Allorhizobium undicola (CIP 105883, LMG 11875, IAM 15378)

Name: Allorhizobium undicola (CIP 105883, LMG 11875, IAM 15378)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 138767

Type strain

Culture col. no. CIP 105883 LMG 11875 IAM 15378 ATCC 700741 JCM 21822 1 more

NCBI tax ID(s) 1370122 78527

Special Collections JCM CIP

History IAM 15378 <-- LMG 11875 <-- P. de Lajudie. CIP <- 1999, LMG <- 1991 de Lajudie, ORSTOM, West Africa: strain ORS 992

Links

Allorhizobium undicola CIP 105883 is a mesophilic, Gram-negative, motile prokaryote of the family Rhizobiaceae.

Gram-negative motile rod-shaped mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 11971

LMG 11875,ATCC 700741,CIP 105883,JCM 21822,CFBP 6719,IAM 15378

@ref 20215

Last LPSN update 2026-02-09 11:33:11

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Hyphomicrobiales

Family Rhizobiaceae

Genus Allorhizobium

Species Allorhizobium undicola

Full scientific name Allorhizobium undicola de Lajudie et al. 1998

Synonyms (1)

Rhizobium undicola

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
125438	negative		97.985
125439	negative		99.7
40508	negative	rod-shaped

Colony morphology

Culture and growth conditions

Culture medium

@ref	Name	Growth	Composition	Medium link
40508	MEDIUM 304 - for Allorhizobium undicola		Distilled water make up to (987.000 ml);Sodium chloride (0.050 g);Agar (20.000 g);Yeast extract (1.000 g);Potassium di-hydrogen phosphate (0.500 g);Sodium glutamate (0.500 g);Mannitol (10.000 g);Solution A - M0556 (10.000 ml);Solution B - M0557 (1.000 ml)
40508	CIP Medium 296			Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
40508	positive	growth	30	mesophilic
40508	positive	growth	15-41
40508	negative	growth	5
40508	negative	growth	45
67770	positive	growth	28	mesophilic

Physiology and metabolism

Spore formation

@ref	Spore formation	Confidence
125438		91.638
125439		99.1

Halophily

@ref	Salt	Growth	Tested relation	Concentration
40508	NaCl	positive	growth	0-6 %
40508	NaCl		growth	8 %
40508	NaCl		growth	10 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
40508	16947 ChEBI	citrate	+	carbon source
40508	4853 ChEBI	esculin	-	hydrolysis
40508	17234 ChEBI	glucose	+	degradation
40508	606565 ChEBI	hippurate	-	hydrolysis
40508	15792 ChEBI	malonate	-	assimilation
40508	17632 ChEBI	nitrate	-	builds gas from
40508	17632 ChEBI	nitrate	-	reduction
40508	17632 ChEBI	nitrate	-	respiration
40508	16301 ChEBI	nitrite	-	builds gas from
40508	16301 ChEBI	nitrite	-	reduction

Antibiotic resistance

@ref	Metabolite	Is sensitive	Is resistant
40508	0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)

Metabolite production

@ref	Chebi-ID	Metabolite	Production
40508	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test	Methylred-test
40508	15688 ChEBI	acetoin	-
40508	17234 ChEBI	glucose		-

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
40508	alcohol dehydrogenase	-	1.1.1.1
68382	alkaline phosphatase	+	3.1.3.1	from API zym
68382	alpha-chymotrypsin	-	3.4.21.1	from API zym
68382	alpha-fucosidase	-	3.2.1.51	from API zym
68382	alpha-galactosidase	-	3.2.1.22	from API zym
68382	alpha-glucosidase	+	3.2.1.20	from API zym
68382	alpha-mannosidase	-	3.2.1.24	from API zym
68382	beta-galactosidase	+	3.2.1.23	from API zym
40508	beta-galactosidase	+	3.2.1.23
68382	beta-glucosidase	+	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
40508	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
40508	gamma-glutamyltransferase	+	2.3.2.2
40508	gelatinase	-
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	lipase (C 14)	-		from API zym
40508	lysine decarboxylase	-	4.1.1.18
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
40508	ornithine decarboxylase	-	4.1.1.17
40508	oxidase	-
40508	phenylalanine ammonia-lyase	+	4.3.1.24
68382	trypsin	+	3.4.21.4	from API zym
40508	tryptophan deaminase	-
40508	urease	+	3.5.1.5
68382	valine arylamidase	-		from API zym

API zym

@ref	Control	Alkaline phosphatase	Esterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	Lipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
40508	-	+	+	+	-	+	-	-	+	-	+	+	-	+	-	+	+	-	-	-

API biotype100

@ref	ControlQ	D-glucose as carbon sourceGLU	D-fructose as carbon sourceFRU	D-galactose as carbon sourceGAL	D-trehalose as carbon sourceTRE	D-mannose as carbon sourceMNE	L-sorbose as carbon sourceSBE	D-melibiose as carbon sourceMEL	sucrose as carbon sourceSAC	D-raffinose as carbon sourceRAF	maltotriose as carbon sourceMTE	maltose as carbon sourceMAL	lactose as carbon sourceLAC	lactulose as carbon sourceLTE	1-O-methyl-beta-galactopyranoside as carbon sourceMbGa	1-O-methyl-alpha-galactopyranoside as carbon sourceMaGa	D-cellobiose as carbon sourceCEL	gentiobiose as carbon sourceGEN	1-O-methyl-beta-D-glucopyranoside as carbon sourceMbGu	esculin as carbon sourceESC	D-ribose as carbon sourceRIB	L-arabinose as carbon sourceARA	D-xylose as carbon sourceXYL	palatinose as carbon sourcePLE	L-rhamnose as carbon sourceRHA	L-fucose as carbon sourceFUC	D-melezitose as carbon sourceMLZ	D-arabitol as carbon sourceDARL	L-arabitol as carbon sourceLARL	xylitol as carbon sourceXLT	dulcitol as carbon sourceDUL	D-tagatose as carbon sourceTAG	glycerol as carbon sourceGLY	myo-inositol as carbon sourceINO	D-mannitol as carbon sourceMAN	maltitol as carbon sourceMTL	D-turanose as carbon sourceTUR	D-sorbitol as carbon sourceSOR	adonitol as carbon sourceADO	hydroxyquinoline-beta-glucuronide as carbon sourceHBG	D-lyxose as carbon sourceLYX	i-erythritol as carbon sourceERY	1-O-methyl-alpha-D-glucoside as carbon sourceMDG	3-O-methyl-D-glucose as carbon source3MDG	D-saccharate as carbon sourceSAT	mucate as carbon sourceMUC	L-tartrate as carbon sourceLTAT	D-tartrate as carbon sourceDTAT	meso-tartrate as carbon sourceMTAT	D-malate as carbon sourceDMLT	L-malate as carbon sourceLMLT	cis-aconitate as carbon sourceCATE	trans-aconitate as carbon sourceTATE	tricarballylate as carbon sourceTTE	citrate as carbon sourceCIT	D-glucuronate as carbon sourceGRT	D-galacturonate as carbon sourceGAT	2-ketogluconate as carbon source2KG	5-ketogluconate as carbon source5KG	tryptophan as carbon sourceTRY	N-acetyl-D-glucosamine as carbon sourceNAG	D-gluconate as carbon sourceGNT	phenylacetate as carbon sourcePAC	protocatechuate as carbon sourcePAT	4-hydroxybenzoate as carbon sourcepOBE	quinate as carbon sourceQAT	gentisate as carbon sourceGTE	3-hydroxybenzoate as carbon sourcemOBE	benzoate as carbon sourceBAT	3-phenylpropionate as carbon sourcePPAT	m-coumarate as carbon sourceCMT	trigonelline as carbon sourceTGE	betaine as carbon sourceBET	putrescine as carbon sourcePCE	4-aminobutyrate as carbon sourceABT	histamine as carbon sourceHIN	DL-lactate as carbon sourceLAT	caprate as carbon sourceCAP	caprylate as carbon sourceCYT	L-histidine as carbon sourceHIS	succinate as carbon sourceSUC	fumarate as carbon sourceFUM	glutarate as carbon sourceGRE	DL-glycerate as carbon sourceGYT	5-aminovalerate as carbon sourceAVT	ethanolamine as carbon sourceETN	tryptamine as carbon sourceTTN	D-glucosamine as carbon sourceGLN	itaconate as carbon sourceITA	3-hydroxybutyrate as carbon source3OBU	L-aspartate as carbon sourceAPT	L-glutamate as carbon sourceGTT	L-proline as carbon sourcePRO	D-alanine as carbon sourceDALA	L-alanine as carbon sourceLALA	L-serine as carbon sourceSER	malonate as carbon sourceMNT	propionate as carbon sourcePROP	L-tyrosine as carbon sourceTYR	2-ketoglutarate as carbon source2KT
40508	not determinedn.d.	+	+	+	-	+	-	-	+	-	-	+	+	+	-	-	+	+	+	+	+	+	+	-	+	-	-	+	-	-	-	-	+	+	+	-	+	+	-	-	+	-	-	-	-	-	-	-	-	+	+	+	-	-	+	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	+	-	+	-	+	-	-	+	+	+	-	-	-	-	-	+	-	+	-	+	+	-	+	-	-	-	-	-

Isolation, sampling and environmental information

Isolation

@ref	Sample type	Host species	Geographic location	Country	Country ISO 3 Code	Continent
40508				Senegal	SEN	Africa
67770	Neptunia natans (aquatic legume)	Neptunia natans	Kaolack	Senegal	SEN	Africa
40508	Neptunia natans, nodules			Senegal	SEN	Africa

Taxonmaps

69479

Global distribution of 16S sequence Y17047 (>99% sequence identity) for Rhizobium undicola subclade from Microbeatlas

Aquatic Samples	32
Soil Samples	30
Animal Samples	33
Plant Samples	3
Total Samples	98

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
40508	1	Risk group (French classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	ASM62166v1 assembly for Allorhizobium undicola ORS 992 = ATCC 700741	scaffold	GCA_000621665	1370122.3	2558860983	1370122	68.66

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
67770	Allorhizobium undicola 16S rRNA gene	Y17047	1433		78527
124043	Rhizobium undicola strain LMG 11875 16S ribosomal RNA gene, partial sequence; internal transcribed spacer, complete sequence; and 23S ribosomal RNA, partial sequence	AF345280	1291		78527

GC content

@ref	GC-content (mol%)	Method
67770	60.1	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: Allorhizobium undicola ORS 992 = ATCC 700741
NCBI: GCA_000621665

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	99.10	no
125439	motility	BacteriaNetⓘ	yes	67.00	no
125439	gram_stain	BacteriaNetⓘ	negative	99.70	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	88.50	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Rhizobium undicola ORS 992 = ATCC 700741
PATRIC: 1370122.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.99	no
125438	anaerobic	anaerobicⓘ	no	95.03	no
125438	spore-forming	spore-formingⓘ	no	91.64	no
125438	aerobic	aerobicⓘ	yes	86.01	no
125438	thermophilic	thermophileⓘ	no	96.36	yes
125438	flagellated	motile2+ⓘ	yes	70.00	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Phylogeny and Phylogeography of Rhizobial Symbionts Nodulating Legumes of the Tribe Genisteae.	Stepkowski T, Banasiewicz J, Granada CE, Andrews M, Passaglia LMP.	Genes (Basel)	10.3390/genes9030163	2018
Phylogeny	Rapid and accurate species and genomic species identification and exhaustive population diversity assessment of Agrobacterium spp. using recA-based PCR.	Shams M, Vial L, Chapulliot D, Nesme X, Lavire C.	Syst Appl Microbiol	10.1016/j.syapm.2013.03.002	2013
Enzymology	Single acquisition of protelomerase gave rise to speciation of a large and diverse clade within the Agrobacterium/Rhizobium supercluster characterized by the presence of a linear chromid.	Ramirez-Bahena MH, Vial L, Lassalle F, Diel B, Chapulliot D, Daubin V, Nesme X, Muller D.	Mol Phylogenet Evol	10.1016/j.ympev.2014.01.005	2014
Genetics	Genomic analysis provides novel insights into diversification and taxonomy of Allorhizobium vitis (i.e. Agrobacterium vitis).	Kuzmanovic N, Biondi E, Overmann J, Pulawska J, Verbarg S, Smalla K, Lassalle F.	BMC Genomics	10.1186/s12864-022-08662-x	2022
Phylogeny	A revision of Rhizobium Frank 1889, with an emended description of the genus, and the inclusion of all species of Agrobacterium Conn 1942 and Allorhizobium undicola de Lajudie et al. 1998 as new combinations: Rhizobium radiobacter, R. rhizogenes, R. rubi, R. undicola and R. vitis.	Young JM, Kuykendall LD, Martinez-Romero E, Kerr A, Sawada H.	Int J Syst Evol Microbiol	10.1099/00207713-51-1-89	2001
Genetics	Plasmids Related to the Symbiotic Nitrogen Fixation Are Not Only Cooperated Functionally but Also May Have Evolved over a Time Span in Family Rhizobiaceae.	Yang LL, Jiang Z, Li Y, Wang ET, Zhi XY.	Genome Biol Evol	10.1093/gbe/evaa152	2020
	New Insights into the Taxonomy of Bacteria in the Genomic Era and a Case Study with Rhizobia.	Ferraz Helene LC, Klepa MS, Hungria M.	Int J Microbiol	10.1155/2022/4623713	2022
Phylogeny	A new species of Devosia that forms a unique nitrogen-fixing root-nodule symbiosis with the aquatic legume Neptunia natans (L.f.) druce.	Rivas R, Velazquez E, Willems A, Vizcaino N, Subba-Rao NS, Mateos PF, Gillis M, Dazzo FB, Martinez-Molina E.	Appl Environ Microbiol	10.1128/aem.68.11.5217-5222.2002	2002
Phylogeny	Methylotrophic Methylobacterium bacteria nodulate and fix nitrogen in symbiosis with legumes.	Sy A, Giraud E, Jourand P, Garcia N, Willems A, de Lajudie P, Prin Y, Neyra M, Gillis M, Boivin-Masson C, Dreyfus B.	J Bacteriol	10.1128/jb.183.1.214-220.2001	2001
Phylogeny	Allorhizobium terrae sp. nov., isolated from paddy soil, and reclassification of Rhizobium oryziradicis (Zhao et al. 2017) as Allorhizobium oryziradicis comb. nov.	Lin SY, Hameed A, Huang HI, Young CC.	Int J Syst Evol Microbiol	10.1099/ijsem.0.003770	2020
Phylogeny	Description of Devosia neptuniae sp. nov. that nodulates and fixes nitrogen in symbiosis with Neptunia natans, an aquatic legume from India.	Rivas R, Willems A, Subba-Rao NS, Mateos PF, Dazzo FB, Kroppenstedt RM, Martinez-Molina E, Gillis M, Velazquez E.	Syst Appl Microbiol	10.1078/072320203322337308	2003
Phylogeny	Allorhizobium undicola gen. nov., sp. nov., nitrogen-fixing bacteria that efficiently nodulate Neptunia natans in Senegal.	de Lajudie P, Laurent-Fulele E, Willems A, Torck U, Coopman R, Collins MD, Kersters K, Dreyfus B, Gillis M	Int J Syst Bacteriol	10.1099/00207713-48-4-1277	1998

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 )
#40508	Collection of Institut Pasteur ; Curators of the CIP; CIP 105883
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#68382	Automatically annotated from API zym .
#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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Allorhizobium undicola (CIP 105883, LMG 11875, IAM 15378)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Spore formation

Halophily

Metabolite utilization

Antibiotic resistance

Metabolite production

Metabolite tests

Enzymes

API zym

API biotype100

Isolation, sampling and environmental information

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000621665

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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