Name: Shewanella fodinae JC15
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 133575

Type strain:

Species: Shewanella fodinae

Strain Designation: JC15

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

Strain history: KCTC 22506 <-- R. Sravan. Kumar et al.; Jawaharlal Nehru Technol. Univ. India; JC15.

NCBI tax ID(s): 552357 (species)

SI-ID 412142

CCUG 57102

Section

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

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	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Pseudomonadota*
	Class	*Gammaproteobacteria*
	Order	*Alteromonadales*
	Family	*Shewanellaceae*
	Genus	*Shewanella*
	Species	**Shewanella fodinae**
	Full Scientific Name (LPSN)	Shewanella fodinae Sravan Kumar et al. 2010

Information on morphological and physiological properties Morphology

[Ref.: #29616]	Gram stain	negative

[Ref.: #29616]	Cell length	2.5 µm

[Ref.: #29616]	Cell width	0.75 µm

[Ref.: #29616]	Cell shape	rod-shaped

[Ref.: #29616]	Motility	yes

[Ref.: #29616]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

	Temperatures	Kind of temperature		Temperature
[Ref.: #61192]			growth	30-37 °C
[Ref.: #67770]			growth	30 °C

[Ref.: #61192]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #29616]			optimum	6
[Ref.: #29616]			growth	05-08

Information on physiology and metabolism Physiology and metabolism

[Ref.: #29616]	Oxygen tolerance	facultative anaerobe
[Ref.: #61192]	Oxygen tolerance	aerobe

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #29616]		NaCl		growth	<9	%
[Ref.: #29616]		NaCl		optimum	5	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #29616]	acetate ChEBI	+	carbon source
[Ref.: #29616]	ethanol ChEBI	+	carbon source
[Ref.: #29616]	formate ChEBI	+	carbon source
[Ref.: #29616]	lactate ChEBI	+	carbon source
[Ref.: #29616]	pyruvate ChEBI	+	carbon source
[Ref.: #29616]	sorbitol ChEBI	+	carbon source
[Ref.: #29616]	succinate ChEBI	+	carbon source
[Ref.: #29616]	valerate ChEBI	+	carbon source

	Metabolite production	Metabolite	Production
[Ref.: #29616]		hydrogen sulfide ChEBI	yes

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #29616]		catalase	+	1.11.1.6
[Ref.: #29616]		cytochrome oxidase	+	1.9.3.1

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

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

[Ref.: #29616]	Sample type/isolated from	Coal mine and marine lagoon

[Ref.: #61192]	Sample type/isolated from	Coal sample,coal mine
[Ref.: #61192]	Sampling date	2008-07-15
[Ref.: #61192]	Country	India
[Ref.: #61192]	Country ISO 3 Code	IND
[Ref.: #61192]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	8 Incline mine
[Ref.: #67770]	Geographic location (country and/or sea, region)	Godavarikhani, Karimnagar District, Andhra Pradesh
[Ref.: #67770]	Country	India
[Ref.: #67770]	Country ISO 3 Code	IND
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Engineered	#Other	#Mine
#Environmental	#Aquatic	#Marine

What are isolation sources categories?

[Ref.: #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

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.: #29616]	Shewanella fodinae partial 16S rRNA gene, strain JC15	FM203122	1458	GenBank	552357 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Shewanella fodinae KCTC 22506	GCA_014651955	contig	GenBank	552357 tax ID	*
[Ref.: #66792]	Shewanella fodinae strain KCTC 22506	552357.4	wgs	PATRIC	552357 tax ID	*
[Ref.: #66792]	Shewanella fodinae CCUG 57102	GCA_023349145	contig	GenBank	552357 tax ID	*

[Ref.: #29616]	GC-content	53.6 mol%
[Ref.: #67770]	GC-content	53.6 mol%	high performance liquid chromatography (HPLC)

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Shewanella fodinae strain KCTC 22506 PATRIC: 552357.4
[Ref.: #69480]	gram-positive	no	98.883	no
[Ref.: #69480]	anaerobic	no	94.965	yes
[Ref.: #69480]	halophile	yes	55.038	yes
[Ref.: #69480]	spore-forming	no	96.452	no
[Ref.: #69480]	glucose-util	yes	86.721	no
[Ref.: #69480]	thermophile	no	98.839	yes
[Ref.: #69480]	aerobic	no	72.229	no
[Ref.: #69480]	motile	yes	93.351	yes
[Ref.: #69480]	flagellated	yes	82.97	no
[Ref.: #69480]	glucose-ferment	no	61.807	no

Availability in culture collections External links

[Ref.: #29616]

Culture collection no.

CCUG 57102, NBRC 105216, KCTC 22506, JCM 32076

[Ref.: #91513]

SI-ID 412142

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 )

#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 (see below)

#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 .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#91513

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-ID412142.1 )

#26006

IJSEM 1649 2010 ( DOI 10.1099/ijs.0.017046-0 , PubMed 19717581 )

* These data were automatically processed and therefore are not curated

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Shewanella fodinae strain KCTC 22506

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