Name: Shinella granuli Ch06
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 13902

Type strain:

Species: Shinella granuli

Strain Designation: Ch06, 55.101

Culture col. no.: CCUG 56487, DSM 18401, JCM 13254, KCTC 12237

Strain history: <- ST Lee, KAIST

NCBI tax ID(s): 323621 (species)

SI-ID 132663

KCTC 12237, JCM 13254, DSM 18401, CCUG 56487

Section

Shinella granuli Ch06 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from granules from an upflow anaerobic sludge blanket reactor .

Gram-negative
motile
rod-shaped
aerobe
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 granuli**
	Full Scientific Name (LPSN)	Shinella granuli An et al. 2006

Information on morphological and physiological properties Morphology

[Ref.: #31635]	Gram stain	negative
[Ref.: #67771]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.99

[Ref.: #31635]	Cell length	04-06 µm

[Ref.: #31635]	Cell width	0.2-0.5 µm

[Ref.: #31635]	Cell shape	rod-shaped

[Ref.: #31635]	Motility	yes
[Ref.: #69480]	Motility	yes Confidence in %95.593

[Ref.: #60986]

Incubation period

1 day

[Ref.: #31635]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #7541]

Culture medium

R2A MEDIUM (DSMZ Medium 830)

[Ref.: #7541]

Culture medium growth

[Ref.: #7541]

Culture medium link

Medium recipe at MediaDive

[Ref.: #7541]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #7541]	growth	30 °C
[Ref.: #31635]	growth	04-40 °C
[Ref.: #31635]	optimum	30 °C
[Ref.: #60986]	growth	37 °C
[Ref.: #67770]	growth	30 °C
[Ref.: #67771]	growth	30 °C

[Ref.: #7541]	Temperature range	mesophilic
[Ref.: #31635]	Temperature range	mesophilic
[Ref.: #60986]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic
[Ref.: #67771]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #31635]			optimum	06-10
[Ref.: #31635]			growth	06-10

Information on physiology and metabolism Physiology and metabolism

[Ref.: #31635]	Oxygen tolerance	aerobe
[Ref.: #60986]	Oxygen tolerance	aerobe
[Ref.: #67771]	Oxygen tolerance	aerobe

[Ref.: #31635]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.996

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #31635]		NaCl		growth	01-04	%
[Ref.: #31635]		NaCl		optimum	01-04	%

[Ref.: #31635]	Observation	aggregates in chains
[Ref.: #67770]	Observation	quinones: Q-10
[Ref.: #67771]	Observation	quinones: Q-10

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #31635]	4-hydroxybenzoate ChEBI	+	carbon source
[Ref.: #31635]	alanine ChEBI	+	carbon source
[Ref.: #31635]	arabinose ChEBI	+	carbon source
[Ref.: #31635]	fucose ChEBI	+	carbon source
[Ref.: #31635]	gluconate ChEBI	+	carbon source
[Ref.: #31635]	malate ChEBI	+	carbon source
[Ref.: #31635]	maltose ChEBI	+	carbon source
[Ref.: #31635]	nitrate ChEBI	+	reduction
[Ref.: #31635]	propionate ChEBI	+	carbon source
[Ref.: #31635]	rhamnose ChEBI	+	carbon source
[Ref.: #31635]	ribose ChEBI	+	carbon source
[Ref.: #31635]	salicin ChEBI	+	carbon source
[Ref.: #31635]	sucrose ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #31635]		catalase	+	1.11.1.6
[Ref.: #31635]		cytochrome oxidase	+	1.9.3.1

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

[Ref.: #7541]	Sample type/isolated from	granules from an upflow anaerobic sludge blanket (UASB) reactor (brewery wastewater-treating)
[Ref.: #7541]	Geographic location (country and/or sea, region)	Daejeon
[Ref.: #7541]	Country	Republic of Korea
[Ref.: #7541]	Country ISO 3 Code	KOR
[Ref.: #7541]	Continent	Asia

[Ref.: #60986]	Sample type/isolated from	Granule sludge
[Ref.: #60986]	Geographic location (country and/or sea, region)	Daejeon
[Ref.: #60986]	Country	Republic of Korea
[Ref.: #60986]	Country ISO 3 Code	KOR
[Ref.: #60986]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	UASB reactor

[Ref.: #67771]	Sample type/isolated from	From granule sludge
[Ref.: #67771]	Geographic location (country and/or sea, region)	Daejeon
[Ref.: #67771]	Country	Republic of Korea
[Ref.: #67771]	Country ISO 3 Code	KOR
[Ref.: #67771]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Engineered	#Biodegradation	#Anaerobic digestor
#Engineered	#Waste	#Wastewater
#Condition	#Anoxic (anaerobic)	-

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AY995149 (>99% sequence identity) for Shinella from Microbeatlas

Aquatic Samples	1019
Soil Samples	353
Animal Samples	568
Plant Samples	143
Total Samples	2083

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

[Ref.: #7541]

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.: #7541]	Shinella granuli strain Ch06 16S ribosomal RNA gene, partial sequence	AY995149	1415	ENA	323621 tax ID
[Ref.: #20218]	Shinella granuli gene for 16S rRNA, partial sequence, strain: Ch06 (= KCTC 12237)	AB187585	1415	ENA	323621 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Shinella granuli DSM 18401	GCA_004341885	scaffold	GenBank	323621 tax ID
[Ref.: #66792]	Shinella granuli strain DSM 18401	323621.6	wgs	PATRIC	323621 tax ID	*
[Ref.: #66792]	Shinella granuli DSM 18401	2802428853	draft	JGI IMG/M	323621 tax ID	*

[Ref.: #7541]	GC-content	66.0 mol%
[Ref.: #31635]	GC-content	66 mol%
[Ref.: #67770]	GC-content	66 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 GenomeNet Sporulation v. 1 based on: Shinella granuli DSM 18401 NCBI: GCA_004341885.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Shinella granuli strain DSM 18401 PATRIC: 323621.6
[Ref.: #69480]	gram-positive	no	98.502	yes
[Ref.: #69480]	anaerobic	no	98.234	no
[Ref.: #69480]	halophile	no	88.634	no
[Ref.: #69480]	spore-forming	no	96.273	no
[Ref.: #69480]	glucose-util	yes	93.771	no
[Ref.: #69480]	motile	yes	89.4	yes
[Ref.: #69480]	flagellated	no	68.361	no
[Ref.: #69480]	aerobic	yes	92.621	yes
[Ref.: #69480]	thermophile	no	98.669	yes
[Ref.: #69480]	glucose-ferment	no	90.932	no

Availability in culture collections External links

[Ref.: #7541]

Culture collection no.

CCUG 56487, DSM 18401, JCM 13254, KCTC 12237

[Ref.: #83077]

SI-ID 132663

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Shinella kummerowiae sp. nov., a symbiotic bacterium isolated from root nodules of the herbal legume Kummerowia stipulacea.	Lin DX, Wang ET, Tang H, Han TX, He YR, Guan SH, Chen WX	Int J Syst Evol Microbiol	10.1099/ijs.0.65723-0	2008	*
Phylogeny	Shinella granuli gen. nov., sp. nov., and proposal of the reclassification of Zoogloea ramigera ATCC 19623 as Shinella zoogloeoides sp. nov.	An DS, Im WT, Yang HC, Lee ST	Int J Syst Evol Microbiol	10.1099/ijs.0.63942-0	2006	*

References

#7541

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 18401

#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 )

#31635

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 #27918 (see below)

#60986 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 56487

#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;
#67771 Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;

#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 )

#83077

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-ID132663.1 )

#27918

IJSEM 443 2006 ( DOI 10.1099/ijs.0.63942-0 , PubMed 16449455 )

* These data were automatically processed and therefore are not curated

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Shinella granuli DSM 18401

Shinella granuli strain DSM 18401

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