Strain identifier
BacDive ID: 10655
Type strain:
Species: Nocardia carnea
Strain Designation: 30
Strain history: CIP <- 1995, IFO <- 1984, ATCC <- NCTC, Actinomyces carneus <- V. Puntoni: strain 30
NCBI tax ID(s): 1206726 (strain), 37328 (species)
General
@ref: 10805
BacDive-ID: 10655
DSM-Number: 43397
keywords: genome sequence, 16S sequence, Bacteria, aerobe, spore-forming, mesophilic, human pathogen
description: Nocardia carnea 30 is an aerobe, spore-forming, mesophilic human pathogen of the family Nocardiaceae.
NCBI tax id
NCBI tax id | Matching level |
---|---|
37328 | species |
1206726 | strain |
strain history
@ref | history |
---|---|
10805 | <- R.E. Gordon, IMRU <- V. Putoni |
67770 | CIP 104509 <-- IFO 14403 <-- ATCC 6847 <-- NCTC 3527 <-- V. Puntoni; 30. |
117186 | CIP <- 1995, IFO <- 1984, ATCC <- NCTC, Actinomyces carneus <- V. Puntoni: strain 30 |
doi: 10.13145/bacdive10655.20230509.8.1
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 carnea
- full scientific name: Nocardia carnea (Rossi Doria 1891) Castellani and Chalmers 1913 (Approved Lists 1980)
synonyms
- @ref: 20215
- synonym: Streptothrix carnea
@ref: 10805
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Nocardiaceae
genus: Nocardia
species: Nocardia carnea
full scientific name: Nocardia carnea (Rossi Doria 1891) Castellani and Chalmers 1913 emend. Nouioui et al. 2018
strain designation: 30
type strain: yes
Morphology
cell morphology
@ref | motility | confidence | gram stain | cell shape |
---|---|---|---|---|
69480 | no | 90.908 | ||
69480 | 100 | positive | ||
117186 | positive | rod-shaped |
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
10805 | GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) | yes | https://mediadive.dsmz.de/medium/65 | Name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) Composition: Agar 18.0 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 |
41222 | MEDIUM 3 - Columbia agar | yes | Columbia agar (39.000 g);distilled water (1000.000 ml) | |
117186 | CIP Medium 3 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
18491 | positive | optimum | 30 | mesophilic |
10805 | positive | growth | 30 | mesophilic |
41222 | positive | growth | 30 | mesophilic |
58021 | positive | growth | 30-37 | mesophilic |
67770 | positive | growth | 28 | mesophilic |
117186 | positive | growth | 30-37 | mesophilic |
117186 | no | growth | 10 | psychrophilic |
117186 | no | growth | 45 | thermophilic |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
58021 | aerobe |
117186 | obligate aerobe |
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | yes | 94 |
69480 | no | 98.477 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
18491 | NaCl | positive | maximum | 7.5 % |
117186 | NaCl | positive | growth | 0-6 % |
117186 | NaCl | no | growth | 8 % |
117186 | NaCl | no | growth | 10 % |
observation
- @ref: 67770
- observation: quinones: MK-8(H4)
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
18491 | 17234 | glucose | + | |
18491 | 22599 | arabinose | - | |
18491 | 17992 | sucrose | - | |
18491 | 18222 | xylose | - | |
18491 | 17268 | myo-inositol | - | |
18491 | 29864 | mannitol | + | |
18491 | 28757 | fructose | - | |
18491 | 26546 | rhamnose | - | |
18491 | 16634 | raffinose | - | |
18491 | 62968 | cellulose | - | |
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 |
117186 | 606565 | hippurate | + | hydrolysis |
117186 | 17632 | nitrate | + | reduction |
117186 | 16301 | nitrite | - | reduction |
metabolite production
@ref | Chebi-ID | metabolite | production |
---|---|---|---|
68368 | 15688 | acetoin | no |
68368 | 35581 | indole | no |
68368 | 16136 | hydrogen sulfide | no |
117186 | 35581 | indole | no |
metabolite tests
@ref | Chebi-ID | metabolite | voges-proskauer-test | indole test |
---|---|---|---|---|
68368 | 15688 | acetoin | - | |
68368 | 35581 | indole | - | |
117186 | 15688 | acetoin | - |
enzymes
@ref | value | activity | ec |
---|---|---|---|
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 |
117186 | oxidase | - | |
117186 | beta-galactosidase | + | 3.2.1.23 |
117186 | alcohol dehydrogenase | - | 1.1.1.1 |
117186 | gelatinase | - | |
117186 | amylase | - | |
117186 | DNase | - | |
117186 | caseinase | - | 3.4.21.50 |
117186 | catalase | + | 1.11.1.6 |
117186 | tween esterase | - | |
117186 | lecithinase | - | |
117186 | lysine decarboxylase | - | 4.1.1.18 |
117186 | ornithine decarboxylase | - | 4.1.1.17 |
117186 | urease | - | 3.5.1.5 |
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 zym
@ref | Control | 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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
117186 | - | + | + | + | - | + | - | - | - | - | + | + | - | - | - | - | + | - | - | - |
API 20E
@ref | ONPG | ADH Arg | LDC Lys | ODC | CIT | H2S | URE | TDA Trp | IND | VP | GEL |
---|---|---|---|---|---|---|---|---|---|---|---|
18491 | - | - | - | - | - | - | + | - | - | - | - |
API biotype100
@ref | GLU | FRU | GAL | TRE | MNE | SBE | MEL | SAC | RAF | MTE | MAL | LAC | LTE | MbGa | MaGa | CEL | GEN | MbGu | ESC | RIB | ARA | XYL | PLE | RHA | FUC | MLZ | DARL | LARL | XLT | DUL | TAG | GLY | INO | MAN | MTL | TUR | SOR | ADO | HBG | LYX | ERY | MDG | 3MDG | SAT | MUC | LTAT | DTAT | MTAT | DMLT | LMLT | CATE | TATE | TTE | CIT | GRT | GAT | 2KG | 5KG | TRY | NAG | GNT | PAC | PAT | pOBE | QAT | GTE | mOBE | BAT | PPAT | CMT | TGE | BET | PCE | ABT | HIN | LAT | CAP | CYT | HIS | SUC | FUM | GRE | GYT | AVT | ETN | TTN | GLN | ITA | 3OBU | APT | GTT | PRO | DALA | LALA | SER | MNT | PROP | TYR | 2KT |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
117186 | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | - | - | - | - | - | - | - | - | - | - | - | - | + | + | - | - | + | - | - | - | - | - | - | - | - | - | - | - | - | + | + | - | - | - | - | - | - | - | + | - | + | - | - | - | - | - | + | - | - |
Isolation, sampling and environmental information
taxonmaps
- @ref: 69479
- File name: preview.99_3551.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_243;97_658;98_2723;99_3551&stattab=map
- Last taxonomy: Nocardia
- 16S sequence: X80607
- Sequence Identity:
- Total samples: 11377
- soil counts: 8278
- aquatic counts: 469
- animal counts: 943
- plant counts: 1687
Safety information
risk assessment
@ref | pathogenicity human | biosafety level | biosafety level comment |
---|---|---|---|
10805 | yes, in single cases | 1 | Risk group (German classification) |
18491 | 1 | ||
117186 | 2 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Nocardia carnea NBRC 14403 16S ribosomal RNA gene, partial sequence | GQ376165 | 1439 | ena | 1206726 |
20218 | Nocardia carnea strain ATCC 6847 clone 1 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, complete sequence; and 23S ribosomal RNA gene, partial sequence | GU236349 | 625 | ena | 1206726 |
20218 | Nocardia carnea strain ATCC 6847 clone 2 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, complete sequence; and 23S ribosomal RNA gene, partial sequence | GU236350 | 625 | ena | 1206726 |
20218 | Nocardia carnea strain ATCC 6847 clone 3 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, complete sequence; and 23S ribosomal RNA gene, partial sequence | GU236351 | 625 | ena | 1206726 |
20218 | Nocardia carnea strain ATCC 6847 clone 4 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, complete sequence; and 23S ribosomal RNA gene, partial sequence | GU236352 | 625 | ena | 1206726 |
20218 | Nocardia carnea strain ATCC 6847 clone 5 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, complete sequence; and 23S ribosomal RNA gene, partial sequence | GU236353 | 625 | ena | 1206726 |
20218 | Nocardia carnea strain ATCC 6847 clone 6 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, complete sequence; and 23S ribosomal RNA gene, partial sequence | GU236354 | 625 | ena | 1206726 |
20218 | Nocardia carnea strain ATCC 6847 16S ribosomal RNA gene, partial sequence | JF797307 | 1412 | ena | 1206726 |
20218 | Nocardia carnea 16S rRNA gene, strain ATCC 6847T | X80602 | 1395 | ena | 1206726 |
20218 | Nocardia carnea strain CGMCC 4.1167 clone 1 16S-23S ribosomal RNA intergenic spacer, complete sequence | DQ518337 | 331 | ena | 1206726 |
20218 | Nocardia carnea strain CGMCC 4.1167 clone 2 16S-23S ribosomal RNA intergenic spacer, complete sequence | DQ518338 | 325 | ena | 1206726 |
20218 | Nocardia carnea strain DSM 43397 16S ribosomal RNA gene, complete sequence | AF430035 | 1492 | ena | 1206726 |
20218 | Nocardia carnea strain DSM 43397 16S-23S ribosomal RNA intergenic spacer, complete sequence | AF536408 | 321 | ena | 1206726 |
20218 | Nocardia carnea strain DSM 43397 16S ribosomal RNA gene, partial sequence | AY756546 | 606 | ena | 1206726 |
20218 | Nocardia carnea 16S rRNA gene, strain DSM43397T | X80607 | 1463 | ena | 1206726 |
20218 | N.carnea gene for 16S ribosomal RNA | Z36929 | 1472 | ena | 1206726 |
20218 | Nocardia carnea strain NRRL B-1336 16S ribosomal RNA gene, partial sequence | JN041599 | 462 | ena | 37328 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Nocardia carnea NBRC 14403 | 1206726.4 | wgs | patric | 1206726 |
66792 | Nocardia carnea NBRC 14403 | 2551306165 | draft | img | 1206726 |
67770 | Nocardia carnea NBRC 14403 | GCA_000308515 | contig | ncbi | 1206726 |
GC content
@ref | GC-content | method |
---|---|---|
67770 | 68 | fluorimetric |
67770 | 67.1 | genome sequence analysis |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | yes | 94 | no |
motile | no | 92.764 | no |
gram-positive | yes | 86.11 | no |
anaerobic | no | 99.43 | yes |
aerobic | yes | 90.324 | yes |
halophile | no | 82.076 | no |
spore-forming | yes | 76.49 | no |
glucose-util | yes | 91.076 | yes |
flagellated | no | 98.463 | no |
thermophile | no | 98.974 | no |
glucose-ferment | no | 92.911 | no |
External links
@ref: 10805
culture collection no.: CCUG 48177, CIP 104509, IFO 14403, JCM 3375, NRRL B-1336, DSM 43397, ATCC 6847, IMRU 3419, NCTC 3527, DSM 43580, JCM 30727, BCRC 13693, CCM 2756, CGMCC 4.1167, CGMCC 4.1733, IFM 0237, IMET 7504, IMSNU 21185, KCTC 9957, NBRC 14403, VKM Ac-814
straininfo link
- @ref: 79925
- straininfo: 92194
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 9734044 | Nocardia flavorosea sp. nov. | Chun J, Seong CN, Bae KS, Lee KJ, Kang SO, Goodfellow M, Hah YC | Int J Syst Bacteriol | 10.1099/00207713-48-3-901 | 1998 | Base Sequence, DNA, Ribosomal/chemistry, Molecular Sequence Data, Nocardia/*classification, RNA, Ribosomal, 16S/genetics | Genetics |
Phylogeny | 21596508 | Nocardia rhamnosiphila sp. nov., isolated from soil. | Everest GJ, Cook AE, le Roes-Hill M, Meyers PR | Syst Appl Microbiol | 10.1016/j.syapm.2011.03.006 | 2011 | Bacterial Typing Techniques, Base Sequence, DNA Gyrase/genetics, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genes, Bacterial, Genes, rRNA, Genotype, Microbial Sensitivity Tests, Molecular Sequence Data, Nocardia/chemistry/*classification/genetics/*isolation & purification/physiology, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil Microbiology, Species Specificity | Genetics |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
10805 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 43397) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-43397 | |||
18491 | Wink, J. | http://www.dsmz.de/microorganisms/wink_pdf/DSM43397.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 | |
41222 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/16426 | ||||
58021 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 48177) | https://www.ccug.se/strain?id=48177 | |||
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 | |||||
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 | |||
79925 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID92194.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
117186 | Curators of the CIP | Collection of Institut Pasteur (CIP 104509) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104509 |