Strain identifier

BacDive ID: 11241

Type strain: Yes

Species: Nocardiopsis flavescens

Strain Designation: SA6

Strain history: J. Zhang SA6.

NCBI tax ID(s): 758803 (species)

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General

@ref: 18195

BacDive-ID: 11241

DSM-Number: 45786

keywords: genome sequence, 16S sequence, Bacteria, mesophilic

description: Nocardiopsis flavescens SA6 is a mesophilic bacterium that builds an aerial mycelium and was isolated from marine sediment at a deph of 20 cm on the seashore of Lianyungang.

NCBI tax id

  • NCBI tax id: 758803
  • Matching level: species

strain history

@refhistory
18195<- JCM; JCM 17424 <- J. Zhang; SA6
67770J. Zhang SA6.

doi: 10.13145/bacdive11241.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Streptosporangiales
  • family: Nocardiopsidaceae
  • genus: Nocardiopsis
  • species: Nocardiopsis flavescens
  • full scientific name: Nocardiopsis flavescens Fang et al. 2011

@ref: 18195

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardiopsaceae

genus: Nocardiopsis

species: Nocardiopsis flavescens

full scientific name: Nocardiopsis flavescens Fang et al. 2011 emend. Nouioui et al. 2018

strain designation: SA6

type strain: yes

Morphology

colony morphology

@refcolony colormedium used
69437Fawn brown (8007), brown beige (1011)suter without tyrosine
69437Clay brown (8003), ochre brown (8001), beige (1001)ISP 3
69437Beige brown (8024), clay brown (8003)ISP 2
69437Light ivory (1015)ISP 7
69437Olive brown (8008), sepia brown (8014)ISP 6
69437Oyster white (1013), ochre yellow (1024)ISP 4
69437Red brown (8012), nut brown (8011), ochre brown (8001)suter with tyrosine
69437Sand yellow (1002)ISP 5

multicellular morphology

@refforms multicellular complexcomplex namecomplex colormedium name
69437yesAerial myceliumSignal white (9003)ISP 2
69437yesAerial myceliumSignal white (9003)ISP 3
69437yesAerial myceliumTraffic white (9016)ISP 4
69437noAerial myceliumISP 5
69437yesAerial myceliumTelegrey 4 (7047)ISP 6
69437noAerial myceliumISP 7
69437yesAerial myceliumSignal white (9003)suter with tyrosine
69437yesAerial myceliumSignal white (9003)suter without tyrosine

pigmentation

@refproductionnamecolor
69437noMelanin
69437yessoluble pigmentOchre brown (8001), sand yellow (1002)

multimedia

@refmultimedia contentcaptionintellectual property rights
18195https://www.dsmz.de/microorganisms/photos/DSM_45786.jpgMedium 535 35°C© Leibniz-Institut DSMZ
69437DSM_45786_image3.jpegPlates (65, ISP2, ISP3, ISP4, ISP5, ISP7)Helmholtz-Zentrum für Infektionsforschung GmbH
69437DSM_45786_image4.jpegPlates (65, ISP2, ISP3, ISP4, ISP5, ISP7)Helmholtz-Zentrum für Infektionsforschung GmbH

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
18195GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)yeshttps://mediadive.dsmz.de/medium/65Name: 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
18195BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)yeshttps://mediadive.dsmz.de/medium/514Name: 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
18195TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://mediadive.dsmz.de/medium/535Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
18195positivegrowth35mesophilic
67770positivegrowth35mesophilic

Physiology and metabolism

halophily

  • @ref: 69437
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-10 %

observation

  • @ref: 67770
  • observation: quinones: MK-10(H2), MK-10(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6943722599arabinose+growth
6943762968cellulose-growth
6943728757fructose+growth
6943717234glucose+growth
6943717268inositol+growth
6943737684mannose+/-growth
6943716634raffinose-growth
6943726546rhamnose+growth
6943717992sucrose+growth
6943718222xylose+growth
6837917632nitrate-reduction
683794853esculin-hydrolysis
6837916199urea-hydrolysis
683795291gelatin+hydrolysis
6837917634D-glucose-fermentation
6837916988D-ribose-fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol-fermentation
6837917306maltose-fermentation
6837917716lactose-fermentation
6837917992sucrose-fermentation
6837928087glycogen-fermentation

enzymes

@refvalueactivityec
68379gelatinase+
68379urease-3.5.1.5
68379beta-glucosidase-3.2.1.21
68379N-acetyl-beta-glucosaminidase+3.2.1.52
68379alpha-glucosidase+3.2.1.20
68379beta-galactosidase+3.2.1.23
68379beta-glucuronidase-3.2.1.31
68379alkaline phosphatase+3.1.3.1
68379pyrrolidonyl arylamidase-3.4.19.3
68379pyrazinamidase-3.5.1.B15
68382alkaline phosphatase+3.1.3.1
68382esterase lipase (C 8)+
68382lipase (C 14)+
68382leucine arylamidase+3.4.11.1
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase+3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382beta-glucosidase+3.2.1.21
68382alpha-mannosidase+3.2.1.24
68382alpha-fucosidase-3.2.1.51

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
69437---+-+++--+--------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
69437++/-++++/----++-+-+++/-+-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
18195marine sediment at a deph of 20 cm on the seashore of LianyungangJiangsu Province, LianyungangChinaCHNAsia
67770Marine sediment at a depth of 20 cm on the seashore of LianyungangJiangsu ProvinceChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Environmental#Aquatic#Sediment

taxonmaps

  • @ref: 69479
  • File name: preview.99_1428.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_152;96_659;97_762;98_1128;99_1428&stattab=map
  • Last taxonomy: Nocardiopsis
  • 16S sequence: GU997639
  • Sequence Identity:
  • Total samples: 11
  • soil counts: 1
  • animal counts: 7
  • plant counts: 3

Safety information

risk assessment

  • @ref: 18195
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 18195
  • description: Nocardiopsis flavescens strain SA6 16S ribosomal RNA gene, partial sequence
  • accession: GU997639
  • length: 1401
  • database: ena
  • NCBI tax ID: 758803

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nocardiopsis flavescens strain CGMCC 4.5723758803.3wgspatric758803
66792Nocardiopsis flavescens CGMCC 4.57232675903133draftimg758803
67770Nocardiopsis flavescens CGMCC 4.5723GCA_900141985scaffoldncbi758803

GC content

@refGC-contentmethod
1819568.6thermal denaturation, midpoint method (Tm)
6777074.1genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno91.67no
flagellatedno98.058no
gram-positiveyes92.787no
anaerobicno99.297no
aerobicyes95.06no
halophileyes55.041no
spore-formingyes95.274no
glucose-utilyes89.806yes
thermophileno97.728yes
glucose-fermentno92.093yes

External links

@ref: 18195

culture collection no.: DSM 45786, CGMCC 4.5723, JCM 17424

straininfo link

  • @ref: 80476
  • straininfo: 406053

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny21148675Nocardiopsis flavescens sp. nov., an actinomycete isolated from marine sediment.Fang C, Zhang J, Pang H, Li Y, Xin Y, Zhang YInt J Syst Evol Microbiol10.1099/ijs.0.027987-02010Actinomycetales/*classification/genetics/*isolation & purification/metabolism, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/metabolism, Geologic Sediments/*microbiology, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiologyMetabolism
Metabolism31270649Enhancement of marinacarboline A biosynthesis by optimizing the riboflavin supplement in marine derived Nocardiopsis flavescens CGMCC 4.5723.Chen Q, Wu C, Zhang Y, Liu X, Chen J, Lei L, Xie YBiotechnol Lett10.1007/s10529-019-02698-y2019Actinobacteria/genetics/*metabolism, Aquatic Organisms/genetics/*metabolism, Biological Products/*metabolism, Biosynthetic Pathways/genetics, Metabolic Engineering/*methods, Riboflavin/*biosynthesis, Vitamin B Complex/*biosynthesis

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
18195Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45786)https://www.dsmz.de/collection/catalogue/details/culture/DSM-45786
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
69437Wink, J.https://cdn.dsmz.de/wink/DSM%2045786.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
69479João 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
80476Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID406053.1StrainInfo: A central database for resolving microbial strain identifiers