Name: Shinella fusca DC-196
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 13906

Type strain:

Species: Shinella fusca

Strain Designation: DC-196

Culture col. no.: DSM 21319, CCUG 55808, LMG 24714

Strain history: <- C. M. Manaia, Escola Superior de Biotecnol., Univ. Católica Portuguesa, Porto, Portugal <- I. Vaz-Moreira et al.; DC.196

NCBI tax ID(s): 544480 (species)

SI-ID 366460

CCUG 55808, LMG 24714, DSM 21319

Section

Shinella fusca DC-196 is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from Domestic wastes compost.

Gram-negative
motile
rod-shaped
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	*Alphaproteobacteria*
	Order	*Hyphomicrobiales*
	Family	*Rhizobiaceae*
	Genus	*Shinella*
	Species	**Shinella fusca**
	Full Scientific Name (LPSN)	Shinella fusca Vaz-Moreira et al. 2010

Information on morphological and physiological properties Morphology

[Ref.: #29251]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.986

[Ref.: #29251]	Cell length	1.19 µm

[Ref.: #29251]	Cell width	0.45 µm

[Ref.: #29251]	Cell shape	rod-shaped

[Ref.: #29251]	Motility	yes
[Ref.: #69480]	Motility	yes Confidence in %91.521

[Ref.: #29251]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #15612]

Culture medium

PLATE COUNT AGAR (DSMZ Medium 464)

[Ref.: #15612]

Culture medium growth

[Ref.: #15612]

Culture medium link

Medium recipe at MediaDive

[Ref.: #15612]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #15612]			growth	28 °C
[Ref.: #29251]			growth	10-40 °C

[Ref.: #15612]

Temperature range

mesophilic

	pH	Kind of pH		pH
[Ref.: #29251]			growth	06-09

Information on physiology and metabolism Physiology and metabolism

[Ref.: #29251]

Oxygen tolerance

anaerobe

[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.992

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #29251]		NaCl		growth	0-3	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #29251]	adipate ChEBI	+	carbon source
[Ref.: #29251]	arabinose ChEBI	+	carbon source
[Ref.: #29251]	cellobiose ChEBI	+	carbon source
[Ref.: #29251]	citrate ChEBI	+	carbon source
[Ref.: #29251]	esculin ChEBI	+	hydrolysis
[Ref.: #29251]	fucose ChEBI	+	carbon source
[Ref.: #29251]	galactose ChEBI	+	carbon source
[Ref.: #29251]	glucose ChEBI	+	carbon source
[Ref.: #29251]	glycerol ChEBI	+	carbon source
[Ref.: #29251]	L-arabitol ChEBI	+	carbon source
[Ref.: #29251]	maltose ChEBI	+	carbon source
[Ref.: #29251]	mannitol ChEBI	+	carbon source
[Ref.: #29251]	mannose ChEBI	+	carbon source
[Ref.: #29251]	N-acetylglucosamine ChEBI	+	carbon source
[Ref.: #29251]	nitrate ChEBI	+	reduction
[Ref.: #29251]	rhamnose ChEBI	+	carbon source
[Ref.: #29251]	ribitol ChEBI	+	carbon source
[Ref.: #29251]	ribose ChEBI	+	carbon source
[Ref.: #29251]	sucrose ChEBI	+	carbon source
[Ref.: #29251]	trehalose ChEBI	+	carbon source
[Ref.: #29251]	xylitol ChEBI	+	carbon source
[Ref.: #29251]	xylose ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Enzyme	Enzyme activity	EC number
[Ref.: #29251]	acid phosphatase	+	3.1.3.2
[Ref.: #29251]	alkaline phosphatase	+	3.1.3.1
[Ref.: #29251]	catalase	+	1.11.1.6
[Ref.: #29251]	cytochrome oxidase	+	1.9.3.1
[Ref.: #29251]	urease	+	3.5.1.5

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

[Ref.: #15612]	Sample type/isolated from	Domestic wastes compost
[Ref.: #15612]	Geographic location (country and/or sea, region)	Porto
[Ref.: #15612]	Country	Portugal
[Ref.: #15612]	Country ISO 3 Code	PRT
[Ref.: #15612]	Continent	Europe

[Ref.: #60744]	Sample type/isolated from	Domestic wastes compost
[Ref.: #60744]	Sampling date	2005
[Ref.: #60744]	Geographic location (country and/or sea, region)	Porto
[Ref.: #60744]	Country	Portugal
[Ref.: #60744]	Country ISO 3 Code	PRT
[Ref.: #60744]	Continent	Europe
* marker position based on {}

Isolation sources categories

#Engineered	#Biodegradation	#Composting
#Engineered	#Waste	#Domestic waste

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence FM177879 (>99% sequence identity) for Shinella from Microbeatlas

Aquatic Samples	53
Soil Samples	30
Animal Samples	14
Plant Samples	7
Total Samples	104

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

[Ref.: #15612]

Biosafety level

Risk group (German classification)
According to TRBA 466

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.: #15612]	Shinella fusca partial 16S rRNA gene, type strain DC-196T	FM177879	1437	ENA	544480 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Shinella fusca DSM 21319	GCA_014203155	scaffold	GenBank	544480 tax ID	*
[Ref.: #66792]	Shinella fusca strain DSM 21319	544480.7	wgs	PATRIC	544480 tax ID	*
[Ref.: #66792]	Shinella fusca DSM 21319	2861721846	draft	JGI IMG/M	544480 tax ID	*

[Ref.: #15612]	GC-content	66.2 mol%	high performance liquid chromatography (HPLC)
[Ref.: #29251]	GC-content	66 mol%

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Shinella fusca DSM 21319 NCBI: GCA_014203155.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Shinella fusca DSM 21319 NCBI: GCA_014203155.1
[Ref.: #69480]	flagellated	no	70.905	no
[Ref.: #69480]	gram-positive	no	98.371	no
[Ref.: #69480]	anaerobic	no	95.957	yes
[Ref.: #69480]	aerobic	yes	87.824	no
[Ref.: #69480]	halophile	no	88.702	no
[Ref.: #69480]	spore-forming	no	94.929	no
[Ref.: #69480]	glucose-util	yes	94.8	yes
[Ref.: #69480]	thermophile	no	99.022	yes
[Ref.: #69480]	motile	yes	87.639	yes
[Ref.: #69480]	glucose-ferment	no	89.298	no

Availability in culture collections External links

[Ref.: #15612]

Culture collection no.

DSM 21319, CCUG 55808, LMG 24714

[Ref.: #83081]

SI-ID 366460

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Shinella pollutisoli sp. nov., isolated from tetrabromobisphenol A-contaminated soil.	Mu Y, Jia WB, Ke Z, Zhuang W, Wang HM, Jiang JD, Chen K, Chen Q	Int J Syst Evol Microbiol	10.1099/ijsem.0.002883	2018	*
Phylogeny	Shinella curvata sp. nov., isolated from hydrocarbon-contaminated desert sands.	Subhash Y, Lee SS	Int J Syst Evol Microbiol	10.1099/ijsem.0.001290	2016	*
Phylogeny	Shinella daejeonensis sp. nov., a nitrate-reducing bacterium isolated from sludge of a leachate treatment plant.	Lee M, Woo SG, Ten LN	Int J Syst Evol Microbiol	10.1099/ijs.0.026435-0	2010	*
Phylogeny	Shinella fusca sp. nov., isolated from domestic waste compost.	Vaz-Moreira I, Faria C, Lopes AR, Svensson LA, Moore ERB, Nunes OC, Manaia CM	Int J Syst Evol Microbiol	10.1099/ijs.0.009498-0	2009	*

References

#15612

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 21319

#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 )

#29251

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 #25671 (see below)

#60744 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 55808

#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) .

#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) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#83081

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-ID366460.1 )

#25671

IJSEM 144 2010 ( DOI 10.1099/ijs.0.009498-0 , PubMed 19648331 )

* These data were automatically processed and therefore are not curated

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Shinella fusca DSM 21319

Shinella fusca DSM 21319

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