Shewanella profunda (DSM 15900, JCM 12080, LT13a)

Name: Shewanella profunda (DSM 15900, JCM 12080, LT13a)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

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

Special Collections DSMZ JCM KCTC CIP Literature strains

History DSMZ <- L. Toffin; LT13a JCM <-- L. Toffin LT13a. CIP <- 2005, JCM <- 2003, L. Toffin, CNRS, Plouzané, France: strain LT13a

Links

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

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

Name and taxonomic classification

SI-ID 134444

DSM 15900,JCM 12080,CIP 108671

@ref 20215

Last LPSN update 2026-05-29 08:28:12

Domain Bacteria

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Alteromonadales

Family Shewanellaceae

Genus Shewanella

Species Shewanella profunda

Full scientific name Shewanella profunda Toffin et al. 2004

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
30157	negative	3 µm	0.6 µm	rod-shaped
125438	negative				98.5
125438					90.423
125439	negative				98.561
121953	negative			rod-shaped

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
6176	BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)	Medium recipe at MediaDive	Name: 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
34010	Marine agar (MA)		Distilled water make up to (1000.000 ml);Marine agar (55.100 g)
121953	CIP Medium 13	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
6176	positive	growth	28
30157	positive	growth	04-37
30157	positive	optimum	27.5
34010	positive	growth	25
67770	positive	growth	25
121953	positive	growth	5-37
121953	negative	growth	41

Culture pH

@ref	Ability	Type	PH
30157	positive	optimum	7
30157	positive	growth	6.5-8

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
30157	facultative anaerobe
121953	obligate aerobe

Spore formation

@ref	Spore formation	Confidence
30157
125438		90.649
125439		99.963

Halophily

@ref	Salt	Growth	Tested relation	Concentration
121953	NaCl	positive	growth	0-4 %
121953	NaCl		growth	6 %
121953	NaCl		growth	8 %
121953	NaCl		growth	10 %

Observation

67770

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

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
30157	22599 ChEBI	arabinose	+	carbon source
30157	16947 ChEBI	citrate	+	carbon source
121953	16947 ChEBI	citrate	-	carbon source
121953	4853 ChEBI	esculin	+	hydrolysis
30157	29987 ChEBI	glutamate	+	carbon source
30157	24996 ChEBI	lactate	+	carbon source
30157	17306 ChEBI	maltose	+	carbon source
30157	37684 ChEBI	mannose	+	carbon source
121953	17632 ChEBI	nitrate	+	reduction
121953	17632 ChEBI	nitrate	-	respiration
121953	16301 ChEBI	nitrite	+	reduction
30157	15361 ChEBI	pyruvate	+	carbon source
121953	132112 ChEBI	sodium thiosulfate	+	builds gas from
30157	30911 ChEBI	sorbitol	+	carbon source
30157	30031 ChEBI	succinate	+	carbon source

Metabolite production

@ref	Chebi-ID	Metabolite	Production
121953	35581 ChEBI	indole

Enzymes

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

API zym

@ref	Control	Alkaline phosphatase	Esterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	Lipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
121953	-	+	+	+	-	+	-	-	+	+	+	+	-	-	-	-	-	-	-	-

API biotype100

@ref	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
121953	not determinedn.d.	-	-	-	-	-	-	-	+	-	+	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Marine
#Environmental	#Aquatic	#Sediment
#Environmental	#Terrestrial	#Core sample

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
6176	marine sediment (depth ~ 5000 m)	Nankai Trough	Japan	JPN	Asia
67770	Deep marine sediment at the Nankai Trough, off the coast of Japan in the Pacific Ocean		Japan	JPN	Asia
121953	Environment, Deep sediment layer	Nankai Trough	Japan	JPN	Asia

Taxonmaps

69479

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

Aquatic Samples	2
Soil Samples	0
Animal Samples	4
Plant Samples	0
Total Samples	6

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
6176	1	Risk group (German classification) According to TRBA 466
121953	1	Risk group (French classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM2328376v1 assembly for Shewanella profunda DSM 15900	contig	GCA_023283765	254793.4	8046302185	254793	54.79

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20218	Shewanella profunda partial 16S rRNA gene, type strain DSM15900T	FR733713	1530		254793
6176	Shewanella profunda strain LT13a 16S ribosomal RNA gene, partial sequence	AY445591	1334		254793

GC content

@ref	GC-content (mol%)	Method
30157	44.9
67770	44.9	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM2328376v1 assembly for Shewanella profunda DSM 15900
NCBI: GCA_023283765

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	85.54	no
125439	gram_stain	BacteriaNetⓘ	negative	98.56	no
125439	motility	BacteriaNetⓘ	yes	75.93	no
125439	spore_formation	BacteriaNetⓘ	no	99.96	no

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	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.50	no
125438	anaerobic	anaerobicⓘ	no	94.18	no
125438	aerobic	aerobicⓘ	yes	57.77	no
125438	spore-forming	spore-formingⓘ	no	90.65	yes
125438	thermophilic	thermophileⓘ	no	98.00	no
125438	flagellated	motile2+ⓘ	yes	90.42	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	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
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

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 )
#26508	IJSEM 1943 2004 ( DOI 10.1099/ijs.0.03007-0 , PubMed 15545415 )
#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
#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 .
#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 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

Content

About us

Shewanella profunda (DSM 15900, JCM 12080, LT13a)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Metabolite production

Enzymes

API zym

API biotype100

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_023283765

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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