Strain identifier

BacDive ID: 8013

Type strain: Yes

Species: Micromonospora pattaloongensis

Strain Designation: TJ2-2

Strain history: C. Thawai TJ2-2.

NCBI tax ID(s): 405436 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 15929

BacDive-ID: 8013

DSM-Number: 45245

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

description: Micromonospora pattaloongensis TJ2-2 is a spore-forming, mesophilic, Gram-positive bacterium that was isolated from Thai mangrove forest.

NCBI tax id

  • NCBI tax id: 405436
  • Matching level: species

strain history

@refhistory
15929<- JCM/RIKEN; JCM 12833 <- C. Thawai; TJ2-2
67770C. Thawai TJ2-2.

doi: 10.13145/bacdive8013.20230509.8.1

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 pattaloongensis
  • full scientific name: Micromonospora pattaloongensis Thawai et al. 2008

@ref: 15929

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Micromonosporaceae

genus: Micromonospora

species: Micromonospora pattaloongensis

full scientific name: Micromonospora pattaloongensis Thawai et al. 2008

strain designation: TJ2-2

type strain: yes

Morphology

cell morphology

@refgram stainmotilityconfidence
32385positiveno
69480positive100

pigmentation

  • @ref: 32385
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
15929TRYPTICASE 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
15929GYM 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
15929NUTRIENT AGAR (DSMZ Medium 1)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium1.pdf

culture temp

@refgrowthtypetemperaturerange
15929positivegrowth28mesophilic
32385positivegrowth25-40
32385positiveoptimum27.5mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
32385yes
69481yes100
69480yes99.447

halophily

  • @ref: 32385
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: <3 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3238522599arabinose+carbon source
3238517057cellobiose+carbon source
3238528757fructose+carbon source
3238528260galactose+carbon source
3238517234glucose+carbon source
3238517716lactose+carbon source
3238533942ribose+carbon source
3238517814salicin+carbon source
3238518222xylose+carbon source
3238517632nitrate+reduction

enzymes

  • @ref: 32385
  • value: gelatinase
  • activity: +

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
15929Thai mangrove forestPattaloong ProvinceThailandTHAAsia
67770Soil from mangrove forestPattaloong ProvinceThailandTHAAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Mangrove
#Environmental#Terrestrial#Forest

Safety information

risk assessment

  • @ref: 15929
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 15929
  • description: Micromonospora pattaloongensis gene for 16S ribosomal RNA, partial sequence
  • accession: AB275607
  • length: 1511
  • database: ena
  • NCBI tax ID: 405436

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Micromonospora pattaloongensis strain DSM 45245405436.4wgspatric405436
66792Micromonospora pattaloongensis DSM 452452693429860draftimg405436
67770Micromonospora pattaloongensis DSM 45245GCA_900107255contigncbi405436

GC content

@refGC-contentmethod
1592971.5
6777071.5high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
gram-positiveyes88.216yes
anaerobicno98.622no
halophileno92.803no
spore-formingyes91.125yes
glucose-utilyes90.255yes
aerobicyes94.375no
flagellatedno91.856yes
motileyes58.076no
thermophileno91.764yes
glucose-fermentno92.058no

External links

@ref: 15929

culture collection no.: DSM 45245, JCM 12833, TISTR 1559, NRRL B-24764

straininfo link

  • @ref: 77443
  • straininfo: 396994

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny18599686Micromonospora pattaloongensis sp. nov., isolated from a Thai mangrove forest.Thawai C, Tanasupawat S, Kudo TInt J Syst Evol Microbiol10.1099/ijs.0.65410-02008Fatty Acids/metabolism, Micromonospora/chemistry/*classification/genetics/ultrastructure, Microscopy, Electron, Scanning, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Soil Microbiology, Species Specificity, Thailand, Trees/*microbiology, VerbenaceaeGenetics
Phylogeny19651739Micromonospora pisi sp. nov., isolated from root nodules of Pisum sativum.C Garcia L, Martinez-Molina E, Trujillo MEInt J Syst Evol Microbiol10.1099/ijs.0.012708-02009Bacterial Proteins/genetics, Base Sequence, DNA Gyrase/genetics, Micromonospora/*classification/genetics/physiology, Molecular Sequence Data, Peas/*microbiology, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Root Nodules, Plant/*microbiology, Sequence Analysis, RNA, SpainGenetics
Phylogeny20305066Micromonospora rhizosphaerae sp. nov., isolated from mangrove rhizosphere soil.Wang C, Xu XX, Qu Z, Wang HL, Lin HP, Xie QY, Ruan JS, Hong KInt J Syst Evol Microbiol10.1099/ijs.0.020461-02010Bacterial Typing Techniques, Base Composition, Carbohydrates/analysis, China, DNA, Bacterial/genetics, Euphorbiaceae/*microbiology, Fatty Acids/analysis, Micromonospora/*classification/genetics/isolation & purification, Molecular Sequence Data, Phospholipids/analysis, Phylogeny, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analysisGenetics
Phylogeny23178729Micromonospora sonneratiae sp. nov., isolated from a root of Sonneratia apetala.Li L, Tang YL, Wei B, Xie QY, Deng Z, Hong KInt J Syst Evol Microbiol10.1099/ijs.0.043570-02012Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Endophytes/classification/genetics/isolation & purification, Fatty Acids/analysis, Genes, Bacterial, Lythraceae/*microbiology, Micromonospora/*classification/genetics/isolation & purification, Molecular Sequence Data, *Phylogeny, Plant Roots/microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil Microbiology, Vitamin K 2/analysisEnzymology
Phylogeny24108323Micromonospora polyrhachis sp. nov., an actinomycete isolated from edible Chinese black ant (Polyrhachis vicina Roger).Xiang W, Yu C, Liu C, Zhao J, Yang L, Xie B, Li L, Hong K, Wang XInt J Syst Evol Microbiol10.1099/ijs.0.055863-02013Animals, Ants/*microbiology, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genes, Bacterial, Micromonospora/*classification/genetics/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/chemistryGenetics
Phylogeny26446196Micromonospora zhanjiangensis sp. nov., isolated from mangrove forest soil.Zhang L, Li L, Deng Z, Hong KInt J Syst Evol Microbiol10.1099/ijsem.0.0006672015Avicennia, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Micromonospora/*classification/genetics/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/chemistry, *WetlandsGenetics
Phylogeny26620702Micromonospora ovatispora sp. nov. isolated from mangrove soil.Li L, Hong KInt J Syst Evol Microbiol10.1099/ijsem.0.0008082015

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
15929Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45245)https://www.dsmz.de/collection/catalogue/details/culture/DSM-45245
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
32385Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2861028776041
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/
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
77443Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID396994.1StrainInfo: A central database for resolving microbial strain identifiers