Strain identifier
BacDive ID: 24236
Type strain:
Species: Mycobacterium sediminis
Strain history: <- S-K Tang, Yunnan Inst., China
NCBI tax ID(s): 1286180 (species)
General
@ref: 20671
BacDive-ID: 24236
DSM-Number: 45643
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-positive, ovoid-shaped
description: Mycobacterium sediminis DSM 45643 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from marine sediment.
NCBI tax id
- NCBI tax id: 1286180
- Matching level: species
strain history
@ref | history |
---|---|
20671 | <- S.-K. Tang, YIM; YIM M13028 <- D.-F. Zhang |
67770 | S.-K. Tang YIM M13028. |
67771 | <- S-K Tang, Yunnan Inst., China |
doi: 10.13145/bacdive24236.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Actinomycetes
- order: Mycobacteriales
- family: Mycobacteriaceae
- genus: Mycobacterium
- species: Mycobacterium sediminis
- full scientific name: Mycobacterium sediminis Zhang et al. 2013
synonyms
- @ref: 20215
- synonym: Mycolicibacterium sediminis
@ref: 20671
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Mycobacteriaceae
genus: Mycobacterium
species: Mycobacterium sediminis
full scientific name: Mycobacterium sediminis Zhang et al. 2013
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell shape | motility | confidence |
---|---|---|---|---|
31044 | positive | ovoid-shaped | no | |
67771 | positive | |||
69480 | no | 93.781 | ||
69480 | positive | 100 |
pigmentation
- @ref: 31044
- production: yes
multimedia
- @ref: 20671
- multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_45643.jpg
- caption: Medium 645 28°C
- intellectual property rights: © Leibniz-Institut DSMZ
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
20671 | 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 |
20671 | MIDDLEBROOK MEDIUM (DSMZ Medium 645) | yes | https://mediadive.dsmz.de/medium/645 | Name: MIDDLEBROOK MEDIUM (DSMZ Medium 645) Composition: Bacto Middlebrook 7H10 agar 20.9945 g/l Glycerol Distilled water |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
20671 | positive | growth | 28 | mesophilic |
31044 | positive | growth | 05-37 | |
31044 | positive | optimum | 28 | mesophilic |
67770 | positive | growth | 28 | mesophilic |
67771 | positive | growth | 28 | mesophilic |
culture pH
@ref | ability | type | pH |
---|---|---|---|
31044 | positive | growth | 6.0-8.0 |
31044 | positive | optimum | 7 |
Physiology and metabolism
oxygen tolerance
- @ref: 67771
- oxygen tolerance: aerobe
spore formation
@ref | spore formation | confidence |
---|---|---|
31044 | no | |
69481 | no | 100 |
69480 | no | 99.876 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
31044 | NaCl | positive | growth | 0-4 % |
31044 | NaCl | positive | optimum | 1 % |
enzymes
@ref | value | activity | ec |
---|---|---|---|
31044 | catalase | + | 1.11.1.6 |
31044 | urease | + | 3.5.1.5 |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent | latitude | longitude |
---|---|---|---|---|---|---|---|
20671 | marine sediment | Yunnan, South China Sea (19° 30.261' N 111° 0.247' E) at a depth of 42 m | China | CHN | Asia | 19.5044 | 111.004 |
67770 | Sediment sample from the South China Sea at a depth of 42 m | ||||||
67771 | From marine sediment | Southe China Sea | China | CHN | Asia |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Environmental | #Aquatic | #Marine |
#Environmental | #Aquatic | #Sediment |
taxonmaps
- @ref: 69479
- File name: preview.99_13681.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_115;97_2631;98_10349;99_13681&stattab=map
- Last taxonomy: Mycolicibacterium
- 16S sequence: KC010490
- Sequence Identity:
- Total samples: 4459
- soil counts: 1808
- aquatic counts: 648
- animal counts: 1323
- plant counts: 680
Safety information
risk assessment
- @ref: 20671
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20671 | Mycobacterium sediminis strain YIM M13028 16S ribosomal RNA gene, partial sequence | KC010490 | 1515 | ena | 1286180 |
67770 | Mycobacterium sediminis strain YIM M13028 16S-23S ribosomal RNA intergenic spacer, complete sequence | KC010492 | 490 | ena | 1286180 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Mycolicibacterium sediminis JCM 17899 | GCA_010731735 | complete | ncbi | 1286180 |
66792 | Mycolicibacterium sediminis strain JCM 17899 | 1286180.8 | complete | patric | 1286180 |
66792 | Mycolicibacterium sediminis JCM 17899 | 2888243993 | complete | img | 1286180 |
66792 | Mycolicibacterium sediminis DSM 45643 | GCA_025822985 | scaffold | ncbi | 1286180 |
GC content
@ref | GC-content | method |
---|---|---|
20671 | 64.1 | high performance liquid chromatography (HPLC) |
31044 | 64.1 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | no | 91.076 | yes |
flagellated | no | 97.857 | yes |
gram-positive | yes | 90.78 | yes |
anaerobic | no | 99.277 | no |
aerobic | yes | 92.421 | no |
halophile | no | 93.931 | yes |
spore-forming | no | 83.703 | yes |
glucose-util | yes | 89.249 | no |
thermophile | no | 99.602 | yes |
glucose-ferment | no | 90.777 | no |
External links
@ref: 20671
culture collection no.: DSM 45643, KCTC 19999, YIM M13028, JCM 17899
straininfo link
- @ref: 88179
- straininfo: 407834
literature
- topic: Phylogeny
- Pubmed-ID: 23728378
- title: Mycobacterium sediminis sp. nov. and Mycobacterium arabiense sp. nov., two rapidly growing members of the genus Mycobacterium.
- authors: Zhang DF, Chen X, Zhang XM, Zhi XY, Yao JC, Jiang Y, Xiong Z, Li WJ
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.050567-0
- year: 2013
- mesh: Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, DNA, Ribosomal Spacer/genetics, Fatty Acids/chemistry, Genes, Bacterial, Geologic Sediments/*microbiology, Molecular Sequence Data, Multilocus Sequence Typing, Mycobacterium/*classification/genetics/isolation & purification, Nucleic Acid Hybridization, Oceans and Seas, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, United Arab Emirates
- topic2: Genetics
Reference
@id | authors | title | doi/url | catalogue | ID_cross_reference | pubmed |
---|---|---|---|---|---|---|
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | 10.1099/ijsem.0.004332 | |||
20671 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-45643 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45643) | |||
31044 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 10.1128/mSphere.00237-17 | 27374 | 28776041 | |
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |||
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
67771 | Curators of the KCTC | https://kctc.kribb.re.kr/En/Kctc | ||||
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. | MicrobeAtlas 1.0 beta | https://microbeatlas.org/ | |||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | Predictions based on the model GenomeNet Sporulation v. 1 | 10.21203/rs.3.rs-2527258/v1 | |||
88179 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | StrainInfo: A central database for resolving microbial strain identifiers | 10.60712/SI-ID407834.1 |