Strain identifier
BacDive ID: 130420
Type strain: 
Species: Paeniglutamicibacter antarcticus
Strain history: LMG 24542 <-- S. Shivaji SPC26 <-- P. K. Pindi.
NCBI tax ID(s): 494023 (species)
version 8.1 (current version)
General
@ref: 21483
BacDive-ID: 130420
DSM-Number: 29880
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-positive, motile, rod-shaped
description: Paeniglutamicibacter antarcticus DSM 29880 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from spade core sediment.
NCBI tax id
- NCBI tax id: 494023
- Matching level: species
strain history
| @ref | history |
|---|---|
| 21483 | <- LMG <- S. Shivaji, CCMB <- P. K. Pindi |
| 67770 | LMG 24542 <-- S. Shivaji SPC26 <-- P. K. Pindi. |
doi: 10.13145/bacdive130420.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Actinomycetes
- order: Micrococcales
- family: Micrococcaceae
- genus: Paeniglutamicibacter
- species: Paeniglutamicibacter antarcticus
- full scientific name: Paeniglutamicibacter antarcticus (Pindi et al. 2010) Busse 2016
synonyms
- @ref: 20215
- synonym: Arthrobacter antarcticus
@ref: 21483
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Micrococcaceae
genus: Paeniglutamicibacter
species: Paeniglutamicibacter antarcticus
full scientific name: Paeniglutamicibacter antarcticus (Pindi et al. 2010) Busse 2016
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell length | cell width | cell shape | motility | confidence |
|---|---|---|---|---|---|---|
| 29430 | positive | 1.5-2.2 µm | 0.2-0.3 µm | rod-shaped | yes | |
| 69480 | positive | 100 |
colony morphology
- @ref: 21483
- incubation period: 3-7 days
pigmentation
- @ref: 29430
- production: yes
Culture and growth conditions
culture medium
- @ref: 21483
- 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 |
|---|---|---|---|---|
| 21483 | positive | growth | 25 | mesophilic |
| 29430 | positive | growth | 04-25 | |
| 29430 | positive | optimum | 22-25 | |
| 67770 | positive | growth | 22 | psychrophilic |
culture pH
| @ref | ability | type | pH | PH range |
|---|---|---|---|---|
| 29430 | positive | growth | 04-10 | alkaliphile |
| 29430 | positive | optimum | 7 |
Physiology and metabolism
oxygen tolerance
- @ref: 29430
- oxygen tolerance: aerobe
spore formation
- @ref: 69480
- spore formation: no
- confidence: 99.945
halophily
| @ref | salt | growth | tested relation | concentration |
|---|---|---|---|---|
| 29430 | NaCl | positive | growth | 0-8 % |
| 29430 | NaCl | positive | optimum | 0-6 % |
observation
| @ref | observation |
|---|---|
| 29430 | aggregates in chains |
| 67770 | quinones: MK-8, MK-9, MK-10 |
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 29430 | 22599 | arabinose | + | carbon source |
| 29430 | 28260 | galactose | + | carbon source |
| 29430 | 17234 | glucose | + | carbon source |
| 29430 | 15792 | malonate | + | carbon source |
| 29430 | 26546 | rhamnose | + | carbon source |
| 29430 | 18222 | xylose | + | carbon source |
enzymes
- @ref: 29430
- value: catalase
- activity: +
- ec: 1.11.1.6
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | continent | latitude | longitude |
|---|---|---|---|---|---|
| 21483 | spade core sediment | Larsemann Hill | Australia and Oceania | -69.3667 | 76.1 |
| 67770 | Southern Ocean sediment from near the Larsemann Hills area of Antarctica |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Terrestrial | #Core sample |
| #Environmental | #Terrestrial | #Sediment |
taxonmaps
- @ref: 69479
- File name: preview.99_5285.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_158;97_169;98_188;99_5285&stattab=map
- Last taxonomy: Paeniglutamicibacter
- 16S sequence: AM931709
- Sequence Identity:
- Total samples: 1613
- soil counts: 596
- aquatic counts: 125
- animal counts: 660
- plant counts: 232
Safety information
risk assessment
- @ref: 21483
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 21483
- description: Arthrobacter antarcticus partial 16S rRNA gene, type strain SPC 26T
- accession: AM931709
- length: 1519
- database: ena
- NCBI tax ID: 494023
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Paeniglutamicibacter antarcticus strain DSM 29880 | 494023.8 | wgs | patric | 494023 |
| 66792 | Arthrobacter antarcticus DSM 29880 | 2918409668 | draft | img | 494023 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 29430 | 68 | |
| 67770 | 67.5-68.5 | thermal denaturation, midpoint method (Tm) |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 72 | no |
| gram-positive | yes | 91.017 | yes |
| anaerobic | no | 99.428 | yes |
| halophile | no | 69.549 | no |
| spore-forming | no | 91.919 | no |
| glucose-util | yes | 84.666 | yes |
| aerobic | yes | 93.821 | no |
| thermophile | no | 99.262 | no |
| motile | no | 94.725 | no |
| flagellated | no | 97.755 | no |
| glucose-ferment | no | 91.292 | no |
External links
@ref: 21483
culture collection no.: DSM 29880, LMG 24542, NCCB 100228, SPC 26, JCM 18952
straininfo link
- @ref: 88952
- straininfo: 343384
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 19783612 | Arthrobacter antarcticus sp. nov., isolated from an Antarctic marine sediment. | Pindi PK, Manorama R, Begum Z, Shivaji S | Int J Syst Evol Microbiol | 10.1099/ijs.0.012989-0 | 2009 | Alanine/analysis, Antarctic Regions, Arthrobacter/chemistry/*classification/genetics/*isolation & purification, Bacterial Typing Techniques, Base Composition, Catalase/metabolism, Cell Wall/chemistry, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Geologic Sediments/*microbiology, Lysine/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/analysis, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA | Genetics |
| Phylogeny | 33555249 | Paeniglutamicibacter terrestris sp. nov., isolated from phenanthrene-degrading consortium enriched from Antarctic soil. | Sakdapetsiri C, Kuntaveesuk A, Ngaemthao W, Suriyachadkun C, Muangchinda C, Chavanich S, Viyakarn V, Chen B, Pinyakong O | Int J Syst Evol Microbiol | 10.1099/ijsem.0.004689 | 2021 |
Reference
| @id | authors | title | doi/url | catalogue | ID_cross_reference | pubmed |
|---|---|---|---|---|---|---|
| 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 | |||
| 21483 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-29880 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 29880) | |||
| 29430 | 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 | 25836 | 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 | |||
| 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 | |||
| 88952 | 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-ID343384.1 |