura et al. 1995

@ref: 3973

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Propionibacteriaceae

genus: Microlunatus

species: Microlunatus phosphovorus

full scientific name: Microlunatus phosphovorus Nakamura et al. 1995

strain designation: NM-1

type strain: yes

Morphology

cell morphology

  • @ref: 121810
  • gram stain: positive
  • cell shape: coccus-shaped
  • motility: no

colony morphology

@refcolony colorincubation periodmedium used
18357Ivory (1014)10-14 days5006
18357Ivory (1014)10-14 days5425
18357Ivory (1014)10-14 days5428
18357Ivory (1014)10-14 daysDSM 776
18357Transparent10-14 daysISP 2

multicellular morphology

@refforms multicellular complexmedium name
18357noISP 2
18357no5006
18357no5425
18357no5428
18357noDSM 776

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
3973MICROLUNATUS MEDIUM (DSMZ Medium 776)yeshttps://mediadive.dsmz.de/medium/776Name: MICROLUNATUS MEDIUM (DSMZ Medium 776) Composition: KH2PO4 0.5 g/l Na glutamate 0.5 g/l Yeast extract 0.5 g/l Peptone 0.5 g/l Glucose 0.5 g/l (NH4)2SO4 0.1 g/l MgSO4 x 7 H2O 0.1 g/l Distilled water
18357ISP 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
183575006yesMedium: 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
183575425yesName: 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
183575428yes
18357DSM 776yesName: DSM 776; MICROLUNATUS MEDIUM Glucose 0.5 g Peptone 0.5 g Yeast extract 0.5 g Na glutamate 0.5 g KH2PO4 0.5 g (NH4)2SO4 0.1 g MgSO4 x 7 H2O 0.1 g Distilled water 1000.0 ml Adjust pH to 7.0.
37178MEDIUM 135 - for Microlunatus phosphovorus and Microsphaera multipartitayesDistilled water make up to (1000.000 ml);Magnesium sulphate heptahydrate (0.100 g);Agar (18.000 g);Glucose (0.500 g);Yeast extract (0.500 g);Ammonium sulphate (0.100 g);Peptone (0.500 g);Potassium di-hydrogen phosphate (0.440 g);Sodium glutamate (0.500 g)
121810CIP Medium 135yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=135
121810CIP Medium 216yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=216

culture temp

@refgrowthtypetemperaturerange
3973positivegrowth30mesophilic
18357positiveoptimum28mesophilic
37178positivegrowth30mesophilic
67770positivegrowth25mesophilic
121810positivegrowth30mesophilic
121810nogrowth5psychrophilic
121810nogrowth10psychrophilic
121810nogrowth22psychrophilic
121810nogrowth37mesophilic
121810nogrowth41thermophilic
121810nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 121810
  • oxygen tolerance: obligate aerobe

murein

  • @ref: 3973
  • murein short key: A42.01
  • type: A3gamma' LL-Dpm-Gly

observation

  • @ref: 67770
  • observation: quinones: MK-9(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
68371lactose-builds acid from17716
68371maltose-builds acid from17306
68371cellobiose-builds acid from17057
68371salicin-builds acid from17814
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
68371N-acetylglucosamine-builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
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-mannose-builds acid from16024
68371D-fructose-builds acid from15824
68371D-galactose-builds acid from12936
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
121810esculin+hydrolysis4853
121810hippurate-hydrolysis606565
121810nitrate+reduction17632
121810nitrite-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
12181035581indoleno

metabolite tests

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

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
121810oxidase+
121810beta-galactosidase+3.2.1.23
121810alcohol dehydrogenase-1.1.1.1
121810gelatinase-
121810DNase-
121810catalase+1.11.1.6
121810coagulase-
121810gamma-glutamyltransferase-2.3.2.2
121810lysine decarboxylase-4.1.1.18
121810ornithine decarboxylase-4.1.1.17
121810urease+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+
68382trypsin+3.4.21.4
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

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
18357---+-+++++-------+-

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
18357+++-+++++++++-+++++
121810+++-++-+-++++-++++--

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
18357++--+-+----

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
121810----------+/--------------+/-------------------------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
121810+++++-+++++++-++++++-+++-+++++-+++++++-+-+------------+----++---+-------+--+------+---+--+++-------

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentisolation date
3973activated sludgeJapanJPNAsia
67770Activated sludge grown on diluted corn steep liquorJapanJPNAsia
121810Environment, Activated sludgeJapanJPNAsia1989

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_8031.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_72;96_3710;97_4562;98_5854;99_8031&stattab=map
  • Last taxonomy: Microlunatus phosphovorus
  • 16S sequence: Z78207
  • Sequence Identity:
  • Total samples: 2841
  • soil counts: 494
  • aquatic counts: 1937
  • animal counts: 341
  • plant counts: 69

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
183571German classification
39731Risk group (German classification)
1218101Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218M.phosphovorus 16S rRNA geneZ782071468ena29405
3973Microlunatus phosphovorus gene for 16S rRNAD261691444ena1032480

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Microlunatus phosphovorus NM-1GCA_000270245completencbi1032480
66792Microlunatus phosphovorus NM-11032480.4completepatric1032480
66792Microlunatus phosphovorus NM-1650716058completeimg1032480

GC content

@refGC-contentmethod
397368high performance liquid chromatography (HPLC)
6777067.9high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno95.074no
flagellatedno98.386no
gram-positiveyes86.509no
anaerobicno99.034no
aerobicyes86.024no
halophileno94.69no
spore-formingno71.231no
thermophileno98.62yes
glucose-utilyes87.827no
glucose-fermentno87.339no

External links

@ref: 3973

culture collection no.: DSM 10555, JCM 9379, ATCC 700054, CIP 104466, FERM P-9771, HAMBI 2303, KCTC 9798, LMG 18116, NBRC 101784, NCIMB 13414, VKM Ac-1990

straininfo link

  • @ref: 81839
  • straininfo: 10852

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny7857797Microlunatus phosphovorus gen. nov., sp. nov., a new gram-positive polyphosphate-accumulating bacterium isolated from activated sludge.Nakamura K, Hiraishi A, Yoshimi Y, Kawaharasaki M, Masuda K, Kamagata YInt J Syst Bacteriol10.1099/00207713-45-1-171995Base Sequence, Gram-Positive Bacteria/*classification/genetics/metabolism, Molecular Sequence Data, Polyphosphates/*metabolism, RNA, Ribosomal, 16S/chemistry/geneticsMetabolism
Phylogeny16478514Isolation, characterization of bacteriophages specific to Microlunatus phosphovorus and their application for rapid host detection.Lee SH, Onuki M, Satoh H, Mino TLett Appl Microbiol10.1111/j.1472-765X.2006.01840.x2006Bacteriolysis, Bacteriophages/classification/*isolation & purification/physiology/ultrastructure, *Environmental Microbiology, Fluorescence, Microscopy, Electron, Transmission, Propionibacteriaceae/isolation & purification/physiology/*virology, Sewage/*microbiology, Species Specificity, Staining and Labeling, TokyoEnzymology
Phylogeny19946055Microlunatus parietis sp. nov., isolated from an indoor wall.Kampfer P, Schafer J, Lodders N, Martin KInt J Syst Evol Microbiol10.1099/ijs.0.020115-02009Bacterial Typing Techniques, Cell Wall/chemistry, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Diaminopimelic Acid/analysis, *Environmental Microbiology, Fatty Acids, Molecular Sequence Data, Mycolic Acids/analysis, Phospholipids/analysis, Phylogeny, Propionibacteriaceae/chemistry/*classification/genetics/*isolation & purification, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAGenetics
Genetics22923697Deciphering the genome of polyphosphate accumulating actinobacterium Microlunatus phosphovorus.Kawakoshi A, Nakazawa H, Fukada J, Sasagawa M, Katano Y, Nakamura S, Hosoyama A, Sasaki H, Ichikawa N, Hanada S, Kamagata Y, Nakamura K, Yamazaki S, Fujita NDNA Res10.1093/dnares/dss0202012Acid Anhydride Hydrolases/genetics, Base Sequence, Genome, Bacterial/*genetics, Molecular Sequence Data, Phosphate Transport Proteins/genetics, Phosphotransferases/genetics, Phylogeny, Physical Chromosome Mapping, Polyhydroxyalkanoates/genetics, Polyphosphates/*metabolism, Propionibacteriaceae/enzymology/*genetics/metabolism, Sequence Analysis, DNAPhylogeny
Metabolism24428681Metagenomic characterization of 'Candidatus Defluviicoccus tetraformis strain TFO71', a tetrad-forming organism, predominant in an anaerobic-aerobic membrane bioreactor with deteriorated biological phosphorus removal.Nobu MK, Tamaki H, Kubota K, Liu WTEnviron Microbiol10.1111/1462-2920.123832014*Bioreactors, DNA, Bacterial/genetics, Genes, Bacterial, Glycogen/metabolism, *Metagenome, Phosphorus/*metabolism, Phylogeny, Polyhydroxyalkanoates/metabolism, Polyphosphates/metabolism, RNA, Ribosomal, 16S/genetics, Rhodospirillaceae/*geneticsPhylogeny
Metabolism31572333The PolS-PolR Two-Component System Regulates Genes Involved in Poly-P Metabolism and Phosphate Transport in Microlunatus phosphovorus.Zhong C, Zhang P, Liu C, Liu M, Chen W, Fu J, Qi X, Cao GFront Microbiol10.3389/fmicb.2019.021272019
Metabolism35320769Carbon uptake bioenergetics of PAOs and GAOs in full-scale enhanced biological phosphorus removal systems.Chen L, Chen H, Hu Z, Tian Y, Wang C, Xie P, Deng X, Zhang Y, Tang X, Lin X, Li B, Wei C, Qiu GWater Res10.1016/j.watres.2022.1182582022Acetates, *Actinomycetales/metabolism, Adenosine Triphosphatases/metabolism, Aspartic Acid, *Betaproteobacteria/metabolism, Bioreactors, Carbon/metabolism, Energy Metabolism, Glutamic Acid/metabolism, Glycogen/metabolism, Phosphorus/metabolism, Polyphosphates/metabolism, Propionates, Propionibacteriaceae, RNA, Ribosomal, 16S/genetics/metabolism, Succinate Dehydrogenase/metabolismPhylogeny

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
3973Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 10555)https://www.dsmz.de/collection/catalogue/details/culture/DSM-10555
18357Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM10555.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
37178Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16377
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/
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
81839Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID10852.1StrainInfo: A central database for resolving microbial strain identifiers
121810Curators of the CIPCollection of Institut Pasteur (CIP 104466)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104466