Kosakonia oryzae (LMG 24251, CGMCC 1.7012, Ola 51)

Name: Kosakonia oryzae (LMG 24251, CGMCC 1.7012, Ola 51)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 133472

Type strain

Culture col. no. LMG 24251 CGMCC 1.7012 Ola 51

NCBI tax ID(s) 497725

Special Collections Literature strains

Links

Kosakonia oryzae LMG 24251 is a facultative anaerobe, Gram-negative, motile bacterium that was isolated from plant endophyte.

Gram-negative motile rod-shaped facultative anaerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 363406

CGMCC 1.7012,LMG 24251

@ref 20215

Last LPSN update 2026-05-29 08:38:06

Domain Bacteria

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Enterobacterales

Family Enterobacteriaceae

Genus Kosakonia

Species Kosakonia oryzae

Full scientific name Kosakonia oryzae (Peng et al. 2009) Brady et al. 2013

Synonyms (1)

Enterobacter oryzae

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
29090	negative	1.7 µm	0.95 µm	rod-shaped
125439	negative				98.621
125438	negative				100

Culture and growth conditions

Culture temp

@ref	Growth	Type	Temperature (°C)
29090	positive	growth	10-40
29090	positive	optimum	32.5

Culture pH

@ref	Ability	Type	PH	PH range
29090	positive	optimum	6.75
29090	positive	growth	3.5-10	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
29090	facultative anaerobe
125439	obligate aerobe	97.324

Spore formation

@ref	Spore formation	Confidence
125439		99.932
125438		92.802

Halophily

@ref	Salt	Growth	Tested relation	Concentration
29090	NaCl	positive	growth	<5 %
29090	NaCl	positive	optimum	<5 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
29090	37054 ChEBI	3-hydroxybutyrate	+	carbon source
29090	35391 ChEBI	aspartate	+	carbon source
29090	16947 ChEBI	citrate	+	carbon source
29090	28757 ChEBI	fructose	+	carbon source
29090	33984 ChEBI	fucose	+	carbon source
29090	25115 ChEBI	malate	+	carbon source
29090	17306 ChEBI	maltose	+	carbon source
29090	29864 ChEBI	mannitol	+	carbon source
29090	28053 ChEBI	melibiose	+	carbon source
29090	37657 ChEBI	methyl D-glucoside	+	carbon source
29090	15963 ChEBI	ribitol	+	carbon source
29090	30911 ChEBI	sorbitol	+	carbon source
29090	17992 ChEBI	sucrose	+	carbon source

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2
#Host	#Other
#Host	#Plants

Isolation

29090

Sample typeplant endophyte

Taxonmaps

69479

Global distribution of 16S sequence EF488759 (>99% sequence identity) for Enterobacteriaceae from Microbeatlas

Aquatic Samples	634
Soil Samples	222
Animal Samples	3824
Plant Samples	458
Total Samples	5138

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
124043	ASM165802v2 assembly for Kosakonia oryzae Ola 51	complete	GCA_001658025	497725.17	2811995292	497725	99.2
66792	IMG-taxon 2675902965 annotated assembly for Kosakonia oryzae CGMCC 1.7012	scaffold	GCA_900112145	497725.6	2675902965	497725	74.83

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
29090	Enterobacter oryzae strain Ola 51 16S ribosomal RNA gene, partial sequence	EF488759	1481		497725

GC content

29090

GC-content (mol%)54.6-55.4

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM165802v2 assembly for Kosakonia oryzae Ola 51
NCBI: GCA_001658025

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	97.32	no
125439	gram_stain	BacteriaNetⓘ	negative	98.62	no
125439	motility	BacteriaNetⓘ	yes	68.12	no
125439	spore_formation	BacteriaNetⓘ	no	99.93	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Kosakonia oryzae CGMCC 1.7012
NCBI: GCA_900112145.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	100.00	no
125438	anaerobic	anaerobicⓘ	no	96.60	no
125438	aerobic	aerobicⓘ	no	74.70	yes
125438	spore-forming	spore-formingⓘ	no	92.80	no
125438	thermophilic	thermophileⓘ	no	100.00	no
125438	flagellated	motile2+ⓘ	yes	72.39	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Comparative Genomics Reveal a Flagellar System, a Type VI Secretion System and Plant Growth-Promoting Gene Clusters Unique to the Endophytic Bacterium Kosakonia radicincitans.	Becker M, Patz S, Becker Y, Berger B, Drungowski M, Bunk B, Overmann J, Sproer C, Reetz J, Tchuisseu Tchakounte GV, Ruppel S.	Front Microbiol	10.3389/fmicb.2018.01997	2018
	Insights into using Kosakonia oryzae AG15 in liquid formulations containing sodium alginate, glycerol, and gum arabic for the sustainable development of Phaseolus vulgaris L.	Ribeiro AAP, Pinheiro TMA, Rossi I, Gomes FM, da Rocha AC, Dos Santos IR, Porto FGM, da Silva MT, Ribeiro AAP, Cardoso VL, de Resende MM.	3 Biotech	10.1007/s13205-025-04537-6	2025
	Bacterial and fungal root endophytes alter survival, growth, and resistance to grazing in a foundation plant species.	Garces KR, Hanley TC, Deckert R, Noble A, Richards C, Gehring C, Hughes AR.	Oecologia	10.1007/s00442-024-05650-8	2024
	Improving NH₃ and H₂S removal efficiency with pilot-scale biotrickling filter by co-immobilizing Kosakonia oryzae FB2-3 and Acinetobacter baumannii L5-4.	Zhu Q, Wu P, Chen B, Wu Q, Cao F, Wang H, Mei Y, Liang Y, Sun X, Chen Z.	Environ Sci Pollut Res Int	10.1007/s11356-022-24426-2	2023
	Bacterial skin infection caused by a plant pathogen Kosakonia cowanii: identification with the MALDI Biotyper sirius one and susceptibility testing.	Merlino J, Pillay K, Rizzo S, Baskar SR, Seed D, Siarakas S, Hettiarachchi R, McKew G, Gray T.	Access Microbiol	10.1099/acmi.0.000923.v3	2025
	Identification and Biodegradation Potential of a Novel Strain of Kosakonia oryzae Isolated from a Polyoxyethylene Tallow Amine Paddy Soil.	Nguyen NT, Pham TTT, Tran TN, Kumar VB, Saikia S, Kiefer R.	Curr Microbiol	10.1007/s00284-021-02592-9	2021
	Simple and sensitive spectrophotometric method for estimating the nitrogen-fixing capacity of bacterial cultures.	Cordova-Rodriguez A, Renteria-Martinez ME, Lopez-Miranda CA, Guzman-Ortiz JM, Moreno-Salazar SF.	MethodsX	10.1016/j.mex.2022.101917	2022
Metabolism	Rapid biodegradation and biofilm-mediated bioremoval of organophosphorus pesticides using an indigenous Kosakonia oryzae strain -VITPSCQ3 in a Vertical-flow Packed Bed Biofilm Bioreactor.	Dash DM, Osborne WJ.	Ecotoxicol Environ Saf	10.1016/j.ecoenv.2020.110290	2020
	Rearranging the sugarcane holobiont via plant growth-promoting bacteria and nitrogen input.	Leite MFA, Dimitrov MR, Freitas-Iorio RP, de Hollander M, Cipriano MAP, Andrade SAL, da Silveira APD, Kuramae EE.	Sci Total Environ	10.1016/j.scitotenv.2021.149493	2021
	A comparative assesment of biostimulants in microbiome-based ecorestoration of polycyclic aromatic hydrocarbon polluted soil.	Ehis-Eriakha CB, Chikere CB, Akaranta O, Akemu SE.	Braz J Microbiol	10.1007/s42770-024-01556-y	2025
	Endophytic bacterial communities in wild rice (Oryza officinalis) and their plant growth-promoting effects on perennial rice.	Tian Q, Gong Y, Liu S, Ji M, Tang R, Kong D, Xue Z, Wang L, Hu F, Huang L, Qin S.	Front Plant Sci	10.3389/fpls.2023.1184489	2023
Phylogeny	Reclassification of Enterobacter sp. FY-07 as Kosakonia oryzendophytica FY-07 and Its Potential to Promote Plant Growth.	Gao G, Zhang Y, Niu S, Chen Y, Wang S, Anwar N, Chen S, Li G, Ma T.	Microorganisms	10.3390/microorganisms10030575	2022
Metabolism	Pectinolytic Bacterial Consortia Reduce Jute Retting Period and Improve Fibre Quality.	Hasan R, Aktar N, Kabir SMT, Honi U, Halim A, Islam R, Sarker MDH, Haque MS, Alam MM, Islam MS.	Sci Rep	10.1038/s41598-020-61898-z	2020
Metabolism	Nitrogen Fixation in Pozol, a Traditional Fermented Beverage.	Rizo J, Rogel MA, Guillen D, Wacher C, Martinez-Romero E, Encarnacion S, Sanchez S, Rodriguez-Sanoja R.	Appl Environ Microbiol	10.1128/aem.00588-20	2020
	Exploring diazotrophic diversity: unveiling Nif core distribution and evolutionary patterns in nitrogen-fixing organisms.	Nichio BTL, Chaves RBR, Pedrosa FO, Raittz RT.	BMC Genomics	10.1186/s12864-024-10994-9	2025
	Soil humus-reducing bacteria in the Xisha islands, South China sea: unveiling diversity and predicting functions.	Deng X, Najeeb S, Liu K, Tan H, Li Y, Wu C, Zhang Y.	BMC Microbiol	10.1186/s12866-025-04137-7	2025
	Microorganisms Capable of Producing Polysaccharides from D-Xylose.	Tsutsui S, Hatano T, Funada R, Kaneko S.	J Appl Glycosci (1999)	10.5458/jag.jag.jag-2022_0008	2022
	Biodegradation of monocrotophos, cypermethrin & fipronil by Proteus myxofaciens VITVJ1: A plant - microbe based remediation.	Vaishnavi J, Osborne JW.	Heliyon	10.1016/j.heliyon.2024.e37384	2024
Phylogeny	Taxonomic evaluation of the genus Enterobacter based on multilocus sequence analysis (MLSA): proposal to reclassify E. nimipressuralis and E. amnigenus into Lelliottia gen. nov. as Lelliottia nimipressuralis comb. nov. and Lelliottia amnigena comb. nov., respectively, E. gergoviae and E. pyrinus into Pluralibacter gen. nov. as Pluralibacter gergoviae comb. nov. and Pluralibacter pyrinus comb. nov., respectively, E. cowanii, E. radicincitans, E. oryzae and E. arachidis into Kosakonia gen. nov. as Kosakonia cowanii comb. nov., Kosakonia radicincitans comb. nov., Kosakonia oryzae comb. nov. and Kosakonia arachidis comb. nov., respectively, and E. turicensis, E. helveticus and E. pulveris into Cronobacter as Cronobacter zurichensis nom. nov., Cronobacter helveticus comb. nov. and Cronobacter pulveris comb. nov., respectively, and emended description of the genera Enterobacter and Cronobacter.	Brady C, Cleenwerck I, Venter S, Coutinho T, De Vos P.	Syst Appl Microbiol	10.1016/j.syapm.2013.03.005	2013
	Root-Derived Endophytic Diazotrophic Bacteria Pantoea cypripedii AF1 and Kosakonia arachidis EF1 Promote Nitrogen Assimilation and Growth in Sugarcane.	Singh RK, Singh P, Guo DJ, Sharma A, Li DP, Li X, Verma KK, Malviya MK, Song XP, Lakshmanan P, Yang LT, Li YR.	Front Microbiol	10.3389/fmicb.2021.774707	2021
	A Novel Salmonella Periplasmic Protein Controlling Cell Wall Homeostasis and Virulence.	Cestero JJ, Castanheira S, Pucciarelli MG, Garcia-Del Portillo F.	Front Microbiol	10.3389/fmicb.2021.633701	2021
	Genotypic Variation of Endophytic Nitrogen-Fixing Activity and Bacterial Flora in Rice Stem Based on Sugar Content.	Okamoto T, Shinjo R, Nishihara A, Uesaka K, Tanaka A, Sugiura D, Kondo M.	Front Plant Sci	10.3389/fpls.2021.719259	2021
Phylogeny	Microbial and Biochemical Profile of Different Types of Greek Table Olives.	Mougiou N, Tsoureki A, Didos S, Bouzouka I, Michailidou S, Argiriou A.	Foods	10.3390/foods12071527	2023
	Contribution of Zinc Solubilizing Bacteria in Growth Promotion and Zinc Content of Wheat.	Kamran S, Shahid I, Baig DN, Rizwan M, Malik KA, Mehnaz S.	Front Microbiol	10.3389/fmicb.2017.02593	2017
	Evidence for Widespread Class II Microcins in Enterobacterales Genomes.	Cole TJ, Parker JK, Feller AL, Wilke CO, Davies BW.	Appl Environ Microbiol	10.1128/aem.01486-22	2022
	The Mexican giant maize of Jala landrace harbour plant-growth-promoting rhizospheric and endophytic bacteria.	Rios-Galicia B, Villagomez-Garfias C, De la Vega-Camarillo E, Guerra-Camacho JE, Medina-Jaritz N, Arteaga-Garibay RI, Villa-Tanaca L, Hernandez-Rodriguez C.	3 Biotech	10.1007/s13205-021-02983-6	2021
Metabolism	Culture-independent analysis of hydrocarbonoclastic bacterial communities in environmental samples during oil-bioremediation.	Dashti N, Ali N, Salamah S, Khanafer M, Al-Shamy G, Al-Awadhi H, Radwan SS.	Microbiologyopen	10.1002/mbo3.630	2019
	Isolation, Characterization, and Evaluation of Native Rhizobacterial Consortia Developed From the Rhizosphere of Rice Grown in Organic State Sikkim, India, and Their Effect on Plant Growth.	Sherpa MT, Sharma L, Bag N, Das S.	Front Microbiol	10.3389/fmicb.2021.713660	2021
	Development and Application of Low-Cost and Eco-Sustainable Bio-Stimulant Containing a New Plant Growth-Promoting Strain Kosakonia pseudosacchari TL13.	Romano I, Ventorino V, Ambrosino P, Testa A, Chouyia FE, Pepe O.	Front Microbiol	10.3389/fmicb.2020.02044	2020
	Zinc biosorption, biochemical and molecular characterization of plant growth-promoting zinc-tolerant bacteria.	Kour R, Jain D, Bhojiya AA, Sukhwal A, Sanadhya S, Saheewala H, Jat G, Singh A, Mohanty SR.	3 Biotech	10.1007/s13205-019-1959-2	2019
Phylogeny	What's in a Name? New Bacterial Species and Changes to Taxonomic Status from 2012 through 2015.	Munson E, Carroll KC.	J Clin Microbiol	10.1128/jcm.01379-16	2017
Genetics	Complete genome sequence of Kosakonia oryzae type strain Ola 51(T).	Li Y, Li S, Chen M, Peng G, Tan Z, An Q	Stand Genomic Sci	10.1186/s40793-017-0240-8	2017
	Precise Species Identification for Enterobacter: a Genome Sequence-Based Study with Reporting of Two Novel Species, Enterobacter quasiroggenkampii sp. nov. and Enterobacter quasimori sp. nov.	Wu W, Feng Y, Zong Z.	mSystems	10.1128/msystems.00527-20	2020
Phylogeny	Enterobacter oryzae sp. nov., a nitrogen-fixing bacterium isolated from the wild rice species Oryza latifolia.	Peng G, Zhang W, Luo H, Xie H, Lai W, Tan Z	Int J Syst Evol Microbiol	10.1099/ijs.0.65484-0	2009

References

#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 )
#25519	IJSEM 1650 2009 ( DOI 10.1099/ijs.0.005967-0 )
#29090	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 #25519
#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 .
#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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Kosakonia oryzae (LMG 24251, CGMCC 1.7012, Ola 51)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Metabolite utilization

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Sequence information

Genome sequences

Genome browser: GCA_001658025

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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