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BacDive ID 16505
Type strain
Strain Designation R-55
Culture col. no. DSM 44705 IFO 16266 JCM 10982 NBRC 16266 R-55 BCRC 16396 1 more
NCBI tax ID(s) 150177
Links
For citation purpose refer to the digital object identifier (doi) of the current version.

Archive

version 9.3 (current version):
version 9.3 (current version)

General

@ref: 11896

BacDive-ID: 16505

DSM-Number: 44705

keywords: genome sequence, 16S sequence, Bacteria, spore-forming, mesophilic

description: Acrocarpospora macrocephala R-55 is a spore-forming, mesophilic bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 150177
  • Matching level: species

strain history

@refhistory
11896<- NBRC <- S. Suzuki, Tanabe Seiyaku Co.; R-55
67770IFO 16266 <-- T. Tamura <-- S. Suzuki R-55.

doi: 10.13145/bacdive16505.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Streptosporangiales
  • family: Streptosporangiaceae
  • genus: Acrocarpospora
  • species: Acrocarpospora macrocephala
  • full scientific name: Acrocarpospora macrocephala Tamura et al. 2000

@ref: 11896

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Streptosporangiaceae

genus: Acrocarpospora

species: Acrocarpospora macrocephala

full scientific name: Acrocarpospora macrocephala Tamura et al. 2000

strain designation: R-55

type strain: yes

Morphology

cell morphology

@refgram stainconfidencemotility
125439positive99.8
12543996.8no

colony morphology

@refcolony colorincubation periodmedium used
19691Brown beige10-14 daysISP 2
19691Brown beige10-14 daysISP 3
19691Brown beige10-14 daysISP 4
19691Brown beige10-14 daysISP 5
19691Brown beige10-14 daysISP 6
19691Brown beige10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
19691noISP 2
19691noISP 3
19691noISP 4
19691noISP 5
19691noISP 6
19691noISP 7

multimedia

  • @ref: 11896
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_44705.jpg
  • caption: Medium 84 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11896ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84)yeshttps://mediadive.dsmz.de/medium/84Name: ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84) Composition: Agar 20.0 g/l Rolled oats 20.0 g/l ZnSO4 x 7 H2O 0.001 g/l MnCl2 x 4 H2O 0.001 g/l FeSO4 x 7 H2O 0.001 g/l Distilled water
11896ISP 5 MEDIUM (DSMZ Medium 993)yeshttps://mediadive.dsmz.de/medium/993Name: ISP 5 MEDIUM (DSMZ Medium 993) Composition: Agar 20.0 g/l Glycerol 10.0 g/l K2HPO4 1.0 g/l L-Asparagine 1.0 g/l FeSO4 x 7 H2O 0.001 g/l MnCl2 x 4 H2O 0.001 g/l ZnSO4 x 7 H2O 0.001 g/l Distilled water
19691ISP 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
19691ISP 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:
19691ISP 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
19691ISP 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
19691ISP 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
19691ISP 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

culture temp

@refgrowthtypetemperature
11896positivegrowth28
67770positivegrowth28

Physiology and metabolism

oxygen tolerance

  • @ref: 125439
  • oxygen tolerance: facultative anaerobe
  • confidence: 94.2

spore formation

  • @ref: 125439
  • spore formation: yes
  • confidence: 94.6

observation

  • @ref: 67770
  • observation: quinones: MK-9(H4), MK-9(H2), MK-9(H6)

metabolite utilization

@refChebi-IDmetaboliteutilization activity
1969117234glucose-
1969122599arabinose+
1969117992sucrose+
1969118222xylose+
1969117268myo-inositol+
1969129864mannitol+
1969128757fructose+
1969126546rhamnose+
1969116634raffinose-
1969162968cellulose+

enzymes

@refvalueactivityec
68382beta-glucosidase+3.2.1.21
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382naphthol-AS-BI-phosphohydrolase-
68382alpha-galactosidase-3.2.1.22
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382valine arylamidase+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382esterase lipase (C 8)+
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase+3.2.1.24
68382beta-galactosidase-3.2.1.23

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
19691+++-++---+----++++-

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentgeographic location
11896soilJapanJPNAsia
67770SoilJapanJPNAsiaSaitama Pref.

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
118961Risk group (German classification)
196911Risk group (German classification)

Sequence information

16S sequences

  • @ref: 11896
  • description: Acrocarpospora macrocephala gene for 16S ribosomal RNA
  • accession: AB025318
  • length: 1449
  • database: nuccore
  • NCBI tax ID: 150177

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Acrocarpospora macrocephala NBRC 16266GCA_009687865scaffoldncbi150177
66792Acrocarpospora macrocephala strain NBRC 16266150177.3wgspatric150177

GC content

@refGC-contentmethod
1189668
6777068.1high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingyes89.483no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no93.219no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes86.827no
125438spore-formingspore-formingAbility to form endo- or exosporesyes86.633no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno92.994yes
125438motile2+flagellatedAbility to perform flagellated movementno87no
125439BacteriaNetspore_formationAbility to form endo- or exosporesyes94.6
125439BacteriaNetmotilityAbility to perform movementno96.8
125439BacteriaNetgram_stainReaction to gram-stainingpositive99.8
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthfacultative anaerobe94.2

External links

@ref: 11896

culture collection no.: DSM 44705, IFO 16266, JCM 10982, NBRC 16266, BCRC 16396

straininfo link

  • @ref: 85538
  • straininfo: 62209

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny10843059Acrocarpospora gen. nov., a new genus of the order Actinomycetales.Tamura T, Suzuki S, Hatano KInt J Syst Evol Microbiol10.1099/00207713-50-3-11632000Actinomycetales/chemistry/*classification/genetics/ultrastructure, Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil MicrobiologyGenetics
Phylogeny23125318Acrocarpospora phusangensis sp. nov., isolated from a temperate peat swamp forest soil.Niemhom N, Suriyachadkun C, Tamura T, Thawai CInt J Syst Evol Microbiol10.1099/ijs.0.046227-02012Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/analysis, Phospholipids/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Thailand, Vitamin K 2/analogs & derivatives/analysis, *WetlandsGenetics
Genetics32801283Diversity of nonribosomal peptide synthetase and polyketide synthase gene clusters in the genus Acrocarpospora.Komaki H, Oguchi A, Tamura T, Hamada M, Ichikawa NJ Gen Appl Microbiol10.2323/jgam.2020.01.0012020Actinobacteria/*genetics, Base Sequence, Genome, Bacterial/*genetics, Multigene Family/genetics, Peptide Biosynthesis, Nucleic Acid-Independent/genetics, Peptide Synthases/*genetics, Polyketide Synthases/*genetics, Sequence Analysis, DNA, Whole Genome SequencingTranscriptome
Phylogeny36129751Acrocarpospora catenulata sp. nov., a novel actinobacterium isolated from lake sediment.Liu C, Guo Y, Li L, Li J, Wang L, Lin J, Wang X, Chu YInt J Syst Evol Microbiol10.1099/ijsem.0.0055262022*Actinomycetales, Bacterial Typing Techniques, Base Composition, Cardiolipins, DNA, Bacterial/genetics, Fatty Acids/chemistry, Glucose, Lakes/analysis, Nucleotides, *Phosphatidylethanolamines, Phospholipids/chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, Ribose, Sequence Analysis, DNA, Soil Microbiology, Vitamin K 2/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitle
11896Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44705)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44705
19691Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44705.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
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/
68382Automatically annotated from API zym
85538Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID62209.1StrainInfo: A central database for resolving microbial strain identifiers
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

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