Strain identifier
BacDive ID: 10727
Type strain:
Species: Nocardia salmonicida
Strain Designation: A-7604, Rucker
Strain history: CIP <- 1995, IFO <- E.B. Shirling: strain ISP 5472 <- Lederle Lab.: strain A-7604, Streptomyces salmonicida
NCBI tax ID(s): 53431 (species)
General
@ref: 9566
BacDive-ID: 10727
DSM-Number: 40472
keywords: Bacteria, 16S sequence, genome sequence, mesophilic
description: Nocardia salmonicida A-7604 is a mesophilic bacterium that was isolated from blueback salmon.
NCBI tax id
- NCBI tax id: 53431
- Matching level: species
strain history
<- E.B. Shirling, ISP, (Streptomyces salmonicida) <- H.D. Tresner, A-7604, strain Rucker |
KCC S-0826 <-- IFO 13393 <-- SAJ <-- ISP 5472 <-- Lederle Labs.; A-7604 <-- R. Rucker. |
doi: 10.13145/bacdive10727.20220920.7
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Actinomycetes
- order: Mycobacteriales
- family: Nocardiaceae
- genus: Nocardia
- species: Nocardia salmonicida
- full scientific name: Nocardia salmonicida (ex Rucker 1949) Isik et al. 1999
@ref: 9566
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Nocardiaceae
genus: Nocardia
species: Nocardia salmonicida subsp. salmonicida
full scientific name: Nocardia salmonicida subsp. salmonicida (Isik et al. 1999) Nouioui et al. 2018
strain designation: A-7604, Rucker
type strain: yes
Morphology
multimedia
- @ref: 9566
- multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_40472.jpg
- caption: Medium 65 28°C
- intellectual property rights: © Leibniz-Institut DSMZ
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
9566 | GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) | yes | https://bacmedia.dsmz.de/medium/65 | Name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) Composition: Agar 12.0 g/l Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l CaCO3 2.0 g/l Distilled water |
35686 | MEDIUM 3 - Columbia agar | yes | Columbia agar (39.000 g);distilled water (1000.000 ml) |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
18597 | positive | optimum | 28 | mesophilic |
9566 | positive | growth | 28 | mesophilic |
35686 | positive | growth | 30 | mesophilic |
67770 | positive | growth | 28 | mesophilic |
Physiology and metabolism
observation
- @ref: 67770
- observation: quinones: MK-8(H4)
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
18597 | 17234 | glucose | + | |
18597 | 22599 | arabinose | - | |
18597 | 17992 | sucrose | - | |
18597 | 18222 | xylose | - | |
18597 | 17268 | myo-inositol | - | |
18597 | 29864 | mannitol | - | |
18597 | 28757 | fructose | + | |
18597 | 26546 | rhamnose | - | |
18597 | 16634 | raffinose | - | |
18597 | 62968 | cellulose | - | |
68379 | 28087 | glycogen | - | fermentation |
68379 | 17992 | sucrose | - | fermentation |
68379 | 17716 | lactose | - | fermentation |
68379 | 17306 | maltose | - | fermentation |
68379 | 16899 | D-mannitol | - | fermentation |
68379 | 65327 | D-xylose | - | fermentation |
68379 | 16988 | D-ribose | - | fermentation |
68379 | 17634 | D-glucose | - | fermentation |
68379 | 5291 | gelatin | - | hydrolysis |
68379 | 16199 | urea | - | hydrolysis |
68379 | 4853 | esculin | + | hydrolysis |
68379 | 17632 | nitrate | - | reduction |
68368 | 5291 | gelatin | - | hydrolysis |
68368 | 27897 | tryptophan | - | energy source |
68368 | 16199 | urea | - | hydrolysis |
68368 | 16947 | citrate | + | assimilation |
68368 | 18257 | ornithine | - | degradation |
68368 | 25094 | lysine | - | degradation |
68368 | 29016 | arginine | - | hydrolysis |
metabolite production
@ref | Chebi-ID | metabolite | production |
---|---|---|---|
68368 | 15688 | acetoin | no |
68368 | 35581 | indole | no |
68368 | 16136 | hydrogen sulfide | no |
metabolite tests
@ref | Chebi-ID | metabolite | voges-proskauer-test | indole test |
---|---|---|---|---|
68368 | 15688 | acetoin | - | |
68368 | 35581 | indole | - |
enzymes
@ref | value | activity | ec |
---|---|---|---|
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 | alkaline phosphatase | + | 3.1.3.1 |
68379 | pyrrolidonyl arylamidase | - | 3.4.19.3 |
68379 | pyrazinamidase | - | 3.5.1.B15 |
68368 | gelatinase | - | |
68368 | tryptophan deaminase | - | 4.1.99.1 |
68368 | urease | - | 3.5.1.5 |
68368 | ornithine decarboxylase | - | 4.1.1.17 |
68368 | lysine decarboxylase | - | 4.1.1.18 |
68368 | arginine dihydrolase | - | 3.5.3.6 |
68368 | beta-galactosidase | - | 3.2.1.23 |
68382 | alkaline phosphatase | + | 3.1.3.1 |
68382 | esterase (C 4) | - | |
68382 | esterase lipase (C 8) | + | |
68382 | lipase (C 14) | + | |
68382 | leucine arylamidase | - | 3.4.11.1 |
68382 | valine arylamidase | - | |
68382 | cystine arylamidase | - | 3.4.11.3 |
68382 | trypsin | + | 3.4.21.4 |
68382 | alpha-chymotrypsin | - | 3.4.21.1 |
68382 | acid phosphatase | + | 3.1.3.2 |
68382 | naphthol-AS-BI-phosphohydrolase | - | |
68382 | alpha-galactosidase | - | 3.2.1.22 |
68382 | beta-galactosidase | - | 3.2.1.23 |
68382 | beta-glucuronidase | + | 3.2.1.31 |
68382 | alpha-glucosidase | + | 3.2.1.20 |
68382 | beta-glucosidase | + | 3.2.1.21 |
68382 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | alpha-fucosidase | - | 3.2.1.51 |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
18597 | - | - | - | + | - | - | + | - | + | - | - | - | - | - | - | - | - | - | - |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
18597 | + | - | + | + | - | - | - | + | - | + | - | - | - | + | + | + | - | - | - |
API 20E
@ref | ONPG | ADH Arg | LDC Lys | ODC | CIT | H2S | URE | TDA Trp | IND | VP | GEL |
---|---|---|---|---|---|---|---|---|---|---|---|
18597 | - | - | - | - | + | - | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | host species |
---|---|---|
9566 | blueback salmon | |
67770 | Blueback salmon (Oncorhynchus nerka) | Oncorhynchus nerka |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Environmental | #Aquatic | #Marine |
#Host | #Fishes | #Salmonidae |
Safety information
risk assessment
@ref | biosafety level | biosafety level comment | pathogenicity animal |
---|---|---|---|
18597 | 2 | German classification | |
9566 | 1 | Risk group (German classification) | yes |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Nocardia salmonicida strain DSM 40472 16S ribosomal RNA gene, complete sequence | AF430050 | 1494 | ena | 53431 |
20218 | Nocardia salmonicida strain DSM 40472 note copy 1 16S-23S ribosomal RNA intergenic spacer, complete sequence | AF536472 | 335 | ena | 53431 |
20218 | Nocardia salmonicida strain DSM 40472 note copy 2 16S-23S ribosomal RNA intergenic spacer, complete sequence | AF536473 | 329 | ena | 53431 |
20218 | Nocardia salmonicida strain JCM 4826 16S ribosomal RNA gene, partial sequence | AY756560 | 606 | ena | 53431 |
20218 | Nocardia salmonicida gene for 16S ribosomal RNA, partial sequence, strain: JCM 4826 | D44392 | 120 | ena | 53431 |
20218 | N.salmonicida gene for 16S ribosomal RNA | Z46750 | 1474 | ena | 53431 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Nocardia salmonicida NBRC 13393 NBRC 13393 | GCA_001613085 | contig | ncbi | 1210085 |
66792 | Nocardia salmonicida NBRC 13393 | 1210085.4 | wgs | patric | 1210085 |
66792 | Nocardia salmonicida NBRC 13393 | 2731957743 | draft | img | 1210085 |
67770 | Nocardia salmonicida NBRC 13393, whole genome shotgun sequencing project | BDBR00000000 | ncbi | 1210085 |
GC content
@ref | GC-content | method |
---|---|---|
9566 | 66.9 | high performance liquid chromatography (HPLC) |
67770 | 66 | fluorimetric |
External links
@ref: 9566
culture collection no.: DSM 40472, ATCC 27463, CBS 694.72, IFO 13393, ISP 5472, JCM 4826, NBRC 13393, NRRL B-2778, RIA 1354, BCRC 12441, CGMCC 4.1136, CGMCC 4.1502, CIP 104517, IFM 10710, IMSNU 21183, KCTC 9372, NRRL B-12385
straininfo link
@ref | passport |
---|---|
20218 | http://www.straininfo.net/strains/123998 |
20218 | http://www.straininfo.net/strains/123993 |
20218 | http://www.straininfo.net/strains/230234 |
20218 | http://www.straininfo.net/strains/123996 |
20218 | http://www.straininfo.net/strains/123994 |
20218 | http://www.straininfo.net/strains/123997 |
20218 | http://www.straininfo.net/strains/334749 |
20218 | http://www.straininfo.net/strains/123999 |
20218 | http://www.straininfo.net/strains/124000 |
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 10319509 | Nocardia salmonicida nom. rev., a fish pathogen. | Isik K, Chun J, Hah YC, Goodfellow M | Int J Syst Bacteriol | 10.1099/00207713-49-2-833 | 1999 | Animals, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fish Diseases/*microbiology, Genes, rRNA, Molecular Sequence Data, Nocardia/*classification/genetics/isolation & purification/physiology, Nocardia Infections/microbiology/*veterinary, Oncorhynchus/*microbiology, Phenotype, RNA, Ribosomal, 16S/genetics | Genetics |
Phylogeny | 26868112 | Nocardia camponoti sp. nov., an actinomycete isolated from the head of an ant (Camponotus japonicas Mayr). | Liu C, Guan X, Li Y, Li W, Ye L, Kong X, Song J, Wang X, Xiang W | Int J Syst Evol Microbiol | 10.1099/ijsem.0.000963 | 2016 | Animals, Ants/*microbiology, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Molecular Sequence Data, Nocardia/*classification/genetics/isolation & purification, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry | Genetics |
Phylogeny | 27510998 | Nocardia lasii sp. nov., a novel actinomycete isolated from the cuticle of an ant (Lasius fuliginosus L). | Liu C, Bai L, Ye L, Zhao J, Yan K, Xiang W, Wang X | Antonie Van Leeuwenhoek | 10.1007/s10482-016-0753-y | 2016 | Animals, Ants/*microbiology, DNA, Bacterial, Molecular Typing, Nocardia/classification/*isolation & purification, Phylogeny, RNA, Ribosomal, 16S/genetics | Enzymology |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
9566 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 40472) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-40472 | |||
18597 | Wink, J. | http://www.dsmz.de/microorganisms/wink_pdf/DSM40472.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 | |||
20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
35686 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/16435 | ||||
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/ | ||||
68368 | Automatically annotated from API 20E | |||||
68379 | Automatically annotated from API Coryne | |||||
68382 | Automatically annotated from API zym |