Name: Pelomonas saccharophila DSM 654
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 2981

Type strain:

Species: Pelomonas saccharophila

Culture col. no.: DSM 654, ATCC 15946, CFBP 2433, CIP 59.18, HAMBI 373, IAM 14368, JCM 15912, LMG 2256, NCCB 46053, VKM B-902, CCUG 32988, BUCSAV 293, CCM 1980, CCUG 15839, IAM 1504, JCM 21181, LMG 7831, NBRC 103037, NCDO 1936, NCIMB 8570, NRRL B-1492

Strain history: DSM 654 <-- ATCC 15946 <-- M. Doudoroff.

NCBI tax ID(s): 304 (species)

Other strains from Pelomonas saccharophila

P. saccharophila CCUG 778
P. saccharophila CCUG 41950 A
P. saccharophila CCUG 52554 B
P. saccharophila CCUG 52623
P. saccharophila CCUG 52667
P. saccharophila CCUG 52669
P. saccharophila CCUG 52671
P. saccharophila CCUG 52681 A
P. saccharophila CCUG 58645

Section

Pelomonas saccharophila DSM 654 is a mesophilic bacterium that was isolated from water.

mesophilic
16S sequence
Bacteria
genome sequence

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

	Last LPSN update	07-12-2022 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Pseudomonadota*
	Class	*Betaproteobacteria*
	Order	*Burkholderiales*
	Family	*Comamonadaceae*
	Genus	*Pelomonas*
	Species	**Pelomonas saccharophila**
	Full Scientific Name (PNU)	Pelomonas saccharophila (Doudoroff 1940) Xie and Yokota 2005

	Synonym	"Roseateles* saccharophilus"*
	Synonym	Pseudomonas saccharophila

Information on morphological and physiological properties Morphology

[Ref.: #69480]	Gram stain	negative Confidence in %99.985

[Ref.: #69480]	Motility	yes Confidence in %93.178

Information on culture and growth conditions Culture and growth conditions

[Ref.: #246]

Culture medium

MINERAL MEDIUM FOR CHEMOLITHOTROPHIC GROWTH (H-3) (DSMZ Medium 81)

[Ref.: #246]

Culture medium growth

[Ref.: #246]

Culture medium link

Medium recipe provided by DSMZ

[Ref.: #246]

Culture medium composition

expand / minimize

[Ref.: #246]

Culture medium

NUTRIENT AGAR (DSMZ Medium 1)

[Ref.: #246]

Culture medium growth

[Ref.: #246]

Culture medium link

Medium recipe provided by DSMZ

[Ref.: #246]

Culture medium composition

expand / minimize

[Ref.: #37699]

Culture medium

MEDIUM 3 - Columbia agar

[Ref.: #37699]

Culture medium growth

[Ref.: #37699]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #246]	growth	30 °C
[Ref.: #37699]	growth	30 °C
[Ref.: #67770]	growth	30 °C

[Ref.: #246]	Temperature range	mesophilic
[Ref.: #37699]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #69481]	Ability of spore formation	no Confidence in %99
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.918

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	Entner Doudoroff pathway	100	10 of 10
[Ref.: #66794]	CMP-KDO biosynthesis	100	4 of 4
[Ref.: #66794]	glycogen metabolism	100	5 of 5
[Ref.: #66794]	photosynthesis	100	14 of 14
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	starch degradation	100	10 of 10
[Ref.: #66794]	valine metabolism	100	9 of 9
[Ref.: #66794]	phenylacetate degradation (aerobic)	100	5 of 5
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	taurine degradation	100	1 of 1
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	cellulose degradation	100	5 of 5
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	denitrification	100	2 of 2
[Ref.: #66794]	ubiquinone biosynthesis	100	7 of 7
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	threonine metabolism	90	9 of 10
[Ref.: #66794]	molybdenum cofactor biosynthesis	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	gluconeogenesis	87.5	7 of 8
[Ref.: #66794]	isoleucine metabolism	87.5	7 of 8
[Ref.: #66794]	reductive acetyl coenzyme A pathway	85.71	6 of 7
[Ref.: #66794]	phenylalanine metabolism	84.62	11 of 13
[Ref.: #66794]	NAD metabolism	83.33	15 of 18
[Ref.: #66794]	proline metabolism	81.82	9 of 11
[Ref.: #66794]	vitamin B6 metabolism	81.82	9 of 11
[Ref.: #66794]	gallate degradation	80	4 of 5
[Ref.: #66794]	ethylmalonyl-CoA pathway	80	4 of 5
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	tetrahydrofolate metabolism	78.57	11 of 14
[Ref.: #66794]	heme metabolism	78.57	11 of 14
[Ref.: #66794]	lysine metabolism	78.57	33 of 42
[Ref.: #66794]	serine metabolism	77.78	7 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	77.78	7 of 9
[Ref.: #66794]	d-mannose degradation	77.78	7 of 9
[Ref.: #66794]	lipid A biosynthesis	77.78	7 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	77.78	7 of 9
[Ref.: #66794]	vitamin B1 metabolism	76.92	10 of 13
[Ref.: #66794]	leucine metabolism	76.92	10 of 13
[Ref.: #66794]	alanine metabolism	75.86	22 of 29
[Ref.: #66794]	pyrimidine metabolism	75.56	34 of 45
[Ref.: #66794]	butanoate fermentation	75	3 of 4
[Ref.: #66794]	glutamate and glutamine metabolism	75	21 of 28
[Ref.: #66794]	phenol degradation	75	15 of 20
[Ref.: #66794]	sulfopterin metabolism	75	3 of 4
[Ref.: #66794]	C4 and CAM-carbon fixation	75	6 of 8
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	purine metabolism	74.47	70 of 94
[Ref.: #66794]	tryptophan metabolism	73.68	28 of 38
[Ref.: #66794]	flavin biosynthesis	73.33	11 of 15
[Ref.: #66794]	pentose phosphate pathway	72.73	8 of 11
[Ref.: #66794]	d-xylose degradation	72.73	8 of 11
[Ref.: #66794]	degradation of sugar acids	72	18 of 25
[Ref.: #66794]	glutathione metabolism	71.43	10 of 14
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	citric acid cycle	71.43	10 of 14
[Ref.: #66794]	tyrosine metabolism	71.43	10 of 14
[Ref.: #66794]	vitamin B12 metabolism	70.59	24 of 34
[Ref.: #66794]	glycolysis	70.59	12 of 17
[Ref.: #66794]	propionate fermentation	70	7 of 10
[Ref.: #66794]	oxidative phosphorylation	69.23	63 of 91
[Ref.: #66794]	urea cycle	69.23	9 of 13
[Ref.: #66794]	selenocysteine biosynthesis	66.67	4 of 6
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	enterobactin biosynthesis	66.67	2 of 3
[Ref.: #66794]	methane metabolism	66.67	2 of 3
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	cysteine metabolism	66.67	12 of 18
[Ref.: #66794]	3-phenylpropionate degradation	66.67	10 of 15
[Ref.: #66794]	arginine metabolism	66.67	16 of 24
[Ref.: #66794]	IAA biosynthesis	66.67	2 of 3
[Ref.: #66794]	L-lactaldehyde degradation	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]	lipid metabolism	64.52	20 of 31
[Ref.: #66794]	degradation of pentoses	64.29	18 of 28
[Ref.: #66794]	ketogluconate metabolism	62.5	5 of 8
[Ref.: #66794]	degradation of sugar alcohols	62.5	10 of 16
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	histidine metabolism	62.07	18 of 29
[Ref.: #66794]	isoprenoid biosynthesis	61.54	16 of 26
[Ref.: #66794]	methionine metabolism	61.54	16 of 26
[Ref.: #66794]	metabolism of amino sugars and derivatives	60	3 of 5
[Ref.: #66794]	vitamin K metabolism	60	3 of 5
[Ref.: #66794]	lipoate biosynthesis	60	3 of 5
[Ref.: #66794]	propanol degradation	57.14	4 of 7
[Ref.: #66794]	androgen and estrogen metabolism	56.25	9 of 16
[Ref.: #66794]	degradation of hexoses	55.56	10 of 18
[Ref.: #66794]	ascorbate metabolism	54.55	12 of 22
[Ref.: #66794]	metabolism of disaccharids	54.55	6 of 11
[Ref.: #66794]	sulfate reduction	53.85	7 of 13
[Ref.: #66794]	cyclohexanol degradation	50	2 of 4
[Ref.: #66794]	glycolate and glyoxylate degradation	50	3 of 6
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	kanosamine biosynthesis II	50	1 of 2
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	ribulose monophosphate pathway	50	1 of 2
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	dTDPLrhamnose biosynthesis	50	4 of 8
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	allantoin degradation	44.44	4 of 9
[Ref.: #66794]	nitrate assimilation	44.44	4 of 9
[Ref.: #66794]	4-hydroxymandelate degradation	44.44	4 of 9
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
[Ref.: #66794]	glycine betaine biosynthesis	40	2 of 5
[Ref.: #66794]	glycine metabolism	40	4 of 10
[Ref.: #66794]	factor 420 biosynthesis	40	2 of 5
[Ref.: #66794]	hydrogen production	40	2 of 5
[Ref.: #66794]	coenzyme M biosynthesis	40	4 of 10
[Ref.: #66794]	D-cycloserine biosynthesis	40	2 of 5
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	polyamine pathway	39.13	9 of 23
[Ref.: #66794]	arachidonic acid metabolism	38.89	7 of 18
[Ref.: #66794]	carnitine metabolism	37.5	3 of 8
[Ref.: #66794]	sulfoquinovose degradation	33.33	1 of 3
[Ref.: #66794]	(5R)-carbapenem carboxylate 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]	carotenoid biosynthesis	31.82	7 of 22
[Ref.: #66794]	phenylpropanoid biosynthesis	30.77	4 of 13
[Ref.: #66794]	4-hydroxyphenylacetate degradation	30	3 of 10
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	29.41	5 of 17
[Ref.: #66794]	benzoyl-CoA degradation	28.57	2 of 7
[Ref.: #66794]	aclacinomycin biosynthesis	28.57	2 of 7
[Ref.: #66794]	cholesterol biosynthesis	27.27	3 of 11
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	vitamin E metabolism	25	1 of 4
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	alginate biosynthesis	25	1 of 4
[Ref.: #66794]	methanogenesis from CO2	25	3 of 12
[Ref.: #66794]	chlorophyll 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.: #246]	Sample type/isolated from	water

[Ref.: #67770]	Sample type/isolated from	Mud from a stagnant pool
* marker position based on {}

Isolation sources categories

#Environmental

#Aquatic

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AM501432 (>99% sequence identity) for Pelomonas from Microbeatlas

Aquatic Samples	1061
Soil Samples	199
Animal Samples	1602
Plant Samples	235
Total Samples	3097

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

[Ref.: #246]

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:

Only first 5 entries are displayed. Click here to see all.

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #20218]	Pelomonas saccharophila partial 16S rRNA gene, type strain ATCC 15946T	AM501428	1471	ENA	304 tax ID	*
[Ref.: #20218]	Pelomonas saccharophila partial 16S rRNA gene, type strain CCUG 32988T	AM501429	1391	ENA	304 tax ID	*
[Ref.: #20218]	Pelomonas saccharophila gene for 16S rRNA, strain: DSM 654	AB021407	1502	ENA	304 tax ID	*
[Ref.: #20218]	Pelomonas saccharophila partial 16S rRNA gene, type strain DSM 654T	AM501431	1345	ENA	304 tax ID	*
[Ref.: #20218]	Pelomonas saccharophila partial 16S rRNA gene, type strain IAM 14368T	AM501432	1391	ENA	304 tax ID	*
[Ref.: #20218]	Pelomonas saccharophila partial 16S rRNA gene, type strain LMG 2256T	AM501430	1386	ENA	304 tax ID	*
[Ref.: #20218]	Pelomonas saccharophila gene for 16S rRNA, partial sequence, strain: NBRC 103037	AB681917	1449	ENA	304 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Pelomonas saccharophila DSM 654	GCA_004342485	scaffold	GenBank	304 tax ID
[Ref.: #66792]	Pelomonas saccharophila strain DSM 654	304.35	wgs	PATRIC	304 tax ID	*
[Ref.: #66792]	Pelomonas saccharophila DSM 654	2802428851	draft	JGI IMG/M	304 tax ID	*

[Ref.: #246]	GC-content	68.9 mol%
[Ref.: #67770]	GC-content	69.1 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 Diaspora project based on: Pelomonas saccharophila DSM 654 NCBI: GCA_004342485.1
[Ref.: #69480]	spore-forming	no	99.918	no
[Ref.: #69480]	anaerobic	no	98.782	no
[Ref.: #69480]	gram-positive	no	99.985	yes
[Ref.: #69480]	thermophile	no	98.843	yes
[Ref.: #69480]	motile	yes	93.178	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Pelomonas saccharophila DSM 654 NCBI: GCA_004342485.1
[Ref.: #69481]	spore-forming	no	99	no

Availability in culture collections External links

[Ref.: #246]

Culture collection no.

DSM 654, ATCC 15946, CFBP 2433, CIP 59.18, HAMBI 373, IAM 14368, JCM 15912, LMG 2256, NCCB 46053, VKM B-902, CCUG 32988, BUCSAV 293, CCM 1980, CCUG 15839, IAM 1504, JCM 21181, LMG 7831, NBRC 103037, NCDO 1936, NCIMB 8570, NRRL B-1492

[Ref.: #20218]

Associated Passport(s) in StrainInfo

53298, 53287, 53296, 232784, 536279, 539275, 53286, 621617, 227764

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Paucibacter oligotrophus sp. nov., isolated from fresh water, and emended description of the genus Paucibacter.	Pheng S, Lee JJ, Eom MK, Lee KH, Kim SG	Int J Syst Evol Microbiol	10.1099/ijsem.0.001931	2017	*
Phylogeny	Description of Pelomonas aquatica sp. nov. and Pelomonas puraquae sp. nov., isolated from industrial and haemodialysis water.	Gomila M, Bowien B, Falsen E, Moore ERB, Lalucat J	Int J Syst Evol Microbiol	10.1099/ijs.0.65149-0	2007	*
Phylogeny	Reclassification of Alcaligenes latus strains IAM 12599T and IAM 12664 and Pseudomonas saccharophila as Azohydromonas lata gen. nov., comb. nov., Azohydromonas australica sp. nov. and Pelomonas saccharophila gen. nov., comb. nov., respectively.	Xie CH, Yokota A	Int J Syst Evol Microbiol	10.1099/ijs.0.63733-0	2005	*

References

#246	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 654

#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 )

#20218

Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )

#37699 ; Curators of the CIP;

#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 )

* These data were automatically processed and therefore are not curated

Change proposal

You found an error in BacDive? Please tell us about it!

Note that changes will be reviewed and judged. If your changes are legitimate, changes will occur within the next BacDive update. Only proposed changes supported by the according reference will be reviewed. The BacDive team reserves the right to reject proposed changes.

Search for species Pelomonas saccharophila in external resources:
SILVA
BRENDA
PANGAEA
StrainInfo
GBIF