Strain identifier

BacDive ID: 12613

Type strain: Yes

Species: Microlunatus capsulatus

Strain Designation: J47, Ben-108

Strain history: CIP <- 2001, M. Dougall, Victoria, Australia: strain Ben-108

NCBI tax ID(s): 99117 (species)

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General

@ref: 4864

BacDive-ID: 12613

DSM-Number: 12936

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

description: Microlunatus capsulatus J47 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from activated sludge.

NCBI tax id

  • NCBI tax id: 99117
  • Matching level: species

strain history

@refhistory
4864<- A.M. Maszenan <- J.A. Soddell; J47 (= Ben 108)
67770DSM 12936 <-- A. M. Maszenan <-- J. A. Soddell J47 (=Ben 108).
117174CIP <- 2001, M. Dougall, Victoria, Australia: strain Ben-108

doi: 10.13145/bacdive12613.20250331.9.3

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 capsulatus
  • full scientific name: Microlunatus capsulatus (Maszenan et al. 1999) Nouioui et al. 2018

  • synonyms

    • @ref: 20215
    • synonym: Friedmanniella capsulata

@ref: 4864

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Propionibacteriaceae

genus: Microlunatus

species: Microlunatus capsulatus

full scientific name: Microlunatus capsulatus (Maszenan et al. 1999) Nouioui et al. 2018

strain designation: J47, Ben-108

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
117174positivecoccus-shapedno
125439positive98
125438no94

colony morphology

@refcolony colorincubation periodmedium used
18503Dahlia yellow (1033)10-14 daysISP 2
18503Dahlia yellow (1033)10-14 daysISP 3
18503Dahlia yellow (1033)10-14 daysISP 4
18503Dahlia yellow (1033)10-14 daysISP 5
18503Dahlia yellow (1033)10-14 daysISP 6
18503Dahlia yellow (1033)10-14 daysISP 7
117174

multicellular morphology

@refforms multicellular complexmedium name
18503noISP 2
18503noISP 3
18503noISP 4
18503noISP 5
18503noISP 6
18503noISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
4864TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yeshttps://mediadive.dsmz.de/medium/92Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water
18503ISP 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
18503ISP 3yesName: ISP 3; 5315 Composition Dog oat flakes 20.0 g/l Trace element solution (5314) 2.5 ml/l Agar 18.0 g/l Preparation: Oat flakes are cooked for 20 minutes, trace element solution and agar are added (in the case of non rolled oat flakes the suspension has to bee filtrated). Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.8 Usage: Maintenance and taxonomy (e.g. SEM As liquid medium for metabolite production) Organisms: All Actinomycetes Trace element solution 5314 Name: Trace element solution 5314; 5314 Composition CaCl2 x H2O 3.0 g/l Fe-III-citrate 1.0 g/l MnSO4 0.2 g/l ZnCl2 0.1 g/l CuSO4 x 5 H2O 0.025 g/l Sodium tetra borate 0.2 g/l CoCl2 x 6 H2O 0.004 g/l Sodium molybdate 0.01 g/l Preparation: Use double destillated water. Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Trace element solution for different media Organisms:
18503ISP 4yesName: ISP 4; DSM 547 Solution I: Difco soluble starch, 10.0 g. Make a paste of the starch with a small amount of cold distilled water and bring to a volume of 500 ml. Solution II: CaCO3 2.0 g K2HPO4 (anhydrous) 1.0 g MgSO4 x 7 H2O 1.0 g NaCl 1.0 g (NH4)2SO4 2.0 g Distilled water 500.0 ml Trace salt solution (see below) 1.0 ml The pH should be between 7.0 and 7.4. Do not adjust if it is within this range. Mix solutions I and II together. Add 20.0 g agar. Liquify agar by steaming at 100°C for 10 to 20 min. Trace element solution: FeSO4 x 7 H2O 0.1 g MnCl2 x 4 H2O 0.1 g ZnSO4 x 7 H2O 0.1 g Distilled water 100.0 ml
18503ISP 5yesName: ISP 5 (5323) Composition L-Asparagine 1.0 g/l Glycerol 10.0 g/l K2HPO4 1.0 g/l Salt solution (see preparation) 1.0 ml/l Agar 20.0 g/l Preparation: Salt solution 1.0 g FeSO4 x 7 H2O 1.0 g MnCl2 x 4 H2O 1.0 g ZNSO4 x 7 H2O in 100 ml water Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.2 Usage: Maintenance and taxonomy Organisms: All Actinomycetes
18503ISP 6yesName: ISP 6 (5318) Composition Peptone 15.0 g/l Proteose peptose 5.0 g/l Ferric ammonium citrate 0.5 g/l Sodium glycerophosphate 1.0 g/l Sodium thiosulfate 0.08 g/l Yeast extract 1.0 g/l Agar 15.0 g/l Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigments Organisms: All Actinomycetes
18503ISP 7yesName: ISP 7 (5322) Composition Glycerol 15.0 g/l L-Tyrosine 0.5 g/l L-Asparagine 1.0 g/l K2HPO4 0.5 g/l NaCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Trace element solution 5343 1.0 ml/l Agar 20.0 Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.3 Usage: Production of melanoid pigments Organisms: All Actinomycetes
33708MEDIUM 4 - Columbia agar with 20 % sterile defibrinated horse serumyesHorse serum (200.000 ml);Columbia agar (39.000 g);Distilled water make up to (1000.000 ml)
117174CIP Medium 4yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=4
117174CIP Medium 6yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=6

culture temp

@refgrowthtypetemperature
4864positivegrowth28
18503positiveoptimum28
33708positivegrowth25
55690positivegrowth37
55690positivegrowth28-37
67770positivegrowth28
117174positivegrowth10-30
117174nogrowth37
117174nogrowth41
117174nogrowth45

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
55690aerobe
55690microaerophile
117174obligate aerobe
125439obligate aerobe99.6

halophily

@refsaltgrowthtested relationconcentration
117174NaClpositivegrowth0-4 %
117174NaClnogrowth6 %
117174NaClnogrowth8 %
117174NaClnogrowth10 %

murein

  • @ref: 4864
  • murein short key: A42.01
  • type: A3gamma' LL-Dpm-Gly

observation

  • @ref: 67770
  • observation: quinones: MK-9(H4), MK-9(H2), MK-7(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1850362968cellulose+
1850316634raffinose+
1850326546rhamnose+
1850328757fructose+
1850329864mannitol+
1850317268myo-inositol+
1850318222xylose+
1850317992sucrose+
1850322599arabinose+
1850317234glucose+
6837928087glycogen-fermentation
6837917992sucrose+fermentation
6837917716lactose-fermentation
6837917306maltose-fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol-fermentation
6837916988D-ribose-fermentation
683795291gelatin-hydrolysis
6837917634D-glucose-fermentation
6837916199urea-hydrolysis
11717416947citrate-carbon source
1171744853esculin+hydrolysis
117174606565hippurate+hydrolysis
11717417632nitrate-reduction
11717416301nitrite-reduction
11717417632nitrate-respiration
683794853esculin+hydrolysis
6837917632nitrate-reduction
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816199urea-hydrolysis
6836816947citrate+assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
11717435581indoleno
6836815688acetoinno
6836835581indoleno
6836816136hydrogen sulfideno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-testindole test
11717415688acetoin-
11717417234glucose-
6836815688acetoin-
6836835581indole-

enzymes

@refvalueactivityec
68382alpha-fucosidase+3.2.1.51
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase-3.2.1.31
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
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382esterase lipase (C 8)+
117174oxidase-
117174beta-galactosidase+3.2.1.23
117174alcohol dehydrogenase-1.1.1.1
117174gelatinase-
117174amylase+
117174DNase-
117174caseinase-3.4.21.50
117174catalase+1.11.1.6
117174tween esterase-
117174gamma-glutamyltransferase+2.3.2.2
117174lysine decarboxylase-4.1.1.18
117174ornithine decarboxylase-4.1.1.17
117174phenylalanine ammonia-lyase-4.3.1.24
117174tryptophan deaminase-
117174urease+3.5.1.5
68379alpha-glucosidase+3.2.1.20
68379beta-galactosidase+3.2.1.23
68379alkaline phosphatase+3.1.3.1
68368gelatinase-
68368urease-3.5.1.5
68382beta-glucosidase+3.2.1.21
68379gelatinase-
68379urease-3.5.1.5
68379beta-glucosidase+3.2.1.21
68379N-acetyl-beta-glucosaminidase-3.2.1.52
68379beta-glucuronidase-3.2.1.31
68379pyrrolidonyl arylamidase+3.4.19.3
68379pyrazinamidase-3.5.1.B15
68368tryptophan deaminase-4.1.99.1
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
18503--++-++-+--------+-

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
18503+-+-++---++++-+++++
117174-++-+----++---++--+-

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
18503----+------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
4864activated sludgeQueensland, Hayman IslandAustraliaAUSAustralia and Oceania
55690Activated sludgeAustraliaAUSAustralia and Oceania
67770Activated sludge biomassHayman Island, QueenslandAustraliaAUSAustralia and Oceania
117174Environment, Activated sludgeAustraliaAUSAustralia and Oceania1992

isolation source categories

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

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
185031
48641Risk group (German classification)
1171741Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
4864Friedmanniella capsulata 16S ribosomal RNA gene, partial sequenceAF0845291477nuccore99117
67770Friedmanniella capsulata gene for 16S ribosomal RNA, partial sequence, strain: JCM 13522LC1139051461nuccore99117

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Microlunatus capsulatus DSM 12936GCA_017876495contigncbi99117
66792Microlunatus capsulatus strain DSM 1293699117.3wgspatric99117
66792Friedmanniella capsulata DSM 129362918354206draftimg99117

GC content

@refGC-contentmethod
486474high performance liquid chromatography (HPLC)
6777074thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingyes87.962no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no96.411yes
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes88.264no
125438spore-formingspore-formingAbility to form endo- or exosporesno54.283no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno97yes
125438motile2+flagellatedAbility to perform flagellated movementno94no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno65.6
125439BacteriaNetmotilityAbility to perform movementno67.8
125439BacteriaNetgram_stainReaction to gram-stainingpositive98
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe99.6

External links

@ref: 4864

culture collection no.: DSM 12936, ACM 5120, JCM 13522, CCUG 43143, Ben 108, CIP 107259, KACC 14261

straininfo link

  • @ref: 81827
  • straininfo: 49384

literature

  • topic: Phylogeny
  • Pubmed-ID: 10555348
  • title: Friedmanniella spumicola sp. nov. and Friedmanniella capsulata sp. nov. from activated sludge foam: gram-positive cocci that grow in aggregates of repeating groups of cocci.
  • authors: Maszenan AM, Seviour RJ, Patel BK, Schumann P, Burghardt J, Webb RI, Soddell JA, Rees GN
  • journal: Int J Syst Bacteriol
  • DOI: 10.1099/00207713-49-4-1667
  • year: 1999
  • mesh: Bacterial Typing Techniques, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Genes, rRNA, Microscopy, Electron, Molecular Sequence Data, Phylogeny, Propionibacteriaceae/*chemistry/*classification/cytology/isolation & purification, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage/*microbiology
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitle
4864Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 12936)https://www.dsmz.de/collection/catalogue/details/culture/DSM-12936
18503Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM12936.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
33708Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/4675
55690Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 43143)https://www.ccug.se/strain?id=43143
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
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
81827Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID49384.1StrainInfo: A central database for resolving microbial strain identifiers
117174Curators of the CIPCollection of Institut Pasteur (CIP 107259)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107259
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1