Ensifer kostiensis (DSM 13372, HAMBI 1489, LMG 15613)

Name: Ensifer kostiensis (DSM 13372, HAMBI 1489, LMG 15613)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 13553

Type strain

Culture col. no. DSM 13372 HAMBI 1489 LMG 15613 TTR 15

NCBI tax ID(s) 76747

Special Collections DSMZ

Links

Ensifer kostiensis DSM 13372 is a mesophilic prokaryote that was isolated from root nodules of Acacia senegal.

mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 13018

LMG 15613,HAMBI 1489,LMG 19227,DSM 13372,NCIMB 13656,ATCC BAA-227,NBRC 100382,KACC 10756

@ref 20215

Last LPSN update 2025-12-16 09:50:07

Domain Pseudomonadati

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Hyphomicrobiales

Family Rhizobiaceae

Genus Ensifer

Species Ensifer kostiensis

Full scientific name Ensifer kostiensis (Nick et al. 1999) Young 2003

Synonyms (1)

Sinorhizobium kostiense

BacDive ID	Other strains from **Ensifer kostiensis** (2)	Type strain
13554	E. kostiensis 34, DSM 13373, HAMBI 1501
13555	E. kostiensis DSM 13374, HAMBI 1679, TTR 1

Morphology

Cell morphology

@ref	Gram stain	Confidence
125438	negative	99
125439	negative	99.1

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
5011	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)	Range
5011	positive	growth	30	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	97.8

Spore formation

@ref	Spore formation	Confidence
125439		97.6

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68369	17128 ChEBI	adipate	-	assimilation	from API 20NE
68369	29016 ChEBI	arginine	-	hydrolysis	from API 20NE
68369	17634 ChEBI	D-glucose	+	assimilation	from API 20NE
68369	17634 ChEBI	D-glucose	-	fermentation	from API 20NE
68369	16899 ChEBI	D-mannitol	+	assimilation	from API 20NE
68369	27689 ChEBI	decanoate	-	assimilation	from API 20NE
68369	4853 ChEBI	esculin	+	hydrolysis	from API 20NE
68369	5291 ChEBI	gelatin	-	hydrolysis	from API 20NE
68369	24265 ChEBI	gluconate	+	assimilation	from API 20NE
68369	30849 ChEBI	L-arabinose	+	assimilation	from API 20NE
68369	25115 ChEBI	malate	+	assimilation	from API 20NE
68369	17306 ChEBI	maltose	+	assimilation	from API 20NE
68369	59640 ChEBI	N-acetylglucosamine	+	assimilation	from API 20NE
68369	17632 ChEBI	nitrate	-	reduction	from API 20NE
68369	27897 ChEBI	tryptophan	-	energy source	from API 20NE
68369	16199 ChEBI	urea	+	hydrolysis	from API 20NE

Metabolite production

@ref	Chebi-ID	Metabolite	Production
68369	35581 ChEBI	indole		from API 20NE

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
68369	35581 ChEBI	indole	-	from API 20NE

Enzymes

@ref	Value	Activity	Ec
68369	arginine dihydrolase	-	3.5.3.6	from API 20NE
68369	beta-glucosidase	+	3.2.1.21	from API 20NE
68369	cytochrome oxidase	+	1.9.3.1	from API 20NE
68369	gelatinase	-		from API 20NE
68369	urease	+	3.5.1.5	from API 20NE

API 20NE

@ref	Reduction of nitratesNO3	TRP	GLU_ Ferm	ADH (Arg)	URE	ESC	GEL	PNPG	GLU_ Assim	ARA	MNE	MAN	NAG	MAL	GNT	CAP	ADI	MLT	CIT	PAC	OX
5011	-	-	-	-	+	+	-	+	+	+	+/-	+	+	+	+	-	-	+	-	-	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Plants	#Tree
#Host Body-Site	#Plant	#Root nodule

Isolation

@ref	Sample type	Host species	Geographic location	Country	Country ISO 3 Code	Continent
5011	root nodules of Acacia senegal	Acacia senegal	Kosti	Sudan	SDN	Africa

Taxonmaps

69479

Global distribution of 16S sequence AM181747 (>99% sequence identity) for Rhizobiaceae from Microbeatlas

Aquatic Samples	1562
Soil Samples	5353
Animal Samples	1094
Plant Samples	1478
Total Samples	9487

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
5011	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	ASM1787459v1 assembly for Sinorhizobium kostiense DSM 13372	contig	GCA_017874595	76747.3	2913295892	76747	74.36

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20218	Sinorhizobium sp. 16S rRNA gene, strain HAMBI 1489	Z78203	1437		42445
5011	Sinorhizobium kostiense partial 16S rRNA gene, strain LMG 19225	AM181747	1426		76747

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Sinorhizobium kostiense DSM 13372
NCBI: GCA_017874595

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	97.60	no
125439	motility	BacteriaNetⓘ	no	52.50	no
125439	gram_stain	BacteriaNetⓘ	negative	99.10	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	97.80	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Sinorhizobium kostiense strain DSM 13372
PATRIC: 76747.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	99.00	no
125438	anaerobic	anaerobicⓘ	no	95.68	no
125438	aerobic	aerobicⓘ	yes	84.36	no
125438	spore-forming	spore-formingⓘ	no	88.41	no
125438	thermophilic	thermophileⓘ	no	99.00	yes
125438	flagellated	motile2+ⓘ	yes	72.58	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Multi locus sequence analysis and symbiotic characterization of novel Ensifer strains nodulating Tephrosia spp. in the Indian Thar Desert.	Tak N, Awasthi E, Bissa G, Meghwal RR, James EK, Sprent JS, Gehlot HS.	Syst Appl Microbiol	10.1016/j.syapm.2016.08.002	2016
Phylogeny	The genus name Ensifer Casida 1982 takes priority over Sinorhizobium Chen et al. 1988, and Sinorhizobium morelense Wang et al. 2002 is a later synonym of Ensifer adhaerens Casida 1982. Is the combination "Sinorhizobium adhaerens" (Casida 1982) Willems et al. 2003 legitimate? Request for an Opinion.	Young JM.	Int J Syst Evol Microbiol	10.1099/ijs.0.02665-0	2003
	Both Alpha- and Beta-Rhizobia Occupy the Root Nodules of Vachellia karroo in South Africa.	Beukes CW, Boshoff FS, Phalane FL, Hassen AI, le Roux MM, Stepkowski T, Venter SN, Steenkamp ET.	Front Microbiol	10.3389/fmicb.2019.01195	2019

References

#5011	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 13372
#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 )
#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) .
#68369	Automatically annotated from API 20NE .
#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 .
#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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Ensifer kostiensis (DSM 13372, HAMBI 1489, LMG 15613)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API 20NE

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_017874595

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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