Name: Propionivibrio dicarboxylicus CreMal1
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 13897

Type strain:

Species: Propionivibrio dicarboxylicus

Strain Designation: CreMal1

Culture col. no.: DSM 5885, JCM 12339, JCM 7784

Strain history: DSM 5885 <-- K. Tanaka strain CreMal1.

NCBI tax ID(s): 1123005 (strain), 83767 (species)

SI-ID 48020

DSM 5885, JCM 7784, JCM 12339

Section

Propionivibrio dicarboxylicus CreMal1 is an anaerobe, mesophilic, motile bacterium that was isolated from anaerobic mud.

motile
anaerobe
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	*Betaproteobacteria*
	Order	*Rhodocyclales*
	Family	*Rhodocyclaceae*
	Genus	*Propionivibrio*
	Species	**Propionivibrio dicarboxylicus**
	Full Scientific Name (LPSN)	Propionivibrio dicarboxylicus Tanaka et al. 1991

Information on morphological and physiological properties Morphology

[Ref.: #69480]	Gram stain	negative Confidence in %100

[Ref.: #69480]	Motility	yes Confidence in %97.65

Information on culture and growth conditions Culture and growth conditions

[Ref.: #2343]

Culture medium

ANAEROBIC FRESHWATER (FWM) MEDIUM (DSMZ Medium 503)

[Ref.: #2343]

Culture medium growth

[Ref.: #2343]

Culture medium link

Medium recipe at MediaDive

[Ref.: #2343]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #2343]			growth	30 °C
[Ref.: #67770]			growth	30 °C

[Ref.: #2343]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #2343]

Oxygen tolerance

anaerobe

[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.998

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	reductive acetyl coenzyme A pathway	100	7 of 7
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	aspartate and asparagine metabolism	100	9 of 9
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	propanol degradation	100	7 of 7
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	ethanol fermentation	100	2 of 2
[Ref.: #66794]	isoleucine metabolism	100	8 of 8
[Ref.: #66794]	tetrahydrofolate metabolism	100	14 of 14
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	ubiquinone biosynthesis	100	7 of 7
[Ref.: #66794]	NAD metabolism	94.44	17 of 18
[Ref.: #66794]	citric acid cycle	92.86	13 of 14
[Ref.: #66794]	photosynthesis	92.86	13 of 14
[Ref.: #66794]	pentose phosphate pathway	90.91	10 of 11
[Ref.: #66794]	threonine metabolism	90	9 of 10
[Ref.: #66794]	propionate fermentation	90	9 of 10
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	serine metabolism	88.89	8 of 9
[Ref.: #66794]	valine metabolism	88.89	8 of 9
[Ref.: #66794]	lipid A biosynthesis	88.89	8 of 9
[Ref.: #66794]	gluconeogenesis	87.5	7 of 8
[Ref.: #66794]	C4 and CAM-carbon fixation	87.5	7 of 8
[Ref.: #66794]	heme metabolism	85.71	12 of 14
[Ref.: #66794]	vitamin B1 metabolism	84.62	11 of 13
[Ref.: #66794]	leucine metabolism	84.62	11 of 13
[Ref.: #66794]	glycolate and glyoxylate degradation	83.33	5 of 6
[Ref.: #66794]	glutamate and glutamine metabolism	82.14	23 of 28
[Ref.: #66794]	proline metabolism	81.82	9 of 11
[Ref.: #66794]	vitamin B6 metabolism	81.82	9 of 11
[Ref.: #66794]	hydrogen production	80	4 of 5
[Ref.: #66794]	Entner Doudoroff pathway	80	8 of 10
[Ref.: #66794]	ethylmalonyl-CoA pathway	80	4 of 5
[Ref.: #66794]	gallate degradation	80	4 of 5
[Ref.: #66794]	methylglyoxal degradation	80	4 of 5
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	vitamin B12 metabolism	79.41	27 of 34
[Ref.: #66794]	alanine metabolism	79.31	23 of 29
[Ref.: #66794]	molybdenum cofactor biosynthesis	77.78	7 of 9
[Ref.: #66794]	d-mannose degradation	77.78	7 of 9
[Ref.: #66794]	purine metabolism	77.66	73 of 94
[Ref.: #66794]	phenylalanine metabolism	76.92	10 of 13
[Ref.: #66794]	glycolysis	76.47	13 of 17
[Ref.: #66794]	degradation of sugar acids	76	19 of 25
[Ref.: #66794]	pyrimidine metabolism	75.56	34 of 45
[Ref.: #66794]	butanoate fermentation	75	3 of 4
[Ref.: #66794]	degradation of pentoses	75	21 of 28
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	ketogluconate metabolism	75	6 of 8
[Ref.: #66794]	sulfopterin metabolism	75	3 of 4
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	dTDPLrhamnose biosynthesis	75	6 of 8
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	flavin biosynthesis	73.33	11 of 15
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	sulfate reduction	69.23	9 of 13
[Ref.: #66794]	degradation of sugar alcohols	68.75	11 of 16
[Ref.: #66794]	cysteine metabolism	66.67	12 of 18
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	sulfoquinovose degradation	66.67	2 of 3
[Ref.: #66794]	CO2 fixation in Crenarchaeota	66.67	6 of 9
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	formaldehyde oxidation	66.67	2 of 3
[Ref.: #66794]	selenocysteine biosynthesis	66.67	4 of 6
[Ref.: #66794]	non-pathway related	65.79	25 of 38
[Ref.: #66794]	tryptophan metabolism	65.79	25 of 38
[Ref.: #66794]	methionine metabolism	65.38	17 of 26
[Ref.: #66794]	glutathione metabolism	64.29	9 of 14
[Ref.: #66794]	tyrosine metabolism	64.29	9 of 14
[Ref.: #66794]	oxidative phosphorylation	62.64	57 of 91
[Ref.: #66794]	arginine metabolism	62.5	15 of 24
[Ref.: #66794]	histidine metabolism	62.07	18 of 29
[Ref.: #66794]	urea cycle	61.54	8 of 13
[Ref.: #66794]	isoprenoid biosynthesis	61.54	16 of 26
[Ref.: #66794]	glycogen metabolism	60	3 of 5
[Ref.: #66794]	phenylacetate degradation (aerobic)	60	3 of 5
[Ref.: #66794]	3-chlorocatechol degradation	60	3 of 5
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
[Ref.: #66794]	lysine metabolism	57.14	24 of 42
[Ref.: #66794]	nitrate assimilation	55.56	5 of 9
[Ref.: #66794]	lipid metabolism	54.84	17 of 31
[Ref.: #66794]	ribulose monophosphate pathway	50	1 of 2
[Ref.: #66794]	adipate degradation	50	1 of 2
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	starch degradation	50	5 of 10
[Ref.: #66794]	degradation of hexoses	50	9 of 18
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	mannosylglycerate biosynthesis	50	1 of 2
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	myo-inositol biosynthesis	50	5 of 10
[Ref.: #66794]	lactate fermentation	50	2 of 4
[Ref.: #66794]	3-phenylpropionate degradation	46.67	7 of 15
[Ref.: #66794]	ascorbate metabolism	45.45	10 of 22
[Ref.: #66794]	4-hydroxymandelate degradation	44.44	4 of 9
[Ref.: #66794]	allantoin degradation	44.44	4 of 9
[Ref.: #66794]	androgen and estrogen metabolism	43.75	7 of 16
[Ref.: #66794]	metabolism of amino sugars and derivatives	40	2 of 5
[Ref.: #66794]	lipoate biosynthesis	40	2 of 5
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	O-antigen biosynthesis	40	2 of 5
[Ref.: #66794]	4-hydroxyphenylacetate degradation	40	4 of 10
[Ref.: #66794]	coenzyme M biosynthesis	40	4 of 10
[Ref.: #66794]	bacilysin biosynthesis	40	2 of 5
[Ref.: #66794]	phenol degradation	40	8 of 20
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	38.46	5 of 13
[Ref.: #66794]	carnitine metabolism	37.5	3 of 8
[Ref.: #66794]	metabolism of disaccharids	36.36	4 of 11
[Ref.: #66794]	cholesterol biosynthesis	36.36	4 of 11
[Ref.: #66794]	d-xylose degradation	36.36	4 of 11
[Ref.: #66794]	polyamine pathway	34.78	8 of 23
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	carotenoid biosynthesis	31.82	7 of 22
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	29.41	5 of 17
[Ref.: #66794]	vitamin E metabolism	25	1 of 4
[Ref.: #66794]	alginate biosynthesis	25	1 of 4
[Ref.: #66794]	catecholamine biosynthesis	25	1 of 4
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	phenylpropanoid biosynthesis	23.08	3 of 13
[Ref.: #66794]	arachidonic acid metabolism	22.22	4 of 18
		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.: #2343]	Sample type/isolated from	anaerobic mud
[Ref.: #2343]	Geographic location (country and/or sea, region)	creek near Lake Kasumigaura
[Ref.: #2343]	Country	Japan
[Ref.: #2343]	Country ISO 3 Code	JPN
[Ref.: #2343]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Anaerobic mud sample from a creek near Lake Kasumigaura
[Ref.: #67770]	Geographic location (country and/or sea, region)	Ibaraki Pref.
[Ref.: #67770]	Country	Japan
[Ref.: #67770]	Country ISO 3 Code	JPN
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Terrestrial	#Mud (Sludge)
#Condition	#Anoxic (anaerobic)	-

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence Y17601 (>99% sequence identity) for Propionivibrio dicarboxylicus subclade from Microbeatlas

Aquatic Samples	61
Soil Samples	3
Animal Samples	1
Plant Samples	4
Total Samples	69

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

[Ref.: #2343]

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.: #2343]	Propionivibrio dicarboxylicus 16S rRNA gene, partial	Y17601	1496	ENA	83767 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Propionivibrio dicarboxylicus DSM 5885	GCA_900099695	scaffold	GenBank	83767 tax ID
[Ref.: #66792]	Propionivibrio dicarboxylicus strain DSM 5885	83767.3	wgs	PATRIC	83767 tax ID	*
[Ref.: #66792]	Propionivibrio dicarboxylicus DSM 5885	2599185173	draft	JGI IMG/M	83767 tax ID	*

[Ref.: #2343]	GC-content	61.0 mol%
[Ref.: #67770]	GC-content	61 mol%	high performance liquid chromatography (HPLC)

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: Propionivibrio dicarboxylicus DSM 5885 NCBI: GCA_900099695.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Propionivibrio dicarboxylicus strain DSM 5885 PATRIC: 83767.3
[Ref.: #69480]	motile	yes	90.717	no
[Ref.: #69480]	flagellated	yes	60.005	no
[Ref.: #69480]	gram-positive	no	99.316	no
[Ref.: #69480]	anaerobic	yes	84.32	yes
[Ref.: #69480]	halophile	no	93.914	no
[Ref.: #69480]	spore-forming	no	95.834	no
[Ref.: #69480]	thermophile	no	97.848	no
[Ref.: #69480]	glucose-util	yes	69.119	no
[Ref.: #69480]	aerobic	no	91.561	no
[Ref.: #69480]	glucose-ferment	no	73.613	no

Availability in culture collections External links

[Ref.: #2343]

Culture collection no.

DSM 5885, JCM 12339, JCM 7784

[Ref.: #83072]

SI-ID 48020

References

#2343

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 5885

#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 )

#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 .

#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 )

#83072

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-ID48020.1 )

* These data were automatically processed and therefore are not curated

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Propionivibrio dicarboxylicus DSM 5885

Propionivibrio dicarboxylicus strain DSM 5885

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