Strain identifier

BacDive ID: 24643

Type strain: Yes

Species: Marininema mesophilum

Strain history: <- J. Li, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China; SCSIO 10219

NCBI tax ID(s): 1048340 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 21233

BacDive-ID: 24643

DSM-Number: 45610

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

description: Marininema mesophilum DSM 45610 is an aerobe, spore-forming, mesophilic bacterium that was isolated from sediments from South China Sea.

NCBI tax id

  • NCBI tax id: 1048340
  • Matching level: species

strain history

  • @ref: 21233
  • history: <- J. Li, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China; SCSIO 10219

doi: 10.13145/bacdive24643.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Caryophanales
  • family: Thermoactinomycetaceae
  • genus: Marininema
  • species: Marininema mesophilum
  • full scientific name: Marininema mesophilum Li et al. 2012

@ref: 21233

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Thermoactinomycetaceae

genus: Marininema

species: Marininema mesophilum

full scientific name: Marininema mesophilum Li et al. 2012

type strain: yes

Morphology

cell morphology

@refgram stainconfidence
30395positive
69480positive100

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
21233TRYPTICASE 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
21233GYM 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
21233NUTRIENT AGAR (DSMZ Medium 1)yeshttps://mediadive.dsmz.de/medium/1Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
21233positivegrowth28mesophilic
30395positivegrowth25-35mesophilic
30395positiveoptimum30mesophilic

culture pH

@refabilitytypepH
30395positivegrowth05-08
30395positiveoptimum6.5

Physiology and metabolism

oxygen tolerance

  • @ref: 30395
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
30395yes
69481yes100
69480yes99.237

enzymes

  • @ref: 30395
  • value: catalase
  • activity: +
  • ec: 1.11.1.6

Isolation, sampling and environmental information

isolation

  • @ref: 21233
  • sample type: sediments from South China Sea
  • geographic location: South China Sea (113° 3.752' E 18° 1.722' N) at a depth of 2105 m
  • country: China
  • origin.country: CHN
  • continent: Asia
  • latitude: 18.0287
  • longitude: 113.063

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_15074.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_358;96_7734;97_9289;98_11402;99_15074&stattab=map
  • Last taxonomy: Marininema mesophilum
  • 16S sequence: JN006758
  • Sequence Identity:
  • Total samples: 522
  • soil counts: 302
  • aquatic counts: 55
  • animal counts: 133
  • plant counts: 32

Safety information

risk assessment

  • @ref: 21233
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 21233
  • description: Marininema mesophilum strain SCSIO 10219 16S ribosomal RNA gene, partial sequence
  • accession: JN006758
  • length: 1540
  • database: ena
  • NCBI tax ID: 1048340

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Marininema mesophilum DSM 45610GCA_900106775scaffoldncbi1048340
66792Marininema mesophilum strain DSM 456101048340.6wgspatric1048340
66792Marininema mesophilum DSM 456102693429881draftimg1048340

GC content

@refGC-contentmethod
2123346.5high performance liquid chromatography (HPLC)
3039546.5

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileno85.957no
glucose-fermentno93.927no
flagellatedno94.298no
gram-positiveyes91.312no
anaerobicno99.155yes
aerobicyes96.192yes
halophileno71.27no
spore-formingyes93.336yes
thermophileyes78.942no
glucose-utilyes87.022no

External links

@ref: 21233

culture collection no.: DSM 45610, CCTCC AA 2011006, SCSIO 10219

straininfo link

  • @ref: 88484
  • straininfo: 406700

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny21828010Marininema mesophilum gen. nov., sp. nov., a thermoactinomycete isolated from deep sea sediment, and emended description of the family Thermoactinomycetaceae.Li J, Zhang GT, Yang J, Tian XP, Wang FZ, Zhang CS, Zhang S, Li WJInt J Syst Evol Microbiol10.1099/ijs.0.035071-02011Bacillales/*classification/genetics/*isolation & purification, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/metabolism, Geologic Sediments/*microbiology, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiologyGenetics
Phylogeny23907227Marininema halotolerans sp. nov., a novel thermoactinomycete isolated from a sediment sample, and emended description of the genus Marininema Li et al. 2012.Zhang XM, He J, Zhang DF, Chen W, Jiang Z, Sahu MK, Sivakumar K, Li WJInt J Syst Evol Microbiol10.1099/ijs.0.052142-02013Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Gram-Positive Bacteria/*classification/genetics/isolation & purification, India, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryGenetics
Phylogeny25249565Salinithrix halophila gen. nov., sp. nov., a halophilic bacterium in the family Thermoactinomycetaceae.Zarparvar P, Amoozegar MA, Nikou MM, Schumann P, Ventosa AInt J Syst Evol Microbiol10.1099/ijs.0.064766-02014Bacillales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Iran, Molecular Sequence Data, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistry, WetlandsGenetics

Reference

@idauthorstitledoi/urlcatalogueID_cross_referencepubmedjournal
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
21233Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-45610Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45610)
30395Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172673228776041
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa102533211880Nucleic Acids Res. 49: D498-D508 2020
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
88484Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID406700.1