Strain identifier
BacDive ID: 7273
Type strain:
Species: Agromyces salentinus
Strain Designation: 108989, 20-5
Strain history: CIP <- 2005, DSMZ <- I. Groth, Hans Knöll Inst., Jena, Germany <- C. Weigel: strain 20-5
NCBI tax ID(s): 269421 (species)
General
@ref: 6320
BacDive-ID: 7273
DSM-Number: 16198
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-positive, rod-shaped
description: Agromyces salentinus 108989 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from soil sample.
NCBI tax id
- NCBI tax id: 269421
- Matching level: species
strain history
@ref | history |
---|---|
6320 | <- I. Groth, HKI; 20-5 <- Ch. Weigel |
67770 | I. Groth 20-5 (=HKI 0320) <-- Ch. Weigel. |
122364 | CIP <- 2005, DSMZ <- I. Groth, Hans Knöll Inst., Jena, Germany <- C. Weigel: strain 20-5 |
doi: 10.13145/bacdive7273.20230509.8.1
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 salentinus
- full scientific name: Agromyces salentinus Jurado et al. 2005
@ref: 6320
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Microbacteriaceae
genus: Agromyces
species: Agromyces salentinus
full scientific name: Agromyces salentinus Jurado et al. 2005
strain designation: 108989, 20-5
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell shape | motility |
---|---|---|---|
31281 | positive | rod-shaped | no |
122364 | positive | rod-shaped | no |
colony morphology
@ref | colony color | incubation period | medium used |
---|---|---|---|
18303 | Rapeseed yellow (1021) | 10-14 days | ISP 2 |
18303 | Rapeseed yellow (1021) | 10-14 days | ISP 3 |
18303 | Rapeseed yellow (1021) | 10-14 days | ISP 4 |
18303 | Rapeseed yellow (1021) | 10-14 days | ISP 5 |
18303 | Rapeseed yellow (1021) | 10-14 days | ISP 6 |
18303 | Rapeseed yellow (1021) | 10-14 days | ISP 7 |
122364 |
multicellular morphology
@ref | forms multicellular complex | medium name |
---|---|---|
18303 | no | ISP 2 |
18303 | no | ISP 3 |
18303 | no | ISP 4 |
18303 | no | ISP 5 |
18303 | no | ISP 6 |
18303 | no | ISP 7 |
pigmentation
- @ref: 31281
- production: yes
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
6320 | R2A MEDIUM (DSMZ Medium 830) | yes | https://mediadive.dsmz.de/medium/830 | Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water |
6320 | TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) | yes | https://mediadive.dsmz.de/medium/92 | Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water |
18303 | 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 | |
18303 | 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: | |
18303 | 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 | |
18303 | 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 | |
18303 | ISP 6 | yes | Name: ISP 6 (5318) Composition Peptone 15.0 g/l Proteose peptose 5.0 g/l Ferric ammonium citrate 0.5 g/l Sodium glycerophosphate 1.0 g/l Sodium thiosulfate 0.08 g/l Yeast extract 1.0 g/l Agar 15.0 g/l Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigments Organisms: All Actinomycetes | |
18303 | 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 | |
36774 | MEDIUM 72- for trypto casein soja agar | yes | Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g) | |
122364 | CIP Medium 72 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72 | |
122364 | CIP Medium 291 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=291 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
18303 | positive | optimum | 28 | mesophilic |
6320 | positive | growth | 28 | mesophilic |
31281 | positive | growth | 10-37 | |
31281 | positive | optimum | 24 | psychrophilic |
36774 | positive | growth | 30 | mesophilic |
67770 | positive | growth | 28 | mesophilic |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
31281 | aerobe |
122364 | obligate aerobe |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
31281 | NaCl | positive | growth | 0-4 % |
31281 | NaCl | positive | optimum | 2 % |
observation
@ref | observation |
---|---|
31281 | aggregates in clumps |
67770 | quinones: MK-12, MK-11, MK-10, MK-13 |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
31281 | 30089 | acetate | + | carbon source |
31281 | 22599 | arabinose | + | carbon source |
31281 | 17057 | cellobiose | + | carbon source |
31281 | 28757 | fructose | + | carbon source |
31281 | 33984 | fucose | + | carbon source |
31281 | 28260 | galactose | + | carbon source |
31281 | 17234 | glucose | + | carbon source |
31281 | 17754 | glycerol | + | carbon source |
31281 | 28087 | glycogen | + | carbon source |
31281 | 17306 | maltose | + | carbon source |
31281 | 16634 | raffinose | + | carbon source |
31281 | 26546 | rhamnose | + | carbon source |
31281 | 33942 | ribose | + | carbon source |
31281 | 17814 | salicin | + | carbon source |
31281 | 17992 | sucrose | + | carbon source |
31281 | 27082 | trehalose | + | carbon source |
31281 | 18222 | xylose | + | carbon source |
31281 | 4853 | esculin | + | hydrolysis |
68371 | Potassium 5-ketogluconate | - | builds acid from | |
68371 | Potassium 2-ketogluconate | - | builds acid from | |
68371 | 24265 | gluconate | - | builds acid from |
68371 | 18403 | L-arabitol | - | builds acid from |
68371 | 18333 | D-arabitol | - | builds acid from |
68371 | 28847 | D-fucose | - | builds acid from |
68371 | 16443 | D-tagatose | - | builds acid from |
68371 | 62318 | D-lyxose | - | builds acid from |
68371 | 17151 | xylitol | - | builds acid from |
68371 | 6731 | melezitose | - | builds acid from |
68371 | 27082 | trehalose | - | builds acid from |
68371 | 17992 | sucrose | + | builds acid from |
68371 | 28053 | melibiose | - | builds acid from |
68371 | 17716 | lactose | - | builds acid from |
68371 | 17306 | maltose | + | builds acid from |
68371 | 17057 | cellobiose | + | builds acid from |
68371 | 17814 | salicin | + | builds acid from |
68371 | 4853 | esculin | + | builds acid from |
68371 | 18305 | arbutin | + | builds acid from |
68371 | 27613 | amygdalin | - | builds acid from |
68371 | 59640 | N-acetylglucosamine | - | builds acid from |
68371 | 320061 | methyl alpha-D-glucopyranoside | - | builds acid from |
68371 | 43943 | methyl alpha-D-mannoside | - | builds acid from |
68371 | 17924 | D-sorbitol | - | builds acid from |
68371 | 16899 | D-mannitol | - | builds acid from |
68371 | 17268 | myo-inositol | - | builds acid from |
68371 | 16813 | galactitol | - | builds acid from |
68371 | 62345 | L-rhamnose | - | builds acid from |
68371 | 17266 | L-sorbose | - | builds acid from |
68371 | 17634 | D-glucose | + | builds acid from |
68371 | 74863 | methyl beta-D-xylopyranoside | - | builds acid from |
68371 | 15963 | ribitol | - | builds acid from |
68371 | 65328 | L-xylose | - | builds acid from |
68371 | 16988 | D-ribose | - | builds acid from |
68371 | 17113 | erythritol | - | builds acid from |
68371 | 17754 | glycerol | - | builds acid from |
122364 | 17632 | nitrate | - | reduction |
122364 | 16301 | nitrite | - | reduction |
68379 | 4853 | esculin | + | hydrolysis |
68379 | 16199 | urea | + | hydrolysis |
68379 | 5291 | gelatin | - | hydrolysis |
68379 | 17992 | sucrose | - | fermentation |
metabolite production
@ref | Chebi-ID | metabolite | production |
---|---|---|---|
31281 | 16136 | hydrogen sulfide | yes |
122364 | 35581 | indole | no |
enzymes
@ref | value | activity | ec |
---|---|---|---|
31281 | catalase | + | 1.11.1.6 |
31281 | cytochrome oxidase | + | 1.9.3.1 |
31281 | urease | + | 3.5.1.5 |
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-galactosidase | + | 3.2.1.23 |
68382 | naphthol-AS-BI-phosphohydrolase | + | |
68382 | acid phosphatase | + | 3.1.3.2 |
68382 | alpha-chymotrypsin | - | 3.4.21.1 |
68382 | trypsin | + | 3.4.21.4 |
68382 | cystine arylamidase | + | 3.4.11.3 |
68382 | valine arylamidase | + | |
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 |
122364 | oxidase | + | |
122364 | alcohol dehydrogenase | - | 1.1.1.1 |
122364 | catalase | + | 1.11.1.6 |
122364 | lysine decarboxylase | - | 4.1.1.18 |
122364 | ornithine decarboxylase | - | 4.1.1.17 |
122364 | urease | - | 3.5.1.5 |
API coryne
@ref | PYZ | PYRA | PAL | beta GUR | beta GAL | alpha GLU | beta NAG | ESC | URE | GEL | SAC |
---|---|---|---|---|---|---|---|---|---|---|---|
18303 | + | + | +/- | - | + | + | - | + | + | - | - |
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 | Control |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
18303 | - | + | + | - | + | + | + | + | - | + | + | + | + | + | + | + | + | + | + | |
122364 | - | + | + | - | + | + | + | + | - | + | + | - | + | - | + | + | + | - | - | - |
API 50CHac
@ref | GLY | ERY | DARA | LARA | RIB | DXYL | LXYL | ADO | MDX | GAL | GLU | FRU | MNE | SBE | RHA | DUL | INO | MAN | SOR | MDM | MDG | NAG | AMY | ARB | ESC | SAL | CEL | MAL | LAC | MEL | SAC | TRE | INU | MLZ | RAF | AMD | GLYG | XLT | GEN | TUR | LYX | TAG | DFUC | LFUC | DARL | LARL | GNT | 2KG | 5KG |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
122364 | - | - | +/- | +/- | - | +/- | - | - | - | +/- | + | +/- | +/- | - | - | - | - | - | - | - | - | - | - | + | + | + | + | + | - | - | + | - | +/- | - | +/- | +/- | +/- | - | +/- | +/- | - | - | - | +/- | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
6320 | soil sample | Porto Badisco | Italy | ITA | Europe |
67770 | Top soil sample collected a few meters from the entrance of Grotta dei Cervi | Porto Badisco | Italy | ITA | Europe |
122364 | Environment, Soil sample | Grotta dei Cervi | Italy | ITA | Europe |
isolation source categories
- Cat1: #Environmental
- Cat2: #Terrestrial
- Cat3: #Soil
taxonmaps
- @ref: 69479
- File name: preview.99_6092.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_852;97_1358;98_4520;99_6092&stattab=map
- Last taxonomy: Agromyces
- 16S sequence: AY507129
- Sequence Identity:
- Total samples: 413
- soil counts: 271
- aquatic counts: 38
- animal counts: 92
- plant counts: 12
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
6320 | 1 | Risk group (German classification) |
122364 | 1 | Risk group (French classification) |
Sequence information
16S sequences
- @ref: 6320
- description: Agromyces salentinus strain 20-5 16S ribosomal RNA gene, partial sequence
- accession: AY507129
- length: 1381
- database: ena
- NCBI tax ID: 269421
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Agromyces salentinus strain JCM 14323 | 269421.3 | wgs | patric | 269421 |
66792 | Agromyces terreus strain JCM 14323 | 424795.3 | wgs | patric | 424795 |
67770 | Agromyces salentinus JCM 14323 | GCA_009749395 | contig | ncbi | 269421 |
GC content
@ref | GC-content | method |
---|---|---|
6320 | 72.3 | |
67770 | 72.3 | thermal denaturation, midpoint method (Tm) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
motile | no | 90.125 | yes |
gram-positive | yes | 93.765 | no |
anaerobic | no | 99.725 | yes |
halophile | no | 89.643 | no |
spore-forming | no | 89.392 | no |
glucose-util | yes | 87.718 | no |
flagellated | no | 97.39 | no |
aerobic | yes | 95.977 | no |
thermophile | no | 99.438 | no |
glucose-ferment | no | 92.381 | no |
External links
@ref: 6320
culture collection no.: DSM 16198, HKI 0320, JCM 14323, CIP 108989, IAM 15297, NCIMB 13989, NCIMB 13990
straininfo link
- @ref: 76724
- straininfo: 362279
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 15653869 | Agromyces salentinus sp. nov. and Agromyces neolithicus sp. nov. | Jurado V, Groth I, Gonzalez JM, Laiz L, Saiz-Jimenez C | Int J Syst Evol Microbiol | 10.1099/ijs.0.63199-0 | 2005 | Actinomycetales/chemistry/*classification/genetics/isolation & purification, Base Composition, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Italy, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology | Genetics |
Phylogeny | 33779960 | Agromyces laixinhei sp. nov. isolated from bat feces in China. | Cheng Y, Bai Y, Huang Y, Yang J, Lu S, Jin D, Pu J, Zheng H, Li J, Huang Y, Wang S, Xu J | J Microbiol | 10.1007/s12275-021-0546-5 | 2021 | Actinobacteria, Actinomycetales/*classification/genetics/*isolation & purification/physiology, Animals, Base Composition, China, Chiroptera/*microbiology, DNA, Bacterial/genetics, Fatty Acids/analysis, Feces/*microbiology, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Whole Genome Sequencing | Transcriptome |
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
---|---|---|---|---|---|---|
6320 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16198) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-16198 | |||
18303 | Wink, J. | http://www.dsmz.de/microorganisms/wink_pdf/DSM16198.pdf | Compendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig | |||
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 | |||
31281 | 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 | 27601 | 28776041 | |
36774 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/6679 | ||||
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/ | ||||
68371 | Automatically annotated from API 50CH acid | |||||
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 | |||
76724 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID362279.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
122364 | Curators of the CIP | Collection of Institut Pasteur (CIP 108989) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108989 |