Strain identifier
BacDive ID: 130646
Type strain: 
Species: Allgaiera indica
Strain Designation: 20V17
Strain history: J. Jiang 20V17.
NCBI tax ID(s): 765699 (species)
version 8.1 (current version)
General
@ref: 22088
BacDive-ID: 130646
DSM-Number: 24802
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative
description: Allgaiera indica 20V17 is a mesophilic, Gram-negative bacterium that was isolated from sulfide chimney of a deep-sea hydrothermal vent.
NCBI tax id
- NCBI tax id: 765699
- Matching level: species
strain history
| @ref | history |
|---|---|
| 22088 | <- L. Jiang, Third Inst. Oceanography, State Oceanic Admin., China; 20V17 |
| 67770 | J. Jiang 20V17. |
doi: 10.13145/bacdive130646.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Rhodobacterales
- family: Paracoccaceae
- genus: Allgaiera
- species: Allgaiera indica
- full scientific name: Allgaiera indica (Jiang et al. 2014) Hördt et al. 2020
synonyms
@ref synonym 20215 Acidimangrovimonas indica 20215 Defluviimonas indica
@ref: 22088
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhodobacterales
family: Rhodobacteraceae
genus: Allgaiera
species: Allgaiera indica
full scientific name: Allgaiera indica (Jiang et al. 2014) Hördt et al. 2020
strain designation: 20V17
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 99.994
colony morphology
- @ref: 22088
- incubation period: 1-2 days
Culture and growth conditions
culture medium
- @ref: 22088
- 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 |
|---|---|---|---|---|
| 22088 | positive | growth | 28 | mesophilic |
| 67770 | positive | growth | 25 | mesophilic |
Physiology and metabolism
spore formation
- @ref: 69480
- spore formation: no
- confidence: 99.993
observation
- @ref: 67770
- observation: quinones: Q10
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent | latitude | longitude |
|---|---|---|---|---|---|---|---|
| 22088 | sulfide chimney of a deep-sea hydrothermal vent | Southwest Indian Ridge (37.78° S 50.64° E at a depth of 2783 m) | China | CHN | Asia | -37.78 | 50.64 |
| 67770 | Deep-sea hydrothermal sulfide in the South-west Indian Ridge |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Hydrothermal vent |
| #Environmental | #Aquatic | #Marine |
| #Condition | #Sulfuric | |
| #Condition | #Thermophilic (>45°C) |
taxonmaps
- @ref: 69479
- File name: preview.99_5924.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_1054;97_3481;98_4402;99_5924&stattab=map
- Last taxonomy: Allgaiera indica subclade
- 16S sequence: HM050420
- Sequence Identity:
- Total samples: 1436
- soil counts: 105
- aquatic counts: 1135
- animal counts: 139
- plant counts: 57
Safety information
risk assessment
- @ref: 22088
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 22088
- description: Defluviimonas indica strain 20V17 16S ribosomal RNA gene, partial sequence
- accession: HM050420
- length: 1431
- database: ena
- NCBI tax ID: 765699
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Allgaiera indica CGMCC 1.10859 | GCA_014653075 | contig | ncbi | 765699 |
| 66792 | Acidimangrovimonas indica strain CGMCC 1.10859 | 765699.5 | wgs | patric | 765699 |
| 66792 | Defluviimonas indica strain DSM 24802 | 765699.3 | wgs | patric | 765699 |
| 66792 | Allgaiera indica DSM 24802 | 2693429897 | draft | img | 765699 |
| 67770 | Defluviimonas sp. 20V17 | GCA_000687435 | contig | ncbi | 1417296 |
| 67770 | Allgaiera indica DSM 24802 | GCA_900106675 | scaffold | ncbi | 765699 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 22088 | 66.3 | sequence analysis |
| 67770 | 66.3 | genome sequence analysis |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 81 | no |
| motile | yes | 51.166 | no |
| flagellated | no | 80.3 | no |
| gram-positive | no | 98.216 | no |
| anaerobic | no | 94.747 | no |
| halophile | no | 59.369 | no |
| spore-forming | no | 94.366 | no |
| glucose-util | yes | 75.533 | no |
| aerobic | yes | 76.503 | no |
| thermophile | no | 92.107 | yes |
| glucose-ferment | no | 90.411 | no |
External links
@ref: 22088
culture collection no.: DSM 24802, CGMCC 1.10859, JCM 17871, MCCC 1A01802
straininfo link
- @ref: 89157
- straininfo: 408247
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 24670896 | Defluviimonas indica sp. nov., a marine bacterium isolated from a deep-sea hydrothermal vent environment. | Jiang L, Xu H, Shao Z, Long M | Int J Syst Evol Microbiol | 10.1099/ijs.0.061614-0 | 2014 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Hydrothermal Vents/*microbiology, Indian Ocean, Molecular Sequence Data, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/analysis/genetics, Rhodobacteraceae/*classification/genetics/isolation & purification, Seawater/microbiology, Sequence Analysis, DNA, Ubiquinone | Genetics |
| Genetics | 24903865 | Draft Genome Sequence of Defluviimonas indica Strain 20V17T, Isolated from a Deep-Sea Hydrothermal Vent Environment in the Southwest Indian Ocean. | Jiang L, Long M, Shao Z | Genome Announc | 10.1128/genomeA.00479-14 | 2014 | Phylogeny | |
| Phylogeny | 28809144 | Defluviimonas nitratireducens sp. nov., isolated from surface seawater. | Liu Y, Lai Q, Wang W, Shao Z | Int J Syst Evol Microbiol | 10.1099/ijsem.0.002015 | 2017 | Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/isolation & purification, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/chemistry | Transcriptome |
| Phylogeny | 29458487 | Defluviimonas pyrenivorans sp. nov., a novel bacterium capable of degrading polycyclic aromatic hydrocarbons. | Zhang S, Sun C, Xie J, Wei H, Hu Z, Wang H | Int J Syst Evol Microbiol | 10.1099/ijsem.0.002629 | 2018 | Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Phospholipids/chemistry, *Phylogeny, Polycyclic Aromatic Hydrocarbons/*metabolism, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/isolation & purification, Rivers/*microbiology, Sequence Analysis, DNA, Ubiquinone/chemistry | Transcriptome |
| Phylogeny | 31169491 | Acidimangrovimonas sediminis gen. nov., sp. nov., isolated from mangrove sediment and reclassification of Defluviimonas indica as Acidimangrovimonas indica comb. nov. and Defluviimonas pyrenivorans as Acidimangrovimonas pyrenivorans comb. nov. | Ren H, Ma H, Li H, Huang L, Luo Y | Int J Syst Evol Microbiol | 10.1099/ijsem.0.003513 | 2019 | Avicennia/*microbiology, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Estuaries, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/isolation & purification, Sequence Analysis, DNA, Ubiquinone/chemistry | Transcriptome |
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 | |
| 22088 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-24802 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 24802) | |
| 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 | |
| 89157 | 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-ID408247.1 |