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BacDive ID 14072
Type strain
Strain Designation LT13a
Culture col. no. DSM 15900 JCM 12080 LT13a KCTC 22433 CIP 108671
NCBI tax ID(s) 254793
Links
For citation purpose refer to the digital object identifier (doi) of the current version.

Archive

version 9.3 (current version):
version 9.3 (current version)

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

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