Strain identifier
BacDive ID: 17636
Type strain:
Species: Catenulispora acidiphila
Strain Designation: ID 139908
Strain history: CIP <- 2006, DSMZ <- L. Cavaletti, Vicuron Pharm., Gerenzano, Italy <- E. Busti, Vicuron Pharm., Gerenzano, Italy: strain ID 139908
NCBI tax ID(s): 479433 (strain), 304895 (species)
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 id | Matching level |
---|---|
479433 | strain |
304895 | species |
strain history
@ref | history |
---|---|
12201 | <- L. Cavaletti <- E. Busti; ID 139908 |
67770 | NBRC 102108 <-- NRRL B-24433 <-- L. Cavaletti <-- E. Busti ID139908. |
116002 | CIP <- 2006, DSMZ <- L. Cavaletti, Vicuron Pharm., Gerenzano, Italy <- E. Busti, Vicuron Pharm., Gerenzano, Italy: strain ID 139908 |
doi: 10.13145/bacdive17636.20230509.8.1
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
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
31588 | positive | 0.4-1 µm | 0.5 µm | rod-shaped | no | |
69480 | no | 92.801 | ||||
69480 | positive | 100 | ||||
116002 | positive | rod-shaped | no |
pigmentation
@ref | production | color | name |
---|---|---|---|
31588 | yes | ||
27877 | yes | brown and white | brownisch whitish, turning yellow/green with ageing |
multimedia
@ref | multimedia content | caption | intellectual property rights |
---|---|---|---|
12201 | https://www.dsmz.de/microorganisms/photos/DSM_44928.jpg | Medium 65 pH5.5 28°C | © Leibniz-Institut DSMZ |
66793 | EM_DSM_44928_1.jpg | electron microscopic image | © HZI/Manfred Rohde |
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
12201 | GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) | yes | https://mediadive.dsmz.de/medium/65 | Name: 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 |
12201 | ISP2 MEDIUM (DSMZ Medium 987) | yes | https://mediadive.dsmz.de/medium/987 | Name: 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 |
33295 | MEDIUM 688 for Catenulispora acidiphila | yes | ||
116002 | CIP Medium 688 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=688 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
12201 | positive | growth | 28 | mesophilic |
31588 | positive | growth | 11-37 | |
31588 | positive | optimum | 22-28 | |
33295 | positive | growth | 30 | mesophilic |
27877 | no | growth | 4 | psychrophilic |
27877 | no | growth | 40 | thermophilic |
67770 | positive | growth | 28 | mesophilic |
culture pH
@ref | ability | type | pH |
---|---|---|---|
31588 | positive | growth | 4.3-6.8 |
31588 | positive | optimum | 6 |
Physiology and metabolism
tolerance
- @ref: 27877
- compound: Lysozyme
- concentration: 100.0 µg/ml
oxygen tolerance
@ref | oxygen tolerance |
---|---|
31588 | aerobe |
116002 | facultative anaerobe |
spore formation
@ref | spore formation | spore description | type of spore | confidence |
---|---|---|---|---|
31588 | yes | |||
27877 | yes | spore surface is rugose, produce chains of more than 20 cylindrical arthrospores | arthrospore | |
69481 | yes | 100 | ||
69480 | yes | 100 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
31588 | NaCl | positive | growth | 0-3 % |
31588 | NaCl | positive | optimum | 0-3 % |
observation
@ref | observation |
---|---|
31588 | aggregates in chains |
67770 | quinones: MK-9(H6), MK-9(H4) |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
31588 | 22599 | arabinose | + | carbon source |
31588 | 28757 | fructose | + | carbon source |
31588 | 17234 | glucose | + | carbon source |
31588 | 17754 | glycerol | + | carbon source |
31588 | 29864 | mannitol | + | carbon source |
31588 | 18222 | xylose | + | carbon source |
27877 | casein | + | hydrolysis | |
27877 | 62968 | cellulose | - | assimilation |
27877 | 5291 | gelatin | + | hydrolysis |
27877 | 17268 | myo-inositol | - | assimilation |
27877 | 17632 | nitrate | - | reduction |
27877 | 26546 | rhamnose | - | assimilation |
27877 | 28017 | starch | + | hydrolysis |
27877 | 17992 | sucrose | - | assimilation |
68371 | Potassium 5-ketogluconate | + | builds acid from | |
68371 | Potassium 2-ketogluconate | - | builds acid from | |
68371 | 24265 | gluconate | - | builds acid from |
68371 | 18403 | L-arabitol | - | builds acid from |
68371 | 18333 | D-arabitol | - | builds acid from |
68371 | 18287 | L-fucose | - | builds acid from |
68371 | 28847 | D-fucose | - | builds acid from |
68371 | 16443 | D-tagatose | - | builds acid from |
68371 | 62318 | D-lyxose | - | builds acid from |
68371 | 28066 | gentiobiose | - | builds acid from |
68371 | 17151 | xylitol | - | builds acid from |
68371 | 28087 | glycogen | - | builds acid from |
68371 | 28017 | starch | - | builds acid from |
68371 | 16634 | raffinose | - | builds acid from |
68371 | 15443 | inulin | - | builds acid from |
68371 | 27082 | trehalose | - | builds acid from |
68371 | 17992 | sucrose | + | builds acid from |
68371 | 28053 | melibiose | - | builds acid from |
68371 | 17716 | lactose | + | builds acid from |
68371 | 17057 | cellobiose | - | builds acid from |
68371 | 17814 | salicin | - | builds acid from |
68371 | 4853 | esculin | - | builds acid from |
68371 | 18305 | arbutin | - | builds acid from |
68371 | 27613 | amygdalin | - | builds acid from |
68371 | 320061 | methyl alpha-D-glucopyranoside | - | builds acid from |
68371 | 43943 | methyl alpha-D-mannoside | - | builds acid from |
68371 | 17924 | D-sorbitol | - | builds acid from |
68371 | 16899 | D-mannitol | - | builds acid from |
68371 | 17268 | myo-inositol | - | builds acid from |
68371 | 16813 | galactitol | - | builds acid from |
68371 | 62345 | L-rhamnose | - | builds acid from |
68371 | 17266 | L-sorbose | - | builds acid from |
68371 | 16024 | D-mannose | - | builds acid from |
68371 | 15824 | D-fructose | + | builds acid from |
68371 | 17634 | D-glucose | + | builds acid from |
68371 | 12936 | D-galactose | + | builds acid from |
68371 | 74863 | methyl beta-D-xylopyranoside | - | builds acid from |
68371 | 15963 | ribitol | - | builds acid from |
68371 | 65328 | L-xylose | - | builds acid from |
68371 | 65327 | D-xylose | - | builds acid from |
68371 | 30849 | L-arabinose | - | builds acid from |
68371 | 17108 | D-arabinose | - | builds acid from |
68371 | 17113 | erythritol | - | builds acid from |
68371 | 17754 | glycerol | + | builds acid from |
116002 | 17632 | nitrate | - | reduction |
116002 | 16301 | nitrite | - | reduction |
antibiotic resistance
@ref | ChEBI | metabolite | is antibiotic | is sensitive | sensitivity conc. | is resistant | resistance conc. |
---|---|---|---|---|---|---|---|
27877 | 28368 | novobiocin | yes | yes | 10 µg/mL | ||
27877 | 29670 | ramoplanin | yes | yes | 10 µg/mL | ||
27877 | 29693 | thiostrepton | yes | yes | 10 µg/mL | ||
27877 | 2790 | apramycin | yes | yes | 10 µg/mL | ||
27877 | 41977 | daunorubicin | yes | yes | 10 µg/mL | ||
27877 | 6104 | kanamycin | yes | yes | 10 µg/mL | ||
27877 | 100147 | nalidixic acid | yes | yes | 10 µg/mL | ||
27877 | 71629 | nisin | yes | yes | 10 µg/mL | ||
27877 | 7809 | oxacillin | yes | yes | 10 µg/mL | ||
27877 | 28077 | rifampicin | yes | yes | 10 µg/mL |
metabolite production
@ref | Chebi-ID | metabolite | production |
---|---|---|---|
31588 | 16136 | hydrogen sulfide | yes |
116002 | 35581 | indole | no |
enzymes
@ref | value | activity | ec |
---|---|---|---|
31588 | catalase | + | 1.11.1.6 |
116002 | oxidase | - | |
116002 | catalase | + | 1.11.1.6 |
116002 | urease | - | 3.5.1.5 |
68382 | valine arylamidase | - | |
68382 | cystine arylamidase | - | 3.4.11.3 |
68382 | trypsin | - | 3.4.21.4 |
68382 | alpha-chymotrypsin | - | 3.4.21.1 |
68382 | naphthol-AS-BI-phosphohydrolase | + | |
68382 | beta-glucosidase | - | 3.2.1.21 |
68382 | alpha-fucosidase | - | 3.2.1.51 |
API zym
@ref | Alkaline phosphatase | Esterase | Esterase Lipase | Lipase | Leucine arylamidase | Valine arylamidase | Cystine arylamidase | Trypsin | alpha- Chymotrypsin | Acid phosphatase | Naphthol-AS-BI-phosphohydrolase | alpha- Galactosidase | beta- Galactosidase | beta- Glucuronidase | alpha- Glucosidase | beta- Glucosidase | N-acetyl-beta- glucosaminidase | alpha- Mannosidase | alpha- Fucosidase | Control |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
19890 | - | - | - | - | - | - | - | - | - | - | + | - | - | - | - | - | - | - | - | |
116002 | + | + | + | + | + | - | - | - | - | + | + | + | + | + | + | - | + | + | - | - |
API 50CHac
@ref | GLY | ERY | DARA | LARA | RIB | DXYL | LXYL | ADO | MDX | GAL | GLU | FRU | MNE | SBE | RHA | DUL | INO | MAN | SOR | MDM | MDG | NAG | AMY | ARB | ESC | SAL | CEL | MAL | LAC | MEL | SAC | TRE | INU | MLZ | RAF | AMD | GLYG | XLT | GEN | TUR | LYX | TAG | DFUC | LFUC | DARL | LARL | GNT | 2KG | 5KG |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
116002 | + | - | - | - | +/- | - | - | - | - | + | + | + | - | - | - | - | - | - | - | - | - | +/- | - | - | - | - | - | +/- | + | - | + | - | - | +/- | - | - | - | - | - | +/- | - | - | - | - | - | - | - | - | + |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
12201 | forest soil | Gerenzano | Italy | ITA | Europe |
67770 | Soil from a wooded area | Gerenzano | Italy | ITA | Europe |
116002 | Environment, Forest soil |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#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
@ref | biosafety level | biosafety level comment |
---|---|---|
12201 | 1 | Risk group (German classification) |
19890 | 1 | Risk group (German classification) |
116002 | 1 | Risk group (French classification) |
Sequence information
16S sequences
- @ref: 12201
- description: Catenulispora acidiphila partial 16S rRNA gene, type strain ID139908T
- accession: AJ865857
- length: 1441
- database: ena
- NCBI tax ID: 479433
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Catenulispora acidiphila DSM 44928 | GCA_000024025 | complete | ncbi | 479433 |
66792 | Catenulispora acidiphila DSM 44928 | 479433.5 | complete | patric | 479433 |
66792 | Catenulispora acidiphila ID139908, DSM 44928 | 644736339 | complete | img | 479433 |
GC content
@ref | GC-content | method |
---|---|---|
12201 | 71.9 | |
31588 | 71.5 | |
67770 | 71.5 | high performance liquid chromatography (HPLC) |
67770 | 69.77 | genome sequence analysis |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | yes | 100 | no |
motile | no | 93.231 | yes |
flagellated | no | 98.48 | yes |
gram-positive | yes | 91.347 | yes |
anaerobic | no | 99.532 | yes |
aerobic | yes | 95.023 | yes |
halophile | no | 93.961 | no |
spore-forming | yes | 93.086 | yes |
thermophile | no | 98.902 | no |
glucose-util | yes | 88.296 | yes |
glucose-ferment | no | 86.805 | no |
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
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 16902001 | Catenulispora 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 S | Int J Syst Evol Microbiol | 10.1099/ijs.0.63858-0 | 2006 | Actinobacteria/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, Trees | Cultivation |
Genetics | 21304647 | Complete 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 HP | Stand Genomic Sci | 10.4056/sigs.17259 | 2009 | ||
Metabolism | 22725258 | Biosynthesis of the class III lantipeptide catenulipeptin. | Wang H, van der Donk WA | ACS Chem Biol | 10.1021/cb3002446 | 2012 | Actinobacteria/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/pharmacology | Genetics |
Metabolism | 24389065 | Identification and characterization of 2-oxoglutarate-dependent dioxygenases catalyzing selective cis-hydroxylation of proline and pipecolinic acid from actinomycetes. | Hara R, Uchiumi N, Kino K | J Biotechnol | 10.1016/j.jbiotec.2013.12.003 | 2013 | Actinobacteria/classification/*enzymology, Bacterial Proteins/genetics/physiology, Carboxylic Acids/*metabolism, Dioxygenases/genetics/*physiology, Hydroxylation, Hydroxyproline/*metabolism, Ketoglutaric Acids/*metabolism, Models, Chemical | Enzymology |
Metabolism | 24554531 | New 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 AK | Chembiochem | 10.1002/cbic.201300712 | 2014 | Actinomycetales/*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/metabolism | Genetics |
Phylogeny | 33360072 | Genomic-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 M | Syst Appl Microbiol | 10.1016/j.syapm.2020.126164 | 2020 | Actinobacteria/*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 Microbiology | Transcriptome |
Reference
@id | authors | catalogue | doi/url | title | pubmed | ID_cross_reference | journal |
---|---|---|---|---|---|---|---|
12201 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44928) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-44928 | ||||
19890 | Wink, J. | http://www.dsmz.de/microorganisms/wink_pdf/DSM44928.pdf | Compendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig | ||||
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | ||||
27877 | 10.1099/ijs.0.63858-0 | 16902001 | |||||
31588 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 28776041 | 27877 | ||
33295 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/7116 | |||||
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | ||||
66793 | Mukherjee et al. | 10.1038/nbt.3886 | GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life | 28604660 | 35: 676-683 2017 | ||
66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | 33211880 | Nucleic Acids Res. 49: D498-D508 2020 | ||
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | |||||
68371 | Automatically annotated from API 50CH acid | ||||||
68382 | Automatically annotated from API zym | ||||||
69479 | João 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 | ||||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | ||||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | ||||
86628 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID295939.1 | StrainInfo: A central database for resolving microbial strain identifiers | ||||
116002 | Curators of the CIP | Collection of Institut Pasteur (CIP 109381) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109381 |