Name: Shinella kummerowiae DSM 19334
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 13904

Type strain:

Species: Shinella kummerowiae

Culture col. no.: DSM 19334, CCBAU 25048, JCM 14778, LMG 24136, CCUG 56777

Strain history: CCBAU 25048.

NCBI tax ID(s): 417745 (species)

SI-ID 293783

JCM 14778, LMG 24136, DSM 19334, CCUG 56777

Section

Shinella kummerowiae DSM 19334 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from root nodules of herbal legume Kummerowia stipulacea.

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 kummerowiae**
	Full Scientific Name (LPSN)	Shinella kummerowiae Lin et al. 2008

Information on morphological and physiological properties Morphology

[Ref.: #32579]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.975

[Ref.: #32579]	Cell length	1.7 µm

[Ref.: #32579]	Cell width	0.6 µm

[Ref.: #32579]	Cell shape	rod-shaped

[Ref.: #32579]	Motility	yes
[Ref.: #69480]	Motility	yes Confidence in %90.43

[Ref.: #61086]

Incubation period

2 days

Information on culture and growth conditions Culture and growth conditions

[Ref.: #8051]

Culture medium

RHIZOBIUM MEDIUM (DSMZ Medium 98)

[Ref.: #8051]

Culture medium growth

[Ref.: #8051]

Culture medium link

Medium recipe at MediaDive

[Ref.: #8051]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #8051]	growth	28 °C
[Ref.: #32579]	growth	25-30 °C
[Ref.: #32579]	optimum	27.5 °C
[Ref.: #61086]	growth	30 °C
[Ref.: #67770]	growth	30 °C

[Ref.: #8051]	Temperature range	mesophilic
[Ref.: #32579]	Temperature range	mesophilic
[Ref.: #61086]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #32579]			optimum	7.5
[Ref.: #32579]			growth	05-11

Information on physiology and metabolism Physiology and metabolism

[Ref.: #32579]	Oxygen tolerance	aerobe
[Ref.: #61086]	Oxygen tolerance	aerobe

[Ref.: #32579]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.995

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #32579]		NaCl		growth	3	%

[Ref.: #67770]

Observation

quinones: Q-10

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #32579]	citrate ChEBI	+	carbon source
[Ref.: #32579]	gluconate ChEBI	+	carbon source
[Ref.: #32579]	malate ChEBI	+	carbon source
[Ref.: #32579]	xylose ChEBI	+	carbon source

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #32579]		catalase	+	1.11.1.6
[Ref.: #32579]		cytochrome oxidase	+	1.9.3.1

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

[Ref.: #8051]	Sample type/isolated from	root nodules of herbal legume Kummerowia stipulacea
[Ref.: #8051]	Host species	Kummerowia stipulacea
[Ref.: #8051]	Geographic location (country and/or sea, region)	Shandong province
[Ref.: #8051]	Country	China
[Ref.: #8051]	Country ISO 3 Code	CHN
[Ref.: #8051]	Continent	Asia

[Ref.: #61086]	Sample type/isolated from	Root nodule of Kummerowia stipulacea
[Ref.: #61086]	Geographic location (country and/or sea, region)	Shandong province
[Ref.: #61086]	Country	China
[Ref.: #61086]	Country ISO 3 Code	CHN
[Ref.: #61086]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Root nodules of Kummerowia stipulacea grown in Shandong provice
[Ref.: #67770]	Host species	Kummerowia stipulacea
[Ref.: #67770]	Country	China
[Ref.: #67770]	Country ISO 3 Code	CHN
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Host Body-Site	#Plant	#Root nodule

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence EF070131 (>99% sequence identity) for Shinella from Microbeatlas

Aquatic Samples	21
Soil Samples	69
Animal Samples	10
Plant Samples	60
Total Samples	160

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

[Ref.: #8051]

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.: #8051]	Shinella kummerowiae strain CCBAU 25048 16S ribosomal RNA gene, partial sequence	EF070131	1372	ENA	417745 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Shinella kummerowiae CCBAU 25048	GCA_009827055	contig	GenBank	417745 tax ID	*
[Ref.: #66792]	Shinella kummerowiae strain CCBAU 25048	417745.4	wgs	PATRIC	417745 tax ID	*

[Ref.: #8051]	GC-content	63.1 mol%
[Ref.: #67770]	GC-content	63.1 mol%	thermal denaturation, midpoint method (Tm)

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 kummerowiae strain CCBAU 25048 PATRIC: 417745.4
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Shinella kummerowiae strain CCBAU 25048 PATRIC: 417745.4
[Ref.: #69480]	gram-positive	no	98.243	no
[Ref.: #69480]	anaerobic	no	97.84	yes
[Ref.: #69480]	halophile	no	90.193	no
[Ref.: #69480]	spore-forming	no	95.349	yes
[Ref.: #69480]	glucose-util	yes	93.536	no
[Ref.: #69480]	aerobic	yes	94.428	yes
[Ref.: #69480]	flagellated	no	62.118	no
[Ref.: #69480]	thermophile	no	99.475	no
[Ref.: #69480]	motile	yes	84.983	no
[Ref.: #69480]	glucose-ferment	no	90.951	no

Availability in culture collections External links

[Ref.: #8051]

Culture collection no.

DSM 19334, CCBAU 25048, JCM 14778, LMG 24136, CCUG 56777

[Ref.: #83079]

SI-ID 293783

Literature:

Topic	Title	Authors	Journal	DOI	Year
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 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	*

References

#8051

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 19334

#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 )

#32579

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 #28794 (see below)

#61086 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 56777

#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;

#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 )

#83079

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-ID293783.1 )

#28794

IJSEM 1409 2008 ( DOI 10.1099/ijs.0.65723-0 , PubMed 18523187 )

* These data were automatically processed and therefore are not curated

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Shinella kummerowiae strain CCBAU 25048

Shinella kummerowiae strain CCBAU 25048

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