Mesorhizobium japonicum (MAFF 303099, LMG 29417, CECT 9101)

Name: Mesorhizobium japonicum (MAFF 303099, LMG 29417, CECT 9101)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 133271

Type strain

Culture col. no. MAFF 303099 LMG 29417 CECT 9101 IAM 15132 JCM 21590

NCBI tax ID(s) 266835 2066070

Special Collections JCM Literature strains

History IAM 15132 <-- MAFF 303099.

Links

Mesorhizobium japonicum MAFF 303099 is an aerobe, Gram-negative, rod-shaped prokaryote that forms circular colonies and was isolated from root nodules of Lotus japonicum.

Gram-negative rod-shaped colony-forming aerobe genome sequence

Name and taxonomic classification

SI-ID 128950

LMG 29417,CECT 9101,JCM 21590,IAM 15132

@ref 20215

Last LPSN update 2025-12-16 10:01:44

Domain Pseudomonadati

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Hyphomicrobiales

Family Phyllobacteriaceae

Genus Mesorhizobium

Species Mesorhizobium japonicum

Full scientific name Mesorhizobium japonicum Martínez-Hidalgo et al. 2016

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
25130	negative	rod-shaped
125438	negative		99.333
125439	negative		98.2

Colony morphology

@ref	Colony size	Colony color	Colony shape	Incubation period	Medium used
25130	1.0-2.0 mm	white	circular	4-5 days	YMA (yeast mannitol agar)

Culture and growth conditions

Culture medium

@ref	Name	Growth
25130	YMA (yeast mannitol agar)

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
25130	positive	growth	15.0-34.0
25130	positive	optimum	28	mesophilic
25130	negative	growth	10
25130	positive	growth	37	mesophilic
67770	positive	growth	28	mesophilic

Culture pH

@ref	Ability	Type	PH
25130	positive	optimum	7
25130	positive	growth	6.0-8.0

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
25130	aerobe
125439	obligate aerobe	98.5

Spore formation

@ref	Spore formation	Confidence
125439		97

Halophily

@ref	Salt	Growth	Tested relation	Concentration
25130	NaCl		maximum	5 %
25130	NaCl		growth	1 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
25130	16808 ChEBI	2-dehydro-D-gluconate	-	assimilation
25130	16808 ChEBI	2-dehydro-D-gluconate	-	builds base from
25130	16193 ChEBI	3-hydroxybenzoate	-	assimilation
25130	37054 ChEBI	3-hydroxybutyrate	+	assimilation
25130	17879 ChEBI	4-hydroxybenzoate	+	assimilation
25130	58143 ChEBI	5-dehydro-D-gluconate	-	assimilation
25130	58143 ChEBI	5-dehydro-D-gluconate	-	builds base from
25130	30089 ChEBI	acetate	+	assimilation
25130	17128 ChEBI	adipate	+	assimilation
25130	27613 ChEBI	amygdalin	-	builds acid from
25130	18305 ChEBI	arbutin	+	assimilation
25130	17968 ChEBI	butyrate	-	assimilation
25130	17057 ChEBI	cellobiose	-	builds acid from
25130	16947 ChEBI	citrate	-	assimilation
25130	17108 ChEBI	D-arabinose	+	builds acid from
25130	18333 ChEBI	D-arabitol	+	builds acid from
25130	15824 ChEBI	D-fructose	+	builds acid from
25130	28847 ChEBI	D-fucose	+	builds acid from
25130	12936 ChEBI	D-galactose	+	builds acid from
25130	17634 ChEBI	D-glucose	+	builds acid from
25130	62318 ChEBI	D-lyxose	+	builds acid from
25130	16899 ChEBI	D-mannitol	+	builds acid from
25130	16024 ChEBI	D-mannose	+	builds acid from
25130	16988 ChEBI	D-ribose	+	assimilation
25130	16988 ChEBI	D-ribose	+	builds acid from
25130	17924 ChEBI	D-sorbitol	+	assimilation
25130	17924 ChEBI	D-sorbitol	+	builds acid from
25130	16443 ChEBI	D-tagatose	-	builds acid from
25130	65327 ChEBI	D-xylose	+	builds acid from
25130	17113 ChEBI	erythritol	-	builds acid from
25130	4853 ChEBI	esculin	+	hydrolysis
25130	4853 ChEBI	esculin	+	assimilation
25130	16813 ChEBI	galactitol	-	builds acid from
25130	28066 ChEBI	gentiobiose	-	builds acid from
25130	24265 ChEBI	gluconate	+	assimilation
25130	17234 ChEBI	glucose	+	assimilation
25130	17754 ChEBI	glycerol	+	builds acid from
25130	28087 ChEBI	glycogen	-	assimilation
25130	28087 ChEBI	glycogen	-	builds acid from
25130	15443 ChEBI	inulin	-	builds acid from
25130	17240 ChEBI	itaconate	-	assimilation
25130	16977 ChEBI	L-alanine	-	assimilation
25130	30849 ChEBI	L-arabinose	+	assimilation
25130	30849 ChEBI	L-arabinose	+	builds acid from
25130	18403 ChEBI	L-arabitol	-	builds acid from
25130	18287 ChEBI	L-fucose	+	assimilation
25130	18287 ChEBI	L-fucose	+	builds acid from
25130	15971 ChEBI	L-histidine	+	assimilation
25130	17203 ChEBI	L-proline	+	assimilation
25130	62345 ChEBI	L-rhamnose	+	assimilation
25130	62345 ChEBI	L-rhamnose	+	builds acid from
25130	17115 ChEBI	L-serine	-	assimilation
25130	17266 ChEBI	L-sorbose	-	builds acid from
25130	65328 ChEBI	L-xylose	+	builds acid from
25130	24996 ChEBI	lactate	+	assimilation
25130	17716 ChEBI	lactose	-	builds acid from
25130	25115 ChEBI	malate	+	assimilation
25130	15792 ChEBI	malonate	-	assimilation
25130	17306 ChEBI	maltose	-	builds acid from
25130	17306 ChEBI	maltose	+	assimilation
25130	29864 ChEBI	mannitol	+	assimilation
25130	37684 ChEBI	mannose	+	assimilation
25130	6731 ChEBI	melezitose	-	builds acid from
25130	28053 ChEBI	melibiose	+	assimilation
25130	28053 ChEBI	melibiose	+	builds acid from
25130	43943 ChEBI	methyl alpha-D-mannoside	-	builds acid from
25130		methyl alpha-D-xylopyranoside	-	builds acid from
25130	37657 ChEBI	methyl D-glucoside	-	builds acid from
25130	17268 ChEBI	myo-inositol	-	builds acid from
25130	17268 ChEBI	myo-inositol	+	assimilation
25130	506227 ChEBI	N-acetylglucosamine	+	assimilation
25130	506227 ChEBI	N-acetylglucosamine	+	builds acid from
25130	17632 ChEBI	nitrate	-	reduction
25130	18401 ChEBI	phenylacetate	-	assimilation
25130	32032 ChEBI	potassium gluconate	-	builds base from
25130	17272 ChEBI	propionate	+	assimilation
25130	16634 ChEBI	raffinose	-	builds acid from
25130	15963 ChEBI	ribitol	+	builds acid from
25130	17814 ChEBI	salicin	-	builds acid from
25130	17814 ChEBI	salicin	+	assimilation
25130	28017 ChEBI	starch	-	builds acid from
25130	9300 ChEBI	suberic acid	-	assimilation
25130	17992 ChEBI	sucrose	+	assimilation
25130	17992 ChEBI	sucrose	+	builds acid from
25130	27082 ChEBI	trehalose	+	builds acid from
25130	32528 ChEBI	turanose	-	builds acid from
25130	31011 ChEBI	valerate	-	assimilation
25130	17151 ChEBI	xylitol	-	builds acid from

Antibiotic resistance

@ref	ChEBI	Metabolite
25130	28971	ampicillin
25130	3515	cefuroxime
25130	100241	ciprofloxacin
25130	49566	cloxacillin
25130	48923	erythromycin
25130	17833	gentamicin
25130	7507	neomycin
25130	17334	penicillin
25130	8309	polymyxin b
25130	27902	tetracycline

Enzymes

@ref	Value	Activity	Ec
25130	arginine dihydrolase	-	3.5.3.6
25130	beta-galactosidase	+	3.2.1.23
25130	gelatinase	-
25130	urease	+	3.5.1.5

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	4-hydroxymandelate degradation	100	9 of 9
66794	biotin biosynthesis	100	4 of 4
66794	ribulose monophosphate pathway	100	2 of 2
66794	allantoin degradation	100	9 of 9
66794	formaldehyde oxidation	100	3 of 3
66794	molybdenum cofactor biosynthesis	100	9 of 9
66794	coenzyme A metabolism	100	4 of 4
66794	sulfopterin metabolism	100	4 of 4
66794	adipate degradation	100	2 of 2
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	methane metabolism	100	3 of 3
66794	aminopropanol phosphate biosynthesis	100	2 of 2
66794	pentose phosphate pathway	100	11 of 11
66794	kanosamine biosynthesis II	100	2 of 2
66794	ethanol fermentation	100	2 of 2
66794	threonine metabolism	100	10 of 10
66794	palmitate biosynthesis	100	22 of 22
66794	ppGpp biosynthesis	100	4 of 4
66794	cardiolipin biosynthesis	100	7 of 7
66794	methylglyoxal degradation	100	5 of 5
66794	butanoate fermentation	100	4 of 4
66794	valine metabolism	100	9 of 9
66794	quinate degradation	100	2 of 2
66794	Entner Doudoroff pathway	100	10 of 10
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	lactate fermentation	100	4 of 4
66794	creatinine degradation	100	5 of 5
66794	glycogen metabolism	100	5 of 5
66794	aspartate and asparagine metabolism	100	9 of 9
66794	C4 and CAM-carbon fixation	100	8 of 8
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	aerobactin biosynthesis	100	1 of 1
66794	gluconeogenesis	100	8 of 8
66794	ceramide biosynthesis	100	1 of 1
66794	glutamate and glutamine metabolism	100	28 of 28
66794	folate polyglutamylation	100	1 of 1
66794	taurine degradation	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	vitamin B12 metabolism	94.12	32 of 34
66794	pyrimidine metabolism	93.33	42 of 45
66794	flavin biosynthesis	93.33	14 of 15
66794	citric acid cycle	92.86	13 of 14
66794	photosynthesis	92.86	13 of 14
66794	phenylalanine metabolism	92.31	12 of 13
66794	leucine metabolism	92.31	12 of 13
66794	proline metabolism	90.91	10 of 11
66794	propionate fermentation	90	9 of 10
66794	alanine metabolism	89.66	26 of 29
66794	serine metabolism	88.89	8 of 9
66794	NAD metabolism	88.89	16 of 18
66794	lipid A biosynthesis	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	CO2 fixation in Crenarchaeota	88.89	8 of 9
66794	ketogluconate metabolism	87.5	7 of 8
66794	isoleucine metabolism	87.5	7 of 8
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	propanol degradation	85.71	6 of 7
66794	tetrahydrofolate metabolism	85.71	12 of 14
66794	heme metabolism	85.71	12 of 14
66794	purine metabolism	85.11	80 of 94
66794	urea cycle	84.62	11 of 13
66794	methionine metabolism	84.62	22 of 26
66794	degradation of sugar acids	84	21 of 25
66794	glycolate and glyoxylate degradation	83.33	5 of 6
66794	histidine metabolism	82.76	24 of 29
66794	glycolysis	82.35	14 of 17
66794	vitamin B6 metabolism	81.82	9 of 11
66794	tryptophan metabolism	81.58	31 of 38
66794	lysine metabolism	80.95	34 of 42
66794	3-chlorocatechol degradation	80	4 of 5
66794	hydrogen production	80	4 of 5
66794	glycine betaine biosynthesis	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	ethylmalonyl-CoA pathway	80	4 of 5
66794	phenylacetate degradation (aerobic)	80	4 of 5
66794	tyrosine metabolism	78.57	11 of 14
66794	degradation of pentoses	78.57	22 of 28
66794	glutathione metabolism	78.57	11 of 14
66794	d-mannose degradation	77.78	7 of 9
66794	vitamin B1 metabolism	76.92	10 of 13
66794	degradation of sugar alcohols	75	12 of 16
66794	acetate fermentation	75	3 of 4
66794	glycogen biosynthesis	75	3 of 4
66794	dTDPLrhamnose biosynthesis	75	6 of 8
66794	degradation of aromatic, nitrogen containing compounds	75	9 of 12
66794	CMP-KDO biosynthesis	75	3 of 4
66794	carnitine metabolism	75	6 of 8
66794	arginine metabolism	75	18 of 24
66794	oxidative phosphorylation	73.63	67 of 91
66794	degradation of hexoses	72.22	13 of 18
66794	ubiquinone biosynthesis	71.43	5 of 7
66794	non-pathway related	71.05	27 of 38
66794	lipid metabolism	70.97	22 of 31
66794	cyanate degradation	66.67	2 of 3
66794	octane oxidation	66.67	2 of 3
66794	cysteine metabolism	66.67	12 of 18
66794	acetoin degradation	66.67	2 of 3
66794	selenocysteine biosynthesis	66.67	4 of 6
66794	3-phenylpropionate degradation	66.67	10 of 15
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	IAA biosynthesis	66.67	2 of 3
66794	bile acid biosynthesis, neutral pathway	64.71	11 of 17
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	sulfate reduction	61.54	8 of 13
66794	phosphatidylethanolamine bioynthesis	61.54	8 of 13
66794	D-cycloserine biosynthesis	60	3 of 5
66794	phenol degradation	60	12 of 20
66794	lipoate biosynthesis	60	3 of 5
66794	cellulose degradation	60	3 of 5
66794	metabolism of amino sugars and derivatives	60	3 of 5
66794	myo-inositol biosynthesis	60	6 of 10
66794	isoprenoid biosynthesis	57.69	15 of 26
66794	nitrate assimilation	55.56	5 of 9
66794	metabolism of disaccharids	54.55	6 of 11
66794	polyamine pathway	52.17	12 of 23
66794	phenylmercury acetate degradation	50	1 of 2
66794	mannosylglycerate biosynthesis	50	1 of 2
66794	cyclohexanol degradation	50	2 of 4
66794	glycine metabolism	50	5 of 10
66794	pantothenate biosynthesis	50	3 of 6
66794	alginate biosynthesis	50	2 of 4
66794	androgen and estrogen metabolism	50	8 of 16
66794	d-xylose degradation	45.45	5 of 11
66794	ascorbate metabolism	45.45	10 of 22
66794	arachidonic acid metabolism	44.44	8 of 18
66794	carotenoid biosynthesis	40.91	9 of 22
66794	coenzyme M biosynthesis	40	4 of 10
66794	O-antigen biosynthesis	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	gallate degradation	40	2 of 5
66794	factor 420 biosynthesis	40	2 of 5
66794	starch degradation	40	4 of 10
66794	bacilysin biosynthesis	40	2 of 5
66794	cholesterol biosynthesis	36.36	4 of 11
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	sphingosine metabolism	33.33	2 of 6
66794	sulfoquinovose degradation	33.33	1 of 3
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	enterobactin biosynthesis	33.33	1 of 3
66794	phenylpropanoid biosynthesis	30.77	4 of 13
66794	4-hydroxyphenylacetate degradation	30	3 of 10
66794	aclacinomycin biosynthesis	28.57	2 of 7
66794	benzoyl-CoA degradation	28.57	2 of 7
66794	chlorophyll metabolism	27.78	5 of 18
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	toluene degradation	25	1 of 4
66794	catecholamine biosynthesis	25	1 of 4
66794	vitamin E metabolism	25	1 of 4

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
25130	root nodules of Lotus japonicum			Japan	JPN	Asia
67770	Lotus corniculatus	Lotus corniculatus	Tochigi	Japan	JPN	Asia

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM962v1 assembly for Mesorhizobium japonicum MAFF 303099	complete	GCA_000009625	266835.9	637000159	266835	98.9

GC content

@ref	GC-content (mol%)	Method
25130	62.9	genome sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Mesorhizobium loti MAFF303099
PATRIC: 266835.9

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	97.00	no
125439	motility	BacteriaNetⓘ	yes	63.10	no
125439	gram_stain	BacteriaNetⓘ	negative	98.20	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	98.50	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Mesorhizobium japonicum MAFF 303099 MAFF 303099
NCBI: GCA_000009625.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	99.33	no
125438	anaerobic	anaerobicⓘ	no	92.02	yes
125438	aerobic	aerobicⓘ	yes	87.89	yes
125438	spore-forming	spore-formingⓘ	no	88.05	no
125438	thermophilic	thermophileⓘ	no	99.00	yes
125438	flagellated	motile2+ⓘ	yes	68.39	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Pathogenicity	RNA-seq analysis of transcription patterns during infection of Mesorhizobium japonicum by phage Cp1R7A-A1.	Gunathilake K, Loos K, Yost C, Hynes MF.	Can J Microbiol	10.1139/cjm-2025-0061	2025
	Rhizobial Secretion of Truncated Exopolysaccharides Severely Impairs the Mesorhizobium-Lotus Symbiosis.	Wightman T, Muszynski A, Kelly SJ, Sullivan JT, Smart CJ, Stougaard J, Ferguson S, Azadi P, Ronson CW.	Mol Plant Microbe Interact	10.1094/mpmi-03-24-0024-r	2024
	A Mesorhizobium japonicum quorum sensing circuit that involves three linked genes and an unusual acyl-homoserine lactone signal.	Suo Z, Cummings DA, Puri AW, Schaefer AL, Greenberg EP.	mBio	10.1128/mbio.01010-23	2023
	Influence of cyclic di-GMP metabolism to T3SS expression, biofilm formation and symbiosis efficiency in Mesorhizobium japonicum MAFF303099.	Escobar MR, Lepek VC, Basile LA.	FEMS Microbiol Lett	10.1093/femsle/fnad087	2023
Genetics	Meta-omics reveals subgingival plaque reconstruction dynamics.	Zhou F, Wu Y, Ren B, Liu Y, Luo K, Li Q, Huang F, Peng X, Li Y, Su Z, Li J.	J Oral Microbiol	10.1080/20002297.2025.2569528	2025
Genetics	Comparative genomic and transcriptomic analyses provide new insight into symbiotic host specificity.	Yuan S, Leng P, Feng Y, Jin F, Zhang H, Zhang C, Huang Y, Shan Z, Yang Z, Hao Q, Chen S, Chen L, Cao D, Guo W, Yang H, Chen H, Zhou X.	iScience	10.1016/j.isci.2024.110207	2024
	Scarcity of fixed carbon transfer in a model microbial phototroph-heterotroph interaction.	Dupuis S, Lingappa UF, Mayali X, Sindermann ES, Chastain JL, Weber PK, Stuart R, Merchant SS.	ISME J	10.1093/ismejo/wrae140	2024
	Evaluation of qPCR to Detect Shifts in Population Composition of the Rhizobial Symbiont Mesorhizobium japonicum during Serial in Planta Transfers.	Quides KW, Lee Y, Hur T, Atamian HS.	Biology (Basel)	10.3390/biology12020277	2023
	A simple and efficient protocol for generating transgenic hairy roots using Agrobacterium rhizogenes.	Ferguson S, Abel NB, Reid D, Madsen LH, Luu TB, Andersen KR, Stougaard J, Radutoiu S.	PLoS One	10.1371/journal.pone.0291680	2023
	Metagenomics and In Vitro Growth-Promoting Experiments Revealed the Potential Roles of Mycorrhizal Fungus Humicolopsis cephalosporioides and Helper Bacteria in Cheilotheca humilis Growth.	Liu Y, Shang Y, Wang X, Li X, Yu Z, Zeng Z, Chen Z, Wang L, Xiang T, Huang X.	Microorganisms	10.3390/microorganisms13102387	2025
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
Pathogenicity	Fungal and bacterial species richness in biodeteriorated seventeenth century Venetian manuscripts.	Stratigaki M, Armirotti A, Ottonello G, Manente S, Traviglia A.	Sci Rep	10.1038/s41598-024-57228-2	2024
Pathogenicity	Guidelines for the description of rhizobial symbiovars.	Martinez-Romero E, Peix A, Hungria M, Mousavi SA, Martinez-Romero J, Young P.	Int J Syst Evol Microbiol	10.1099/ijsem.0.006373	2024
	The Type IV Secretion System (T4SS) Mediates Symbiosis between Bradyrhizobium sp. SUTN9-2 and Legumes.	Wangthaisong P, Piromyou P, Songwattana P, Wongdee J, Teamtaisong K, Tittabutr P, Boonkerd N, Teaumroong N.	Appl Environ Microbiol	10.1128/aem.00040-23	2023
	The putative type 4 secretion system effector BspD is involved in maintaining envelope integrity of the pathogen Brucella.	Ketterer M, Chiquet P, Esposito M, Sedzicki J, Quebatte M, Dehio C.	mSphere	10.1128/msphere.00232-24	2024
	Synergy between Rhizobial Co-Microsymbionts Leads to an Increase in the Efficiency of Plant-Microbe Interactions.	Safronova V, Sazanova A, Belimov A, Guro P, Kuznetsova I, Karlov D, Chirak E, Yuzikhin O, Verkhozina A, Afonin A, Tikhonovich I.	Microorganisms	10.3390/microorganisms11051206	2023
	RhizoBindingSites v2.0 Is a Bioinformatic Database of DNA Motifs Potentially Involved in Transcriptional Regulation Deduced From Their Genomic Sites.	Taboada-Castro H, Hernandez-Alvarez AJ, Castro-Mondragon JA, Encarnacion-Guevara S.	Bioinform Biol Insights	10.1177/11779322241272395	2024
Metabolism	A novel way to synthesize pantothenate in bacteria involves beta-alanine synthase present in uracil degradation pathway.	Lopez-Samano M, Beltran LFL, Sanchez-Thomas R, Davalos A, Villasenor T, Garcia-Garcia JD, Garcia-de Los Santos A.	Microbiologyopen	10.1002/mbo3.1006	2020
Genetics	Leveraging comparative genomics to uncover alien genes in bacterial genomes.	Sengupta S, Azad RK.	Microb Genom	10.1099/mgen.0.000939	2023
	Mesorhizobium sp. J8 can establish symbiosis with Glycyrrhiza uralensis, increasing glycyrrhizin production.	Kusaba I, Nakao T, Maita H, Sato S, Chijiiwa R, Yamada E, Arima S, Kojoma M, Ishimaru K, Akashi R, Suzuki A.	Plant Biotechnol (Tokyo)	10.5511/plantbiotechnology.20.1124a	2021
Genetics	Assessment of Physicochemical, Microbiological and Toxicological Hazards at an Illegal Landfill in Central Poland.	Szulc J, Okrasa M, Nowak A, Niziol J, Ruman T, Kuberski S.	Int J Environ Res Public Health	10.3390/ijerph19084826	2022
	Identification of EcpK, a bacterial tyrosine pseudokinase important for exopolysaccharide biosynthesis in Myxococcus xanthus.	Blocher L, Schwabe J, Glatter T, Sogaard-Andersen L.	J Bacteriol	10.1128/jb.00499-24	2025
Enzymology	Structural comparison of p-hydroxybenzoate hydroxylase (PobA) from Pseudomonas putida with PobA from other Pseudomonas spp. and other monooxygenases.	Lazar JT, Shuvalova L, Rosas-Lemus M, Kiryukhina O, Satchell KJF, Minasov G.	Acta Crystallogr F Struct Biol Commun	10.1107/s2053230x19008653	2019
	Exposure of Pseudomonas aeruginosa to Cinnamaldehyde Selects Multidrug Resistant Mutants.	Tetard A, Gaillot S, Dubois E, Aarras S, Valot B, Phan G, Plesiat P, Llanes C.	Antibiotics (Basel)	10.3390/antibiotics11121790	2022
	Evolution of diverse effective N₂-fixing microsymbionts of Cicer arietinum following horizontal transfer of the Mesorhizobium ciceri CC1192 symbiosis integrative and conjugative element.	Hill Y, Colombi E, Bonello E, Haskett T, Ramsay J, O'Hara G, Terpolilli J.	Appl Environ Microbiol	10.1128/aem.02558-20	2021
	Legumes of the Sardinia Island: Knowledge on Symbiotic and Endophytic Bacteria and Interactive Software Tool for Plant Species Determination.	Muresu R, Porceddu A, Concheri G, Stevanato P, Squartini A.	Plants (Basel)	10.3390/plants11111521	2022
	DUF2285 is a novel helix-turn-helix domain variant that orchestrates both activation and antiactivation of conjugative element transfer in proteobacteria.	Jowsey WJ, Morris CRP, Hall DA, Sullivan JT, Fagerlund RD, Eto KY, Solomon PD, Mackay JP, Bond CS, Ramsay JP, Ronson CW.	Nucleic Acids Res	10.1093/nar/gkad457	2023
Metabolism	Combining SIMS and mechanistic modelling to reveal nutrient kinetics in an algal-bacterial mutualism.	Laeverenz Schlogelhofer H, Peaudecerf FJ, Bunbury F, Whitehouse MJ, Foster RA, Smith AG, Croze OA.	PLoS One	10.1371/journal.pone.0251643	2021
	Lotus Accessions Possess Multiple Checkpoints Triggered by Different Type III Secretion System Effectors of the Wide-Host-Range Symbiont Bradyrhizobium elkanii USDA61.	Kusakabe S, Higasitani N, Kaneko T, Yasuda M, Miwa H, Okazaki S, Saeki K, Higashitani A, Sato S.	Microbes Environ	10.1264/jsme2.me19141	2020
	Characterization, expression and application of a zearalenone degrading enzyme from Neurospora crassa.	Bi K, Zhang W, Xiao Z, Zhang D.	AMB Express	10.1186/s13568-018-0723-z	2018
	Rapid HILIC-Z ion mobility mass spectrometry (RHIMMS) method for untargeted metabolomics of complex biological samples.	Picmanova M, Moses T, Cortada-Garcia J, Barrett G, Florance H, Pandor S, Burgess K.	Metabolomics	10.1007/s11306-022-01871-1	2022
	Magnetizing Biotech-Advances in (In Vivo) Magnetic Enzyme Immobilization.	Olcucu G, Jaeger KE, Krauss U.	Eng Life Sci	10.1002/elsc.70000	2025
	Sphingomonas sediminicola Is an Endosymbiotic Bacterium Able to Induce the Formation of Root Nodules in Pea (Pisum sativum L.) and to Enhance Plant Biomass Production.	Mazoyon C, Hirel B, Pecourt A, Catterou M, Gutierrez L, Sarazin V, Dubois F, Duclercq J.	Microorganisms	10.3390/microorganisms11010199	2023
Genetics	COG database update: focus on microbial diversity, model organisms, and widespread pathogens.	Galperin MY, Wolf YI, Makarova KS, Vera Alvarez R, Landsman D, Koonin EV.	Nucleic Acids Res	10.1093/nar/gkaa1018	2021
Genetics	Phylogenomic Reconstruction and Metabolic Potential of the Genus Aminobacter.	Artuso I, Turrini P, Pirolo M, Lugli GA, Ventura M, Visca P.	Microorganisms	10.3390/microorganisms9061332	2021
	Cyclic Isothiocyanate Goitrin Impairs Lotus japonicus Nodulation, Affects the Proteomes of Nodules and Free Mesorhizobium loti, and Induces the Formation of Caffeic Acid Derivatives in Bacterial Cultures.	Jeong S, Schutz V, Demir F, Preusche M, Huesgen P, Bigler L, Kovacic F, Gutbrod K, Dormann P, Schulz M.	Plants (Basel)	10.3390/plants13202897	2024
	RhizoBindingSites, a Database of DNA-Binding Motifs in Nitrogen-Fixing Bacteria Inferred Using a Footprint Discovery Approach.	Taboada-Castro H, Castro-Mondragon JA, Aguilar-Vera A, Hernandez-Alvarez AJ, van Helden J, Encarnacion-Guevara S.	Front Microbiol	10.3389/fmicb.2020.567471	2020
Metabolism	alpha-proteobacteria synthesize biotin precursor pimeloyl-ACP using BioZ 3-ketoacyl-ACP synthase and lysine catabolism.	Hu Y, Cronan JE.	Nat Commun	10.1038/s41467-020-19251-5	2020
Genetics	Ancient Bacterial Class Alphaproteobacteria Cytochrome P450 Monooxygenases Can Be Found in Other Bacterial Species.	Nzuza N, Padayachee T, Syed PR, Krys JD, Chen W, Gront D, Nelson DR, Syed K.	Int J Mol Sci	10.3390/ijms22115542	2021
Phylogeny	Whole-Genome Sequencing of Bradyrhizobium diazoefficiens 113-2 and Comparative Genomic Analysis Provide Molecular Insights Into Species Specificity and Host Specificity.	Li R, Feng Y, Chen H, Zhang C, Huang Y, Chen L, Hao Q, Cao D, Yuan S, Zhou X.	Front Microbiol	10.3389/fmicb.2020.576800	2020
Phylogeny	Plant Growth Promotion Abilities of Phylogenetically Diverse Mesorhizobium Strains: Effect in the Root Colonization and Development of Tomato Seedlings.	Menendez E, Perez-Yepez J, Hernandez M, Rodriguez-Perez A, Velazquez E, Leon-Barrios M.	Microorganisms	10.3390/microorganisms8030412	2020
	Characterization of the genomically encoded fosfomycin resistance enzyme from Mycobacterium abscessus.	Travis S, Shay MR, Manabe S, Gilbert NC, Frantom PA, Thompson MK.	Medchemcomm	10.1039/c9md00372j	2019
	Visualizing the superfamily of metallo-beta-lactamases through sequence similarity network neighborhood connectivity analysis.	Gonzalez JM.	Heliyon	10.1016/j.heliyon.2020.e05867	2021
Enzymology	Dual activity of PNGM-1 pinpoints the evolutionary origin of subclass B3 metallo-beta-lactamases: a molecular and evolutionary study.	Lee JH, Takahashi M, Jeon JH, Kang LW, Seki M, Park KS, Hong MK, Park YS, Kim TY, Karim AM, Lee JH, Nashimoto M, Lee SH.	Emerg Microbes Infect	10.1080/22221751.2019.1692638	2019
	Differential mechanisms of tolerance to extreme environmental conditions in tardigrades.	Carrero D, Perez-Silva JG, Quesada V, Lopez-Otin C.	Sci Rep	10.1038/s41598-019-51471-8	2019
	Rhizobium leguminosarum bv. trifolii NodD2 Enhances Competitive Nodule Colonization in the Clover-Rhizobium Symbiosis.	Ferguson S, Major AS, Sullivan JT, Bourke SD, Kelly SJ, Perry BJ, Ronson CW.	Appl Environ Microbiol	10.1128/aem.01268-20	2020
	Legume-rhizobium dance: an agricultural tool that could be improved?	Basile LA, Lepek VC.	Microb Biotechnol	10.1111/1751-7915.13906	2021
Metabolism	Biochemical and structural characterization of the BioZ enzyme engaged in bacterial biotin synthesis pathway.	Zhang S, Xu Y, Guan H, Cui T, Liao Y, Wei W, Li J, Hassan BH, Zhang H, Jia X, Ouyang S, Feng Y.	Nat Commun	10.1038/s41467-021-22360-4	2021
	Evolution of Wolbachia mutualism and reproductive parasitism: insight from two novel strains that co-infect cat fleas.	Driscoll TP, Verhoeve VI, Brockway C, Shrewsberry DL, Plumer M, Sevdalis SE, Beckmann JF, Krueger LM, Macaluso KR, Azad AF, Gillespie JJ.	PeerJ	10.7717/peerj.10646	2020
	Rational Design of the Soluble Variant of l-Pipecolic Acid Hydroxylase using the alpha-Helix Rule and the Hydropathy Contradiction Rule.	Shinoda S, Itakura A, Sasano H, Miyake R, Kawabata H, Asano Y.	ACS Omega	10.1021/acsomega.2c04247	2022
	Cycad Coralloid Roots Contain Bacterial Communities Including Cyanobacteria and Caulobacter spp. That Encode Niche-Specific Biosynthetic Gene Clusters.	Gutierrez-Garcia K, Bustos-Diaz ED, Corona-Gomez JA, Ramos-Aboites HE, Selem-Mojica N, Cruz-Morales P, Perez-Farrera MA, Barona-Gomez F, Cibrian-Jaramillo A.	Genome Biol Evol	10.1093/gbe/evy266	2019
Biotechnology	Phenolic Acids Induce Nod Factor Production in Lotus japonicus-Mesorhizobium Symbiosis.	Shimamura M, Kumaki T, Hashimoto S, Saeki K, Ayabe SI, Higashitani A, Akashi T, Sato S, Aoki T	Microbes Environ	10.1264/jsme2.ME21094	2022
Phylogeny	Two Broad Host Range Rhizobial Strains Isolated From Relict Legumes Have Various Complementary Effects on Symbiotic Parameters of Co-inoculated Plants.	Safronova V, Belimov A, Sazanova A, Chirak E, Kuznetsova I, Andronov E, Pinaev A, Tsyganova A, Seliverstova E, Kitaeva A, Tsyganov V, Tikhonovich I	Front Microbiol	10.3389/fmicb.2019.00514	2019
Phylogeny	traG Gene Is Conserved across Mesorhizobium spp. Able to Nodulate the Same Host Plant and Expressed in Response to Root Exudates.	Paco A, da-Silva JR, Eliziario F, Brigido C, Oliveira S, Alexandre A	Biomed Res Int	10.1155/2019/3715271	2019
Phylogeny	Mesorhizobium sanjuanii sp. nov., isolated from nodules of Lotus tenuis in the saline-alkaline lowlands of Flooding Pampa, Argentina.	Sannazzaro AI, Torres Tejerizo G, Fontana MF, Cumpa Velasquez LM, Hansen LH, Pistorio M, Estrella MJ.	Int J Syst Evol Microbiol	10.1099/ijsem.0.002924	2018
Phylogeny	Mesorhizobium carmichaelinearum sp. nov., isolated from Carmichaelineae spp. root nodules.	De Meyer SE, Andrews M, James EK, Willems A	Int J Syst Evol Microbiol	10.1099/ijsem.0.003120	2018
Phylogeny	Reclassification of strains MAFF 303099T and R7A into Mesorhizobiumjaponicum sp. nov.	Martinez-Hidalgo P, Ramirez-Bahena MH, Flores-Felix JD, Igual JM, Sanjuan J, Leon-Barrios M, Peix A, Velazquez E	Int J Syst Evol Microbiol	10.1099/ijsem.0.001448	2016

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 )
#25130	P. R.-B. Martínez-Hidalgo, M. H.,Flores-Félix, J. D.,Igual, J. M.,Sanjuán, J.,León-Barrios, M.,Peix, A.,Velázquez, E.: Reclassification of strains MAFF 303099T and R7A into Mesorhizobium japonicum sp. nov. IJSEM 66: 4936 - 4941 2016 ( DOI 10.1099/ijsem.0.001448 , PubMed 27565417 )
#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) .
#66794	Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#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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Mesorhizobium japonicum (MAFF 303099, LMG 29417, CECT 9101)

Name and taxonomic classification

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Oxygen tolerance

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