Strain identifier

BacDive ID: 14072

Type strain: Yes

Species: Shewanella profunda

Strain Designation: LT13a

Strain history: CIP <- 2005, JCM <- 2003, L. Toffin, CNRS, Plouzané, France: strain LT13a

NCBI tax ID(s): 254793 (species)

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General

@ref: 6176

BacDive-ID: 14072

DSM-Number: 15900

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

description: Shewanella profunda LT13a is a facultative anaerobe, mesophilic, Gram-negative bacterium that was isolated from marine sediment .

NCBI tax id

  • NCBI tax id: 254793
  • Matching level: species

strain history

@refhistory
6176<- L. Toffin; LT13a
67770L. Toffin LT13a.
121953CIP <- 2005, JCM <- 2003, L. Toffin, CNRS, Plouzané, France: strain LT13a

doi: 10.13145/bacdive14072.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Alteromonadales
  • family: Shewanellaceae
  • genus: Shewanella
  • species: Shewanella profunda
  • full scientific name: Shewanella profunda Toffin et al. 2004

@ref: 6176

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Alteromonadales

family: Shewanellaceae

genus: Shewanella

species: Shewanella profunda

full scientific name: Shewanella profunda Toffin et al. 2004

strain designation: LT13a

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
30157negative3 µm0.6 µmrod-shapedyes
121953negativerod-shapedyes
125439negative99.6
125438yes90.423
125438negative98.5

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6176BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)yeshttps://mediadive.dsmz.de/medium/514Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water
34010Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
121953CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperature
6176positivegrowth28
30157positivegrowth04-37
30157positiveoptimum27.5
34010positivegrowth25
67770positivegrowth25
121953positivegrowth5-37
121953nogrowth41

culture pH

@refabilitytypepH
30157positivegrowth6.5-8
30157positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
30157facultative anaerobe
121953obligate aerobe

spore formation

@refspore formationconfidence
30157no
125439no99.8
125438no90.649

halophily

@refsaltgrowthtested relationconcentration
121953NaClpositivegrowth0-4 %
121953NaClnogrowth6 %
121953NaClnogrowth8 %
121953NaClnogrowth10 %

observation

  • @ref: 67770
  • observation: quinones: Q-8, Q-7, MMK-7, MK-7, MMK-8, MK-8

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3015722599arabinose+carbon source
3015716947citrate+carbon source
3015729987glutamate+carbon source
3015724996lactate+carbon source
3015717306maltose+carbon source
3015737684mannose+carbon source
3015715361pyruvate+carbon source
3015730911sorbitol+carbon source
3015730031succinate+carbon source
12195316947citrate-carbon source
1219534853esculin+hydrolysis
12195317632nitrate+reduction
12195316301nitrite+reduction
121953132112sodium thiosulfate+builds gas from
12195317632nitrate-respiration

metabolite production

  • @ref: 121953
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
30157gelatinase+
30157cytochrome oxidase+1.9.3.1
68382alpha-fucosidase-3.2.1.51
68382alpha-glucosidase-3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin+3.4.21.1
68382trypsin+3.4.21.4
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382leucine arylamidase+3.4.11.1
68382esterase lipase (C 8)+
68382esterase (C 4)+
121953oxidase+
121953beta-galactosidase-3.2.1.23
121953alcohol dehydrogenase-1.1.1.1
121953gelatinase+
121953amylase+
121953DNase+
121953caseinase+3.4.21.50
121953catalase+1.11.1.6
121953tween esterase+
121953lecithinase+
121953lipase+
121953lysine decarboxylase-4.1.1.18
121953ornithine decarboxylase+4.1.1.17
121953protease+
121953tryptophan deaminase-
121953urease-3.5.1.5
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase-3.2.1.21
68382lipase (C 14)-
68382alkaline phosphatase+3.1.3.1

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
121953-+++-+--++++--------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
121953-------+-++----------------------------------------------------------------------------------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
6176marine sediment (depth ~ 5000 m)Nankai TroughJapanJPNAsia
67770Deep marine sediment at the Nankai Trough, off the coast of Japan in the Pacific OceanJapanJPNAsia
121953Environment, Deep sediment layerNankai TroughJapanJPNAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Environmental#Aquatic#Sediment
#Environmental#Terrestrial#Core sample

taxonmaps

  • @ref: 69479
  • File name: preview.99_3799.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_59;96_126;97_134;98_151;99_3799&stattab=map
  • Last taxonomy: Shewanella
  • 16S sequence: FR733713
  • Sequence Identity:
  • Total samples: 6
  • aquatic counts: 2
  • animal counts: 4

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
61761Risk group (German classification)
1219531Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Shewanella profunda partial 16S rRNA gene, type strain DSM15900TFR7337131530nuccore254793
6176Shewanella profunda strain LT13a 16S ribosomal RNA gene, partial sequenceAY4455911334nuccore254793

Genome sequences

  • @ref: 66792
  • description: Shewanella profunda DSM 15900
  • accession: GCA_023283765
  • assembly level: contig
  • database: ncbi
  • NCBI tax ID: 254793

GC content

@refGC-contentmethod
3015744.9
6777044.9high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingno98.5no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no94.18no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes57.772no
125438spore-formingspore-formingAbility to form endo- or exosporesno90.649yes
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno98no
125438motile2+flagellatedAbility to perform flagellated movementyes90.423no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno99.8
125439BacteriaNetmotilityAbility to perform movementyes81.9
125439BacteriaNetgram_stainReaction to gram-stainingnegative99.6
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe85.5

External links

@ref: 6176

culture collection no.: DSM 15900, JCM 12080, CIP 108671, KCTC 22433

straininfo link

  • @ref: 83241
  • straininfo: 134444

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15545415Shewanella profunda sp. nov., isolated from deep marine sediment of the Nankai Trough.Toffin L, Bidault A, Pignet P, Tindall BJ, Slobodkin A, Kato C, Prieur DInt J Syst Evol Microbiol10.1099/ijs.0.03007-02004Anaerobiosis, Base Composition, Cystine/metabolism, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, Fatty Acids/analysis/isolation & purification, Ferric Compounds/metabolism, Flagella, Fumarates/metabolism, Genes, rRNA, Geologic Sediments/*microbiology, Hydrostatic Pressure, Japan, Molecular Sequence Data, Nitrates/metabolism, Nucleic Acid Hybridization, Organic Chemicals/metabolism, Oxygen/metabolism, Pacific Ocean, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Shewanella/*classification/cytology/*isolation & purification/physiology, Temperature, *Water MicrobiologyMetabolism
Phylogeny25096326Psychrobium conchae gen. nov., sp. nov., a psychrophilic marine bacterium isolated from the Iheya North hydrothermal field.Nogi Y, Abe M, Kawagucci S, Hirayama HInt J Syst Evol Microbiol10.1099/ijs.0.066738-02014Animals, Bacterial Typing Techniques, Base Composition, Bivalvia/*microbiology, DNA, Bacterial/genetics, Fatty Acids/chemistry, Gammaproteobacteria/*classification/genetics/isolation & purification, Hydrothermal Vents, Japan, Molecular Sequence Data, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater, Sequence Analysis, DNA, Ubiquinone/chemistryGenetics
25653646Iron reduction by the deep-sea bacterium Shewanella profunda LT13a under subsurface pressure and temperature conditions.Picard A, Testemale D, Wagenknecht L, Hazael R, Daniel IFront Microbiol10.3389/fmicb.2014.007962015
Phylogeny35861494Shewanella oncorhynchi sp. nov., a novel member of the genus Shewanella, isolated from Rainbow Trout (Oncorhynchus mykiss).Altun S, Duman M, Ay H, Saticioglu IBInt J Syst Evol Microbiol10.1099/ijsem.0.0054602022Animals, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Oncorhynchus mykiss, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater, Sequence Analysis, DNA, *Shewanella, UbiquinoneTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
6176Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15900)https://www.dsmz.de/collection/catalogue/details/culture/DSM-15900
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
30157Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604126508
34010Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6325
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
83241Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID134444.1StrainInfo: A central database for resolving microbial strain identifiers
121953Curators of the CIPCollection of Institut Pasteur (CIP 108671)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108671
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1