Strain identifier

BacDive ID: 133508

Type strain: Yes

Species: Marinifilum fragile

Strain Designation: JC2469

Strain history: J. Chun JC2469.

NCBI tax ID(s): 1236979 (strain), 570161 (species)

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General

@ref: 29231

BacDive-ID: 133508

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, Gram-negative, rod-shaped

description: Marinifilum fragile JC2469 is a facultative anaerobe, Gram-negative, rod-shaped bacterium that was isolated from marine sediment.

NCBI tax id

NCBI tax idMatching level
570161species
1236979strain

strain history

  • @ref: 67770
  • history: J. Chun JC2469.

doi: 10.13145/bacdive133508.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Bacteroidia
  • order: Bacteroidales
  • family: Marinifilaceae
  • genus: Marinifilum
  • species: Marinifilum fragile
  • full scientific name: Marinifilum fragile Na et al. 2009

@ref: 29231

domain: Bacteria

phylum: Bacteroidetes

class: Bacteroidia

order: Bacteroidales

family: Marinifilaceae

genus: Marinifilum

species: Marinifilum fragile

strain designation: JC2469

type strain: yes

Morphology

cell morphology

@refgram staincell widthcell shapemotilityconfidence
29231negative0.5 µmrod-shapedno
69480negative99.999

Culture and growth conditions

culture temp

@refgrowthtypetemperaturerange
29231positivegrowth20-37.4
29231positiveoptimum33.8mesophilic
67770positivegrowth30mesophilic

culture pH

@refabilitytypepH
29231positivegrowth06-08
29231positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 29231
  • oxygen tolerance: facultative anaerobe

spore formation

@refspore formationconfidence
29231no
69481no99
69480no99.967

halophily

@refsaltgrowthtested relationconcentration
29231NaClpositivegrowth01-07 %
29231NaClpositiveoptimum3 %

observation

  • @ref: 67770
  • observation: quinones: MK-7

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2923128260galactose+carbon source
2923117234glucose+carbon source
2923117754glycerol+carbon source
2923117716lactose+carbon source
2923117306maltose+carbon source
2923128053melibiose+carbon source
29231506227N-acetylglucosamine+carbon source
2923117632nitrate+reduction

enzymes

@refvalueactivityec
29231acid phosphatase+3.1.3.2
29231alkaline phosphatase+3.1.3.1
29231gelatinase+
29231cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
29231marine sediment
67770Tidal flat sediment of YeochaGanghwa IslandRepublic of KoreaKORAsia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_128.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15786;96_98;97_105;98_114;99_128&stattab=map
  • Last taxonomy: Marinifilum fragile subclade
  • 16S sequence: FJ394546
  • Sequence Identity:
  • Total samples: 5180
  • soil counts: 343
  • aquatic counts: 2183
  • animal counts: 2588
  • plant counts: 66

Sequence information

16S sequences

  • @ref: 29231
  • description: Marinifilum fragile CECT 7942 strain JC2469 16S ribosomal RNA gene, partial sequence
  • accession: FJ394546
  • length: 1452
  • database: nuccore
  • NCBI tax ID: 1218172

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Marinifilum fragile JCM 155791236979.6wgspatric1236979
66792Marinifilum fragile JCM 155792728369664draftimg1236979
67770Marinifilum fragile JCM 15579GCA_001310955contigncbi1236979

GC content

@refGC-contentmethod
2923145
6777045high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno99no
motileno89.021yes
gram-positiveno97.42no
anaerobicno68.782no
aerobicno92.359yes
halophileno58.597no
spore-formingno92.792no
thermophileno98.544no
glucose-utilyes89.044yes
flagellatedno94.107yes
glucose-fermentno65.549no

External links

@ref: 29231

culture collection no.: IMSNU 14138, KCTC 22488, JCM 15579

straininfo link

  • @ref: 91475
  • straininfo: 364153

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19620374Marinifilum fragile gen. nov., sp. nov., isolated from tidal flat sediment.Na H, Kim S, Moon EY, Chun JInt J Syst Evol Microbiol10.1099/ijs.0.009027-02009Bacterial Typing Techniques, Bacteroidetes/chemistry/*classification/genetics/*isolation & purification, Cluster Analysis, Cytophaga/genetics, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Geologic Sediments/*microbiology, Humans, Korea, Microscopy, Electron, Scanning, Microscopy, Electron, Transmission, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analysisPathogenicity
Phylogeny23337028Marinifilum flexuosum sp. nov., a new Bacteroidetes isolated from coastal Mediterranean Sea water and emended description of the genus Marinifilum Na et al., 2009.Ruvira MA, Lucena T, Pujalte MJ, Arahal DR, Macian MCSyst Appl Microbiol10.1016/j.syapm.2012.12.0032013Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/isolation & purification/ultrastructure, Mediterranean Sea, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiologyGenetics
Phylogeny27470589Description of Ancylomarina subtilis gen. nov., sp. nov., isolated from coastal sediment, proposal of Marinilabiliales ord. nov. and transfer of Marinilabiliaceae, Prolixibacteraceae and Marinifilaceae to the order Marinilabiliales.Wu WJ, Zhao JX, Chen GJ, Du ZJInt J Syst Evol Microbiol10.1099/ijsem.0.0013422016Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/isolation & purification, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny27498985Marinifilum albidiflavum sp. nov., isolated from coastal sediment.Xu ZX, Mu X, Zhang HX, Chen GJ, Du ZJInt J Syst Evol Microbiol10.1099/ijsem.0.0013952016Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/isolation & purification, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNATranscriptome
Phylogeny30230441Marinifilum breve sp. nov., a marine bacterium isolated from the Yongle Blue Hole in the South China Sea and emended description of the genus Marinifilum.Fu T, Jia C, Fu L, Zhou S, Yao P, Du R, Sun H, Yang Z, Shi X, Zhang XHInt J Syst Evol Microbiol10.1099/ijsem.0.0030272018Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/isolation & purification, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Temperature, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorstitledoi/urlID_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
29231Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172565228776041
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
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.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
91475Reimer, 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-ID364153.1