Shewanella fodinae (CCUG 57102, NBRC 105216, KCTC 22506)

Name: Shewanella fodinae (CCUG 57102, NBRC 105216, KCTC 22506)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 133575

Type strain

Strain Designation JC15

Culture col. no. CCUG 57102 NBRC 105216 KCTC 22506 JC15 JCM 32076

NCBI tax ID(s) 552357

Special Collections CCUG JCM KCTC Literature strains

Links

Shewanella fodinae JC15 is a facultative anaerobe, mesophilic, Gram-negative prokaryote that was isolated from Coal mine and marine lagoon.

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

Name and taxonomic classification

SI-ID 412142

KCTC 22506,NBRC 105216,CCUG 57102

@ref 20215

Last LPSN update 2025-12-16 10:01:49

Domain Pseudomonadati

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Alteromonadales

Family Shewanellaceae

Genus Shewanella

Species Shewanella fodinae

Full scientific name Shewanella fodinae Sravan Kumar et al. 2010

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
29616	negative	2.5 µm	0.75 µm	rod-shaped
125439	negative				99.6
125438	negative				98

Pigmentation

29616

Productionyes

Culture and growth conditions

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
61192	positive	growth	30-37	mesophilic
67770	positive	growth	30	mesophilic

Culture pH

@ref	Ability	Type	PH
29616	positive	optimum	6
29616	positive	growth	05-08

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
29616	facultative anaerobe
61192	aerobe
125439	obligate aerobe	92.7

Spore formation

@ref	Spore formation	Confidence
125439		99.7

Halophily

@ref	Salt	Growth	Tested relation	Concentration
29616	NaCl	positive	growth	<9 %
29616	NaCl	positive	optimum	5 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
29616	30089 ChEBI	acetate	+	carbon source
29616	16236 ChEBI	ethanol	+	carbon source
29616	15740 ChEBI	formate	+	carbon source
29616	24996 ChEBI	lactate	+	carbon source
29616	15361 ChEBI	pyruvate	+	carbon source
29616	30911 ChEBI	sorbitol	+	carbon source
29616	30031 ChEBI	succinate	+	carbon source
29616	31011 ChEBI	valerate	+	carbon source

Metabolite production

@ref	Chebi-ID	Metabolite	Production
29616	16136 ChEBI	hydrogen sulfide

Enzymes

@ref	Value	Activity	Ec
29616	catalase	+	1.11.1.6
29616	cytochrome oxidase	+	1.9.3.1

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	L-lactaldehyde degradation	100	3 of 3
66794	formaldehyde oxidation	100	3 of 3
66794	vitamin K metabolism	100	5 of 5
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	reductive acetyl coenzyme A pathway	100	7 of 7
66794	palmitate biosynthesis	100	22 of 22
66794	adipate degradation	100	2 of 2
66794	CMP-KDO biosynthesis	100	4 of 4
66794	acetate fermentation	100	4 of 4
66794	biotin biosynthesis	100	4 of 4
66794	coenzyme A metabolism	100	4 of 4
66794	enterobactin biosynthesis	100	3 of 3
66794	suberin monomers biosynthesis	100	2 of 2
66794	methylglyoxal degradation	100	5 of 5
66794	folate polyglutamylation	100	1 of 1
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	tetrahydrofolate metabolism	100	14 of 14
66794	ubiquinone biosynthesis	100	7 of 7
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	ppGpp biosynthesis	100	4 of 4
66794	photosynthesis	92.86	13 of 14
66794	threonine metabolism	90	9 of 10
66794	valine metabolism	88.89	8 of 9
66794	NAD metabolism	88.89	16 of 18
66794	chorismate metabolism	88.89	8 of 9
66794	isoleucine metabolism	87.5	7 of 8
66794	heme metabolism	85.71	12 of 14
66794	leucine metabolism	84.62	11 of 13
66794	alanine metabolism	82.76	24 of 29
66794	pentose phosphate pathway	81.82	9 of 11
66794	purine metabolism	80.85	76 of 94
66794	peptidoglycan biosynthesis	80	12 of 15
66794	starch degradation	80	8 of 10
66794	glutamate and glutamine metabolism	78.57	22 of 28
66794	molybdenum cofactor biosynthesis	77.78	7 of 9
66794	aspartate and asparagine metabolism	77.78	7 of 9
66794	lipid A biosynthesis	77.78	7 of 9
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	serine metabolism	77.78	7 of 9
66794	phenylalanine metabolism	76.92	10 of 13
66794	pyrimidine metabolism	75.56	34 of 45
66794	butanoate fermentation	75	3 of 4
66794	glycogen biosynthesis	75	3 of 4
66794	sulfopterin metabolism	75	3 of 4
66794	gluconeogenesis	75	6 of 8
66794	C4 and CAM-carbon fixation	75	6 of 8
66794	proline metabolism	72.73	8 of 11
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	glutathione metabolism	71.43	10 of 14
66794	propanol degradation	71.43	5 of 7
66794	citric acid cycle	71.43	10 of 14
66794	Entner Doudoroff pathway	70	7 of 10
66794	lipid metabolism	67.74	21 of 31
66794	d-mannose degradation	66.67	6 of 9
66794	octane oxidation	66.67	2 of 3
66794	flavin biosynthesis	66.67	10 of 15
66794	acetoin degradation	66.67	2 of 3
66794	selenocysteine biosynthesis	66.67	4 of 6
66794	glycolate and glyoxylate degradation	66.67	4 of 6
66794	cyanate degradation	66.67	2 of 3
66794	methionine metabolism	65.38	17 of 26
66794	glycolysis	64.71	11 of 17
66794	vitamin B6 metabolism	63.64	7 of 11
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	cysteine metabolism	61.11	11 of 18
66794	non-pathway related	60.53	23 of 38
66794	hydrogen production	60	3 of 5
66794	glycogen metabolism	60	3 of 5
66794	propionate fermentation	60	6 of 10
66794	arginine metabolism	58.33	14 of 24
66794	isoprenoid biosynthesis	57.69	15 of 26
66794	histidine metabolism	55.17	16 of 29
66794	metabolism of disaccharids	54.55	6 of 11
66794	ethanol fermentation	50	1 of 2
66794	pantothenate biosynthesis	50	3 of 6
66794	degradation of aromatic, nitrogen containing compounds	50	6 of 12
66794	dTDPLrhamnose biosynthesis	50	4 of 8
66794	ketogluconate metabolism	50	4 of 8
66794	phenylmercury acetate degradation	50	1 of 2
66794	glycine metabolism	50	5 of 10
66794	tryptophan metabolism	50	19 of 38
66794	tyrosine metabolism	50	7 of 14
66794	lysine metabolism	47.62	20 of 42
66794	urea cycle	46.15	6 of 13
66794	oxidative phosphorylation	45.05	41 of 91
66794	nitrate assimilation	44.44	4 of 9
66794	arachidonic acid metabolism	44.44	8 of 18
66794	benzoyl-CoA degradation	42.86	3 of 7
66794	glycine betaine biosynthesis	40	2 of 5
66794	coenzyme M biosynthesis	40	4 of 10
66794	lipoate biosynthesis	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	factor 420 biosynthesis	40	2 of 5
66794	gallate degradation	40	2 of 5
66794	vitamin B1 metabolism	38.46	5 of 13
66794	sulfate reduction	38.46	5 of 13
66794	polyamine pathway	34.78	8 of 23
66794	methane metabolism	33.33	1 of 3
66794	degradation of hexoses	33.33	6 of 18
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	IAA biosynthesis	33.33	1 of 3
66794	3-phenylpropionate degradation	33.33	5 of 15
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	vitamin B12 metabolism	32.35	11 of 34
66794	androgen and estrogen metabolism	31.25	5 of 16
66794	phosphatidylethanolamine bioynthesis	30.77	4 of 13
66794	degradation of sugar acids	28	7 of 25
66794	ascorbate metabolism	27.27	6 of 22
66794	phenol degradation	25	5 of 20
66794	degradation of sugar alcohols	25	4 of 16
66794	lactate fermentation	25	1 of 4
66794	cyclohexanol degradation	25	1 of 4
66794	methanogenesis from CO2	25	3 of 12
66794	toluene degradation	25	1 of 4
66794	degradation of pentoses	25	7 of 28
66794	4-hydroxymandelate degradation	22.22	2 of 9

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Other	#Mine
#Environmental	#Aquatic	#Marine

Isolation

@ref	Sample type	Sampling date	Country	Country ISO 3 Code	Continent	Geographic location
29616	Coal mine and marine lagoon
61192	Coal sample,coal mine	2008-07-15	India	IND	Asia
67770	8 Incline mine		India	IND	Asia	Godavarikhani, Karimnagar District, Andhra Pradesh

Taxonmaps

69479

Global distribution of 16S sequence FM203122 (>99% sequence identity) for Shewanella fodinae from Microbeatlas

Aquatic Samples	163
Soil Samples	40
Animal Samples	53
Plant Samples	13
Total Samples	269

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM1465195v1 assembly for Shewanella fodinae KCTC 22506	contig	GCA_014651955	552357.4	8110937187	552357	67.06
66792	ASM2334914v1 assembly for Shewanella fodinae CCUG 57102	contig	GCA_023349145	552357.13	8113441556	552357	66.58

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
29616	Shewanella fodinae partial 16S rRNA gene, strain JC15	FM203122	1458	552357
124043	Shewanella fodinae gene for 16S rRNA, partial sequence, strain: NBRC 105216.	AB682248	1468	552357
124043	Shewanella fodinae strain KCTC 22506 16S ribosomal RNA gene, partial sequence.	MT758084	1328	552357
124043	Shewanella fodinae strain KCTC 22506 16S ribosomal RNA gene, partial sequence.	MT759847	1325	552357

GC content

@ref	GC-content (mol%)	Method
29616	53.6
67770	53.6	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: Shewanella fodinae KCTC 22506
NCBI: GCA_014651955

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	99.70	no
125439	motility	BacteriaNetⓘ	yes	86.90	no
125439	gram_stain	BacteriaNetⓘ	negative	99.60	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	92.70	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Shewanella fodinae strain KCTC 22506
PATRIC: 552357.4

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.00	yes
125438	anaerobic	anaerobicⓘ	no	91.73	no
125438	spore-forming	spore-formingⓘ	no	88.91	no
125438	aerobic	aerobicⓘ	no	57.92	no
125438	thermophilic	thermophileⓘ	no	95.50	no
125438	flagellated	motile2+ⓘ	yes	86.05	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Shewanella fodinae sp. nov., isolated from a coal mine and from a marine lagoon.	Sravan Kumar R, Sasi Jyothsna TS, Sasikala C, Seong CN, Lim CH, Park SC, Ramana CV	Int J Syst Evol Microbiol	10.1099/ijs.0.017046-0	2009

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 )
#26006	IJSEM 1649 2010 ( DOI 10.1099/ijs.0.017046-0 , PubMed 19717581 )
#29616	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 #26006
#61192	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 57102
#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) .
#66794	Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#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 .
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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 )

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Shewanella fodinae (CCUG 57102, NBRC 105216, KCTC 22506)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Metabolite utilization

Metabolite production

Enzymes

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Sequence information

Genome sequences

Genome browser: GCA_014651955

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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