Name: Plasticicumulans lactativorans YD
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 24761

Type strain:

Species: Plasticicumulans lactativorans

Strain Designation: YD

Culture col. no.: DSM 25287, NCCB 100398

Strain history: <- Y. Jiang, Dept. Biotechnology, Delft Univ. of Technology, The Netherlands; YD

NCBI tax ID(s): 1133106 (species)

SI-ID 406661

DSM 25287

Section

Plasticicumulans lactativorans YD is an aerobe, mesophilic, Gram-negative bacterium that was isolated from lactate-fed bioreactor inoculated with activated sludge from a sewage treatment plant.

coccus-shaped
Gram-negative
motile
aerobe
mesophilic
16S sequence
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Pseudomonadota*
	Class	*Gammaproteobacteria*
	Order	[Gammaproteobacteria, not assigned to order]
	Family	"Candidatus Competibacteraceae"
	Genus	*Plasticicumulans*
	Species	**Plasticicumulans lactativorans**
	Full Scientific Name (LPSN)	Plasticicumulans lactativorans Jiang et al. 2014

Information on morphological and physiological properties Morphology

[Ref.: #31063]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.993

[Ref.: #31063]	Cell length	3.5 µm

[Ref.: #31063]	Cell width	3.25 µm

[Ref.: #31063]	Cell shape	coccus-shaped

[Ref.: #31063]	Motility	yes
[Ref.: #69480]	Motility	yes Confidence in %96.69

Multimedia content

[Ref.: #21223]

Intellectual property rights:

Information on culture and growth conditions Culture and growth conditions

[Ref.: #21223]

Culture medium

R2A MEDIUM (DSMZ Medium 830)

[Ref.: #21223]

Culture medium growth

[Ref.: #21223]

Culture medium link

Medium recipe at MediaDive

[Ref.: #21223]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #21223]	growth	30 °C
[Ref.: #31063]	growth	20-45 °C
[Ref.: #31063]	optimum	40 °C

[Ref.: #21223]	Temperature range	mesophilic
[Ref.: #31063]	Temperature range	thermophilic

	pH	Kind of pH		pH
[Ref.: #31063]			optimum	7
[Ref.: #31063]			growth	06-08

Information on physiology and metabolism Physiology and metabolism

[Ref.: #31063]

Oxygen tolerance

aerobe

[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.988

[Ref.: #21223]

Name of produced compound

poly(ß-hydroxybutyric acid)

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #31063]		NaCl		optimum	1.16	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #31063]	acetate ChEBI	+	carbon source
[Ref.: #31063]	butanol ChEBI	+	carbon source
[Ref.: #31063]	ethanol ChEBI	+	carbon source
[Ref.: #31063]	fructose ChEBI	+	carbon source
[Ref.: #31063]	galactose ChEBI	+	carbon source
[Ref.: #31063]	glucosamine ChEBI	+	carbon source
[Ref.: #31063]	glucose ChEBI	+	carbon source
[Ref.: #31063]	glycerol ChEBI	+	carbon source
[Ref.: #31063]	lactate ChEBI	+	carbon source
[Ref.: #31063]	maltose ChEBI	+	carbon source
[Ref.: #31063]	melibiose ChEBI	+	carbon source
[Ref.: #31063]	nitrate ChEBI	+	reduction
[Ref.: #31063]	propionate ChEBI	+	carbon source
[Ref.: #31063]	pyruvate ChEBI	+	carbon source
[Ref.: #31063]	raffinose ChEBI	+	carbon source
[Ref.: #31063]	succinate ChEBI	+	carbon source
[Ref.: #31063]	sucrose ChEBI	+	carbon source
[Ref.: #31063]	valerate ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #31063]		catalase	+	1.11.1.6
[Ref.: #31063]		cytochrome oxidase	+	1.9.3.1

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	butanoate fermentation	100	4 of 4
[Ref.: #66794]	phenylacetate degradation (aerobic)	100	5 of 5
[Ref.: #66794]	Entner Doudoroff pathway	100	10 of 10
[Ref.: #66794]	cardiolipin biosynthesis	100	7 of 7
[Ref.: #66794]	CMP-KDO biosynthesis	100	4 of 4
[Ref.: #66794]	threonine metabolism	100	10 of 10
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	ethanol fermentation	100	2 of 2
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	molybdenum cofactor biosynthesis	100	9 of 9
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	valine metabolism	100	9 of 9
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	kanosamine biosynthesis II	100	2 of 2
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	ubiquinone biosynthesis	100	7 of 7
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	reductive acetyl coenzyme A pathway	100	7 of 7
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	photosynthesis	92.86	13 of 14
[Ref.: #66794]	tetrahydrofolate metabolism	92.86	13 of 14
[Ref.: #66794]	phenylalanine metabolism	92.31	12 of 13
[Ref.: #66794]	4-hydroxymandelate degradation	88.89	8 of 9
[Ref.: #66794]	NAD metabolism	88.89	16 of 18
[Ref.: #66794]	aspartate and asparagine metabolism	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	arginine metabolism	87.5	21 of 24
[Ref.: #66794]	gluconeogenesis	87.5	7 of 8
[Ref.: #66794]	citric acid cycle	85.71	12 of 14
[Ref.: #66794]	glutamate and glutamine metabolism	85.71	24 of 28
[Ref.: #66794]	leucine metabolism	84.62	11 of 13
[Ref.: #66794]	glycolysis	82.35	14 of 17
[Ref.: #66794]	proline metabolism	81.82	9 of 11
[Ref.: #66794]	lipid metabolism	80.65	25 of 31
[Ref.: #66794]	cellulose degradation	80	4 of 5
[Ref.: #66794]	3-chlorocatechol degradation	80	4 of 5
[Ref.: #66794]	3-phenylpropionate degradation	80	12 of 15
[Ref.: #66794]	hydrogen production	80	4 of 5
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	tyrosine metabolism	78.57	11 of 14
[Ref.: #66794]	glutathione metabolism	78.57	11 of 14
[Ref.: #66794]	heme metabolism	78.57	11 of 14
[Ref.: #66794]	lipid A biosynthesis	77.78	7 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	77.78	7 of 9
[Ref.: #66794]	serine metabolism	77.78	7 of 9
[Ref.: #66794]	vitamin B1 metabolism	76.92	10 of 13
[Ref.: #66794]	urea cycle	76.92	10 of 13
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	sulfopterin metabolism	75	3 of 4
[Ref.: #66794]	ketogluconate metabolism	75	6 of 8
[Ref.: #66794]	C4 and CAM-carbon fixation	75	6 of 8
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	flavin biosynthesis	73.33	11 of 15
[Ref.: #66794]	vitamin B6 metabolism	72.73	8 of 11
[Ref.: #66794]	alanine metabolism	72.41	21 of 29
[Ref.: #66794]	propionate fermentation	70	7 of 10
[Ref.: #66794]	purine metabolism	69.15	65 of 94
[Ref.: #66794]	d-mannose degradation	66.67	6 of 9
[Ref.: #66794]	IAA biosynthesis	66.67	2 of 3
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	enterobactin biosynthesis	66.67	2 of 3
[Ref.: #66794]	glycolate and glyoxylate degradation	66.67	4 of 6
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	non-pathway related	65.79	25 of 38
[Ref.: #66794]	histidine metabolism	65.52	19 of 29
[Ref.: #66794]	methionine metabolism	65.38	17 of 26
[Ref.: #66794]	pyrimidine metabolism	64.44	29 of 45
[Ref.: #66794]	d-xylose degradation	63.64	7 of 11
[Ref.: #66794]	pentose phosphate pathway	63.64	7 of 11
[Ref.: #66794]	oxidative phosphorylation	62.64	57 of 91
[Ref.: #66794]	degradation of sugar alcohols	62.5	10 of 16
[Ref.: #66794]	lysine metabolism	61.9	26 of 42
[Ref.: #66794]	cysteine metabolism	61.11	11 of 18
[Ref.: #66794]	degradation of hexoses	61.11	11 of 18
[Ref.: #66794]	gallate degradation	60	3 of 5
[Ref.: #66794]	starch degradation	60	6 of 10
[Ref.: #66794]	phenol degradation	60	12 of 20
[Ref.: #66794]	myo-inositol biosynthesis	60	6 of 10
[Ref.: #66794]	lipoate biosynthesis	60	3 of 5
[Ref.: #66794]	glycogen metabolism	60	3 of 5
[Ref.: #66794]	tryptophan metabolism	57.89	22 of 38
[Ref.: #66794]	isoprenoid biosynthesis	57.69	15 of 26
[Ref.: #66794]	propanol degradation	57.14	4 of 7
[Ref.: #66794]	nitrate assimilation	55.56	5 of 9
[Ref.: #66794]	sulfate reduction	53.85	7 of 13
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	lactate fermentation	50	2 of 4
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	cyclohexanol degradation	50	2 of 4
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	50	6 of 12
[Ref.: #66794]	arachidonic acid metabolism	50	9 of 18
[Ref.: #66794]	dTDPLrhamnose biosynthesis	50	4 of 8
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	resorcinol degradation	50	1 of 2
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	46.15	6 of 13
[Ref.: #66794]	metabolism of disaccharids	45.45	5 of 11
[Ref.: #66794]	allantoin degradation	44.44	4 of 9
[Ref.: #66794]	polyamine pathway	43.48	10 of 23
[Ref.: #66794]	degradation of pentoses	42.86	12 of 28
[Ref.: #66794]	degradation of sugar acids	40	10 of 25
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	glycine betaine biosynthesis	40	2 of 5
[Ref.: #66794]	ethylmalonyl-CoA pathway	40	2 of 5
[Ref.: #66794]	metabolism of amino sugars and derivatives	40	2 of 5
[Ref.: #66794]	selenocysteine biosynthesis	33.33	2 of 6
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	vitamin B12 metabolism	32.35	11 of 34
[Ref.: #66794]	ascorbate metabolism	31.82	7 of 22
[Ref.: #66794]	androgen and estrogen metabolism	31.25	5 of 16
[Ref.: #66794]	4-hydroxyphenylacetate degradation	30	3 of 10
[Ref.: #66794]	coenzyme M biosynthesis	30	3 of 10
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	29.41	5 of 17
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	vitamin E metabolism	25	1 of 4
[Ref.: #66794]	carnitine metabolism	25	2 of 8
		Only first 10 entries are displayed. Click here to see all.

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #21223]	Sample type/isolated from	lactate-fed bioreactor inoculated with activated sludge from a sewage treatment plant
[Ref.: #21223]	Geographic location (country and/or sea, region)	Kralingseveer, Rotterdam, Netherlands
[Ref.: #21223]	Country	Netherlands
[Ref.: #21223]	Country ISO 3 Code	NLD
[Ref.: #21223]	Continent	Europe
* marker position based on {}

Isolation sources categories

#Engineered	#Bioreactor	-
#Engineered	#Waste	#Activated sludge
#Engineered	#Waste	#Water treatment plant

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence JN565849 (>99% sequence identity) for Plasticicumulans lactativorans subclade from Microbeatlas

Aquatic Samples	1557
Soil Samples	1664
Animal Samples	444
Plant Samples	160
Total Samples	3825

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #21223]

Biosafety level

Risk group (German classification)
According to TRBA 466

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #21223]	Plasticicumulans lactativorans strain YD 16S ribosomal RNA gene, partial sequence	JN565849	1476	ENA	1133106 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Plasticicumulans lactativorans DSM 25287	GCA_004341245	scaffold	GenBank	1133106 tax ID	*
[Ref.: #66792]	Plasticicumulans lactativorans strain DSM 25287	1133106.8	wgs	PATRIC	1133106 tax ID	*
[Ref.: #66792]	Plasticicumulans lactativorans DSM 25287	2795385449	draft	JGI IMG/M	1133106 tax ID	*

[Ref.: #21223]	GC-content	68.5 mol%	thermal denaturation, midpoint method (Tm)
[Ref.: #31063]	GC-content	68.5 mol%

Data predicted using genome information as a basis Genome-based predictions

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Plasticicumulans lactativorans DSM 25287 NCBI: GCA_004341245.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Plasticicumulans lactativorans DSM 25287 NCBI: GCA_004341245.1
[Ref.: #69480]	motile	yes	86.437	no
[Ref.: #69480]	flagellated	yes	62.926	no
[Ref.: #69480]	gram-positive	no	99.031	yes
[Ref.: #69480]	anaerobic	no	96.208	yes
[Ref.: #69480]	aerobic	yes	67.263	no
[Ref.: #69480]	halophile	no	92.624	yes
[Ref.: #69480]	spore-forming	no	96.048	no
[Ref.: #69480]	thermophile	no	94.341	no
[Ref.: #69480]	glucose-util	yes	91.014	yes
[Ref.: #69480]	glucose-ferment	no	82.721	no

Availability in culture collections External links

[Ref.: #21223]

Culture collection no.

DSM 25287, NCCB 100398

[Ref.: #88588]

SI-ID 406661

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Plasticicumulans lactativorans sp. nov., a polyhydroxybutyrate-accumulating gammaproteobacterium from a sequencing-batch bioreactor fed with lactate.	Jiang Y, Sorokin DY, Junicke H, Kleerebezem R, van Loosdrecht MCM	Int J Syst Evol Microbiol	10.1099/ijs.0.051045-0	2013	*

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 )

#21223

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 25287

#31063

Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #27392 (see below)

#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 )

#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 .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#88588

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID406661.1 )

#27392

IJSEM 33 2014 ( DOI 10.1099/ijs.0.051045-0 , PubMed 24002473 )

* These data were automatically processed and therefore are not curated

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Plasticicumulans lactativorans DSM 25287

Plasticicumulans lactativorans DSM 25287

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