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BacDive ID 17636
Type strain
Strain Designation ID 139908
Culture col. no. DSM 44928 NRRL B-24433 ID 139908 NBRC 102108 CIP 109381 BCRC 16841 JCM 14897 2 more
NCBI tax ID(s) 479433 304895
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: 12201

BacDive-ID: 17636

DSM-Number: 44928

keywords: genome sequence, 16S sequence, Bacteria, aerobe, spore-forming, mesophilic, Gram-positive, rod-shaped

description: Catenulispora acidiphila ID 139908 is an aerobe, spore-forming, mesophilic bacterium that was isolated from forest soil.

NCBI tax id

NCBI tax idMatching level
304895species
479433strain

strain history

@refhistory
12201<- L. Cavaletti <- E. Busti; ID 139908
67770NBRC 102108 <-- NRRL B-24433 <-- L. Cavaletti <-- E. Busti ID139908.
116002CIP <- 2006, DSMZ <- L. Cavaletti, Vicuron Pharm., Gerenzano, Italy <- E. Busti, Vicuron Pharm., Gerenzano, Italy: strain ID 139908

doi: 10.13145/bacdive17636.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Catenulisporales
  • family: Catenulisporaceae
  • genus: Catenulispora
  • species: Catenulispora acidiphila
  • full scientific name: Catenulispora acidiphila Busti et al. 2006

@ref: 12201

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Catenulisporaceae

genus: Catenulispora

species: Catenulispora acidiphila

full scientific name: Catenulispora acidiphila Busti et al. 2006 emend. Nouioui et al. 2018

strain designation: ID 139908

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31588positive0.4-1 µm0.5 µmrod-shapedno
125439positive99.9
125439no96.9
116002positiverod-shapedno

pigmentation

@refproductioncolorname
31588yes
27877yesbrown and whitebrownisch whitish, turning yellow/green with ageing

multimedia

@refmultimedia contentcaptionintellectual property rights
12201https://www.dsmz.de/microorganisms/photos/DSM_44928.jpgMedium 65 pH5.5 28°C© Leibniz-Institut DSMZ
66793EM_DSM_44928_1.jpgelectron microscopic image© HZI/Manfred Rohde

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
12201GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)yeshttps://mediadive.dsmz.de/medium/65Name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) Composition: Agar 18.0 g/l Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l CaCO3 2.0 g/l Distilled water
12201ISP2 MEDIUM (DSMZ Medium 987)yeshttps://mediadive.dsmz.de/medium/987Name: ISP 2 MEDIUM (DSMZ Medium 987) Composition: Agar 20.0 g/l Malt extract 10.0 g/l Dextrose 4.0 g/l Yeast extract 4.0 g/l Distilled water
33295MEDIUM 688 for Catenulispora acidiphilayes
116002CIP Medium 688yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=688
12201ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium84.pdf

culture temp

@refgrowthtypetemperature
12201positivegrowth28
31588positivegrowth11-37
31588positiveoptimum22-28
33295positivegrowth30
27877nogrowth4
27877nogrowth40
67770positivegrowth28

culture pH

@refabilitytypepH
31588positivegrowth4.3-6.8
31588positiveoptimum6

Physiology and metabolism

tolerance

  • @ref: 27877
  • compound: Lysozyme
  • concentration: 100.0 µg/ml

oxygen tolerance

@refoxygen toleranceconfidence
31588aerobe
116002facultative anaerobe
125439obligate aerobe99.3

spore formation

@refspore formationspore descriptiontype of sporeconfidence
31588yes
27877yesspore surface is rugose, produce chains of more than 20 cylindrical arthrosporesarthrospore
125439yes96.5

halophily

@refsaltgrowthtested relationconcentration
31588NaClpositivegrowth0-3 %
31588NaClpositiveoptimum0-3 %

observation

@refobservation
31588aggregates in chains
67770quinones: MK-9(H6), MK-9(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3158822599arabinose+carbon source
3158828757fructose+carbon source
3158817234glucose+carbon source
3158817754glycerol+carbon source
3158829864mannitol+carbon source
3158818222xylose+carbon source
27877casein+hydrolysis
2787762968cellulose-assimilation
278775291gelatin+hydrolysis
2787717268myo-inositol-assimilation
2787717632nitrate-reduction
2787726546rhamnose-assimilation
2787728017starch+hydrolysis
2787717992sucrose-assimilation
11600217632nitrate-reduction
11600216301nitrite-reduction
68371Potassium 5-ketogluconate+builds acid from
6837117634D-glucose+builds acid from
6837112936D-galactose+builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837128066gentiobiose-builds acid from
6837117151xylitol-builds acid from
6837128087glycogen-builds acid from
6837128017starch-builds acid from
6837116634raffinose-builds acid from
6837115443inulin-builds acid from
6837127082trehalose-builds acid from
6837117992sucrose+builds acid from
6837128053melibiose-builds acid from
6837117716lactose+builds acid from
6837117057cellobiose-builds acid from
6837117814salicin-builds acid from
683714853esculin-builds acid from
6837118305arbutin-builds acid from
6837127613amygdalin-builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol-builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose-builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose-builds acid from
6837115824D-fructose+builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose-builds acid from
6837130849L-arabinose-builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol+builds acid from

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitivesensitivity conc.is resistantresistance conc.
2787728368novobiocinyesyes10 µg/mL
2787729670ramoplaninyesyes10 µg/mL
2787729693thiostreptonyesyes10 µg/mL
278772790apramycinyesyes10 µg/mL
2787741977daunorubicinyesyes10 µg/mL
278776104kanamycinyesyes10 µg/mL
27877100147nalidixic acidyesyes10 µg/mL
2787771629nisinyesyes10 µg/mL
278777809oxacillinyesyes10 µg/mL
2787728077rifampicinyesyes10 µg/mL

metabolite production

@refChebi-IDmetaboliteproduction
3158816136hydrogen sulfideyes
11600235581indoleno

enzymes

@refvalueactivityec
31588catalase+1.11.1.6
68382beta-glucosidase-3.2.1.21
68382alpha-fucosidase-3.2.1.51
68382alpha-chymotrypsin-3.4.21.1
68382naphthol-AS-BI-phosphohydrolase+
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
116002oxidase-
116002catalase+1.11.1.6
116002urease-3.5.1.5
68382trypsin-3.4.21.4

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
19890----------+--------
116002+++++----++++++-++--

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
116002+---+/-----+++---------+/------+/-+-+--+/------+/---------+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
12201forest soilGerenzanoItalyITAEurope
67770Soil from a wooded areaGerenzanoItalyITAEurope
116002Environment, Forest soil

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Forest
#Environmental#Terrestrial#Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_6314.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_94;96_3004;97_3691;98_4676;99_6314&stattab=map
  • Last taxonomy: Catenulispora
  • 16S sequence: AJ865857
  • Sequence Identity:
  • Total samples: 21098
  • soil counts: 16042
  • aquatic counts: 870
  • animal counts: 1233
  • plant counts: 2953

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
122011Risk group (German classification)
198901Risk group (German classification)
1160021Risk group (French classification)

Sequence information

16S sequences

  • @ref: 12201
  • description: Catenulispora acidiphila partial 16S rRNA gene, type strain ID139908T
  • accession: AJ865857
  • length: 1441
  • database: nuccore
  • NCBI tax ID: 479433

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Catenulispora acidiphila DSM 44928GCA_000024025completencbi479433
66792Catenulispora acidiphila DSM 44928479433.5completepatric479433
66792Catenulispora acidiphila ID139908, DSM 44928644736339completeimg479433

GC content

@refGC-contentmethod
1220171.9
3158871.5
6777071.5high performance liquid chromatography (HPLC)
6777069.77genome sequence analysis

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingyes88.389yes
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no97.311yes
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes88.448no
125438spore-formingspore-formingAbility to form endo- or exosporesyes89.142yes
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno94.5no
125438motile2+flagellatedAbility to perform flagellated movementno88.5no
125439BacteriaNetspore_formationAbility to form endo- or exosporesyes96.5
125439BacteriaNetmotilityAbility to perform movementno96.9
125439BacteriaNetgram_stainReaction to gram-stainingpositive99.9
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe99.3

External links

@ref: 12201

culture collection no.: DSM 44928, NRRL B-24433, JCM 14897, BCRC 16841, CIP 109381, NBRC 102108

straininfo link

  • @ref: 86628
  • straininfo: 295939

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16902001Catenulispora acidiphila gen. nov., sp. nov., a novel, mycelium-forming actinomycete, and proposal of Catenulisporaceae fam. nov.Busti E, Cavaletti L, Monciardini P, Schumann P, Rohde M, Sosio M, Donadio SInt J Syst Evol Microbiol10.1099/ijs.0.63858-02006Actinobacteria/chemistry/*classification/isolation & purification/physiology, Base Composition, Culture Media, Cyanoacrylates/analysis, Hydrogen-Ion Concentration, Italy, Lipids/analysis, Molecular Sequence Data, Peptidoglycan/analysis, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Homology, Nucleic Acid, Soil Microbiology, Species Specificity, TreesCultivation
Genetics21304647Complete genome sequence of Catenulispora acidiphila type strain (ID 139908).Copeland A, Lapidus A, Glavina Del Rio T, Nolan M, Lucas S, Chen F, Tice H, Cheng JF, Bruce D, Goodwin L, Pitluck S, Mikhailova N, Pati A, Ivanova N, Mavromatis K, Chen A, Palaniappan K, Chain P, Land M, Hauser L, Chang YJ, Jeffries CD, Chertkov O, Brettin T, Detter JC, Han C, Ali Z, Tindall BJ, Goker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HPStand Genomic Sci10.4056/sigs.172592009
Metabolism22725258Biosynthesis of the class III lantipeptide catenulipeptin.Wang H, van der Donk WAACS Chem Biol10.1021/cb30024462012Actinobacteria/chemistry/*enzymology/genetics/metabolism, Alanine/*analogs & derivatives/chemistry/genetics/metabolism/pharmacology, Amino Acid Sequence, Genes, Bacterial, Molecular Sequence Data, Multigene Family, Peptides/*chemistry/genetics/*metabolism/pharmacology, Protein Sorting Signals, Streptomyces coelicolor/drug effects/growth & development, Sulfides/*chemistry/*metabolism/pharmacologyGenetics
Metabolism24389065Identification and characterization of 2-oxoglutarate-dependent dioxygenases catalyzing selective cis-hydroxylation of proline and pipecolinic acid from actinomycetes.Hara R, Uchiumi N, Kino KJ Biotechnol10.1016/j.jbiotec.2013.12.0032013Actinobacteria/classification/*enzymology, Bacterial Proteins/genetics/physiology, Carboxylic Acids/*metabolism, Dioxygenases/genetics/*physiology, Hydroxylation, Hydroxyproline/*metabolism, Ketoglutaric Acids/*metabolism, Models, ChemicalEnzymology
Metabolism24554531New aminocoumarins from the rare actinomycete Catenulispora acidiphila DSM 44928: identification, structure elucidation, and heterologous production.Zettler J, Xia H, Burkard N, Kulik A, Grond S, Heide L, Apel AKChembiochem10.1002/cbic.2013007122014Actinomycetales/*chemistry/genetics/metabolism, Aminocoumarins/*chemistry/metabolism/pharmacology, Anti-Bacterial Agents/biosynthesis/*chemistry/pharmacology, Bacterial Proteins/genetics/metabolism, Biological Products/chemistry/metabolism/pharmacology, Genome, Bacterial, Gram-Negative Bacteria/drug effects, Gram-Positive Bacteria/drug effects, Molecular Conformation, Multigene Family, Pyrroles/*chemistry/metabolism/pharmacology, Recombinant Proteins/biosynthesis/genetics, Streptomyces/metabolismGenetics
Phylogeny33360072Genomic-based classification of Catenulispora pinisilvae sp. nov., novel actinobacteria isolated from a pine forest soil in Poland and emended description of Catenulispora rubra.Swiecimska M, Golinska P, Wypij M, Goodfellow MSyst Appl Microbiol10.1016/j.syapm.2020.1261642020Actinobacteria/*classification/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, *Forests, Nucleic Acid Hybridization, Peptidoglycan/chemistry, *Phylogeny, Pinus, Poland, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil MicrobiologyTranscriptome

Reference

@idauthorscataloguedoi/urltitlepubmedID_cross_referencejournal
12201Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44928)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44928
19890Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44928.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
2787710.1099/ijs.0.63858-016902001
31588Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604127877
33295Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7116
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 life28604660 35: 676-683 2017
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 updates33211880Nucleic Acids Res. 49: D498-D508 2020
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68371Automatically annotated from API 50CH acid
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
86628Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID295939.1StrainInfo: A central database for resolving microbial strain identifiers
116002Curators of the CIPCollection of Institut Pasteur (CIP 109381)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109381
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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