Strain identifier
BacDive ID: 23226
Type strain: 
Species: Pannonibacter indicus
Strain Designation: HT23
Strain history: S. K. Das HT23.
NCBI tax ID(s): 466044 (species)
version 8.1 (current version)
General
@ref: 19211
BacDive-ID: 23226
DSM-Number: 23407
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative
description: Pannonibacter indicus HT23 is a mesophilic, Gram-negative bacterium that was isolated from hot spring sediment.
NCBI tax id
- NCBI tax id: 466044
- Matching level: species
strain history
| @ref | history |
|---|---|
| 19211 | <- S. K. Das, Inst. Life Sci., Bhubaneswar, India; HT23 |
| 67770 | S. K. Das HT23. |
doi: 10.13145/bacdive23226.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Hyphomicrobiales
- family: Stappiaceae
- genus: Pannonibacter
- species: Pannonibacter indicus
- full scientific name: Pannonibacter indicus corrig. Bandyopadhyay et al. 2013
synonyms
- @ref: 20215
- synonym: Pannonibacter indica
@ref: 19211
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhodobacterales
family: Rhodobacteraceae
genus: Pannonibacter
species: Pannonibacter indicus
full scientific name: Pannonibacter indicus Bandyopadhyay et al. 2013
strain designation: HT23
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 99.994
Culture and growth conditions
culture temp
- @ref: 67770
- growth: positive
- type: growth
- temperature: 30
- range: mesophilic
Physiology and metabolism
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 100 |
| 69480 | no | 99.919 |
observation
- @ref: 67770
- observation: quinones: Q-10, Q-9
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 19211 | hot spring sediment | Orissa, Athamallik | India | IND | Asia |
| 67770 | Hot spring sediment sample collected from Athamallik | Orissa | India | IND | Asia |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Sediment |
| #Environmental | #Aquatic | #Thermal spring |
| #Condition | #Thermophilic (>45°C) |
taxonmaps
- @ref: 69479
- File name: preview.99_5252.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_5;96_2552;97_3118;98_3917;99_5252&stattab=map
- Last taxonomy: Pannonibacter
- 16S sequence: EF608175
- Sequence Identity:
- Total samples: 12794
- soil counts: 2317
- aquatic counts: 5053
- animal counts: 4774
- plant counts: 650
Safety information
risk assessment
- @ref: 19211
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 19211
- description: Pannonibacter indicus strain HT23 16S ribosomal RNA gene, partial sequence
- accession: EF608175
- length: 1405
- database: ena
- NCBI tax ID: 466044
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Pannonibacter indicus strain DSM 23407 | 466044.4 | wgs | patric | 466044 |
| 66792 | Pannonibacter indicus DSM 23407 | 2615840614 | draft | img | 466044 |
| 67770 | Pannonibacter indicus DSM 23407 | GCA_001517385 | scaffold | ncbi | 466044 |
| 67770 | Pannonibacter indicus DSM 23407 | GCA_001418225 | scaffold | ncbi | 466044 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 19211 | 63.3 | |
| 67770 | 63.3 | high performance liquid chromatography (HPLC) |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| gram-positive | no | 98.789 | no |
| anaerobic | no | 97.006 | no |
| halophile | no | 67.058 | no |
| spore-forming | no | 95.577 | no |
| glucose-util | yes | 90.871 | no |
| aerobic | yes | 86.702 | no |
| flagellated | yes | 71.04 | no |
| thermophile | no | 93.886 | yes |
| motile | yes | 90.542 | no |
| glucose-ferment | no | 90.921 | no |
External links
@ref: 19211
culture collection no.: DSM 23407, JCM 16851, LMG 25769
straininfo link
- @ref: 87452
- straininfo: 369747
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 22940883 | Pannonibacter indica sp. nov., a highly arsenate-tolerant bacterium isolated from a hot spring in India. | Bandyopadhyay S, Schumann P, Das SK | Arch Microbiol | 10.1007/s00203-012-0840-z | 2012 | Arsenates/pharmacology, Base Composition, Geologic Sediments/microbiology, Hot Springs/*microbiology, India, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/drug effects/genetics/ultrastructure | Genetics |
| Metabolism | 26915994 | Functional analysis of ars gene cluster of Pannonibacter indicus strain HT23(T) (DSM 23407(T)) and identification of a proline residue essential for arsenate reductase activity. | Bandyopadhyay S, Das SK | Appl Microbiol Biotechnol | 10.1007/s00253-016-7390-2 | 2016 | Amino Acid Substitution, Arsenate Reductases/*genetics/metabolism, Arsenic/metabolism, Bacterial Proteins/*genetics/metabolism, Cloning, Molecular, Escherichia coli/genetics/metabolism, *Gene Expression Regulation, Bacterial, Kinetics, *Multigene Family, Mutagenesis, Site-Directed, Open Reading Frames, Operon, Oxidation-Reduction, Plasmids/chemistry/metabolism, Proline/*chemistry/metabolism, Protein Folding, Protein Tyrosine Phosphatases/genetics/metabolism, Recombinant Proteins/genetics/metabolism, Rhodobacteraceae/enzymology/*genetics, Structure-Activity Relationship | Enzymology |
| Genetics | 28473384 | Draft Genome Sequence of Pannonibacter indicus Strain HT23(T) (DSM 23407(T)), a Highly Arsenate-Tolerant Bacterium Isolated from a Hot Spring in India. | Bandyopadhyay S, Whitman WB, Das SK | Genome Announc | 10.1128/genomeA.00283-17 | 2017 | Phylogeny | |
| Phylogeny | 29693544 | Pannonibacter carbonis sp. nov., isolated from coal mine water. | Xi L, Qiao N, Liu D, Li J, Zhang J, Liu J | Int J Syst Evol Microbiol | 10.1099/ijsem.0.002794 | 2018 | Bacterial Typing Techniques, Base Composition, China, *Coal, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Mining, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/isolation & purification, Sequence Analysis, DNA, Ubiquinone/analogs & derivatives/chemistry, *Water Microbiology | Transcriptome |
Reference
| @id | authors | catalogue | doi/url | title |
|---|---|---|---|---|
| 19211 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23407) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-23407 | |
| 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 | |
| 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 | |
| 69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |
| 69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |
| 87452 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID369747.1 | StrainInfo: A central database for resolving microbial strain identifiers |