Strain identifier
BacDive ID: 7281
Type strain:
Species: Agromyces atrinae
Strain Designation: P27
Strain history: <- JW Bae, KRIBB
NCBI tax ID(s): 592376 (species)
General
@ref: 17418
BacDive-ID: 7281
DSM-Number: 23870
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-positive, rod-shaped
description: Agromyces atrinae P27 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from traditional fermented seafood.
NCBI tax id
- NCBI tax id: 592376
- Matching level: species
strain history
@ref | history |
---|---|
17418 | <- JCM <- J.-W. Bae, Kyung Hee Univ., Seoul, Republic of Korea; P27 <- KCTC |
67770 | J.-W. Bae P27. |
67771 | <- JW Bae, KRIBB |
doi: 10.13145/bacdive7281.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Actinomycetes
- order: Micrococcales
- family: Microbacteriaceae
- genus: Agromyces
- species: Agromyces atrinae
- full scientific name: Agromyces atrinae Park et al. 2010
@ref: 17418
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Microbacteriaceae
genus: Agromyces
species: Agromyces atrinae
full scientific name: Agromyces atrinae Park et al. 2010
strain designation: P27
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
29397 | positive | 1.5 µm | 0.75 µm | rod-shaped | no | |
67771 | positive | |||||
69480 | positive | 100 |
colony morphology
@ref | colony color | incubation period | medium used |
---|---|---|---|
21416 | Rape yellow (1021) | 10-14 days | ISP 2 |
21416 | 10-14 days | ISP 3 | |
21416 | Oyster white (1013) | 10-14 days | ISP 4 |
21416 | 10-14 days | ISP 5 | |
21416 | Rape yellow (1021) | 10-14 days | ISP 7 |
multicellular morphology
@ref | forms multicellular complex | medium name |
---|---|---|
21416 | no | ISP 2 |
21416 | no | ISP 3 |
21416 | no | ISP 4 |
21416 | no | ISP 5 |
21416 | no | ISP 7 |
21416 |
pigmentation
- @ref: 29397
- production: yes
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
17418 | BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) | yes | https://mediadive.dsmz.de/medium/514 | 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 |
21416 | ISP 2 | yes | Name: ISP 2 / Yeast Malt Agar (5265); 5265 Composition Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l Agar 15.0 g/l Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.0 Usage: Maintenance and Taxonomy Organisms: All Actinomycetes | |
21416 | ISP 3 | yes | Name: ISP 3; 5315 Composition Dog oat flakes 20.0 g/l Trace element solution (5314) 2.5 ml/l Agar 18.0 g/l Preparation: Oat flakes are cooked for 20 minutes, trace element solution and agar are added (in the case of non rolled oat flakes the suspension has to bee filtrated). Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.8 Usage: Maintenance and taxonomy (e.g. SEM As liquid medium for metabolite production) Organisms: All Actinomycetes Trace element solution 5314 Name: Trace element solution 5314; 5314 Composition CaCl2 x H2O 3.0 g/l Fe-III-citrate 1.0 g/l MnSO4 0.2 g/l ZnCl2 0.1 g/l CuSO4 x 5 H2O 0.025 g/l Sodium tetra borate 0.2 g/l CoCl2 x 6 H2O 0.004 g/l Sodium molybdate 0.01 g/l Preparation: Use double destillated water. Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Trace element solution for different media Organisms: | |
21416 | ISP 4 | yes | Name: ISP 4; DSM 547 Solution I: Difco soluble starch, 10.0 g. Make a paste of the starch with a small amount of cold distilled water and bring to a volume of 500 ml. Solution II: CaCO3 2.0 g K2HPO4 (anhydrous) 1.0 g MgSO4 x 7 H2O 1.0 g NaCl 1.0 g (NH4)2SO4 2.0 g Distilled water 500.0 ml Trace salt solution (see below) 1.0 ml The pH should be between 7.0 and 7.4. Do not adjust if it is within this range. Mix solutions I and II together. Add 20.0 g agar. Liquify agar by steaming at 100°C for 10 to 20 min. Trace element solution: FeSO4 x 7 H2O 0.1 g MnCl2 x 4 H2O 0.1 g ZnSO4 x 7 H2O 0.1 g Distilled water 100.0 ml | |
21416 | ISP 5 | yes | Name: ISP 5 (5323) Composition L-Asparagine 1.0 g/l Glycerol 10.0 g/l K2HPO4 1.0 g/l Salt solution (see preparation) 1.0 ml/l Agar 20.0 g/l Preparation: Salt solution 1.0 g FeSO4 x 7 H2O 1.0 g MnCl2 x 4 H2O 1.0 g ZNSO4 x 7 H2O in 100 ml water Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.2 Usage: Maintenance and taxonomy Organisms: All Actinomycetes | |
21416 | ISP 7 | yes | Name: ISP 7 (5322) Composition Glycerol 15.0 g/l L-Tyrosine 0.5 g/l L-Asparagine 1.0 g/l K2HPO4 0.5 g/l NaCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Trace element solution 5343 1.0 ml/l Agar 20.0 Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.3 Usage: Production of melanoid pigments Organisms: All Actinomycetes |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
17418 | positive | growth | 28 | mesophilic |
29397 | positive | growth | 10-37 | |
29397 | positive | optimum | 30 | mesophilic |
67770 | positive | growth | 37 | mesophilic |
67771 | positive | growth | 37 | mesophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
29397 | positive | growth | 06-10 | alkaliphile |
29397 | positive | optimum | 6.5 |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
29397 | aerobe |
67771 | aerobe |
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 92 |
69480 | no | 99.997 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
21416 | NaCl | positive | maximum | 2.5 % |
29397 | NaCl | positive | growth | 0-4 % |
29397 | NaCl | positive | optimum | 2 % |
observation
- @ref: 67770
- observation: quinones: MK-12, MK-11, MK-10
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
21416 | 17234 | glucose | + | |
21416 | 22599 | arabinose | + | |
21416 | 17992 | sucrose | + | |
21416 | 18222 | xylose | + | |
21416 | 17268 | myo-inositol | - | |
21416 | 37684 | mannose | - | |
21416 | 28757 | fructose | - | |
21416 | 26546 | rhamnose | - | |
21416 | 16634 | raffinose | + | |
21416 | 62968 | cellulose | - | |
29397 | 30089 | acetate | + | carbon source |
29397 | 17057 | cellobiose | + | carbon source |
29397 | 23652 | dextrin | + | carbon source |
29397 | 28757 | fructose | + | carbon source |
29397 | 28260 | galactose | + | carbon source |
29397 | 24265 | gluconate | + | carbon source |
29397 | 17234 | glucose | + | carbon source |
29397 | 17754 | glycerol | + | carbon source |
29397 | 28087 | glycogen | + | carbon source |
29397 | 17596 | inosine | + | carbon source |
29397 | 17716 | lactose | + | carbon source |
29397 | 17306 | maltose | + | carbon source |
29397 | 29864 | mannitol | + | carbon source |
29397 | 37684 | mannose | + | carbon source |
29397 | 15361 | pyruvate | + | carbon source |
29397 | 51850 | methyl pyruvate | + | carbon source |
29397 | 33942 | ribose | + | carbon source |
29397 | 17814 | salicin | + | carbon source |
29397 | 17992 | sucrose | + | carbon source |
29397 | 17748 | thymidine | + | carbon source |
29397 | 27082 | trehalose | + | carbon source |
29397 | 53423 | tween 40 | + | carbon source |
29397 | 53426 | tween 80 | + | carbon source |
29397 | 16704 | uridine | + | carbon source |
29397 | 18222 | xylose | + | carbon source |
29397 | 17632 | nitrate | + | reduction |
68379 | 17632 | nitrate | - | reduction |
68379 | 4853 | esculin | + | hydrolysis |
68379 | 16199 | urea | - | hydrolysis |
68379 | 5291 | gelatin | + | hydrolysis |
68379 | 17634 | D-glucose | - | fermentation |
68379 | 16988 | D-ribose | - | fermentation |
68379 | 65327 | D-xylose | - | fermentation |
68379 | 16899 | D-mannitol | - | fermentation |
68379 | 17306 | maltose | - | fermentation |
68379 | 17716 | lactose | - | fermentation |
68379 | 17992 | sucrose | + | fermentation |
68379 | 28087 | glycogen | + | fermentation |
enzymes
@ref | value | activity | ec |
---|---|---|---|
29397 | acid phosphatase | + | 3.1.3.2 |
29397 | alpha-galactosidase | + | 3.2.1.22 |
29397 | catalase | + | 1.11.1.6 |
68382 | alpha-fucosidase | - | 3.2.1.51 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68382 | beta-glucosidase | + | 3.2.1.21 |
68382 | alpha-glucosidase | + | 3.2.1.20 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | beta-galactosidase | + | 3.2.1.23 |
68382 | alpha-galactosidase | - | 3.2.1.22 |
68382 | naphthol-AS-BI-phosphohydrolase | + | |
68382 | alpha-chymotrypsin | - | 3.4.21.1 |
68382 | trypsin | - | 3.4.21.4 |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | lipase (C 14) | - | |
68382 | esterase lipase (C 8) | + | |
68382 | esterase (C 4) | + | |
68382 | alkaline phosphatase | + | 3.1.3.1 |
68379 | gelatinase | + | |
68379 | urease | - | 3.5.1.5 |
68379 | beta-glucosidase | + | 3.2.1.21 |
68379 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68379 | alpha-glucosidase | + | 3.2.1.20 |
68379 | beta-galactosidase | + | 3.2.1.23 |
68379 | beta-glucuronidase | - | 3.2.1.31 |
68379 | pyrrolidonyl arylamidase | - | 3.4.19.3 |
68379 | pyrazinamidase | - | 3.5.1.B15 |
API coryne
@ref | NIT | PYZ | PYRA | PAL | beta GUR | beta GAL | alpha GLU | beta NAG | ESC | URE | GEL | GLU | RIB | XYL | MAN | MAL | LAC | SAC | GLYG |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
21416 | - | - | - | +/- | - | + | + | - | + | - | + | - | - | - | - | - | - | + | + |
API zym
@ref | Alkaline phosphatase | Esterase | Esterase Lipase | Lipase | Leucine arylamidase | Valine arylamidase | Cystine arylamidase | Trypsin | alpha- Chymotrypsin | Acid phosphatase | Naphthol-AS-BI-phosphohydrolase | alpha- Galactosidase | beta- Galactosidase | beta- Glucuronidase | alpha- Glucosidase | beta- Glucosidase | N-acetyl-beta- glucosaminidase | alpha- Mannosidase | alpha- Fucosidase |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
21416 | + | + | + | - | + | +/- | +/- | - | - | +/- | + | - | + | - | + | + | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | country | origin.country | continent |
---|---|---|---|---|
17418 | traditional fermented seafood | Republic of Korea | KOR | Asia |
67770 | Traditional fermented seafood | Republic of Korea | KOR | Asia |
67771 | From Jeotgal, fermented shellfisg | Republic of Korea | KOR | Asia |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Engineered | #Food production | #Seafood |
#Engineered | #Food production | #Fermented |
taxonmaps
- @ref: 69479
- File name: preview.99_63152.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_852;97_34675;98_44713;99_63152&stattab=map
- Last taxonomy: Agromyces atrinae subclade
- 16S sequence: FJ607310
- Sequence Identity:
- Total samples: 907
- soil counts: 315
- aquatic counts: 136
- animal counts: 246
- plant counts: 210
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
17418 | 1 | Risk group (German classification) |
21416 | L1 | German classification |
Sequence information
16S sequences
- @ref: 17418
- description: Agromyces atrinae strain P27 16S ribosomal RNA gene, partial sequence
- accession: FJ607310
- length: 1477
- database: ena
- NCBI tax ID: 592376
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Agromyces atrinae strain DSM 23870 | 592376.3 | wgs | patric | 592376 |
66792 | Agromyces atrinae strain DSM 23870 | 592376.5 | wgs | patric | 592376 |
66792 | Agromyces atrinae DSM 23870 | 2844837950 | draft | img | 592376 |
67770 | Agromyces atrinae DSM 23870 | GCA_013407835 | contig | ncbi | 592376 |
67770 | Agromyces atrinae DSM 23870 | GCA_004134805 | scaffold | ncbi | 592376 |
GC content
@ref | GC-content | method |
---|---|---|
17418 | 69.0 | thermal denaturation, midpoint method (Tm) |
29397 | 69 | |
67770 | 69 | thermal denaturation, midpoint method (Tm) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 92 | no |
gram-positive | yes | 92.576 | no |
anaerobic | no | 99.603 | no |
halophile | no | 89.922 | no |
spore-forming | no | 90.526 | no |
glucose-util | yes | 86.419 | no |
thermophile | no | 99.613 | yes |
flagellated | no | 98.054 | yes |
aerobic | yes | 91.98 | yes |
motile | no | 91.156 | yes |
glucose-ferment | no | 86.992 | yes |
External links
@ref: 17418
culture collection no.: DSM 23870, JCM 15913, KCTC 19593
straininfo link
- @ref: 76732
- straininfo: 399040
literature
- topic: Phylogeny
- Pubmed-ID: 19666805
- title: Agromyces atrinae sp. nov., isolated from fermented seafood.
- authors: Park EJ, Kim MS, Jung MJ, Roh SW, Chang HW, Shin KS, Bae JW
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.012294-0
- year: 2009
- mesh: Actinomycetales/*classification/genetics/*isolation & purification/physiology, Bacterial Typing Techniques, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Fermentation, Genes, rRNA, Genotype, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Seafood/*microbiology, Sequence Analysis, DNA, Species Specificity
- topic2: Genetics
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed | journal |
---|---|---|---|---|---|---|---|
17418 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23870) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-23870 | ||||
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 | ||||
21416 | Wink, J. | http://www.dsmz.de/microorganisms/wink_pdf/DSM23870.pdf | Compendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig | ||||
29397 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 25804 | 28776041 | ||
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) | ||||
66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | 33211880 | Nucleic Acids Res. 49: D498-D508 2020 | ||
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | |||||
67771 | Curators of the KCTC | https://kctc.kribb.re.kr/En/Kctc | |||||
68379 | Automatically annotated from API Coryne | ||||||
68382 | Automatically annotated from API zym | ||||||
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 | ||||
76732 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID399040.1 | StrainInfo: A central database for resolving microbial strain identifiers |