Strain identifier

BacDive ID: 8016

Type strain: Yes

Species: Micromonospora marina

Strain Designation: JSM1-1

Strain history: S. Tanasupawat; Chulalongkorn Univ., Thailand; JSM1-1.

NCBI tax ID(s): 307120 (species)

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General

@ref: 17434

BacDive-ID: 8016

DSM-Number: 45555

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

description: Micromonospora marina JSM1-1 is an aerobe, spore-forming, mesophilic bacterium that was isolated from sand collected along the sea shore.

NCBI tax id

  • NCBI tax id: 307120
  • Matching level: species

strain history

@refhistory
17434<- JCM <- S. Tanasupawat; JSM1-1
67770S. Tanasupawat; Chulalongkorn Univ., Thailand; JSM1-1.

doi: 10.13145/bacdive8016.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micromonosporales
  • family: Micromonosporaceae
  • genus: Micromonospora
  • species: Micromonospora marina
  • full scientific name: Micromonospora marina Tanasupawat et al. 2010

@ref: 17434

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Micromonosporaceae

genus: Micromonospora

species: Micromonospora marina

full scientific name: Micromonospora marina Tanasupawat et al. 2010

strain designation: JSM1-1

type strain: yes

Morphology

cell morphology

@refgram stainmotilityconfidence
29486positive
125438no91
125438positive90.304
125439positive99.8

pigmentation

  • @ref: 29486
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
17434N-Z-AMINE-MEDIUM (DSMZ Medium 554)yeshttps://mediadive.dsmz.de/medium/554Name: N-Z-AMINE-MEDIUM (DSMZ Medium 554) Composition: Starch 20.0 g/l Agar 20.0 g/l Glucose 10.0 g/l N-Z amine 5.0 g/l Yeast extract 5.0 g/l CaCO3 1.0 g/l Distilled water
17434GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium65.pdf
17434TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium535.pdf

culture temp

@refgrowthtypetemperature
17434positivegrowth28
29486positivegrowth15-45
29486positiveoptimum27.5
67770positivegrowth28

culture pH

  • @ref: 29486
  • ability: positive
  • type: growth
  • pH: 05-09
  • PH range: alkaliphile

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
29486aerobe
125438aerobe90.084
125439obligate aerobe99.7

spore formation

@refspore formationconfidence
29486yes
125438yes92.745
125439yes92.4

halophily

  • @ref: 29486
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 7 %

observation

  • @ref: 67770
  • observation: quinones: MK-10(H4), MK-10(H6), MK-10(H8)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2948622599arabinose+carbon source
2948628757fructose+carbon source
2948628260galactose+carbon source
2948617234glucose+carbon source
2948617754glycerol+carbon source
2948629864mannitol+carbon source
2948628053melibiose+carbon source
2948616634raffinose+carbon source
2948626546rhamnose+carbon source
2948618222xylose+carbon source

enzymes

  • @ref: 29486
  • value: gelatinase
  • activity: +

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
17434sand collected along the sea shorePrajuabkirikhun Province, Hua-HinThailandTHAAsia
67770Sand along the sea shore in Hua-HinPrajuabkirikhun ProvinceThailandTHAAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Coast
#Environmental#Terrestrial#Sandy

taxonmaps

  • @ref: 69479
  • File name: preview.99_1923.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_94;96_404;97_1111;98_1509;99_1923&stattab=map
  • Last taxonomy: Micromonospora
  • 16S sequence: AB196712
  • Sequence Identity:
  • Total samples: 804
  • soil counts: 470
  • aquatic counts: 188
  • animal counts: 133
  • plant counts: 13

Safety information

risk assessment

  • @ref: 17434
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 17434
  • description: Micromonospora marina gene for 16S rRNA, partial sequence, strain: JSM1-1
  • accession: AB196712
  • length: 1437
  • database: nuccore
  • NCBI tax ID: 307120

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Micromonospora marina strain DSM 45555307120.5wgspatric307120
66792Micromonospora marina DSM 455552622736534draftimg307120
67770Micromonospora marina DSM 45555GCA_900091565scaffoldncbi307120

GC content

@refGC-contentmethod
1743472high performance liquid chromatography (HPLC)
2948672
6777072.83genome sequence analysis

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingyes90.304yes
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no97.355yes
125438spore-formingspore-formingAbility to form endo- or exosporesyes92.745no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes90.084yes
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno95yes
125438motile2+flagellatedAbility to perform flagellated movementno91no
125439BacteriaNetspore_formationAbility to form endo- or exosporesyes92.4
125439BacteriaNetmotilityAbility to perform movementno89.7
125439BacteriaNetgram_stainReaction to gram-stainingpositive99.8
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe99.7

External links

@ref: 17434

culture collection no.: DSM 45555, JCM 12870, PCU 269, TISTR 1566

straininfo link

  • @ref: 77446
  • straininfo: 403844

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19656925Micromonospora marina sp. nov., isolated from sea sand.Tanasupawat S, Jongrungruangchok S, Kudo TInt J Syst Evol Microbiol10.1099/ijs.0.014068-02009DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/chemistry/metabolism, Geologic Sediments/*microbiology, Micromonospora/*classification/genetics/*isolation & purification/metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, ThailandMetabolism
Phylogeny20562246Micromonospora humi sp. nov., isolated from peat swamp forest soil.Songsumanus A, Tanasupawat S, Thawai C, Suwanborirux K, Kudo TInt J Syst Evol Microbiol10.1099/ijs.0.024281-02010DNA, Bacterial/genetics, Micromonospora/*classification/genetics/*isolation & purification, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil Microbiology, Thailand, Trees/microbiologyGenetics
Phylogeny22523170Micromonospora sediminicola sp. nov., isolated from marine sediment.Supong K, Suriyachadkun C, Tanasupawat S, Suwanborirux K, Pittayakhajonwut P, Kudo T, Thawai CInt J Syst Evol Microbiol10.1099/ijs.0.041103-02012Bacterial Typing Techniques, Base Composition, Carbohydrates/analysis, DNA, Bacterial/genetics, Fatty Acids/analysis, Geologic Sediments/*microbiology, Micromonospora/*classification/genetics/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, ThailandGenetics
Phylogeny22523171Micromonospora maritima sp. nov., isolated from mangrove soil.Songsumanus A, Tanasupawat S, Igarashi Y, Kudo TInt J Syst Evol Microbiol10.1099/ijs.0.039180-02012Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/analysis, Micromonospora/*classification/genetics/metabolism, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Thailand, Vitamin K 2/analysisGenetics
Phylogeny23667141Micromonospora schwarzwaldensis sp. nov., a producer of telomycin, isolated from soil.Gurovic MSV, Muller S, Domin N, Seccareccia I, Nietzsche S, Martin K, Nett MInt J Syst Evol Microbiol10.1099/ijs.0.051623-02013DNA, Bacterial/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Germany, Micromonospora/*classification/genetics/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, Peptides/*metabolism, Peptidoglycan/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analysisGenetics
Phylogeny33174828Micromonospora fluminis sp. nov., isolated from mountain river sediment.Camacho Pozo MI, Wieme AD, Rodriguez Perez S, Llaurado Maury G, Peeters C, Snauwaert C, Lescaylle Veranes Y, Pena Zamora L, Schumann P, Vandamme PAInt J Syst Evol Microbiol10.1099/ijsem.0.0045542020Bacterial Typing Techniques, Base Composition, Cuba, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Micromonospora/*classification/isolation & purification, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rivers/*microbiology, Sequence Analysis, DNA, Vitamin K 2/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
17434Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45555)https://www.dsmz.de/collection/catalogue/details/culture/DSM-45555
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
29486Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2588628776041
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)
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
77446Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID403844.1StrainInfo: A central database for resolving microbial strain identifiers
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1