Strain identifier

BacDive ID: 3783

Type strain: Yes

Species: Emticicia oligotrophica

Strain Designation: GPTSA100-15

Strain history: <- MTCC <- P. Saha and T. Chakrabarti; GPTSA100-15

NCBI tax ID(s): 929562 (strain), 312279 (species)

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General

@ref: 6989

BacDive-ID: 3783

DSM-Number: 17448

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, rod-shaped

description: Emticicia oligotrophica GPTSA100-15 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from warm spring water.

NCBI tax id

NCBI tax idMatching level
312279species
929562strain

strain history

  • @ref: 6989
  • history: <- MTCC <- P. Saha and T. Chakrabarti; GPTSA100-15

doi: 10.13145/bacdive3783.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Cytophagia
  • order: Cytophagales
  • family: Spirosomataceae
  • genus: Emticicia
  • species: Emticicia oligotrophica
  • full scientific name: Emticicia oligotrophica Saha and Chakrabarti 2006

@ref: 6989

domain: Bacteria

phylum: Bacteroidetes

class: Cytophagia

order: Cytophagales

family: Spirosomaceae

genus: Emticicia

species: Emticicia oligotrophica

full scientific name: Emticicia oligotrophica Saha and Chakrabarti 2006 emend. Hahnke et al. 2016

strain designation: GPTSA100-15

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31704negative02-05 µm0.3-0.4 µmrod-shapedno
69480no95.187
69480negative99.993

pigmentation

  • @ref: 31704
  • production: yes

multimedia

  • @ref: 66793
  • multimedia content: EM_DSM_17448_1.jpg
  • caption: electron microscopic image
  • intellectual property rights: © HZI/Manfred Rohde

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6989R2A MEDIUM (DSMZ Medium 830)yeshttps://mediadive.dsmz.de/medium/830Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
6989DILUTED TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545a)yeshttps://mediadive.dsmz.de/medium/545aName: DILUTED TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545a) Composition: Casein peptone 0.17 g/l NaCl 0.05 g/l Soy peptone 0.03 g/l K2HPO4 0.025 g/l D(+)-Glucose 0.025 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
6989positivegrowth28mesophilic
31704positivegrowth15-42
31704positiveoptimum37mesophilic

culture pH

@refabilitytypepHPH range
31704positivegrowth05-11alkaliphile
31704positiveoptimum08-11

Physiology and metabolism

oxygen tolerance

  • @ref: 31704
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
31704no
69481no100
69480no99.99

observation

  • @ref: 31704
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3170422599arabinose+carbon source
3170417057cellobiose+carbon source
3170428757fructose+carbon source
3170428260galactose+carbon source
3170417234glucose+carbon source
3170417754glycerol+carbon source
3170417716lactose+carbon source
3170428053melibiose+carbon source
3170416634raffinose+carbon source
3170417992sucrose+carbon source
3170417632nitrate+reduction

enzymes

@refvalueactivityec
31704catalase+1.11.1.6
31704gelatinase+
31704cytochrome oxidase+1.9.3.1
31704urease+3.5.1.5

Isolation, sampling and environmental information

isolation

  • @ref: 6989
  • sample type: warm spring water
  • geographic location: Assam, Jorhat
  • country: India
  • origin.country: IND
  • continent: Asia

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic
  • Cat3: #Thermal spring

taxonmaps

  • @ref: 69479
  • File name: preview.99_5782.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_535;96_2772;97_3409;98_4304;99_5782&stattab=map
  • Last taxonomy: Emticicia oligotrophica subclade
  • 16S sequence: AY904352
  • Sequence Identity:
  • Total samples: 1499
  • soil counts: 68
  • aquatic counts: 1267
  • animal counts: 102
  • plant counts: 62

Safety information

risk assessment

  • @ref: 6989
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 6989
  • description: Emticicia oligotrophica strain GPTSA100-15 16S ribosomal RNA gene, partial sequence
  • accession: AY904352
  • length: 1385
  • database: ena
  • NCBI tax ID: 929562

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Emticicia oligotrophica DSM 17448GCA_000263195completencbi929562
66792Emticicia oligotrophica DSM 17448929562.9plasmidpatric929562
66792Emticicia oligotrophica DSM 17448929562.8plasmidpatric929562
66792Emticicia oligotrophica DSM 17448929562.7plasmidpatric929562
66792Emticicia oligotrophica DSM 17448929562.6plasmidpatric929562
66792Emticicia oligotrophica DSM 17448929562.10plasmidpatric929562
66792Emticicia oligotrophica DSM 17448929562.3completepatric929562
66792Emticicia oligotrophica GPTSA100-15, DSM 174482506485001completeimg929562

GC content

@refGC-contentmethod
698936.9
698935.6sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno94.608yes
flagellatedno97.126yes
gram-positiveno97.686yes
anaerobicno99.03yes
aerobicyes85.535yes
halophileno96.382no
spore-formingno94.822yes
glucose-utilyes85.745yes
thermophileno96.228no
glucose-fermentno90.234no

External links

@ref: 6989

culture collection no.: DSM 17448, CIP 109782, MTCC 6937

straininfo link

  • @ref: 73295
  • straininfo: 396940

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16627643Emticicia oligotrophica gen. nov., sp. nov., a new member of the family 'Flexibacteraceae', phylum Bacteroidetes.Saha P, Chakrabarti TInt J Syst Evol Microbiol10.1099/ijs.0.64086-02006Bacterial Typing Techniques, Base Composition, Culture Media/chemistry, Cytophagaceae/chemistry/*classification/isolation & purification/physiology, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis/isolation & purification, Genes, rRNA/genetics, Molecular Sequence Data, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Water MicrobiologyEnzymology
Phylogeny18450696Emticicia ginsengisoli sp. nov., a species of the family 'Flexibacteraceae' isolated from soil of a ginseng field.Liu QM, Ten LN, Yu HS, Jin FX, Im WT, Lee STInt J Syst Evol Microbiol10.1099/ijs.0.65386-02008Bacterial Typing Techniques, Base Composition, Cytophagaceae/chemistry/*classification/genetics/isolation & purification, DNA, Bacterial/analysis/isolation & purification, Fatty Acids/analysis, Genes, rRNA, Genotype, Korea, Molecular Sequence Data, *Panax, Phenotype, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Species SpecificityGenetics
Phylogeny24994775Lacihabitans soyangensis gen. nov., sp. nov., a new member of the family Cytophagaceae, isolated from a freshwater reservoir.Joung Y, Kim H, Kang H, Lee BI, Ahn TS, Joh KInt J Syst Evol Microbiol10.1099/ijs.0.058511-02014Bacterial Typing Techniques, Base Composition, Cytophagaceae/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Fresh Water/*microbiology, Molecular Sequence Data, Phosphatidylethanolamines/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryGenetics
Phylogeny25933620Emticicia sediminis sp. nov. isolated from sediment of a shallow stream.Park SE, Lee S, Kim H, Ahn TYInt J Syst Evol Microbiol10.1099/ijs.0.0002922015Bacterial Typing Techniques, Base Composition, Cytophagaceae/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Rivers/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryGenetics
Phylogeny26341781Taeseokella kangwonensis gen. nov., sp. nov., isolated from a freshwater reservoir.Joung Y, Hong S, Kim H, Kang H, Farrance CE, Joh KInt J Syst Evol Microbiol10.1099/ijsem.0.0005822015Bacterial Typing Techniques, Base Composition, Cytophagaceae/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Fresh Water/*microbiology, Molecular Sequence Data, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryGenetics
Phylogeny26346054Emticicia aquatica sp. nov., a species of the family Cytophagaceae isolated from fresh water.Joung Y, Seo MA, Kang H, Kim H, Ahn TS, Cho JC, Joh KInt J Syst Evol Microbiol10.1099/ijsem.0.0005772015Bacterial Typing Techniques, Base Composition, Cytophagaceae/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Fresh Water/*microbiology, Molecular Sequence Data, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNAGenetics
Phylogeny27264529Emticicia paludis sp. nov., isolated from wetland freshwater.Kang H, Kim H, Joung Y, Joh KInt J Syst Evol Microbiol10.1099/ijsem.0.0012052016Bacterial Typing Techniques, Base Composition, Cytophagaceae/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Fresh Water/*microbiology, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry, *WetlandsTranscriptome
Phylogeny27613103Emticiciafontis sp. nov., isolated from a freshwater pond.Nam GG, Joung Y, Song J, Lim Y, Cho JCInt J Syst Evol Microbiol10.1099/ijsem.0.0014902016Bacterial Typing Techniques, Base Composition, Cytophagaceae/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Ponds/*microbiology, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny28150574Emticicia aquatilis sp. nov., isolated from a freshwater sample.Ngo HTT, Trinh H, Yang JE, Won KH, Chu DH, Kook M, Yi THInt J Syst Evol Microbiol10.1099/ijsem.0.0018402017Bacterial Typing Techniques, Base Composition, Cytophagaceae/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Fresh Water/*microbiology, Glycolipids/chemistry, Nucleic Acid Hybridization, Phosphatidylethanolamines/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
6989Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17448)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17448
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
31704Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2798128776041
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)
66793Mukherjee et al.10.1038/nbt.3886GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life28604660 35: 676-683 2017
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
73295Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID396940.1StrainInfo: A central database for resolving microbial strain identifiers