Strain identifier
BacDive ID: 18119
Type strain: 
Species: Exiguobacterium profundum
Strain Designation: 10c
Strain history: <- M.-L. Fardeau; 10c
NCBI tax ID(s): 307643 (species)
version 8.1 (current version)
General
@ref: 6874
BacDive-ID: 18119
DSM-Number: 17289
keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, mesophilic, Gram-positive, motile, rod-shaped
description: Exiguobacterium profundum 10c is a facultative anaerobe, mesophilic, Gram-positive bacterium that was isolated from mud .
NCBI tax id
- NCBI tax id: 307643
- Matching level: species
strain history
- @ref: 6874
- history: <- M.-L. Fardeau; 10c
doi: 10.13145/bacdive18119.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Bacilli
- order: Caryophanales
- family: Bacillaceae
- genus: Exiguobacterium
- species: Exiguobacterium profundum
- full scientific name: Exiguobacterium profundum Crapart et al. 2007
@ref: 6874
domain: Bacteria
phylum: Firmicutes
class: Bacilli
order: Bacillales
family: Bacilli, not assigned to family
genus: Exiguobacterium
species: Exiguobacterium profundum
full scientific name: Exiguobacterium profundum Crapart et al. 2007
strain designation: 10c
type strain: yes
Morphology
cell morphology
- @ref: 31911
- gram stain: positive
- cell length: 6 µm
- cell width: 0.75 µm
- cell shape: rod-shaped
- motility: yes
pigmentation
- @ref: 31911
- production: no
Culture and growth conditions
culture medium
- @ref: 6874
- name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)
- growth: yes
- link: https://mediadive.dsmz.de/medium/514
- composition: Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 6874 | positive | growth | 30 | mesophilic |
| 31911 | positive | growth | 12-49 | |
| 31911 | positive | optimum | 45 | thermophilic |
| 59059 | positive | growth | 30-42 |
culture pH
| @ref | ability | type | pH | PH range |
|---|---|---|---|---|
| 31911 | positive | growth | 5.5-9.5 | alkaliphile |
| 31911 | positive | optimum | 7 |
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance |
|---|---|
| 31911 | facultative anaerobe |
| 59059 | aerobe |
spore formation
- @ref: 31911
- spore formation: no
halophily
| @ref | salt | growth | tested relation | concentration |
|---|---|---|---|---|
| 31911 | NaCl | positive | growth | 0-11 % |
| 31911 | NaCl | positive | optimum | 2 % |
observation
- @ref: 31911
- observation: aggregates in chains
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 31911 | 30089 | acetate | + | carbon source |
| 31911 | 17057 | cellobiose | + | carbon source |
| 31911 | 28757 | fructose | + | carbon source |
| 31911 | 28260 | galactose | + | carbon source |
| 31911 | 17234 | glucose | + | carbon source |
| 31911 | 24996 | lactate | + | carbon source |
| 31911 | 17716 | lactose | + | carbon source |
| 31911 | 17306 | maltose | + | carbon source |
| 31911 | 29864 | mannitol | + | carbon source |
| 31911 | 37684 | mannose | + | carbon source |
| 31911 | 28053 | melibiose | + | carbon source |
| 31911 | 506227 | N-acetylglucosamine | + | carbon source |
| 31911 | 15361 | pyruvate | + | carbon source |
| 31911 | 16634 | raffinose | + | carbon source |
| 31911 | 33942 | ribose | + | carbon source |
| 31911 | 17814 | salicin | + | carbon source |
| 31911 | 17992 | sucrose | + | carbon source |
| 31911 | 27082 | trehalose | + | carbon source |
| 31911 | 4853 | esculin | + | hydrolysis |
| 31911 | 17632 | nitrate | + | reduction |
enzymes
- @ref: 31911
- value: catalase
- activity: +
- ec: 1.11.1.6
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country |
|---|---|---|---|
| 6874 | mud (deep-sea hydrothermal vent) | East Pacific Rise (2600), Grandbonum vent site | International waters |
| 59059 | Deep-sea hydrothermal vent | 13°N East-Paciifc Rise at 2600m |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Hydrothermal vent |
| #Environmental | #Terrestrial | #Mud (Sludge) |
| #Condition | #Thermophilic (>45°C) |
taxonmaps
- @ref: 69479
- File name: preview.99_2494.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_130;96_715;97_837;98_973;99_2494&stattab=map
- Last taxonomy: Exiguobacterium
- 16S sequence: AY818050
- Sequence Identity:
- Total samples: 1790
- soil counts: 61
- aquatic counts: 453
- animal counts: 1235
- plant counts: 41
Safety information
risk assessment
- @ref: 6874
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 6874
- description: Exiguobacterium profundum strain 10C 16S ribosomal RNA gene, partial sequence
- accession: AY818050
- length: 1510
- database: ena
- NCBI tax ID: 307643
Genome sequences
- @ref: 66792
- description: Exiguobacterium profundum 10C
- accession: GCA_025234635
- assembly level: contig
- database: ncbi
- NCBI tax ID: 307643
GC content
- @ref: 6874
- GC-content: 50.4
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| motile | yes | 90.548 | no |
| flagellated | yes | 75.027 | no |
| gram-positive | yes | 88.488 | yes |
| anaerobic | no | 99.124 | no |
| aerobic | yes | 64.189 | no |
| halophile | yes | 74.126 | no |
| spore-forming | no | 67.848 | no |
| glucose-ferment | no | 78.711 | no |
| thermophile | no | 99.747 | no |
| glucose-util | yes | 89.319 | yes |
External links
@ref: 6874
culture collection no.: DSM 17289, CCUG 50949, CNCM I-2962
straininfo link
- @ref: 87107
- straininfo: 297183
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 17267965 | Exiguobacterium profundum sp. nov., a moderately thermophilic, lactic acid-producing bacterium isolated from a deep-sea hydrothermal vent. | Crapart S, Fardeau ML, Cayol JL, Thomas P, Sery C, Ollivier B, Combet-Blanc Y | Int J Syst Evol Microbiol | 10.1099/ijs.0.64639-0 | 2007 | Anaerobiosis, Bacillaceae/*classification/cytology/*isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, Carbohydrate Metabolism, Catalase/analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis/chemistry, Genes, rRNA, Hot Springs/*microbiology, Hydrogen-Ion Concentration, Lactic Acid/metabolism, Molecular Sequence Data, Nitrates/metabolism, Nitrites/metabolism, Oxidation-Reduction, Oxidoreductases/analysis, Pacific Ocean, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sodium Chloride, Spores, Bacterial, Temperature | Metabolism |
| Phylogeny | 23229437 | Exiguobacterium himgiriensis sp. nov. a novel member of the genus Exiguobacterium, isolated from the Indian Himalayas. | Singh NK, Raichand R, Kaur I, Kaur C, Pareek S, Mayilraj S | Antonie Van Leeuwenhoek | 10.1007/s10482-012-9861-5 | 2012 | Bacillales/*classification/genetics/*isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, India, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, Pigments, Biological/metabolism, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology | Genetics |
Reference
| @id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
|---|---|---|---|---|---|---|
| 6874 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17289) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-17289 | |||
| 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 | |||
| 31911 | 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 | 28168 | 28776041 | |
| 59059 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 50949) | https://www.ccug.se/strain?id=50949 | |||
| 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) | |||
| 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 | |||
| 87107 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID297183.1 | StrainInfo: A central database for resolving microbial strain identifiers |