Strain identifier
BacDive ID: 12011
Type strain: 
Species: Bhargavaea cecembensis
Strain Designation: DSE10
Strain history: S. Shivaji DSE10.
NCBI tax ID(s): 394098 (species)
version 8.1 (current version)
General
@ref: 16151
BacDive-ID: 12011
DSM-Number: 22132
keywords: genome sequence, 16S sequence, Bacteria, aerobe, Gram-positive, rod-shaped
description: Bhargavaea cecembensis DSE10 is an aerobe, Gram-positive, rod-shaped bacterium that was isolated from Deep-sea sediments.
NCBI tax id
- NCBI tax id: 394098
- Matching level: species
strain history
| @ref | history |
|---|---|
| 16151 | <- S. Shivaji, Centre for Cellular and Molecular Biology, Hyderabad, India; DSE10 |
| 67770 | S. Shivaji DSE10. |
doi: 10.13145/bacdive12011.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Bacilli
- order: Caryophanales
- family: Caryophanaceae
- genus: Bhargavaea
- species: Bhargavaea cecembensis
- full scientific name: Bhargavaea cecembensis Manorama et al. 2009
@ref: 16151
domain: Bacteria
phylum: Firmicutes
class: Bacilli
order: Bacillales
family: Planococcaceae
genus: Bhargavaea
species: Bhargavaea cecembensis
full scientific name: Bhargavaea cecembensis Manorama et al. 2009 emend. Verma et al. 2012
strain designation: DSE10
type strain: yes
Morphology
cell morphology
- @ref: 28963
- gram stain: positive
- cell length: 6 µm
- cell width: 2 µm
- cell shape: rod-shaped
- motility: no
Culture and growth conditions
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 28963 | positive | growth | 15-55 | |
| 28963 | positive | optimum | 37 | mesophilic |
| 67770 | positive | growth | 30 | mesophilic |
culture pH
- @ref: 28963
- ability: positive
- type: growth
- pH: 7-7.5
Physiology and metabolism
oxygen tolerance
- @ref: 28963
- oxygen tolerance: aerobe
spore formation
- @ref: 28963
- spore formation: no
halophily
- @ref: 28963
- salt: NaCl
- growth: positive
- tested relation: growth
- concentration: <6 %
murein
- @ref: 16151
- murein short key: A31
- type: A1gamma m-Dpm-direct
observation
- @ref: 67770
- observation: quinones: MK-8
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 28963 | 15963 | ribitol | + | carbon source |
| 28963 | 17306 | maltose | + | carbon source |
| 28963 | 53425 | tween 60 | + | carbon source |
| 28963 | 17632 | nitrate | + | reduction |
metabolite production
- @ref: 28963
- Chebi-ID: 16136
- metabolite: hydrogen sulfide
- production: yes
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 28963 | catalase | + | 1.11.1.6 |
| 28963 | cytochrome oxidase | + | 1.9.3.1 |
| 28963 | urease | + | 3.5.1.5 |
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent | latitude | longitude |
|---|---|---|---|---|---|---|---|
| 16151 | Deep-sea sediments | Indian Ocean, Chagos–Laccadive ridge system, 111060 S, 721310 E | India | IND | Asia | ||
| 67770 | Deep-sea sediment sample collected from the Chagos-Laccadive ridge system (111060 S, 721310 E) | Indian Ocean | 1.1106 | 72.131 |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Marine |
| #Environmental | #Aquatic | #Sediment |
taxonmaps
- @ref: 69479
- File name: preview.99_5557.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_2682;97_3294;98_4145;99_5557&stattab=map
- Last taxonomy: Bhargavaea
- 16S sequence: AM286423
- Sequence Identity:
- Total samples: 1707
- soil counts: 871
- aquatic counts: 273
- animal counts: 344
- plant counts: 219
Safety information
risk assessment
- @ref: 16151
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 20218 | Bhargavaea cecembensis strain DSE10 16S ribosomal RNA gene, partial sequence | HQ424469 | 1516 | ena | 394098 |
| 16151 | Bhargavaea cecembensis partial 16S rRNA gene, type strain DSE10T | AM286423 | 1544 | ena | 394098 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Bhargavaea cecembensis DSE10 | 1235279.3 | wgs | patric | 1235279 |
| 66792 | Bhargavaea cecembensis DSE10 | 2537561877 | draft | img | 1235279 |
| 67770 | Bhargavaea cecembensis DSE10 | GCA_000348905 | contig | ncbi | 1235279 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 16151 | 53.7 | thermal denaturation, midpoint method (Tm) |
| 16151 | 59.5 | thermal denaturation, midpoint method (Tm) |
| 28963 | 59.5 | |
| 67770 | 57-62 | thermal denaturation, midpoint method (Tm) |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| motile | no | 87.777 | no |
| gram-positive | yes | 92.693 | yes |
| anaerobic | no | 99.243 | yes |
| aerobic | yes | 95.043 | yes |
| halophile | yes | 90.194 | yes |
| spore-forming | yes | 64.529 | no |
| glucose-util | yes | 85.544 | no |
| flagellated | no | 93.174 | no |
| thermophile | no | 99.313 | yes |
| glucose-ferment | no | 89.318 | no |
External links
@ref: 16151
culture collection no.: DSM 22132, JCM 14375, LMG 24411
straininfo link
- @ref: 81230
- straininfo: 323184
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 19625444 | Bhargavaea cecembensis gen. nov., sp. nov., isolated from the Chagos-Laccadive ridge system in the Indian Ocean. | Manorama R, Pindi PK, Reddy GS, Shivaji S | Int J Syst Evol Microbiol | 10.1099/ijs.0.002691-0 | 2009 | DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/chemistry/metabolism, Geologic Sediments/microbiology, Gram-Positive Rods/chemistry/classification/genetics/*isolation & purification, Indian Ocean, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology | Genetics |
| Phylogeny | 22155760 | Reclassification of Bacillus beijingensis Qiu et al. 2009 and Bacillus ginsengi Qiu et al. 2009 as Bhargavaea beijingensis comb. nov. and Bhargavaea ginsengi comb. nov. and emended description of the genus Bhargavaea. | Verma P, Pandey PK, Gupta AK, Seong CN, Park SC, Choe HN, Baik KS, Patole MS, Shouche YS | Int J Syst Evol Microbiol | 10.1099/ijs.0.034850-0 | 2011 | Bacillus/*classification/genetics/metabolism, Bacterial Typing Techniques, Base Composition, DNA Gyrase/genetics, DNA, Bacterial/genetics, Fatty Acids/analysis, Genes, Bacterial, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/analysis, *Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA | Genetics |
| Phylogeny | 23243092 | Bhargavaea ullalensis sp. nov., isolated from coastal sand. | Glaeser SP, Arun AB, Rekha PD, Prabhu S, Busse HJ, Kampfer P | Int J Syst Evol Microbiol | 10.1099/ijs.0.045062-0 | 2012 | Bacillales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/analysis, Genes, Bacterial, India, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/analysis, *Phylogeny, Polyamines/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Silicon Dioxide, Vitamin K 2/analogs & derivatives/analysis | Genetics |
| Genetics | 23766406 | Draft Genome Sequence of Bhargavaea cecembensis Strain DSE10T, Isolated from a Deep-Sea Sediment Sample Collected at a Depth of 5,904 m from the Chagos-Laccadive Ridge System in the Indian Ocean. | Shivaji S, Ara S, Begum Z, Ruth M, Singh A, Kumar Pinnaka A | Genome Announc | 10.1128/genomeA.00346-13 | 2013 | Phylogeny | |
| Phylogeny | 30151776 | Bhargavaea changchunensis sp. nov. isolated from soil in China. | Tian FH, Fan DY, Zhang C, Jia CW, Gao W, Li Y, Li CT | Arch Microbiol | 10.1007/s00203-018-1563-6 | 2018 | Base Composition, China, DNA, Bacterial/chemistry, Fatty Acids/analysis, Nucleic Acid Hybridization, Phylogeny, Planococcaceae/*classification/genetics/isolation & purification, RNA, Ribosomal, 16S/genetics, *Soil Microbiology | Enzymology |
| Phylogeny | 30801243 | Pradoshia eiseniae gen. nov., sp. nov., a spore-forming member of the family Bacillaceae capable of assimilating 3-nitropropionic acid, isolated from the anterior gut of the earthworm Eisenia fetida. | Saha T, Ranjan VK, Ganguli S, Thakur S, Chakraborty B, Barman P, Ghosh W, Chakraborty R | Int J Syst Evol Microbiol | 10.1099/ijsem.0.003304 | 2019 | Animals, Bacillaceae/*classification/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genome, Bacterial, India, Nitro Compounds/*metabolism, Oligochaeta/*microbiology, *Phylogeny, Propionates/*metabolism, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry | Genetics |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed | ID_cross_reference |
|---|---|---|---|---|---|---|---|
| 16151 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22132) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-22132 | ||||
| 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 | ||
| 28963 | 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 | 25400 | ||
| 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 | ||||
| 81230 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID323184.1 | StrainInfo: A central database for resolving microbial strain identifiers |