Strain identifier
BacDive ID: 23819
Type strain: 
Species: Arcobacter anaerophilus
Strain Designation: JC84
Strain history: <- Ch Sasikala, Centre for Environment, IST, JNTU
NCBI tax ID(s): 877500 (species)
version 8.1 (current version)
General
@ref: 20311
BacDive-ID: 23819
DSM-Number: 24636
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-negative, rod-shaped
description: Arcobacter anaerophilus JC84 is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from estuarine sediment.
NCBI tax id
- NCBI tax id: 877500
- Matching level: species
strain history
| @ref | history |
|---|---|
| 20311 | <- C. Sasikala <- T. S. Sasi Jyothsna, Jawaharlal Nehru Technological Univ., Hyderabad, India; JC84 |
| 67771 | <- Ch Sasikala, Centre for Environment, IST, JNTU |
doi: 10.13145/bacdive23819.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Epsilonproteobacteria
- order: Campylobacterales
- family: Arcobacteraceae
- genus: Arcobacter
- species: Arcobacter anaerophilus
- full scientific name: Arcobacter anaerophilus Sasi Jyothsna et al. 2013
synonyms
@ref synonym 20215 Haloarcobacter anaerophilus 20215 Halarcobacter anaerophilus
@ref: 20311
domain: Bacteria
phylum: Proteobacteria
class: Epsilonproteobacteria
order: Campylobacterales
family: Campylobacteraceae
genus: Arcobacter
species: Arcobacter anaerophilus
full scientific name: Arcobacter anaerophilus Sasi Jyothsna et al. 2013
strain designation: JC84
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell length | cell width | cell shape | motility | confidence |
|---|---|---|---|---|---|---|
| 31159 | negative | 1.5 µm | 0.2 µm | rod-shaped | no | |
| 67771 | rod-shaped | no | ||||
| 67771 | negative | |||||
| 69480 | yes | 96.033 | ||||
| 69480 | negative | 100 |
colony morphology
- @ref: 20311
- incubation period: 1-2 days
pigmentation
- @ref: 31159
- production: yes
Culture and growth conditions
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 31159 | positive | growth | 25-37 | mesophilic |
| 31159 | positive | optimum | 30 | mesophilic |
| 67771 | positive | growth | 30 | mesophilic |
culture pH
| @ref | ability | type | pH | PH range |
|---|---|---|---|---|
| 31159 | positive | growth | 07-10 | alkaliphile |
| 31159 | positive | optimum | 7.5 |
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance |
|---|---|
| 20311 | anaerobe |
| 31159 | anaerobe |
| 67771 | anaerobe |
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 31159 | no | |
| 69481 | no | 95 |
| 69480 | no | 99.744 |
halophily
| @ref | salt | growth | tested relation | concentration |
|---|---|---|---|---|
| 31159 | NaCl | positive | growth | 0-6 % |
| 31159 | NaCl | positive | optimum | 2 % |
observation
| @ref | observation |
|---|---|
| 31159 | aggregates in clumps |
| 67771 | quinones: MK-6 |
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 31159 | 30089 | acetate | + | carbon source |
| 31159 | 22599 | arabinose | + | carbon source |
| 31159 | 18403 | L-arabitol | + | carbon source |
| 31159 | 17057 | cellobiose | + | carbon source |
| 31159 | 17596 | inosine | + | carbon source |
| 31159 | 17716 | lactose | + | carbon source |
| 31159 | 37684 | mannose | + | carbon source |
| 31159 | 28053 | melibiose | + | carbon source |
| 31159 | 50048 | phenylethylamine | + | carbon source |
| 31159 | 17632 | nitrate | + | reduction |
metabolite production
- @ref: 31159
- Chebi-ID: 16136
- metabolite: hydrogen sulfide
- production: yes
enzymes
- @ref: 31159
- value: cytochrome oxidase
- activity: +
- ec: 1.9.3.1
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 20311 | estuarine sediment | West Bengal, Gangasagar | India | IND | Asia |
| 67771 | From sediment sample from Gangasagar | West Bengal | India | IND | Asia |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Estuary |
| #Environmental | #Aquatic | #Sediment |
| #Environmental | #Aquatic | #Brackish |
taxonmaps
- @ref: 69479
- File name: preview.99_3670.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_53;96_1897;97_2280;98_2805;99_3670&stattab=map
- Last taxonomy: Arcobacter anaerophilus subclade
- 16S sequence: MG195889
- Sequence Identity:
- Total samples: 1821
- soil counts: 77
- aquatic counts: 1570
- animal counts: 144
- plant counts: 30
Safety information
risk assessment
- @ref: 20311
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 20311 | Arcobacter anaerophilus partial 16S rRNA gene, strain JC84, isolate D09-53 | FR686494 | 1389 | ena | 877500 |
| 67771 | Arcobacter anaerophilus strain DSM 24636T 16S ribosomal RNA gene, partial sequence | MG195889 | 1505 | ena | 877500 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Halarcobacter anaerophilus DSM 24636 | GCA_006459125 | complete | ncbi | 877500 |
| 66792 | Halarcobacter anaerophilus DSM 24636 | GCA_004116345 | contig | ncbi | 877500 |
| 66792 | Arcobacter anaerophilus strain DSM 24636 | 877500.16 | wgs | patric | 877500 |
| 66792 | Arcobacter anaerophilus strain DSM 24636 | 877500.17 | complete | patric | 877500 |
| 66792 | Arcobacter anaerophilus DSM 24636 | 2871084118 | draft | img | 877500 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 20311 | 24.6 | high performance liquid chromatography (HPLC) |
| 31159 | 24.6 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 95 | no |
| motile | yes | 89.007 | yes |
| flagellated | yes | 67.798 | yes |
| gram-positive | no | 98.831 | yes |
| anaerobic | yes | 55.971 | yes |
| aerobic | no | 92.477 | yes |
| halophile | no | 76.675 | no |
| spore-forming | no | 92.526 | yes |
| thermophile | no | 94.613 | no |
| glucose-util | no | 63.881 | no |
| glucose-ferment | no | 88.399 | no |
External links
@ref: 20311
culture collection no.: DSM 24636, KCTC 15071, MTCC 10956, CECT 9783
literature
- topic: Phylogeny
- Pubmed-ID: 23918794
- title: Arcobacter anaerophilus sp. nov., isolated from an estuarine sediment and emended description of the genus Arcobacter.
- authors: Sasi Jyothsna TS, Rahul K, Ramaprasad EVV, Sasikala C, Ramana CV
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.054155-0
- year: 2013
- mesh: Arcobacter/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, *Estuaries, Fatty Acids/chemistry, Genes, Bacterial, Geologic Sediments/*microbiology, Hydrogen Sulfide/metabolism, India, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry
- topic2: Genetics
Reference
| @id | authors | title | doi/url | catalogue | ID_cross_reference | pubmed | journal |
|---|---|---|---|---|---|---|---|
| 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 | ||||
| 20311 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-24636 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 24636) | ||||
| 31159 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 10.1128/mSphere.00237-17 | 27487 | 28776041 | ||
| 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 | ||||
| 66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | 10.1093/nar/gkaa1025 | 33211880 | Nucleic Acids Res. 49: D498-D508 2020 | ||
| 67771 | Curators of the KCTC | https://kctc.kribb.re.kr/En/Kctc | |||||
| 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 | ||||
| 69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | Predictions based on the model GenomeNet Sporulation v. 1 | 10.21203/rs.3.rs-2527258/v1 |