Strain identifier

BacDive ID: 13267

Type strain: Yes

Species: Amycolatopsis marina

Strain Designation: Ms392A

Strain history: CGMCC 4.3568 <-- J. Bian et al. Ms392A.

NCBI tax ID(s): 490629 (species)

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General

@ref: 17661

BacDive-ID: 13267

DSM-Number: 45569

keywords: genome sequence, 16S sequence, Bacteria, aerobe, spore-forming, mesophilic, Gram-positive

description: Amycolatopsis marina Ms392A is an aerobe, spore-forming, mesophilic bacterium that was isolated from ocean-sediment.

NCBI tax id

  • NCBI tax id: 490629
  • Matching level: species

strain history

@refhistory
17661<- NBRC <- CGMCC <- J. Bian, Chinese Acad. Sci.; Ms392A
67770CGMCC 4.3568 <-- J. Bian et al. Ms392A.

doi: 10.13145/bacdive13267.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Pseudonocardiales
  • family: Pseudonocardiaceae
  • genus: Amycolatopsis
  • species: Amycolatopsis marina
  • full scientific name: Amycolatopsis marina Bian et al. 2009

@ref: 17661

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Pseudonocardiaceae

genus: Amycolatopsis

species: Amycolatopsis marina

full scientific name: Amycolatopsis marina Bian et al. 2009 emend. Nouioui et al. 2018

strain designation: Ms392A

type strain: yes

Morphology

cell morphology

@refgram stainmotilityconfidence
28874positiveno
69480no93.221
69480positive100

pigmentation

  • @ref: 28874
  • production: no

Culture and growth conditions

culture medium

  • @ref: 17661
  • name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/65
  • composition: 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

culture temp

@refgrowthtypetemperaturerange
17661positivegrowth28mesophilic
28874positivegrowth10-55
28874positiveoptimum28mesophilic
67770positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
28874positivegrowth6.0-9.0alkaliphile
28874positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

  • @ref: 28874
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481yes99
69480yes99.998

halophily

@refsaltgrowthtested relationconcentration
28874NaClpositivegrowth0.5-12 %
28874NaClpositiveoptimum5 %

observation

  • @ref: 67770
  • observation: quinones: MK-8(H4), MK-9(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2887417057cellobiose+carbon source
2887428757fructose+carbon source
2887428260galactose+carbon source
288745291gelatin+carbon source
2887417306maltose+carbon source
2887429864mannitol+carbon source
2887426546rhamnose+carbon source
2887427082trehalose+carbon source

enzymes

  • @ref: 28874
  • value: catalase
  • activity: +
  • ec: 1.11.1.6

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
17661ocean-sedimentSouth China SeaChinaCHNAsia
67770Deep-ocean sedimentSouth China Sea

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_69285.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_29751;97_37567;98_48712;99_69285&stattab=map
  • Last taxonomy: Amycolatopsis marina
  • 16S sequence: EU329845
  • Sequence Identity:
  • Total samples: 458
  • soil counts: 157
  • aquatic counts: 28
  • animal counts: 183
  • plant counts: 90

Safety information

risk assessment

  • @ref: 17661
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 17661
  • description: Amycolatopsis marina strain MS392A 16S ribosomal RNA gene, partial sequence
  • accession: EU329845
  • length: 1485
  • database: ena
  • NCBI tax ID: 490629

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Amycolatopsis marina strain CGMCC 4.3568490629.6wgspatric490629
66792Amycolatopsis marina CGMCC 4.35682667527405draftimg490629
67770Amycolatopsis marina CGMCC 4.3568GCA_900111885scaffoldncbi490629

GC content

@refGC-contentmethod
1766170.1
6777068.2genome sequence analysis
6777070.1high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes99no
gram-positiveyes86.143yes
anaerobicno99.122yes
halophileno50no
spore-formingyes71.592no
glucose-utilyes88.09no
aerobicyes93.409yes
thermophileno94.986yes
motileno92.936yes
flagellatedno97.069no
glucose-fermentno93.865no

External links

@ref: 17661

culture collection no.: DSM 45569, CGMCC 4.3568, NBRC 104263, JCM 16121

straininfo link

  • @ref: 82471
  • straininfo: 404573

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19244425Amycolatopsis marina sp. nov., an actinomycete isolated from an ocean sediment.Bian J, Li Y, Wang J, Song FH, Liu M, Dai HQ, Ren B, Gao H, Hu X, Liu ZH, Li WJ, Zhang LXInt J Syst Evol Microbiol10.1099/ijs.0.000026-02009Actinomycetales/chemistry/*classification/genetics/isolation & purification, China, DNA, Bacterial/analysis, DNA, Ribosomal Spacer/analysis, Genes, rRNA, Geologic Sediments/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, RNA, Ribosomal, 23S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Species SpecificityGenetics
Phylogeny19666809Amycolatopsis halophila sp. nov., a halophilic actinomycete isolated from a salt lake.Tang SK, Wang Y, Guan TW, Lee JC, Kim CJ, Li WJInt J Syst Evol Microbiol10.1099/ijs.0.012427-02009Actinomycetales/*classification/genetics/*isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Fresh Water/chemistry/*microbiology, Genes, rRNA, Genotype, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Sodium Chloride, Species SpecificityGenetics
Phylogeny26233655Amycolatopsis flava sp. nov., a halophilic actinomycete isolated from Dead Sea.Wei X, Jiang Y, Chen X, Jiang Y, Lai HAntonie Van Leeuwenhoek10.1007/s10482-015-0542-z2015Actinobacteria/*classification/*isolation & purification, Bacterial Typing Techniques, Base Composition, Carbohydrates/analysis, Cell Wall/chemistry, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Geologic Sediments/*microbiology, Hydrogen-Ion Concentration, Israel, Microscopy, Electron, Scanning, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride/metabolism, Temperature, Vitamin K 2/analysisGenetics
Genetics31164159Integrating vectors for genetic studies in the rare Actinomycete Amycolatopsis marina.Gao H, Murugesan B, Hossbach J, Evans SK, Stark WM, Smith MCMBMC Biotechnol10.1186/s12896-019-0521-y2019Actinobacteria/*genetics/virology, Amycolatopsis, Attachment Sites, Microbiological/genetics, Base Sequence, Genetic Vectors/*genetics, Genome, Bacterial/*genetics, Integrases/genetics/metabolism, *Recombination, Genetic, Sequence Homology, Nucleic Acid, Viral Proteins/genetics/metabolismMetabolism

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
17661Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45569)https://www.dsmz.de/collection/catalogue/details/culture/DSM-45569
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
28874Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2531428776041
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 updates33211880Nucleic Acids Res. 49: D498-D508 2020
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
82471Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID404573.1StrainInfo: A central database for resolving microbial strain identifiers