Shinella kummerowiae (DSM 19334, CCBAU 25048, JCM 14778)

Name: Shinella kummerowiae (DSM 19334, CCBAU 25048, JCM 14778)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 13904

Type strain

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

NCBI tax ID(s) 417745

Special Collections DSMZ CCUG JCM Literature strains

History DSMZ <- W. X. Chen, China Agric. Univ., College Biol. Sci., Beijing; CCBAU 25048 <- D. X. Lin JCM <-- CCBAU 25048.

Links

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

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

Name and taxonomic classification

SI-ID 293783

JCM 14778,LMG 24136,DSM 19334,CCUG 56777

@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 kummerowiae

Full scientific name Shinella kummerowiae Lin et al. 2008

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
32579	negative	1.7 µm	0.6 µm	rod-shaped
125439	negative				92.558
125438	negative				98.5

Colony morphology

61086

Incubation period2 days

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
8051	RHIZOBIUM MEDIUM (DSMZ Medium 98)		Medium recipe at MediaDive	Name: RHIZOBIUM MEDIUM (DSMZ Medium 98) Composition: air-dried garden soil 80.0 g/l Agar 15.0 g/l Mannitol 10.0 g/l Yeast extract 1.0 g/l Na2CO3 0.2 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
8051	positive	growth	28
32579	positive	growth	25-30
32579	positive	optimum	27.5
61086	positive	growth	30
67770	positive	growth	30

Culture pH

@ref	Ability	Type	PH	PH range
32579	positive	optimum	7.5
32579	positive	growth	05-11	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
32579	aerobe
61086	aerobe
125439	obligate aerobe	94.239

Spore formation

@ref	Spore formation	Confidence
32579
125438		90.95
125439		99.34

Halophily

@ref	Salt	Growth	Tested relation	Concentration
32579	NaCl	positive	growth	3 %

Observation

67770

Observationquinones: Q-10

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
32579	16947 ChEBI	citrate	+	carbon source
32579	24265 ChEBI	gluconate	+	carbon source
32579	25115 ChEBI	malate	+	carbon source
32579	18222 ChEBI	xylose	+	carbon source

Enzymes

@ref	Value	Activity	Ec
32579	catalase	+	1.11.1.6
32579	cytochrome oxidase	+	1.9.3.1

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Host Body-Site	#Plant	#Root nodule

Isolation

@ref	Sample type	Host species	Geographic location	Country	Country ISO 3 Code	Continent
8051	root nodules of herbal legume Kummerowia stipulacea	Kummerowia stipulacea	Shandong province	China	CHN	Asia
61086	Root nodule of Kummerowia stipulacea		Shandong province	China	CHN	Asia
67770	Root nodules of Kummerowia stipulacea grown in Shandong provice	Kummerowia stipulacea		China	CHN	Asia

Taxonmaps

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

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
8051	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
66792	ASM982705v1 assembly for Shinella kummerowiae CCBAU 25048	contig	GCA_009827055	417745.4	2989349275	417745	70.26

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
8051	Shinella kummerowiae strain CCBAU 25048 16S ribosomal RNA gene, partial sequence	EF070131	1372		417745
124043	Shinella kummerowiae strain CCBAU 25048 (T) 16S ribosomal RNA gene, partial sequence.	MK424305	1370		417745

GC content

@ref	GC-content (mol%)	Method
8051	63.1
67770	63.1	thermal denaturation, midpoint method (Tm)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM982705v1 assembly for Shinella kummerowiae CCBAU 25048
BV-BRC: 417745.4

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	94.24	no
125439	gram_stain	BacteriaNetⓘ	negative	92.56	no
125439	spore_formation	BacteriaNetⓘ	no	99.34	no
125439	motility	BacteriaNetⓘ	yes	51.56	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Shinella kummerowiae strain CCBAU 25048
PATRIC: 417745.4

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.50	no
125438	anaerobic	anaerobicⓘ	no	96.18	no
125438	spore-forming	spore-formingⓘ	no	90.95	yes
125438	aerobic	aerobicⓘ	yes	85.28	yes
125438	thermophilic	thermophileⓘ	no	98.75	yes
125438	flagellated	motile2+ⓘ	yes	70.06	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Integrating metagenomics and culturomics to uncover the soil bacterial community in Asparagus cochinchinensis cultivation.	Yu J, Yang S, Zhang X, Liu X, Tang X, Wang L, Chen J, Luo H, Liu C, Song C.	Front Microbiol	10.3389/fmicb.2024.1467864	2024
	Pollution pressure drives microbial assemblages that improve the phytoremediation potential of heavy metals by Ricinus communis.	Rubio-Noguez D, Breton-Deval L, Salinas-Peralta I, Juarez K, Galicia L.	World J Microbiol Biotechnol	10.1007/s11274-024-04025-8	2024
Enzymology	Isolation and Characterization of Levoglucosan-Metabolizing Bacteria.	Arya AS, Hang MTH, Eiteman MA.	Appl Environ Microbiol	10.1128/aem.01868-21	2022
	Shinella sedimenti sp. nov., isolated from sediment of Zhairuo Island located in the East China Sea.	Chen G, He M, Li KJ, Zheng KW, Tang XX, Debnath SC, Wang PM, Guo Z, Hong Y, Zheng DQ.	Int J Syst Evol Microbiol	10.1099/ijsem.0.006000	2023
	Bacteria Belonging to Pseudomonas typographi sp. nov. from the Bark Beetle Ips typographus Have Genomic Potential to Aid in the Host Ecology.	Peral-Aranega E, Saati-Santamaria Z, Kolarik M, Rivas R, Garcia-Fraile P.	Insects	10.3390/insects11090593	2020
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 )
#28794	IJSEM 1409 2008 ( DOI 10.1099/ijs.0.65723-0 , PubMed 18523187 )
#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
#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 .
#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 )

Rate our new design

Content

About us

Shinella kummerowiae (DSM 19334, CCBAU 25048, JCM 14778)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

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_009827055

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

Help

Social Media