Strain identifier
BacDive ID: 130542
Type strain: 
Species: Microbacter margulisiae
Strain Designation: ADRI
Strain history: I. Sánchez-Andrea strain ADRI.
NCBI tax ID(s): 1350067 (species)
version 9.1 (current version)
General
@ref: 22129
BacDive-ID: 130542
DSM-Number: 27471
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, Gram-negative
description: Microbacter margulisiae ADRI is an anaerobe, Gram-negative bacterium that was isolated from sediment of an acid rock drainage environment.
NCBI tax id
- NCBI tax id: 1350067
- Matching level: species
strain history
| @ref | history |
|---|---|
| 22129 | <- I. Sánchez-Andrea, Univ. Wageningen; ADRI <- I. Sánchez-Andrea, Universidad Autónoma de Madrid, Spain |
| 67770 | I. Sánchez-Andrea strain ADRI. |
doi: 10.13145/bacdive130542.20240916.9.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacteroidota
- domain: Bacteria
- phylum: Bacteroidota
- class: Bacteroidia
- order: Bacteroidales
- family: Porphyromonadaceae
- genus: Microbacter
- species: Microbacter margulisiae
- full scientific name: Microbacter margulisiae Sánchez-Andrea et al. 2014
@ref: 22129
domain: Bacteria
phylum: Bacteroidetes
class: Bacteroidia
order: Bacteroidales
family: Porphyromonadaceae
genus: Microbacter
species: Microbacter margulisiae
full scientific name: Microbacter margulisiae Sánchez-Andrea et al. 2014
strain designation: ADRI
type strain: yes
Morphology
cell morphology
| @ref | gram stain | confidence | motility |
|---|---|---|---|
| 69480 | negative | 93.198 | |
| 69480 | 92 | no |
colony morphology
- @ref: 22129
- incubation period: 3-7 days
Culture and growth conditions
culture medium
- @ref: 22129
- name: MICROBACTER MEDIUM (DSMZ Medium 1571)
- growth: yes
- link: https://mediadive.dsmz.de/medium/1571
- composition: Name: MICROBACTER MEDIUM (DSMZ Medium 1571) Composition: Yeast extract 2.0 g/l Na2HPO4 x 2 H2O 0.53 g/l Resazurin 0.5 g/l L-Cysteine 0.5 g/l KH2PO4 0.41 g/l Na2S x 9 H2O 0.36 g/l NH4Cl 0.3 g/l NaCl 0.3 g/l MgCl2 x 6 H2O 0.1 g/l CaCl2 x 2 H2O 0.01 g/l HCl 0.0025 g/l FeCl2 x 4 H2O 0.0015 g/l NaOH 0.00025 g/l CoCl2 x 6 H2O 0.00019 g/l MnCl2 x 4 H2O 0.0001 g/l ZnCl2 7e-05 g/l Na2MoO4 x 2 H2O 3.6e-05 g/l NiCl2 x 6 H2O 2.4e-05 g/l H3BO3 6e-06 g/l Pyridoxine hydrochloride 5e-06 g/l Lipoic acid 2.5e-06 g/l p-Aminobenzoic acid 2.5e-06 g/l D-Calcium pantothenate 2.5e-06 g/l Nicotinic acid 2.5e-06 g/l Riboflavin 2.5e-06 g/l Thiamine-HCl x 2 H2O 2.5e-06 g/l Na2WO4 x 2 H2O 2e-06 g/l CuCl2 x 2 H2O 2e-06 g/l Na2SeO3 x 5 H2O 1.5e-06 g/l Biotin 1e-06 g/l Folic acid 1e-06 g/l Vitamin B12 5e-08 g/l Distilled water
culture temp
| @ref | growth | type | temperature |
|---|---|---|---|
| 22129 | positive | growth | 30 |
| 67770 | positive | growth | 30 |
Physiology and metabolism
oxygen tolerance
- @ref: 22129
- oxygen tolerance: anaerobe
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69480 | no | 92.5 |
| 69481 | no | 100 |
observation
- @ref: 67770
- observation: quinones: MK-8, MK-9
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 22129 | sediment of an acid rock drainage environment | Huelva, Tinto River | Spain | ESP | Europe |
| 67770 | Sediment of an acid rock drainage environment | Tinto River | Spain | ESP | Europe |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Sediment |
| #Environmental | #Terrestrial | #Geologic |
| #Condition | #Acidic |
taxonmaps
- @ref: 69479
- File name: preview.99_69925.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_662;96_29962;97_37854;98_49109;99_69925&stattab=map
- Last taxonomy: Microbacter margulisiae subclade
- 16S sequence: LM643867
- Sequence Identity:
- Total samples: 1678
- soil counts: 91
- aquatic counts: 207
- animal counts: 1367
- plant counts: 13
Safety information
risk assessment
- @ref: 22129
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 22129
- description: Microbacter margulisiae partial 16S rRNA gene, strain DSM 27471, isolate ADRI
- accession: LM643867
- length: 1488
- database: nuccore
- NCBI tax ID: 1350067
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Microbacter margulisiae DSM 27471 | GCA_014192515 | contig | ncbi | 1350067 |
| 66792 | Microbacter margulisiae strain DSM 27471 | 1350067.3 | wgs | patric | 1350067 |
| 66792 | Microbacter margulisiae DSM 27471 | 2824490045 | draft | img | 1350067 |
GC content
- @ref: 22129
- GC-content: 39.9
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
| @ref | trait | model | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 69481 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 100 | no |
| 69480 | gram-positive | gram-positive | Positive reaction to Gram-staining | no | 93.198 | no |
| 69480 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | yes | 75.986 | yes |
| 69480 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 92.5 | no |
| 69480 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | no | 77.514 | no |
| 69480 | thermophilic | thermophile | Ability to grow at temperatures above or equal to 45°C | no | 90.167 | yes |
| 69480 | flagellated | motile2+ | Ability to perform flagellated movement | no | 92 | no |
External links
@ref: 22129
culture collection no.: DSM 27471, JCM 19374
straininfo link
- @ref: 89063
- straininfo: 408032
literature
- topic: Phylogeny
- Pubmed-ID: 25201913
- title: Microbacter margulisiae gen. nov., sp. nov., a propionigenic bacterium isolated from sediments of an acid rock drainage pond.
- authors: Sanchez-Andrea I, Sanz JL, Stams AJM
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.066241-0
- year: 2014
- mesh: Acids, Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/isolation & purification, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Molecular Sequence Data, *Phylogeny, Ponds/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Spain, Vitamin K 2/analogs & derivatives/chemistry
- topic2: Genetics
Reference
| @id | authors | title | doi/url | catalogue |
|---|---|---|---|---|
| 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 | |
| 22129 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-27471 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 27471) | |
| 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/ | ||
| 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 | |
| 89063 | 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-ID408032.1 |