Strain identifier
BacDive ID: 3830
Type strain: 
Species: Pontibacter actiniarum
Strain history: <- O. I. Nedashkovskaya, Pacific Inst. Bioorg. Chem., RAS, Vladivostok; KMM 6156 <- L. S. Shevchenko
NCBI tax ID(s): 709015 (strain), 323450 (species)
version 8.1 (current version)
General
@ref: 8128
BacDive-ID: 3830
DSM-Number: 19842
keywords: genome sequence, 16S sequence, Bacteria, mesophilic
description: Pontibacter actiniarum DSM 19842 is a mesophilic bacterium that was isolated from unidentified actinians.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 323450 | species |
| 709015 | strain |
strain history
- @ref: 8128
- history: <- O. I. Nedashkovskaya, Pacific Inst. Bioorg. Chem., RAS, Vladivostok; KMM 6156 <- L. S. Shevchenko
doi: 10.13145/bacdive3830.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacteroidota
- domain: Bacteria
- phylum: Bacteroidota
- class: Cytophagia
- order: Cytophagales
- family: Hymenobacteraceae
- genus: Pontibacter
- species: Pontibacter actiniarum
- full scientific name: Pontibacter actiniarum Nedashkovskaya et al. 2005
@ref: 8128
domain: Bacteria
phylum: Bacteroidetes
class: Cytophagia
order: Cytophagales
family: Hymenobacteraceae
genus: Pontibacter
species: Pontibacter actiniarum
full scientific name: Pontibacter actiniarum Nedashkovskaya et al. 2005 emend. Hahnke et al. 2016
type strain: yes
Morphology
multimedia
- @ref: 66793
- multimedia content: EM_DSM_19842_1.jpg
- caption: electron microscopic image
- intellectual property rights: © HZI/Manfred Rohde
Culture and growth conditions
culture medium
- @ref: 8128
- 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: 8128
- growth: positive
- type: growth
- temperature: 28
- range: mesophilic
Isolation, sampling and environmental information
isolation
- @ref: 8128
- sample type: unidentified actinians
- geographic location: Pacific Ocean, Rudnaya Bay
- country: Russia
- origin.country: RUS
- continent: Asia
isolation source categories
- Cat1: #Host
- Cat2: #Invertebrates (Other)
- Cat3: #Cnidaria (Corals)
taxonmaps
- @ref: 69479
- File name: preview.99_2450.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_60;96_1325;97_1572;98_1911;99_2450&stattab=map
- Last taxonomy: Pontibacter actiniarum subclade
- 16S sequence: AY989908
- Sequence Identity:
- Total samples: 39
- soil counts: 9
- aquatic counts: 23
- animal counts: 6
- plant counts: 1
Safety information
risk assessment
- @ref: 8128
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 8128
- description: Pontibacter actiniarum strain KMM 6156 16S ribosomal RNA gene, partial sequence
- accession: AY989908
- length: 1435
- database: ena
- NCBI tax ID: 709015
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Pontibacter actiniarum DSM 19842 | GCA_003585765 | complete | ncbi | 323450 |
| 66792 | Pontibacter actiniarum DSM 19842 | GCA_000472485 | contig | ncbi | 709015 |
| 66792 | Pontibacter actiniarum DSM 19842 | 709015.3 | wgs | patric | 709015 |
| 66792 | Pontibacter actiniarum strain DSM 19842 | 323450.3 | complete | patric | 323450 |
| 66792 | Pontibacter actiniarum DSM 19842 | 2834962495 | complete | img | 709015 |
| 66792 | Pontibacter actiniarum DSM 19842 | 2502545039 | draft | img | 709015 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 8128 | 48.7 | |
| 8128 | 53.1 | sequence analysis |
External links
@ref: 8128
culture collection no.: DSM 19842, KCTC 12367, KMM 6156, LMG 23027
straininfo link
- @ref: 73341
- straininfo: 138409
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 16280531 | Pontibacter actiniarum gen. nov., sp. nov., a novel member of the phylum 'Bacteroidetes', and proposal of Reichenbachiella gen. nov. as a replacement for the illegitimate prokaryotic generic name Reichenbachia Nedashkovskaya et al. 2003. | Nedashkovskaya OI, Kim SB, Suzuki M, Shevchenko LS, Lee MS, Lee KH, Park MS, Frolova GM, Oh HW, Bae KS, Park HY, Mikhailov VV | Int J Syst Evol Microbiol | 10.1099/ijs.0.63819-0 | 2005 | Bacteroidetes/chemistry/*classification/genetics/isolation & purification, Base Composition, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Molecular Sequence Data, RNA, Ribosomal, 16S/analysis/genetics | Genetics |
| Phylogeny | 16825654 | Effluviibacter roseus gen. nov., sp. nov., isolated from muddy water, belonging to the family "Flexibacteraceae". | Suresh K, Mayilraj S, Chakrabarti T | Int J Syst Evol Microbiol | 10.1099/ijs.0.64144-0 | 2006 | Aerobiosis, Amino Acids/metabolism, Bacterial Typing Techniques, Base Composition, Carbohydrate Metabolism, Cytophagaceae/*classification/cytology/*isolation & purification/physiology, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis/chemistry, Genes, rRNA, Gentian Violet, Molecular Sequence Data, Phenazines, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, *Water Microbiology | Metabolism |
| Phylogeny | 18450715 | Pontibacter korlensis sp. nov., isolated from the desert of Xinjiang, China. | Zhang L, Zhang Q, Luo X, Tang Y, Dai J, Li Y, Wang Y, Chen G, Fang C | Int J Syst Evol Microbiol | 10.1099/ijs.0.65667-0 | 2008 | Bacterial Typing Techniques, Base Composition, China, Cytophagaceae/*classification/genetics/isolation & purification/physiology, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, *Desert Climate, Fatty Acids/analysis, Genes, rRNA, Genotype, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Species Specificity | Genetics |
| Phylogeny | 23907224 | Erythrobacter odishensis sp. nov. and Pontibacter odishensis sp. nov. isolated from dry soil of a solar saltern. | Subhash Y, Tushar L, Sasikala C, Ramana CV | Int J Syst Evol Microbiol | 10.1099/ijs.0.052183-0 | 2013 | Bacterial Typing Techniques, Cytophagaceae/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, India, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Sphingomonadaceae/*classification/genetics/isolation & purification, Triterpenes/chemistry, Ubiquinone/chemistry | Enzymology |
| Phylogeny | 31273482 | Pontibacter oryzae sp. nov., a carotenoid-producing species isolated from a rice paddy field. | Chhetri G, Kim J, Kim H, Kim I, Seo T | Antonie Van Leeuwenhoek | 10.1007/s10482-019-01298-0 | 2019 | Carotenoids/*metabolism, Cytophagaceae/*classification/genetics/*metabolism, Genomics/methods, Oryza/*microbiology, Phenotype, Phylogeny, Plant Diseases/*microbiology | Metabolism |
| Phylogeny | 34633922 | Pontibacter flavimaris sp. nov., of the family Hymenobacteraceae, isolated from marine sediment. | Liu D, Xiong Q, Zhao J, Fang Z, Zhang G | Int J Syst Evol Microbiol | 10.1099/ijsem.0.004958 | 2021 | Bacterial Typing Techniques, Bacteroidetes/*classification/isolation & purification, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Geologic Sediments/microbiology, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry | Transcriptome |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 8128 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19842) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-19842 | |||
| 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) | |||
| 66793 | Mukherjee et al. | 10.1038/nbt.3886 | GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life | 35: 676-683 2017 | 28604660 | |
| 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 | |||
| 73341 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID138409.1 | StrainInfo: A central database for resolving microbial strain identifiers |