Name: Shewanella profunda LT13a
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 14072

Type strain:

Species: Shewanella profunda

Strain Designation: LT13a

Culture col. no.: DSM 15900, JCM 12080, CIP 108671, KCTC 22433

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

NCBI tax ID(s): 254793 (species)

SI-ID 134444

DSM 15900, JCM 12080, CIP 108671

Special Collections

Section

When using BacDive for research please cite our paper

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

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

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	09-12-2024 (DD-MM-YYYY)
	Domain	*Bacteria*
	Phylum	*Pseudomonadota*
	Class	*Gammaproteobacteria*
	Order	*Alteromonadales*
	Family	*Shewanellaceae*
	Genus	*Shewanella*
	Species	**Shewanella profunda**
	Full Scientific Name (LPSN)	Shewanella profunda Toffin et al. 2004

Information on morphological and physiological properties Morphology

[Ref.: #30157]	Gram stain	negative
[Ref.: #121953]	Gram stain	negative
[Ref.: #125439]	Gram stain	negative Confidence in %99.6
[Ref.: #125438]	Gram stain	negative Confidence in %98.5

[Ref.: #30157]	Cell length	3 µm

[Ref.: #30157]	Cell width	0.6 µm

[Ref.: #30157]	Cell shape	rod-shaped
[Ref.: #121953]	Cell shape	rod-shaped

[Ref.: #30157]	Motility	yes
[Ref.: #121953]	Motility	yes
[Ref.: #125438]	Motility	yes Confidence in %90.423

Information on culture and growth conditions Culture and growth conditions

[Ref.: #6176]

Culture medium

BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)

[Ref.: #6176]

Culture medium growth

[Ref.: #6176]

Culture medium link

Medium recipe at MediaDive

[Ref.: #6176]

Culture medium composition

expand / minimize

[Ref.: #34010]

Culture medium

Marine agar (MA)

[Ref.: #34010]

Culture medium growth

[Ref.: #34010]

Culture medium composition

expand / minimize

[Ref.: #121953]

Culture medium

CIP Medium 13

[Ref.: #121953]

Culture medium growth

[Ref.: #121953]

Culture medium link

Medium recipe provided by DSMZ

	Kind of temperature		Temperature
[Ref.: #6176]		growth	28 °C
[Ref.: #30157]		growth	04-37 °C
[Ref.: #30157]		optimum	27.5 °C
[Ref.: #34010]		growth	25 °C
[Ref.: #67770]		growth	25 °C
[Ref.: #121953]		growth	5-37 °C
[Ref.: #121953]	no	growth	41 °C

	pH	Kind of pH		pH
[Ref.: #30157]			optimum	7
[Ref.: #30157]			growth	6.5-8

Information on physiology and metabolism Physiology and metabolism

[Ref.: #30157]	Oxygen tolerance	facultative anaerobe
[Ref.: #121953]	Oxygen tolerance	obligate aerobe

[Ref.: #30157]	Ability of spore formation	no
[Ref.: #125439]	Ability of spore formation	no Confidence in %99.8
[Ref.: #125438]	Ability of spore formation	no Confidence in %90.649

	Salt	Tested relation		Salt conc.
[Ref.: #121953]	NaCl		growth	0-4	%
[Ref.: #121953]	NaCl	no	growth	6	%
[Ref.: #121953]	NaCl	no	growth	8	%
[Ref.: #121953]	NaCl	no	growth	10	%

[Ref.: #67770]

Observation

quinones: Q-8, Q-7, MMK-7, MK-7, MMK-8, MK-8

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #30157]	arabinose ChEBI	+	carbon source
[Ref.: #30157]	citrate ChEBI	+	carbon source
[Ref.: #121953]	citrate ChEBI	-	carbon source
[Ref.: #121953]	esculin ChEBI	+	hydrolysis
[Ref.: #30157]	glutamate ChEBI	+	carbon source
[Ref.: #30157]	lactate ChEBI	+	carbon source
[Ref.: #30157]	maltose ChEBI	+	carbon source
[Ref.: #30157]	mannose ChEBI	+	carbon source
[Ref.: #121953]	nitrate ChEBI	+	reduction
[Ref.: #121953]	nitrate ChEBI	-	respiration
[Ref.: #121953]	nitrite ChEBI	+	reduction
[Ref.: #30157]	pyruvate ChEBI	+	carbon source
[Ref.: #121953]	sodium thiosulfate ChEBI	+	builds gas from
[Ref.: #30157]	sorbitol ChEBI	+	carbon source
[Ref.: #30157]	succinate ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #121953]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #121953]	alcohol dehydrogenase	-	1.1.1.1
[Ref.: #68382]	alkaline phosphatase	+	3.1.3.1	* from API zym
[Ref.: #68382]	alpha-chymotrypsin	+	3.4.21.1	* from API zym
[Ref.: #68382]	alpha-fucosidase	-	3.2.1.51	* from API zym
[Ref.: #68382]	alpha-galactosidase	-	3.2.1.22	* from API zym
[Ref.: #68382]	alpha-glucosidase	-	3.2.1.20	* from API zym
[Ref.: #68382]	alpha-mannosidase	-	3.2.1.24	* from API zym
[Ref.: #121953]	amylase	+
[Ref.: #121953]	beta-galactosidase	-	3.2.1.23
[Ref.: #68382]	beta-galactosidase	-	3.2.1.23	* from API zym
[Ref.: #68382]	beta-glucosidase	-	3.2.1.21	* from API zym
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym
[Ref.: #121953]	caseinase	+	3.4.21.50
[Ref.: #121953]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #30157]	cytochrome oxidase	+	1.9.3.1
[Ref.: #121953]	DNase	+
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	+		* from API zym
[Ref.: #30157]	gelatinase	+
[Ref.: #121953]	gelatinase	+
[Ref.: #121953]	lecithinase	+
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #121953]	lipase	+
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #121953]	lysine decarboxylase	-	4.1.1.18
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #121953]	ornithine decarboxylase	+	4.1.1.17
[Ref.: #121953]	oxidase	+
[Ref.: #121953]	protease	+
[Ref.: #68382]	trypsin	+	3.4.21.4	* from API zym
[Ref.: #121953]	tryptophan deaminase	-
[Ref.: #121953]	tween esterase	+
[Ref.: #121953]	urease	-	3.5.1.5
[Ref.: #68382]	valine arylamidase	-		* from API zym
	Only first 10 entries are displayed. Click here to see all.

API® Biotype100:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	ControlQ	D-glucose as carbon sourceGLU	D-fructose as carbon sourceFRU	D-galactose as carbon sourceGAL	D-trehalose as carbon sourceTRE	D-mannose as carbon sourceMNE	L-sorbose as carbon sourceSBE	D-melibiose as carbon sourceMEL	sucrose as carbon sourceSAC	D-raffinose as carbon sourceRAF	maltotriose as carbon sourceMTE	maltose as carbon sourceMAL	lactose as carbon sourceLAC	lactulose as carbon sourceLTE	1-O-methyl-beta-galactopyranoside as carbon sourceMbGa	1-O-methyl-alpha-galactopyranoside as carbon sourceMaGa	D-cellobiose as carbon sourceCEL	gentiobiose as carbon sourceGEN	1-O-methyl-beta-D-glucopyranoside as carbon sourceMbGu	esculin as carbon sourceESC	D-ribose as carbon sourceRIB	L-arabinose as carbon sourceARA	D-xylose as carbon sourceXYL	palatinose as carbon sourcePLE	L-rhamnose as carbon sourceRHA	L-fucose as carbon sourceFUC	D-melezitose as carbon sourceMLZ	D-arabitol as carbon sourceDARL	L-arabitol as carbon sourceLARL	xylitol as carbon sourceXLT	dulcitol as carbon sourceDUL	D-tagatose as carbon sourceTAG	glycerol as carbon sourceGLY	myo-inositol as carbon sourceINO	D-mannitol as carbon sourceMAN	maltitol as carbon sourceMTL	D-turanose as carbon sourceTUR	D-sorbitol as carbon sourceSOR	adonitol as carbon sourceADO	hydroxyquinoline-beta-glucuronide as carbon sourceHBG	D-lyxose as carbon sourceLYX	i-erythritol as carbon sourceERY	1-O-methyl-alpha-D-glucoside as carbon sourceMDG	3-O-methyl-D-glucose as carbon source3MDG	D-saccharate as carbon sourceSAT	mucate as carbon sourceMUC	L-tartrate as carbon sourceLTAT	D-tartrate as carbon sourceDTAT	meso-tartrate as carbon sourceMTAT	D-malate as carbon sourceDMLT	L-malate as carbon sourceLMLT	cis-aconitate as carbon sourceCATE	trans-aconitate as carbon sourceTATE	tricarballylate as carbon sourceTTE	citrate as carbon sourceCIT	D-glucuronate as carbon sourceGRT	D-galacturonate as carbon sourceGAT	2-ketogluconate as carbon source2KG	5-ketogluconate as carbon source5KG	tryptophan as carbon sourceTRY	N-acetyl-D-glucosamine as carbon sourceNAG	D-gluconate as carbon sourceGNT	phenylacetate as carbon sourcePAC	protocatechuate as carbon sourcePAT	4-hydroxybenzoate as carbon sourcepOBE	quinate as carbon sourceQAT	gentisate as carbon sourceGTE	3-hydroxybenzoate as carbon sourcemOBE	benzoate as carbon sourceBAT	3-phenylpropionate as carbon sourcePPAT	m-coumarate as carbon sourceCMT	trigonelline as carbon sourceTGE	betaine as carbon sourceBET	putrescine as carbon sourcePCE	4-aminobutyrate as carbon sourceABT	histamine as carbon sourceHIN	DL-lactate as carbon sourceLAT	caprate as carbon sourceCAP	caprylate as carbon sourceCYT	L-histidine as carbon sourceHIS	succinate as carbon sourceSUC	fumarate as carbon sourceFUM	glutarate as carbon sourceGRE	DL-glycerate as carbon sourceGYT	5-aminovalerate as carbon sourceAVT	ethanolamine as carbon sourceETN	tryptamine as carbon sourceTTN	D-glucosamine as carbon sourceGLN	itaconate as carbon sourceITA	3-hydroxybutyrate as carbon source3OBU	L-aspartate as carbon sourceAPT	L-glutamate as carbon sourceGTT	L-proline as carbon sourcePRO	D-alanine as carbon sourceDALA	L-alanine as carbon sourceLALA	L-serine as carbon sourceSER	malonate as carbon sourceMNT	propionate as carbon sourcePROP	L-tyrosine as carbon sourceTYR	2-ketoglutarate as carbon source2KT
[Ref.: #121953]	2866	not determinedn.d.	-	-	-	-	-	-	-	+	-	+	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-

API® zym:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Control	2-naphthyl phosphateAlkaline phosphatase	2-naphthyl butyrateEsterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	2-naphthyl myristateLipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	N-benzoyl-DL-arginine-2-naphthylamideTrypsin	N-glutaryl-phenylalanine-2-naphthylamidealpha- Chymotrypsin	2-naphthyl phosphateAcid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	6-Br-2-naphthyl-alphaD-galactpyranosidealpha- Galactosidase	2-naphthyl-betaD-galactpyranosidebeta- Galactosidase	Naphthol-AS-BI-betaD-glucuronidebeta- Glucuronidase	2-naphthyl-alphaD-glucopyranosidealpha- Glucosidase	6-Br-2-naphthyl-betaD-glucopyranosidebeta- Glucosidase	1-naphthyl-N-acetyl-betaD-glucosaminideN-acetyl-beta- glucosaminidase	6-Br-2-naphthyl-alphaD-mannopyranosidealpha- Mannosidase	2-naphthyl-alphaL-fucopyranosidealpha- Fucosidase
[Ref.: #121953]	11376	-	+	+	+	-	+	-	-	+	+	+	+	-	-	-	-	-	-	-	-

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #6176]	Sample type/isolated from	marine sediment (depth ~ 5000 m)
[Ref.: #6176]	Geographic location (country and/or sea, region)	Nankai Trough
[Ref.: #6176]	Country	Japan
[Ref.: #6176]	Country ISO 3 Code	JPN
[Ref.: #6176]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Deep marine sediment at the Nankai Trough, off the coast of Japan in the Pacific Ocean
[Ref.: #67770]	Country	Japan
[Ref.: #67770]	Country ISO 3 Code	JPN
[Ref.: #67770]	Continent	Asia

[Ref.: #121953]	Sample type/isolated from	Environment, Deep sediment layer
[Ref.: #121953]	Geographic location (country and/or sea, region)	Nankai Trough
[Ref.: #121953]	Country	Japan
[Ref.: #121953]	Country ISO 3 Code	JPN
[Ref.: #121953]	Continent	Asia
* marker position based on {}

Isolation sources categories

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

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence FR733713 (>99% sequence identity) for Shewanella from Microbeatlas

Aquatic Samples	2
Soil Samples
Animal Samples	4
Plant Samples
Total Samples	6

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #6176]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #121953]	Biosafety level	1	Risk group (French classification)

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #6176]	Shewanella profunda strain LT13a 16S ribosomal RNA gene, partial sequence	AY445591	1334	GenBank ENA	254793 tax ID
[Ref.: #20218]	Shewanella profunda partial 16S rRNA gene, type strain DSM15900T	FR733713	1530	GenBank ENA	254793 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Shewanella profunda DSM 15900	GCA_023283765	contig	GenBank ENA	254793 tax ID	*

[Ref.: #30157]	GC-content	44.9 mol%
[Ref.: #67770]	GC-content	44.9 mol%	high performance liquid chromatography (HPLC)

Data predicted using genome information as a basis Genome-based predictions

	Model	Trait	Prediction	Confidence in %	In training data
	Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Shewanella profunda DSM 15900 NCBI: GCA_023283765.1
[Ref.: #125438]	gram-positive	gram-positiveⓘ	no	98.5	no
[Ref.: #125438]	anaerobic	anaerobicⓘ	no	94.18	no
[Ref.: #125438]	aerobic	aerobicⓘ	yes	57.772	no
[Ref.: #125438]	spore-forming	spore-formingⓘ	no	90.649	yes
[Ref.: #125438]	thermophile	thermophilicⓘ	no	98	no
[Ref.: #125438]	motile2+	flagellatedⓘ	yes	90.423	no

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Shewanella profunda DSM 15900 NCBI: GCA_023283765
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	no	99.8
[Ref.: #125439]	BacteriaNet	motilityⓘ	yes	81.9
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	negative	99.6
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	obligate aerobe	85.5

Availability in culture collections External links

[Ref.: #6176]

Culture collection no.

DSM 15900, JCM 12080, CIP 108671, KCTC 22433

[Ref.: #83241]

SI-ID 134444

Literature:

	Title	Authors	Journal	DOI	Year
Phylogeny	Psychrobium conchae gen. nov., sp. nov., a psychrophilic marine bacterium isolated from the Iheya North hydrothermal field.	Nogi Y, Abe M, Kawagucci S, Hirayama H	Int J Syst Evol Microbiol	10.1099/ijs.0.066738-0	2014	*
Phylogeny	Shewanella 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 D	Int J Syst Evol Microbiol	10.1099/ijs.0.03007-0	2004	*
Phylogeny	Shewanella oncorhynchi sp. nov., a novel member of the genus Shewanella, isolated from Rainbow Trout (Oncorhynchus mykiss).	Altun S, Duman M, Ay H, Saticioglu IB	Int J Syst Evol Microbiol	10.1099/ijsem.0.005460	2022	*
	Iron reduction by the deep-sea bacterium Shewanella profunda LT13a under subsurface pressure and temperature conditions.	Picard A, Testemale D, Wagenknecht L, Hazael R, Daniel I	Front Microbiol	10.3389/fmicb.2014.00796	2015	*

References

#6176

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 15900

#20215

Parte, 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 DSMZ. IJSEM ( DOI 10.1099/ijsem.0.004332 )

#20218

Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )

#30157

Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #26508 (see below)

#34010 ; Curators of the CIP;

#66792

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;

#68382

Automatically annotated from API zym .

#69479

João 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 beta .

#83241

Reimer, 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 identifiers . ( DOI 10.60712/SI-ID134444.1 )

#121953 Collection of Institut Pasteur ; Curators of the CIP; CIP 108671

#125438

Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )

#125439

Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .

#26508

IJSEM 1943 2004 ( DOI 10.1099/ijs.0.03007-0 , PubMed 15545415 )

* These data were automatically processed and therefore are not curated

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Shewanella profunda DSM 15900

Shewanella profunda DSM 15900

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