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, spore-forming, Gram-positive

description: Nocardiopsis flavescens SA6 is a spore-forming, Gram-positive 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/bacdive11241.20240916.9.1

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

cell morphology

@refmotilityconfidencegram stain
69480no93.1
6948092.23positive

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

@refgrowthtypetemperature
18195positivegrowth35
67770positivegrowth35

Physiology and metabolism

oxygen tolerance

  • @ref: 69480
  • oxygen tolerance: aerobe
  • confidence: 92.16

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: nuccore
  • 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

@reftraitmodeldescriptionpredictionconfidencetraining_data
69480gram-positivegram-positivePositive reaction to Gram-stainingyes92.23no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no97.653no
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes92.16no
69480spore-formingspore-formingAbility to form endo- or exosporesyes87.801no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno92.614no
69480flagellatedmotile2+Ability to perform flagellated movementno93.1no

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
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
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