Shewanella waksmanii (CIP 107701, KMM 3823, ATCC BAA-643)

Name: Shewanella waksmanii (CIP 107701, KMM 3823, ATCC BAA-643)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 139569

Type strain

Culture col. no. CIP 107701 KMM 3823 ATCC BAA-643

NCBI tax ID(s) 1336233 213783

Special Collections CIP

History CIP <- 2002, E. Ivanova, Swinburne Inst., Victoria, Australia <- O. Nedashkovskaya

Links

Shewanella waksmanii CIP 107701 is a Gram-negative, motile, rod-shaped bacterium of the family Shewanellaceae.

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

Name and taxonomic classification

SI-ID 99590

ATCC BAA-643,CIP 107701,KCTC 12233

@ref 20215

Last LPSN update 2026-05-29 08:39:31

Domain Bacteria

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Alteromonadales

Family Shewanellaceae

Genus Shewanella

Species Shewanella waksmanii

Full scientific name Shewanella waksmanii Ivanova et al. 2003

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Motility	Confidence
41998	negative	rod-shaped
125439	negative			99.31

Culture and growth conditions

Culture medium

@ref	Name	Growth	Composition	Medium link
41998	Marine agar (MA)		Distilled water make up to (1000.000 ml);Marine agar (55.100 g)
41998	CIP Medium 13			Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
41998	positive	growth	25
41998	positive	growth	10-30
41998	negative	growth	5
41998	negative	growth	37
41998	negative	growth	41

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	97.635

Spore formation

@ref	Spore formation	Confidence
125439		99.931

Halophily

@ref	Salt	Growth	Tested relation	Concentration
41998	NaCl	positive	growth	2-8 %
41998	NaCl		growth	0 %
41998	NaCl		growth	10 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
41998	16947 ChEBI	citrate	-	carbon source
41998	4853 ChEBI	esculin	+	hydrolysis
41998	17632 ChEBI	nitrate	-	reduction
41998	16301 ChEBI	nitrite	-	reduction
41998	132112 ChEBI	sodium thiosulfate	-	builds gas from

Metabolite production

@ref	Chebi-ID	Metabolite	Production
41998	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
41998	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
41998	amylase	+
68382	beta-galactosidase	-	3.2.1.23	from API zym
41998	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
41998	caseinase	+	3.4.21.50
41998	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
41998	gelatinase	+/-
41998	lecithinase	-
68382	leucine arylamidase	+	3.4.11.1	from API zym
41998	lipase	+
68382	lipase (C 14)	-		from API zym
41998	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
41998	ornithine decarboxylase	-	4.1.1.17
41998	oxidase	+
41998	protease	+
68382	trypsin	-	3.4.21.4	from API zym
41998	tryptophan deaminase	-
41998	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
41998	-	+	+	+	-	+	-	-	-	+	+	+	-	-	-	-	-	+	-	-

Isolation, sampling and environmental information

Isolation

@ref	Sample type	Country	Country ISO 3 Code	Continent
41998		Japan	JPN	Asia
41998	Sipuncula, Phascolosoma japonicum	Japan	JPN	Asia

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
41998	1	Risk group (French classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
124043	ASM51880v1 assembly for Shewanella waksmanii ATCC BAA-643	scaffold	GCA_000518805	1336233.3	2546825523	1336233	61.56

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
124043	Shewanella waksmanii 16S ribosomal RNA gene, partial sequence.	AY170366	1540		213783

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM51880v1 assembly for Shewanella waksmanii ATCC BAA-643
NCBI: GCA_000518805

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	97.64	no
125439	motility	BacteriaNetⓘ	yes	77.32	no
125439	gram_stain	BacteriaNetⓘ	negative	99.31	no
125439	spore_formation	BacteriaNetⓘ	no	99.93	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Whole-Genome Sequencing Redefines Shewanella Taxonomy.	Thorell K, Meier-Kolthoff JP, Sjoling A, Martin-Rodriguez AJ.	Front Microbiol	10.3389/fmicb.2019.01861	2019
	Effects of poly(3-hydroxybutyrate) [P(3HB)] coating on the bacterial communities of artificial structures.	Chai YJ, Syauqi TA, Sudesh K, Ee TL, Ban CC, Kar Mun AC, Anne Strain EM, Merican F, Rahim MA, Md Salleh K, Yin CS.	PLoS One	10.1371/journal.pone.0300929	2024
Metabolism	Improved utilization of soybean meal through fermentation with commensal Shewanella sp. MR-7 in turbot (Scophthalmus maximus L.).	Li C, Zhang B, Wang X, Pi X, Wang X, Zhou H, Mai K, He G.	Microb Cell Fact	10.1186/s12934-019-1265-z	2019
Genetics	Genomic insights into biosynthetic gene cluster diversity and structural variability in marine bacteria.	Al-Siyabi N, Al-Ansari A, Abri MAA, Sivakumar N.	Sci Rep	10.1038/s41598-025-21523-3	2025
	Isolation of a Novel Bacterial Strain Capable of Producing Abundant Extracellular Membrane Vesicles Carrying a Single Major Cargo Protein and Analysis of Its Transport Mechanism.	Chen C, Kawamoto J, Kawai S, Tame A, Kato C, Imai T, Kurihara T.	Front Microbiol	10.3389/fmicb.2019.03001	2019
Phylogeny	Shewanella waksmanii sp. nov., isolated from a sipuncula (Phascolosoma japonicum).	Ivanova EP, Nedashkovskaya OI, Zhukova NV, Nicolau DV, Christen R, Mikhailov VV	Int J Syst Evol Microbiol	10.1099/ijs.0.02630-0	2003

References

#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 )
#41998	Collection of Institut Pasteur ; Curators of the CIP; CIP 107701
#68382	Automatically annotated from API zym .
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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 )

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Shewanella waksmanii (CIP 107701, KMM 3823, ATCC BAA-643)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Metabolite utilization

Metabolite production

Enzymes

API zym

Isolation, sampling and environmental information

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000518805

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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