Paracoccus laeviglucosivorans (DSM 100094, JCM 30587, 43P)

Name: Paracoccus laeviglucosivorans (DSM 100094, JCM 30587, 43P)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 131503

Type strain

Strain Designation 43P

Culture col. no. DSM 100094 JCM 30587 43P

NCBI tax ID(s) 1197861

Special Collections DSMZ JCM

History <- A. Nakamura, Graduate School Life and Environmental Sci., Univ. Tsukuba, Japan; 43P <- T. Shimizu A. Nakamura; Univ. of Tsukuba, Japan; 43P.

Links

Paracoccus laeviglucosivorans 43P is a mesophilic prokaryote that was isolated from soil from a cabbage field.

mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 401986

JCM 30587,DSM 100094

@ref 20215

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

Domain Pseudomonadati

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Rhodobacterales

Family Paracoccaceae

Genus Paracoccus

Species Paracoccus laeviglucosivorans

Full scientific name Paracoccus laeviglucosivorans Nakamura 2015

Morphology

Cell morphology

@ref	Gram stain	Confidence
125439	negative	98.8
125438	negative	98.5

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
22730	TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545)		Medium recipe at MediaDive	Name: TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545) Composition: Casein peptone 17.0 g/l NaCl 5.0 g/l Soy peptone 3.0 g/l D(+)-Glucose 2.5 g/l K2HPO4 2.5 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
22730	positive	growth	28	mesophilic
67770	positive	growth	30	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	99

Spore formation

@ref	Spore formation	Confidence
125439		98.1

Observation

67770

Observationquinones: Q-10

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	cyanate degradation	100	3 of 3
66794	allantoin degradation	100	9 of 9
66794	enterobactin biosynthesis	100	3 of 3
66794	octane oxidation	100	3 of 3
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	Entner Doudoroff pathway	100	10 of 10
66794	sulfopterin metabolism	100	4 of 4
66794	methylglyoxal degradation	100	5 of 5
66794	ppGpp biosynthesis	100	4 of 4
66794	coenzyme A metabolism	100	4 of 4
66794	reductive acetyl coenzyme A pathway	100	7 of 7
66794	adipate degradation	100	2 of 2
66794	C4 and CAM-carbon fixation	100	8 of 8
66794	gluconeogenesis	100	8 of 8
66794	valine metabolism	100	9 of 9
66794	suberin monomers biosynthesis	100	2 of 2
66794	folate polyglutamylation	100	1 of 1
66794	palmitate biosynthesis	100	22 of 22
66794	biotin biosynthesis	100	4 of 4
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	formaldehyde oxidation	100	3 of 3
66794	photosynthesis	92.86	13 of 14
66794	tetrahydrofolate metabolism	92.86	13 of 14
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	serine metabolism	88.89	8 of 9
66794	d-mannose degradation	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	NAD metabolism	88.89	16 of 18
66794	ketogluconate metabolism	87.5	7 of 8
66794	glutathione metabolism	85.71	12 of 14
66794	phenylalanine metabolism	84.62	11 of 13
66794	glycolate and glyoxylate degradation	83.33	5 of 6
66794	vitamin B12 metabolism	82.35	28 of 34
66794	glutamate and glutamine metabolism	82.14	23 of 28
66794	proline metabolism	81.82	9 of 11
66794	gallate degradation	80	4 of 5
66794	propionate fermentation	80	8 of 10
66794	phenylacetate degradation (aerobic)	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	threonine metabolism	80	8 of 10
66794	glycogen metabolism	80	4 of 5
66794	ethylmalonyl-CoA pathway	80	4 of 5
66794	alanine metabolism	79.31	23 of 29
66794	citric acid cycle	78.57	11 of 14
66794	heme metabolism	78.57	11 of 14
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	pyrimidine metabolism	77.78	35 of 45
66794	4-hydroxymandelate degradation	77.78	7 of 9
66794	lipid A biosynthesis	77.78	7 of 9
66794	purine metabolism	77.66	73 of 94
66794	leucine metabolism	76.92	10 of 13
66794	vitamin B1 metabolism	76.92	10 of 13
66794	lysine metabolism	76.19	32 of 42
66794	degradation of sugar acids	76	19 of 25
66794	acetate fermentation	75	3 of 4
66794	isoleucine metabolism	75	6 of 8
66794	glycogen biosynthesis	75	3 of 4
66794	CMP-KDO biosynthesis	75	3 of 4
66794	flavin biosynthesis	73.33	11 of 15
66794	pentose phosphate pathway	72.73	8 of 11
66794	vitamin B6 metabolism	72.73	8 of 11
66794	ubiquinone biosynthesis	71.43	5 of 7
66794	propanol degradation	71.43	5 of 7
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	oxidative phosphorylation	68.13	62 of 91
66794	degradation of pentoses	67.86	19 of 28
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	methane metabolism	66.67	2 of 3
66794	arginine metabolism	66.67	16 of 24
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	3-phenylpropionate degradation	66.67	10 of 15
66794	acetoin degradation	66.67	2 of 3
66794	selenocysteine biosynthesis	66.67	4 of 6
66794	degradation of aromatic, nitrogen containing compounds	66.67	8 of 12
66794	non-pathway related	65.79	25 of 38
66794	histidine metabolism	65.52	19 of 29
66794	degradation of sugar alcohols	62.5	10 of 16
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	urea cycle	61.54	8 of 13
66794	lipid metabolism	61.29	19 of 31
66794	vitamin K metabolism	60	3 of 5
66794	creatinine degradation	60	3 of 5
66794	cellulose degradation	60	3 of 5
66794	myo-inositol biosynthesis	60	6 of 10
66794	glycolysis	58.82	10 of 17
66794	tryptophan metabolism	57.89	22 of 38
66794	nitrate assimilation	55.56	5 of 9
66794	aspartate and asparagine metabolism	55.56	5 of 9
66794	d-xylose degradation	54.55	6 of 11
66794	isoprenoid biosynthesis	53.85	14 of 26
66794	methionine metabolism	53.85	14 of 26
66794	dTDPLrhamnose biosynthesis	50	4 of 8
66794	kanosamine biosynthesis II	50	1 of 2
66794	pantothenate biosynthesis	50	3 of 6
66794	mannosylglycerate biosynthesis	50	1 of 2
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	ribulose monophosphate pathway	50	1 of 2
66794	cyclohexanol degradation	50	2 of 4
66794	coenzyme M biosynthesis	50	5 of 10
66794	glycine metabolism	50	5 of 10
66794	quinate degradation	50	1 of 2
66794	butanoate fermentation	50	2 of 4
66794	ethanol fermentation	50	1 of 2
66794	cysteine metabolism	50	9 of 18
66794	resorcinol degradation	50	1 of 2
66794	tyrosine metabolism	50	7 of 14
66794	polyamine pathway	47.83	11 of 23
66794	sulfate reduction	46.15	6 of 13
66794	metabolism of disaccharids	45.45	5 of 11
66794	ascorbate metabolism	45.45	10 of 22
66794	phenol degradation	45	9 of 20
66794	arachidonic acid metabolism	44.44	8 of 18
66794	metabolism of amino sugars and derivatives	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	hydrogen production	40	2 of 5
66794	lipoate biosynthesis	40	2 of 5
66794	3-chlorocatechol degradation	40	2 of 5
66794	glycine betaine biosynthesis	40	2 of 5
66794	degradation of hexoses	38.89	7 of 18
66794	phenylpropanoid biosynthesis	38.46	5 of 13
66794	carnitine metabolism	37.5	3 of 8
66794	androgen and estrogen metabolism	37.5	6 of 16
66794	IAA biosynthesis	33.33	1 of 3
66794	sphingosine metabolism	33.33	2 of 6
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	starch degradation	30	3 of 10
66794	benzoyl-CoA degradation	28.57	2 of 7
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	lactate fermentation	25	1 of 4
66794	alginate biosynthesis	25	1 of 4
66794	toluene degradation	25	1 of 4
66794	bile acid biosynthesis, neutral pathway	23.53	4 of 17
66794	phosphatidylethanolamine bioynthesis	23.08	3 of 13

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Agriculture	#Field
#Environmental	#Terrestrial	#Soil
#Host	#Plants	#Herbaceous plants (Grass,Crops)

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude
22730	soil from a cabbage field	Ibaraki, Tsukuba	Japan	JPN	Asia	36.03	140.08 36.03/140.08
67770	Soil of cabbage field in Tsukuba,(36.115N, 140.091E)	Ibaraki Pref.	Japan	JPN	Asia	36.115	140.091 36.115/140.091

Taxonmaps

69479

Global distribution of 16S sequence AB727354 (>99% sequence identity) for Paracoccus from Microbeatlas

Aquatic Samples	16
Soil Samples	3
Animal Samples	42
Plant Samples	1
Total Samples	62

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
22730	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	IMG-taxon 2724679710 annotated assembly for Paracoccus laeviglucosivorans DSM 100094	contig	GCA_900182695	1197861.3	2724679710	1197861	60.76

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
22730	Paracoccus laeviglucosivorans gene for 16S rRNA, partial sequence	AB727354	1372		1197861

GC content

@ref	GC-content (mol%)	Method
22730	64.1	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: Paracoccus laeviglucosivorans DSM 100094
NCBI: GCA_900182695

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	98.10	no
125439	motility	BacteriaNetⓘ	yes	57.40	no
125439	gram_stain	BacteriaNetⓘ	negative	98.80	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.00	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Paracoccus laeviglucosivorans strain DSM 100094
PATRIC: 1197861.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.50	no
125438	anaerobic	anaerobicⓘ	no	96.79	no
125438	spore-forming	spore-formingⓘ	no	89.97	no
125438	aerobic	aerobicⓘ	yes	87.36	no
125438	thermophilic	thermophileⓘ	no	97.68	yes
125438	flagellated	motile2+ⓘ	yes	50.11	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Paracoccus laeviglucosivorans sp. nov., an l-glucose-utilizing bacterium isolated from soil.	Nakamura A	Int J Syst Evol Microbiol	10.1099/ijsem.0.000508	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 )
#22730	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 100094
#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;
#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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Paracoccus laeviglucosivorans (DSM 100094, JCM 30587, 43P)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Observation

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_900182695

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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