Strain identifier
BacDive ID: 8029
Type strain: 
Species: Micromonospora gifhornensis
Strain Designation: 1-2
Strain history: DSM 44337 <-- H. Rheims HR1-2.
NCBI tax ID(s): 84594 (species)
version 8.1 (current version)
General
@ref: 11683
BacDive-ID: 8029
DSM-Number: 44337
keywords: genome sequence, 16S sequence, Bacteria, spore-forming, mesophilic, Gram-positive
description: Micromonospora gifhornensis 1-2 is a spore-forming, mesophilic, Gram-positive bacterium that was isolated from peat sample.
NCBI tax id
- NCBI tax id: 84594
- Matching level: species
strain history
| @ref | history |
|---|---|
| 11683 | <- H. Rheims, 1-2 |
| 67770 | DSM 44337 <-- H. Rheims HR1-2. |
doi: 10.13145/bacdive8029.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Actinomycetes
- order: Micromonosporales
- family: Micromonosporaceae
- genus: Micromonospora
- species: Micromonospora gifhornensis
- full scientific name: Micromonospora gifhornensis (Rheims et al. 1998) Nouioui et al. 2018
synonyms
- @ref: 20215
- synonym: Verrucosispora gifhornensis
@ref: 11683
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Micromonosporaceae
genus: Micromonospora
species: Micromonospora gifhornensis
full scientific name: Micromonospora gifhornensis (Rheims et al. 1998) Nouioui et al. 2018
strain designation: 1-2
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: positive
- confidence: 100
multimedia
- @ref: 11683
- multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_44337.jpg
- caption: Medium 65 37°C
- intellectual property rights: © Leibniz-Institut DSMZ
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 11683 | 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 |
| 11683 | GPHF-MEDIUM (DSMZ Medium 553) | yes | https://mediadive.dsmz.de/medium/553 | Name: GPHF-MEDIUM (DSMZ Medium 553) Composition: Agar 20.0 g/l Glucose 10.0 g/l Beef extract 5.0 g/l Yeast extract 5.0 g/l Casein peptone 5.0 g/l CaCl2 x 2 H2O 0.74 g/l Distilled water |
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 11683 | positive | growth | 37 | mesophilic |
| 67770 | positive | growth | 28 | mesophilic |
Physiology and metabolism
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | yes | 100 |
| 69480 | yes | 100 |
observation
- @ref: 67770
- observation: quinones: MK-9(H4), MK-9(H6), MK-10(H4), MK-9(H2)
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 11683 | peat sample | Gifhorn, Großes Moor | Germany | DEU | Europe |
| 67770 | Peat from a peat bog near Gifhorn | Lower Saxony | Germany | DEU | Europe |
isolation source categories
- Cat1: #Environmental
- Cat2: #Terrestrial
- Cat3: #Wetland (Swamp)
taxonmaps
- @ref: 69479
- File name: preview.99_4596.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_94;96_404;97_2781;98_3452;99_4596&stattab=map
- Last taxonomy: Micromonospora
- 16S sequence: Y15523
- Sequence Identity:
- Total samples: 449
- soil counts: 308
- aquatic counts: 47
- animal counts: 71
- plant counts: 23
Safety information
risk assessment
- @ref: 11683
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 20218 | Verrucosispora gifhornensis DSM 44337 16S-23S ribosomal RNA intergenic spacer | AY371892 | 361 | ena | 84594 |
| 20218 | Verrucosispora gifhornensis 16S rRNA gene | Y15523 | 1462 | ena | 84594 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Micromonospora gifhornensis NBRC 16317 | GCA_016863515 | contig | ncbi | 84594 |
| 66792 | Micromonospora gifhornensis strain NBRC 16317 | 84594.3 | wgs | patric | 84594 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 11683 | 70.4 | |
| 67770 | 70 | high performance liquid chromatography (HPLC) |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | yes | 100 | no |
| motile | no | 93.912 | no |
| flagellated | no | 97.166 | no |
| gram-positive | yes | 90.808 | no |
| anaerobic | no | 99.291 | no |
| halophile | no | 95.545 | no |
| spore-forming | yes | 95.612 | no |
| thermophile | no | 98.662 | no |
| glucose-util | yes | 88.196 | no |
| aerobic | yes | 93.637 | no |
| glucose-ferment | no | 90.976 | no |
External links
@ref: 11683
culture collection no.: DSM 44337, BCC 49510, IFO 16317, JCM 10457, NBRC 16317, CGMCC 4.5502, IMSNU 22178, KACC 20946
straininfo link
- @ref: 77459
- straininfo: 50577
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 9828414 | Verrucosispora gifhornensis gen. nov., sp. nov., a new member of the actinobacterial family Micromonosporaceae. | Rheims H, Schumann P, Rohde M, Stackebrandt E | Int J Syst Bacteriol | 10.1099/00207713-48-4-1119 | 1998 | Anti-Bacterial Agents/pharmacology, Base Composition, DNA, Bacterial/chemistry, DNA, Ribosomal/chemistry, Genes, rRNA, Microbial Sensitivity Tests, Micromonosporaceae/*classification/drug effects/growth & development/isolation & purification, Molecular Sequence Data, Phylogeny, Polymerase Chain Reaction/methods, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Species Specificity, Spores, Bacterial, Terminology as Topic | Genetics |
| Phylogeny | 19620381 | Verrucosispora lutea sp. nov., isolated from a mangrove sediment sample. | Liao ZL, Tang SK, Guo L, Zhang YQ, Tian XP, Jiang CL, Xu LH, Li WJ | Int J Syst Evol Microbiol | 10.1099/ijs.0.008813-0 | 2009 | Aerobiosis, Bacterial Typing Techniques, Base Composition, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Glucose/analysis, Micromonosporaceae/chemistry/*classification/genetics/*isolation & purification, Microscopy, Electron, Scanning, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/analysis, Phospholipids/analysis, Phylogeny, Plants/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Spores, Bacterial/cytology, Vitamin K 2/analysis, Xylose/analysis | Genetics |
| Phylogeny | 21989685 | Verrucosispora maris sp. nov., a novel deep-sea actinomycete isolated from a marine sediment which produces abyssomicins. | Goodfellow M, Stach JE, Brown R, Bonda AN, Jones AL, Mexson J, Fiedler HP, Zucchi TD, Bull AT | Antonie Van Leeuwenhoek | 10.1007/s10482-011-9651-5 | 2011 | Amino Acids/analysis, Anti-Bacterial Agents/*metabolism, Bacterial Typing Techniques, Base Composition, Carbohydrates/analysis, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Geologic Sediments/*microbiology, Micromonosporaceae/*classification/genetics/*isolation & purification/physiology, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA | Genetics |
| Phylogeny | 23111784 | Verrucosispora fiedleri sp. nov., an actinomycete isolated from a fjord sediment which synthesizes proximicins. | Goodfellow M, Brown R, Ahmed L, Pathom-Aree W, Bull AT, Jones AL, Stach JE, Zucchi TD, Zhang L, Wang J | Antonie Van Leeuwenhoek | 10.1007/s10482-012-9831-y | 2012 | Bacterial Typing Techniques, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Estuaries, Geologic Sediments/*microbiology, Micromonosporaceae/*classification/genetics/*isolation & purification, Molecular Sequence Data, Norway, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA | Genetics |
| Phylogeny | 23710052 | Verrucosispora andamanensis sp. nov., isolated from a marine sponge. | Supong K, Suriyachadkun C, Suwanborirux K, Pittayakhajonwut P, Thawai C | Int J Syst Evol Microbiol | 10.1099/ijs.0.050906-0 | 2013 | Animals, Bacterial Typing Techniques, Base Composition, Carbohydrates/chemistry, Cell Wall/chemistry, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Micromonosporaceae/*classification/genetics/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, Porifera/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Thailand | Genetics |
| Phylogeny | 30605079 | Micromonospora craniellae sp. nov., isolated from a marine sponge, and reclassification of Jishengella endophytica as Micromonospora endophytica comb. nov. | Li L, Zhu HR, Xu QH, Lin HW, Lu YH | Int J Syst Evol Microbiol | 10.1099/ijsem.0.003209 | 2019 | Animals, Bacterial Typing Techniques, China, DNA, Bacterial/genetics, Genes, Bacterial, Micromonospora/*classification/isolation & purification, Micromonosporaceae/classification, Nucleic Acid Hybridization, *Phylogeny, Porifera/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA | Transcriptome |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 11683 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44337) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-44337 | |||
| 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 | |||
| 20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
| 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) | |||
| 67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
| 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 | |||
| 77459 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID50577.1 | StrainInfo: A central database for resolving microbial strain identifiers |