Mesorhizobium sophorae (ICMP 19535, LMG 28223, HAMBI 3606)

Name: Mesorhizobium sophorae (ICMP 19535, LMG 28223, HAMBI 3606)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 141125

Type strain

Culture col. no. ICMP 19535 LMG 28223 HAMBI 3606

NCBI tax ID(s) 1300294

Special Collections Literature strains

Links

Mesorhizobium sophorae ICMP 19535 is a Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from root nodules of Sophora microphylla from a river outwash fan.

Gram-negative rod-shaped colony-forming genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 393610

LMG 28223,HAMBI 3606,ICMP 19535

@ref 20215

Last LPSN update 2026-05-29 08:39:53

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Hyphomicrobiales

Family Bartonellaceae

Genus Mesorhizobium

Species Mesorhizobium sophorae

Full scientific name Mesorhizobium sophorae De Meyer et al. 2016

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
44033	negative	2 µm	1 µm	rod-shaped
125438	negative				98.5

Colony morphology

@ref	Colony size	Colony color	Colony shape	Medium used
44033	0.2-0.7 mm	light cream	circular	YMA

Culture and growth conditions

Culture medium

@ref	Name	Growth
44033	YMA
44033	YMB

Culture temp

@ref	Growth	Type	Temperature (°C)
44033	positive	growth	15-30
44033	negative	growth	4
44033	negative	growth	7
44033	negative	growth	37
44033	positive	growth	28

Culture pH

@ref	Ability	Type	PH	PH range
44033	positive	growth	4.0-7.0	acidophile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	98.886

Spore formation

@ref	Spore formation	Confidence
125439		98.788

Halophily

@ref	Salt	Growth	Tested relation	Concentration
44033	NaCl	positive	growth	1-8 %(w/v)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
44033		1 % sodium lactate	+/-	respiration
44033	64552 ChEBI	2-hydroxybutyrate	-	respiration
44033	16763 ChEBI	2-oxobutanoate	-	respiration
44033	30916 ChEBI	2-oxoglutarate	-	respiration
44033	37054 ChEBI	3-hydroxybutyrate	+	respiration
44033	73918 ChEBI	3-O-methyl-D-glucose	-	respiration
44033	18101 ChEBI	4-hydroxyphenylacetic acid	+/-	respiration
44033	30089 ChEBI	acetate	+	respiration
44033	13705 ChEBI	acetoacetate	+	respiration
44033	17925 ChEBI	alpha-D-glucose	+	respiration
44033	36219 ChEBI	alpha-lactose	+	respiration
44033	161680 ChEBI	aztreonam	+	respiration
44033	73706 ChEBI	bromosuccinate	-	respiration
44033	17057 ChEBI	cellobiose	+	respiration
44033	16947 ChEBI	citrate	-	respiration
44033	18333 ChEBI	D-arabitol	+	respiration
44033	29990 ChEBI	D-aspartate	+/-	respiration
44033	15824 ChEBI	D-fructose	+	respiration
44033	78697 ChEBI	D-fructose 6-phosphate	-	respiration
44033	28847 ChEBI	D-fucose	+	respiration
44033	12936 ChEBI	D-galactose	+	respiration
44033	18024 ChEBI	D-galacturonic acid	+/-	respiration
44033	8391 ChEBI	D-gluconate	-	respiration
44033	17634 ChEBI	D-glucose	+	assimilation
44033	14314 ChEBI	D-glucose 6-phosphate	-	respiration
44033	15748 ChEBI	D-glucuronate	+/-	respiration
44033	15588 ChEBI	D-malate	-	respiration
44033	16899 ChEBI	D-mannitol	+	respiration
44033	16024 ChEBI	D-mannose	+	respiration
44033	33801 ChEBI	D-saccharate	-	respiration
44033	16523 ChEBI	D-serine	-	respiration
44033	17924 ChEBI	D-sorbitol	+/-	respiration
44033	16551 ChEBI	D-trehalose	+	respiration
44033	23652 ChEBI	dextrin	+/-	respiration
44033	15740 ChEBI	formate	+/-	respiration
44033	71321 ChEBI	fusidate	+/-	respiration
44033	16537 ChEBI	galactarate	-	respiration
44033	16865 ChEBI	gamma-aminobutyric acid	+	respiration
44033	5291 ChEBI	gelatin	-	respiration
44033	28066 ChEBI	gentiobiose	+	respiration
44033	32323 ChEBI	glucuronamide	+/-	respiration
44033	17754 ChEBI	glycerol	+	respiration
44033	70744 ChEBI	glycine-proline	+/-	respiration
44033	32735 ChEBI	guanidinium chloride	-	respiration
44033	17596 ChEBI	inosine	-	respiration
44033	16977 ChEBI	L-alanine	+	respiration
44033	30849 ChEBI	L-arabinose	+	assimilation
44033	16467 ChEBI	L-arginine	+	respiration
44033	29991 ChEBI	L-aspartate	+	respiration
44033	18287 ChEBI	L-fucose	+	respiration
44033	17464 ChEBI	L-galactonic acid gamma-lactone	-	respiration
44033	29985 ChEBI	L-glutamate	+/-	respiration
44033	15971 ChEBI	L-histidine	+/-	respiration
44033	15589 ChEBI	L-malate	+	respiration
44033	18183 ChEBI	L-pyroglutamic acid	-	respiration
44033	62345 ChEBI	L-rhamnose	+	respiration
44033	17115 ChEBI	L-serine	-	respiration
44033	24996 ChEBI	lactate	+	respiration
44033	6472 ChEBI	lincomycin	+	respiration
44033	48607 ChEBI	lithium chloride	+/-	respiration
44033	17306 ChEBI	maltose	+	assimilation
44033	17306 ChEBI	maltose	+	respiration
44033	28053 ChEBI	melibiose	+	respiration
44033	74611 ChEBI	methyl (R)-lactate	-	respiration
44033	37657 ChEBI	methyl D-glucoside	+	respiration
44033	51850 ChEBI	methyl pyruvate	-	respiration
44033	50694 ChEBI	minocycline	+/-	respiration
44033	17268 ChEBI	myo-inositol	+	respiration
44033	63154 ChEBI	N-acetyl-beta-D-mannosamine	+/-	respiration
44033	28037 ChEBI	N-acetylgalactosamine	+	respiration
44033	506227 ChEBI	N-acetylglucosamine	+	respiration
44033	35418 ChEBI	n-acetylneuraminate	-	respiration
44033	100147 ChEBI	nalidixic acid	+	respiration
44033	75273 ChEBI	niaproof	-	respiration
44033	17309 ChEBI	pectin	-	respiration
44033	75248 ChEBI	potassium tellurite	+/-	respiration
44033	17272 ChEBI	propionate	+	respiration
44033	26490 ChEBI	quinate	-	respiration
44033	16634 ChEBI	raffinose	+	respiration
44033	29673 ChEBI	rifamycin sv	+	respiration
44033	17814 ChEBI	salicin	+/-	respiration
44033	75229 ChEBI	sodium bromate	-	respiration
44033	64103 ChEBI	sodium butyrate	+/-	respiration
44033	17164 ChEBI	stachyose	-	respiration
44033	17992 ChEBI	sucrose	+/-	respiration
44033	75198 ChEBI	tetrazolium blue	+	respiration
44033	75193 ChEBI	tetrazolium violet	+/-	respiration
44033	45735 ChEBI	troleandomycin	-	respiration
44033	32528 ChEBI	turanose	+/-	respiration
44033	53423 ChEBI	tween 40	+/-	respiration
44033	28001 ChEBI	vancomycin	+/-	respiration

Antibiotic resistance

@ref	ChEBI	Metabolite	Resistance conc.	Sensitivity conc.
44033	17698	chloramphenicol	30 µg (disc)
44033	48923	erythromycin	15 µg (disc)
44033	17833	gentamicin		10 µg (disc)
44033	6104	kanamycin	30 µg (disc)
44033	17076	streptomycin		25 µg (disc)

Enzymes

@ref	Value	Activity	Ec
44033	arginine dihydrolase	+/-	3.5.3.6
44033	catalase	-	1.11.1.6
44033	cytochrome oxidase	+	1.9.3.1

Fatty acid profile

Metadata FA analysis

@ref

44033

Fatty acid	Percentage
C18:1ω7c	48.8
C16:0	21.4
11-methyl-C18:1ω7c	12
C19:0cycloω8c	10.1
C17:0 iso	5.3
C16:1ω7c / C15:0iso2-OH	2.4

Isolation, sampling and environmental information

Isolation source categories

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

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
44033	root nodules of Sophora microphylla from a river outwash fan	Pororari River, Westland	New Zealand	NZL	Australia and Oceania

Taxonmaps

69479

Global distribution of 16S sequence KC237424 (>99% sequence identity) for Mesorhizobium from Microbeatlas

Aquatic Samples	5652
Soil Samples	18576
Animal Samples	4689
Plant Samples	1771
Total Samples	30688

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM227041v1 assembly for Mesorhizobium sophorae ICMP 19535	contig	GCA_002270415	1300294.3	2791355123	1300294	73.49

16S sequences

@ref	Description	Accession	Database
44033	Mesorhizobium sophorae strain ICMP 19535 16S ribosomal RNA gene, partial sequence	KC237424

GC content

@ref	GC-content (mol%)	Method
44033	62.6	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM227041v1 assembly for Mesorhizobium sophorae ICMP 19535
NCBI: GCA_002270415

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	98.89	no
125439	gram_stain	BacteriaNetⓘ	negative	89.56	no
125439	spore_formation	BacteriaNetⓘ	no	98.79	no
125439	motility	BacteriaNetⓘ	yes	51.29	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Mesorhizobium sophorae strain ICMP 19535
PATRIC: 1300294.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.50	yes
125438	anaerobic	anaerobicⓘ	no	93.18	no
125438	spore-forming	spore-formingⓘ	no	87.70	no
125438	aerobic	aerobicⓘ	yes	85.29	no
125438	thermophilic	thermophileⓘ	no	99.50	yes
125438	flagellated	motile2+ⓘ	yes	56.31	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Phylogenomic analyses and reclassification of the Mesorhizobium complex: proposal for 9 novel genera and reclassification of 15 species.	Li Y, Guo T, Sun L, Wang ET, Young JPW, Tian CF.	BMC Genomics	10.1186/s12864-024-10333-y	2024
Genetics	Complete Genome Sequence of Mesorhizobium sophorae ICMP 19535(T), a Highly Specific, Nitrogen-Fixing Symbiont of New Zealand Endemic Sophora spp.	De Meyer SE, Nguyen DT, Wang P, Andrews M	Genome Announc	10.1128/genomeA.00958-17	2017
Phylogeny	Mesorhizobium terrae sp. nov., a novel species isolated from soil in Jangsu, Korea.	Jung YJ, Kim HJ, Hur M	Antonie Van Leeuwenhoek	10.1007/s10482-020-01435-0	2020
Phylogeny	Mesorhizobium calcicola sp. nov., Mesorhizobium waitakense sp. nov., Mesorhizobium sophorae sp. nov., Mesorhizobium newzealandense sp. nov. and Mesorhizobium kowhaii sp. nov. isolated from Sophora root nodules.	De Meyer SE, Tan HW, Andrews M, Heenan PB, Willems A	Int J Syst Evol Microbiol	10.1099/ijsem.0.000796	2015

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 )
#44033	Soe E. De Meyer, Heng Wee Tan, Mitchell Andrews, Peter B. Heenan and Anne Willems: Mesorhizobium calcicola sp. nov., Mesorhizobium waitakense sp. nov., Mesorhizobium sophorae sp. nov., Mesorhizobium newzealandense sp. nov. and Mesorhizobium kowhaii sp. nov. isolated from Sophora root nodules. IJSEM 66: 786 - 795 2016 ( DOI 10.1099/ijsem.0.000796 , PubMed 26610329 )
#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 .
#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 sophorae (ICMP 19535, LMG 28223, HAMBI 3606)

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

Metabolite utilization

Antibiotic resistance

Enzymes

Fatty acid profile

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Sequence information

Genome sequences

Genome browser: GCA_002270415

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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