Shinella granuli (CCUG 56487, DSM 18401, JCM 13254)

Name: Shinella granuli (CCUG 56487, DSM 18401, JCM 13254)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 13902

Type strain

Strain Designation Ch06, 55.101

Culture col. no. CCUG 56487 DSM 18401 JCM 13254 KCTC 12237 Ch06 1 more

NCBI tax ID(s) 323621

Special Collections DSMZ CCUG JCM KCTC Literature strains

History DSMZ <- S.-T. Lee, KAIST; Ch06 <- W.-T. Im JCM <-- S.-T. Lee Ch06. KCTC <- ST Lee, KAIST

Links

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

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

Name and taxonomic classification

SI-ID 132663

KCTC 12237,JCM 13254,DSM 18401,CCUG 56487

@ref 20215

Last LPSN update 2026-05-29 08:28:09

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Hyphomicrobiales

Family Rhizobiaceae

Genus Shinella

Species Shinella granuli

Full scientific name Shinella granuli An et al. 2006

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
31635	negative	04-06 µm	0.2-0.5 µm	rod-shaped
67771	negative
125438	negative				99.333

Colony morphology

60986

Incubation period1 day

Pigmentation

31635

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
7541	R2A MEDIUM (DSMZ Medium 830)		Medium recipe at MediaDive	Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
7541	NUTRIENT AGAR (DSMZ Medium 1)		Medium recipe at MediaDive	Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
7541	positive	growth	28
31635	positive	growth	04-40
31635	positive	optimum	30
60986	positive	growth	37
67770	positive	growth	30
67771	positive	growth	30

Culture pH

@ref	Ability	Type	PH	PH range
31635	positive	optimum	06-10
31635	positive	growth	06-10	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
31635	aerobe
60986	aerobe
67771	aerobe
125439	obligate aerobe	94.707

Spore formation

@ref	Spore formation	Confidence
31635
125439		97.853
125438		92.199

Halophily

@ref	Salt	Growth	Tested relation	Concentration
31635	NaCl	positive	growth	01-04 %
31635	NaCl	positive	optimum	01-04 %

Observation

@ref	Observation
31635	aggregates in chains
67770	quinones: Q-10
67771	quinones: Q-10

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
31635	17879 ChEBI	4-hydroxybenzoate	+	carbon source
31635	16449 ChEBI	alanine	+	carbon source
31635	22599 ChEBI	arabinose	+	carbon source
31635	33984 ChEBI	fucose	+	carbon source
31635	24265 ChEBI	gluconate	+	carbon source
31635	25115 ChEBI	malate	+	carbon source
31635	17306 ChEBI	maltose	+	carbon source
31635	17632 ChEBI	nitrate	+	reduction
31635	17272 ChEBI	propionate	+	carbon source
31635	26546 ChEBI	rhamnose	+	carbon source
31635	33942 ChEBI	ribose	+	carbon source
31635	17814 ChEBI	salicin	+	carbon source
31635	17992 ChEBI	sucrose	+	carbon source

Enzymes

@ref	Value	Activity	Ec
31635	catalase	+	1.11.1.6
31635	cytochrome oxidase	+	1.9.3.1

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Biodegradation	#Anaerobic digestor
#Engineered	#Waste	#Wastewater
#Condition	#Anoxic (anaerobic)	-

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
7541	granules from an upflow anaerobic sludge blanket (UASB) reactor (brewery wastewater-treating)	Daejeon	Republic of Korea	KOR	Asia
60986	Granule sludge	Daejeon	Republic of Korea	KOR	Asia
67770	UASB reactor
67771	From granule sludge	Daejeon	Republic of Korea	KOR	Asia

Taxonmaps

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

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
7541	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
124043	ASM3954007v1 assembly for Shinella granuli JCM 13254	contig	GCA_039540075			323621	73.64
67770	ASM434188v1 assembly for Shinella granuli DSM 18401	scaffold	GCA_004341885	323621.6	2802428853	323621	56.53
124043	ASM4242944v1 assembly for Shinella granuli JCM 13254	scaffold	GCA_042429445			323621	48.56

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20218	Shinella granuli gene for 16S rRNA, partial sequence, strain: Ch06 (= KCTC 12237)	AB187585	1415		323621
7541	Shinella granuli strain Ch06 16S ribosomal RNA gene, partial sequence	AY995149	1415		323621

GC content

@ref	GC-content (mol%)	Method
7541	66.0
31635	66
67770	66	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: ASM3954007v1 assembly for Shinella granuli JCM 13254
NCBI: GCA_039540075

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	94.71	no
125439	gram_stain	BacteriaNetⓘ	negative	81.55	no
125439	motility	BacteriaNetⓘ	yes	42.97	no
125439	spore_formation	BacteriaNetⓘ	no	97.85	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Shinella granuli strain DSM 18401
PATRIC: 323621.6

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	99.33	no
125438	anaerobic	anaerobicⓘ	no	97.37	yes
125438	spore-forming	spore-formingⓘ	no	92.20	no
125438	aerobic	aerobicⓘ	yes	86.62	yes
125438	thermophilic	thermophileⓘ	no	98.25	yes
125438	flagellated	motile2+ⓘ	yes	71.38	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Phylogenomic analyses and reclassification of the Mesorhizobium complex: proposal for 9 novel genera and reclassification of 15 species.	Li Y, Guo T, Sun L, Wang ET, Young JPW, Tian CF.	BMC Genomics	10.1186/s12864-024-10333-y	2024
	Complete Genome Sequences of Kinneretia sp. Strain XES5, Shinella sp. Strain XGS7, and Vogesella sp. Strain XCS3, Isolated from Xenopus laevis Skin.	Hudson DT, Chapman PA, Day RC, Morgan XC, Beck CW.	Microbiol Resour Announc	10.1128/mra.01050-21	2021
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 )
#27918	IJSEM 443 2006 ( DOI 10.1099/ijs.0.63942-0 , PubMed 16449455 )
#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
#60986	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 56487
#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 .
#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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Shinella granuli (CCUG 56487, DSM 18401, JCM 13254)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Enzymes

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_039540075

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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