Bosea lathyri (DSM 26656, CCUG 61247, LMG 26379)

Name: Bosea lathyri (DSM 26656, CCUG 61247, LMG 26379)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 1791

Type strain

Strain Designation R-46060

Culture col. no. DSM 26656 CCUG 61247 LMG 26379 R-46060

NCBI tax ID(s) 1036778

Special Collections DSMZ CCUG Literature strains

History <- LMG <- A. Willems, Group Biochemistry and Microbiology, University of Ghent <- S. De Meyer, Group Biochemistry and Microbiology, University of Ghent

Links

Bosea lathyri R-46060 is an aerobe, Gram-negative, motile bacterium that was isolated from root nodules of Lathyrus latifolius.

Gram-negative motile rod-shaped aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 371088

LMG 26379,CCUG 61247,DSM 26656

@ref 20215

Last LPSN update 2026-02-09 11:18:11

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Hyphomicrobiales

Family Boseaceae

Genus Bosea

Species Bosea lathyri

Full scientific name Bosea lathyri De Meyer and Willems 2012

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
23325	negative	1.2-2.0 µm	0.6-0.8 µm	rod-shaped
125438	negative				97.333
125439	negative				97.9

Colony morphology

@ref	Colony size	Colony color	Medium used
23325	1.5-2.0 mm	white	YMA
23325	1.0-1.5 mm	white	YMA

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
23325	YMA
18268	REACTIVATION WITH LIQUID MEDIUM 1 (DSMZ Medium 1a)		Medium recipe at MediaDive	Name: REACTIVATION WITH LIQUID MEDIUM 1 (DSMZ Medium 1a) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
18268	positive	growth	28
23325	positive	growth	25
23325	positive	growth	28
23325	positive	growth	33
23325	negative	growth	42
62588	positive	growth	30

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
62588	aerobe
125439	obligate aerobe	95.9

Spore formation

@ref	Spore formation	Confidence
125438		90.164
125439		97.7

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
23325	17128 ChEBI	adipate	+/-	assimilation
68369	17128 ChEBI	adipate	+	assimilation	from API 20NE
68369	29016 ChEBI	arginine	-	hydrolysis	from API 20NE
23325	16947 ChEBI	citrate	+/-	assimilation
23325	17634 ChEBI	D-glucose	-	assimilation
68369	17634 ChEBI	D-glucose	-	assimilation	from API 20NE
68369	17634 ChEBI	D-glucose	-	fermentation	from API 20NE
23325	16899 ChEBI	D-mannitol	-	assimilation
68369	16899 ChEBI	D-mannitol	-	assimilation	from API 20NE
23325	16024 ChEBI	D-mannose	+/-	assimilation
68369	16024 ChEBI	D-mannose	-	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
23325	30849 ChEBI	L-arabinose	-	assimilation
68369	30849 ChEBI	L-arabinose	-	assimilation	from API 20NE
23325	25115 ChEBI	malate	+	assimilation
68369	25115 ChEBI	malate	+	assimilation	from API 20NE
23325	17306 ChEBI	maltose	-	assimilation
68369	17306 ChEBI	maltose	-	assimilation	from API 20NE
23325	506227 ChEBI	N-acetylglucosamine	-	assimilation
68369	59640 ChEBI	N-acetylglucosamine	-	assimilation	from API 20NE
23325	17632 ChEBI	nitrate	+	reduction
68369	17632 ChEBI	nitrate	+	reduction	from API 20NE
23325	18401 ChEBI	phenylacetate	-	assimilation
23325	32032 ChEBI	potassium gluconate	+	assimilation
68369	27897 ChEBI	tryptophan	-	energy source	from API 20NE
68369	16199 ChEBI	urea	+	hydrolysis	from API 20NE

Antibiotic resistance

@ref	ChEBI	Metabolite
23325	2676	amoxicillin
23325	50845	doxycycline
23325	17334	penicillin

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
23325	beta-glucosidase	+	3.2.1.21
68369	beta-glucosidase	-	3.2.1.21	from API 20NE
23325	catalase	+	1.11.1.6
23325	cytochrome oxidase	+	1.9.3.1
68369	cytochrome oxidase	+	1.9.3.1	from API 20NE
68369	gelatinase	-		from API 20NE
23325	urease	+	3.5.1.5
68369	urease	+	3.5.1.5	from API 20NE

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	propanol degradation	100	7 of 7
66794	CO2 fixation in Crenarchaeota	100	9 of 9
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	suberin monomers biosynthesis	100	2 of 2
66794	methylglyoxal degradation	100	5 of 5
66794	valine metabolism	100	9 of 9
66794	ketogluconate metabolism	100	8 of 8
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	allantoin degradation	100	9 of 9
66794	pentose phosphate pathway	100	11 of 11
66794	formaldehyde oxidation	100	3 of 3
66794	denitrification	100	2 of 2
66794	sulfopterin metabolism	100	4 of 4
66794	coenzyme A metabolism	100	4 of 4
66794	starch degradation	100	10 of 10
66794	ribulose monophosphate pathway	100	2 of 2
66794	molybdenum cofactor biosynthesis	100	9 of 9
66794	taurine degradation	100	1 of 1
66794	4-hydroxymandelate degradation	100	9 of 9
66794	folate polyglutamylation	100	1 of 1
66794	acetate fermentation	100	4 of 4
66794	cardiolipin biosynthesis	100	7 of 7
66794	ethanol fermentation	100	2 of 2
66794	palmitate biosynthesis	100	22 of 22
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	ppGpp biosynthesis	100	4 of 4
66794	adipate degradation	100	2 of 2
66794	C4 and CAM-carbon fixation	100	8 of 8
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	gluconeogenesis	100	8 of 8
66794	degradation of sugar acids	96	24 of 25
66794	photosynthesis	92.86	13 of 14
66794	leucine metabolism	92.31	12 of 13
66794	phenylalanine metabolism	92.31	12 of 13
66794	degradation of aromatic, nitrogen containing compounds	91.67	11 of 12
66794	threonine metabolism	90	9 of 10
66794	Entner Doudoroff pathway	90	9 of 10
66794	propionate fermentation	90	9 of 10
66794	serine metabolism	88.89	8 of 9
66794	NAD metabolism	88.89	16 of 18
66794	chorismate metabolism	88.89	8 of 9
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	glutathione metabolism	85.71	12 of 14
66794	citric acid cycle	85.71	12 of 14
66794	glutamate and glutamine metabolism	85.71	24 of 28
66794	ubiquinone biosynthesis	85.71	6 of 7
66794	proline metabolism	81.82	9 of 11
66794	flavin biosynthesis	80	12 of 15
66794	3-chlorocatechol degradation	80	4 of 5
66794	glycogen metabolism	80	4 of 5
66794	ethylmalonyl-CoA pathway	80	4 of 5
66794	phenylacetate degradation (aerobic)	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	gallate degradation	80	4 of 5
66794	purine metabolism	79.79	75 of 94
66794	vitamin B12 metabolism	79.41	27 of 34
66794	lysine metabolism	78.57	33 of 42
66794	aspartate and asparagine metabolism	77.78	7 of 9
66794	lipid A biosynthesis	77.78	7 of 9
66794	glycolysis	76.47	13 of 17
66794	alanine metabolism	75.86	22 of 29
66794	glycogen biosynthesis	75	3 of 4
66794	isoleucine metabolism	75	6 of 8
66794	degradation of pentoses	75	21 of 28
66794	dTDPLrhamnose biosynthesis	75	6 of 8
66794	butanoate fermentation	75	3 of 4
66794	toluene degradation	75	3 of 4
66794	biotin biosynthesis	75	3 of 4
66794	CMP-KDO biosynthesis	75	3 of 4
66794	phenol degradation	75	15 of 20
66794	tryptophan metabolism	73.68	28 of 38
66794	methionine metabolism	73.08	19 of 26
66794	vitamin B6 metabolism	72.73	8 of 11
66794	d-xylose degradation	72.73	8 of 11
66794	cysteine metabolism	72.22	13 of 18
66794	heme metabolism	71.43	10 of 14
66794	tyrosine metabolism	71.43	10 of 14
66794	urea cycle	69.23	9 of 13
66794	vitamin B1 metabolism	69.23	9 of 13
66794	oxidative phosphorylation	69.23	63 of 91
66794	histidine metabolism	68.97	20 of 29
66794	pyrimidine metabolism	68.89	31 of 45
66794	non-pathway related	68.42	26 of 38
66794	lipid metabolism	67.74	21 of 31
66794	d-mannose degradation	66.67	6 of 9
66794	cyanate degradation	66.67	2 of 3
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	octane oxidation	66.67	2 of 3
66794	glycolate and glyoxylate degradation	66.67	4 of 6
66794	methane metabolism	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	sulfoquinovose degradation	66.67	2 of 3
66794	IAA biosynthesis	66.67	2 of 3
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	arginine metabolism	66.67	16 of 24
66794	tetrahydrofolate metabolism	64.29	9 of 14
66794	metabolism of disaccharids	63.64	7 of 11
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	degradation of sugar alcohols	62.5	10 of 16
66794	myo-inositol biosynthesis	60	6 of 10
66794	cellulose degradation	60	3 of 5
66794	3-phenylpropionate degradation	60	9 of 15
66794	lipoate biosynthesis	60	3 of 5
66794	metabolism of amino sugars and derivatives	60	3 of 5
66794	hydrogen production	60	3 of 5
66794	ascorbate metabolism	59.09	13 of 22
66794	sulfate reduction	53.85	7 of 13
66794	isoprenoid biosynthesis	53.85	14 of 26
66794	polyamine pathway	52.17	12 of 23
66794	mannosylglycerate biosynthesis	50	1 of 2
66794	lactate fermentation	50	2 of 4
66794	androgen and estrogen metabolism	50	8 of 16
66794	glycine metabolism	50	5 of 10
66794	pantothenate biosynthesis	50	3 of 6
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	4-hydroxyphenylacetate degradation	50	5 of 10
66794	coenzyme M biosynthesis	50	5 of 10
66794	phenylmercury acetate degradation	50	1 of 2
66794	alginate biosynthesis	50	2 of 4
66794	resorcinol degradation	50	1 of 2
66794	quinate degradation	50	1 of 2
66794	bile acid biosynthesis, neutral pathway	47.06	8 of 17
66794	phosphatidylethanolamine bioynthesis	46.15	6 of 13
66794	nitrate assimilation	44.44	4 of 9
66794	benzoyl-CoA degradation	42.86	3 of 7
66794	creatinine degradation	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	factor 420 biosynthesis	40	2 of 5
66794	arachidonic acid metabolism	38.89	7 of 18
66794	degradation of hexoses	38.89	7 of 18
66794	carnitine metabolism	37.5	3 of 8
66794	carotenoid biosynthesis	36.36	8 of 22
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	chlorophyll metabolism	33.33	6 of 18
66794	sphingosine metabolism	33.33	2 of 6
66794	enterobactin biosynthesis	33.33	1 of 3
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	phenylpropanoid biosynthesis	30.77	4 of 13
66794	catecholamine biosynthesis	25	1 of 4
66794	cyclohexanol degradation	25	1 of 4
66794	vitamin E metabolism	25	1 of 4
66794	daunorubicin biosynthesis	22.22	2 of 9

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
18268	+	-	-	-	+	-	-	-	-	-	-	-	-	-	+	-	+	+	-	-	+
18268	+	-	-	-	+	-	-	-	-	-	-	-	-	-	+	-	+	+	-	-	+

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	Sampling date	Geographic location	Country	Country ISO 3 Code	Continent
23325	root nodules of Lathyrus latifolius		Flanders	Belgium	BEL	Europe
62588	Root nodule,Lathyrus latifolius	2008-07-25	Flanders,Zwalm	Belgium	BEL	Europe
18268	root nodules of Lupinus polyphyllus		Flanders near river Zwalm	Belgium	BEL	Europe

Taxonmaps

69479

Global distribution of 16S sequence FR774993 (>99% sequence identity) for Bosea from Microbeatlas

Aquatic Samples	781
Soil Samples	922
Animal Samples	515
Plant Samples	240
Total Samples	2458

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
18268	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	IMG-taxon 2622736433 annotated assembly for Bosea lathyri DSM 26656	scaffold	GCA_900108245	1036778.3	2622736433	1036778	73.96

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
18268	Bosea lathyri partial 16S rRNA gene, type strain R-46060T	FR774993	1441		1036778
124043	Bosea lathyri 16S-23S ribosomal RNA intergenic spacer and 23S ribosomal RNA gene, partial sequence.	KM065742	809		1036778

GC content

@ref	GC-content (mol%)	Method
18268	66.9
23325	66.4	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: Bosea lathyri DSM 26656
NCBI: GCA_900108245

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	95.90	no
125439	gram_stain	BacteriaNetⓘ	negative	97.90	no
125439	motility	BacteriaNetⓘ	yes	59.80	no
125439	spore_formation	BacteriaNetⓘ	no	97.70	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Bosea lathyri DSM 26656
NCBI: GCA_900108245.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.33	no
125438	anaerobic	anaerobicⓘ	no	94.72	no
125438	aerobic	aerobicⓘ	yes	85.73	yes
125438	spore-forming	spore-formingⓘ	no	90.16	no
125438	thermophilic	thermophileⓘ	no	96.96	no
125438	flagellated	motile2+ⓘ	yes	73.02	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Draft genome sequence of Bosea sp. WAO an arsenite and sulfide oxidizer isolated from a pyrite rock outcrop in New Jersey.	Walczak AB, Yee N, Young LY.	Stand Genomic Sci	10.1186/s40793-018-0312-4	2018
Phylogeny	Bosea caraganae sp. nov. a new species of slow-growing bacteria isolated from root nodules of the relict species Caragana jubata (Pall.) Poir. originating from Mongolia.	Sazanova AL, Safronova VI, Kuznetsova IG, Karlov DS, Belimov AA, Andronov EE, Chirak ER, Popova JP, Verkhozina AV, Willems A, Tikhonovich IA	Int J Syst Evol Microbiol	10.1099/ijsem.0.003509	2019
Phylogeny	Bosea psychrotolerans sp. nov., a psychrotrophic alphaproteobacterium isolated from Lake Michigan water.	Albert RA, McGuine M, Pavlons SC, Roecker J, Bruess J, Mossman S, Sun S, King M, Hong S, Farrance CE, Danner J, Joung Y, Shapiro N, Whitman WB, Busse HJ	Int J Syst Evol Microbiol	10.1099/ijsem.0.003319	2019
Phylogeny	Bosea vaviloviae sp. nov., a new species of slow-growing rhizobia isolated from nodules of the relict species Vavilovia formosa (Stev.) Fed.	Safronova VI, Kuznetsova IG, Sazanova AL, Kimeklis AK, Belimov AA, Andronov EE, Pinaev AG, Chizhevskaya EP, Pukhaev AR, Popov KP, Willems A, Tikhonovich IA	Antonie Van Leeuwenhoek	10.1007/s10482-015-0383-9	2015
Phylogeny	Multilocus sequence analysis of Bosea species and description of Bosea lupini sp. nov., Bosea lathyri sp. nov. and Bosea robiniae sp. nov., isolated from legumes.	De Meyer SE, Willems A	Int J Syst Evol Microbiol	10.1099/ijs.0.035477-0	2011

References

#18268	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 26656
#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 )
#23325	Sofie E. De Meyer, Anne Willems: Multilocus sequence analysis of Bosea species and description of Bosea lupini sp. nov., Bosea lathyri sp. nov. and Bosea robiniae sp. nov., isolated from legumes. IJSEM 62: 2505 - 2510 2012 ( DOI 10.1099/ijs.0.035477-0 , PubMed 22155761 )
#62588	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 61247
#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 )
#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 .
#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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Bosea lathyri (DSM 26656, CCUG 61247, LMG 26379)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Metabolite utilization

Antibiotic resistance

Metabolite production

Metabolite tests

Enzymes

Pathway annotation

API 20NE

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_900108245

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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