Strain identifier

BacDive ID: 24770

Type strain: Yes

Species: Vallitalea guaymasensis

Strain Designation: Ra 1766F, Ra1766G1

Strain history: M.-L. Fardeau Ra1766G1.

NCBI tax ID(s): 1185412 (species)

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General

@ref: 21265

BacDive-ID: 24770

DSM-Number: 24848

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

description: Vallitalea guaymasensis Ra 1766F is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from deep sea sediments, 2002 m depth.

NCBI tax id

  • NCBI tax id: 1185412
  • Matching level: species

strain history

@refhistory
21265<- M.-L. Fardeau, Lab. Microbiol. de l'IRD/ESIL, Univ. de Provence et de la Méditerranée, Marseille, France; Ra1766G1 <- R. Lakhal {2011}
67770M.-L. Fardeau Ra1766G1.

doi: 10.13145/bacdive24770.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Clostridia
  • order: Eubacteriales
  • family: Vallitaleaceae
  • genus: Vallitalea
  • species: Vallitalea guaymasensis
  • full scientific name: Vallitalea guaymasensis Lakhal et al. 2013

  • synonyms

    • @ref: 20215
    • synonym: Abyssivirga alkaniphila

@ref: 21265

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Clostridia, not assigned to order

family: Vallitaleaceae

genus: Vallitalea

species: Vallitalea guaymasensis

full scientific name: Vallitalea guaymasensis Lakhal et al. 2013

strain designation: Ra 1766F, Ra1766G1

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
30840negative6 µm0.75 µmrod-shapedno
125439positive90.5

Culture and growth conditions

culture medium

  • @ref: 21265
  • name: MARIDESULFOVIBRIO MEDIUM (DSMZ Medium 1040)
  • growth: yes
  • link: https://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium1040.pdf

culture temp

@refgrowthtypetemperature
21265positivegrowth30
30840positivegrowth20-40
30840positiveoptimum32.5
67770positivegrowth30

culture pH

@refabilitytypepH
30840positivegrowth6.0-8.0
30840positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
21265anaerobe
30840anaerobe
125439anaerobe93.4

spore formation

  • @ref: 30840
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
30840NaClpositivegrowth0.5-7.5 %
30840NaClpositiveoptimum2.5 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3084022599arabinose+carbon source
3084017057cellobiose+carbon source
3084028260galactose+carbon source
3084017234glucose+carbon source
3084017306maltose+carbon source
3084029864mannitol+carbon source
3084037684mannose+carbon source
3084015361pyruvate+carbon source
3084016634raffinose+carbon source
3084033942ribose+carbon source
3084017992sucrose+carbon source
3084018222xylose+carbon source

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitude
21265deep sea sediments, 2002 m depthGulf of California, Guaymas BasinMexicoMEXNorth America27.0122-111.415
67770Sediment o Guaymas Basin

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_27294.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_922;96_13533;97_16476;98_20440;99_27294&stattab=map
  • Last taxonomy: Eubacteriales
  • 16S sequence: NR_117645
  • Sequence Identity:
  • Total samples: 216
  • soil counts: 16
  • aquatic counts: 115
  • animal counts: 85

Safety information

risk assessment

  • @ref: 21265
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
21265Vallitalea guaymasensis strain Ra1766G1 16S ribosomal RNA, partial sequenceNR_1176451444nuccore1185412
67770Vallitalea guaymasensis partial 16S rRNA gene, type strain Ra1766G1THE8056401444nuccore1185412

Genome sequences

  • @ref: 66792
  • description: Vallitalea guaymasensis Ra1766G1
  • accession: GCA_018141425
  • assembly level: complete
  • database: ncbi
  • NCBI tax ID: 1185412

GC content

@refGC-contentmethod
2126531.2high performance liquid chromatography (HPLC)
3084031.2

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingyes57.552yes
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)yes79.707no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no90.531yes
125438spore-formingspore-formingAbility to form endo- or exosporesyes51.053yes
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno91.068yes
125438motile2+flagellatedAbility to perform flagellated movementyes75.61no
125439BacteriaNetspore_formationAbility to form endo- or exosporesyes80.2
125439BacteriaNetmotilityAbility to perform movementyes75
125439BacteriaNetgram_stainReaction to gram-stainingpositive90.5
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthanaerobe93.4

External links

@ref: 21265

culture collection no.: DSM 24848, JCM 17997

straininfo link

  • @ref: 88596
  • straininfo: 397699

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny23396717Vallitalea guaymasensis gen. nov., sp. nov., isolated from marine sediment.Lakhal R, Pradel N, Postec A, Hamdi M, Ollivier B, Godfroy A, Fardeau MLInt J Syst Evol Microbiol10.1099/ijs.0.045708-02013Bacteria, Anaerobic/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Geologic Sediments/*microbiology, Molecular Sequence Data, Pacific Ocean, Phospholipids/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAGenetics
Phylogeny30540237Vallitalea okinawensis sp. nov., isolated from Okinawa Trough sediment and emended description of the genus Vallitalea.Sun YT, Zhou N, Wang BJ, Liu XD, Jiang CY, Ge X, Liu SJInt J Syst Evol Microbiol10.1099/ijsem.0.0031582018Bacterial Typing Techniques, Base Composition, Clostridiales/*classification/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Glycolipids/chemistry, Pacific Ocean, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNATranscriptome

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
21265Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-24848Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 24848)
30840Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172717028776041
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/
88596Reimer, 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-ID397699.1
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg OvermannPredicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets10.1101/2024.08.12.607695
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardydeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1https://github.com/GenomeNet/deepG