Strain identifier

BacDive ID: 24460

Type strain: Yes

Species: Longimycelium tulufanense

Strain history: <- J. Nakagawa; NBRC 107726 <- ; CGMCC 4.5737 <- Y. Huang, Chinese Acad. Sci.; TRM 46004

NCBI tax ID(s): 907463 (species)

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General

@ref: 21269

BacDive-ID: 24460

DSM-Number: 46696

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

description: Longimycelium tulufanense DSM 46696 is an aerobe, spore-forming, mesophilic bacterium that was isolated from sediment.

NCBI tax id

  • NCBI tax id: 907463
  • Matching level: species

strain history

  • @ref: 21269
  • history: <- J. Nakagawa; NBRC 107726 <- ; CGMCC 4.5737 <- Y. Huang, Chinese Acad. Sci.; TRM 46004

doi: 10.13145/bacdive24460.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Pseudonocardiales
  • family: Pseudonocardiaceae
  • genus: Longimycelium
  • species: Longimycelium tulufanense
  • full scientific name: Longimycelium tulufanense Xia et al. 2013

@ref: 21269

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Pseudonocardiaceae

genus: Longimycelium

species: Longimycelium tulufanense

full scientific name: Longimycelium tulufanense Xia et al. 2013

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
30780positivecoccus-shaped
69480no94.309
69480positive100

pigmentation

  • @ref: 30780
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 21269
  • 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
21269positivegrowth37mesophilic
30780positivegrowth20-45
30780positiveoptimum37mesophilic

culture pH

@refabilitytypepHPH range
30780positivegrowth05-09alkaliphile
30780positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 30780
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
30780yes
69481yes100
69480yes100

halophily

@refsaltgrowthtested relationconcentration
30780NaClpositivegrowth01-08 %
30780NaClpositiveoptimum2 %

observation

  • @ref: 30780
  • observation: aggregates in clumps

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3078033984fucose+carbon source
3078028260galactose+carbon source
3078017234glucose+carbon source
3078026546rhamnose+carbon source
3078033942ribose+carbon source
3078030911sorbitol+carbon source
3078017992sucrose+carbon source
3078018222xylose+carbon source
3078017632nitrate+reduction
6836927689decanoate-assimilation
6836916024D-mannose-assimilation
6836917634D-glucose+assimilation
683695291gelatin+hydrolysis
6836916199urea+hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate-reduction

metabolite production

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
30780catalase+1.11.1.6
68369gelatinase+
68369urease+3.5.1.5
68369arginine dihydrolase-3.5.3.6
68382alkaline phosphatase+3.1.3.1
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
68382alpha-chymotrypsin+3.4.21.1
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
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382alpha-mannosidase+3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
21269-++/-+/-+/-+++/-+/-++/-+/----+-++-

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPAC
21269----++/-++/-++/--+/-+/-+/-+/--+/-+/-+/--

Isolation, sampling and environmental information

isolation

  • @ref: 21269
  • sample type: sediment
  • geographic location: Tulufan Basin, Aiding Lake
  • country: China
  • origin.country: CHN
  • continent: Asia

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Sediment
#Environmental#Terrestrial#Sediment

taxonmaps

  • @ref: 69479
  • File name: preview.99_174526.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_14904;96_64942;97_84260;98_114253;99_174526&stattab=map
  • Last taxonomy: Longimycelium tulufanense subclade
  • 16S sequence: HQ229000
  • Sequence Identity:
  • Total samples: 914
  • soil counts: 559
  • aquatic counts: 87
  • animal counts: 230
  • plant counts: 38

Safety information

risk assessment

  • @ref: 21269
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 21269
  • description: Longimycelium tulufanense strain TRM 46004 16S ribosomal RNA gene, partial sequence
  • accession: HQ229000
  • length: 1454
  • database: ena
  • NCBI tax ID: 907463

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Longimycelium tulufanense CGMCC 4.5737GCA_014645795scaffoldncbi907463
66792Longimycelium tulufanense strain CGMCC 4.5737907463.3wgspatric907463

GC content

  • @ref: 21269
  • GC-content: 65.2

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
flagellatedno97.725no
gram-positiveyes91.424yes
anaerobicno98.831yes
aerobicyes90.941no
halophileno82.931no
spore-formingyes88.848no
glucose-utilyes86.831yes
thermophileno93.562yes
motileno92.844no
glucose-fermentno91.436no

External links

@ref: 21269

culture collection no.: DSM 46696, CGMCC 4.5737, NBRC 107726, TRM 46004

straininfo link

  • @ref: 88335
  • straininfo: 400681

literature

  • topic: Phylogeny
  • Pubmed-ID: 23315412
  • title: Longimycelium tulufanense gen. nov., sp. nov., a filamentous actinomycete of the family Pseudonocardiaceae.
  • authors: Xia ZF, Guan TW, Ruan JS, Huang Y, Zhang LL
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.044222-0
  • year: 2013
  • mesh: Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/analysis, Geologic Sediments/*microbiology, Lakes/microbiology, Molecular Sequence Data, Phospholipids/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/analysis
  • topic2: Genetics

Reference

@idauthorstitledoi/urlcatalogueID_cross_referencepubmed
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
21269Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-46696Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 46696)
30780Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172711128776041
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
68369Automatically annotated from API 20NE
68382Automatically annotated from API zym
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
88335Reimer, 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-ID400681.1