Name: Desulfocucumis palustris NAW-5
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 140353

Type strain:

Species: Desulfocucumis palustris

Strain Designation: NAW-5

Culture col. no.: DSM 102911, NBRC 112242

Strain history: <- M. Watanabe, Hokkaido University, Sapporo, Japan; NAW-5 <- M. Watanabe {2016}

NCBI tax ID(s): 1898651 (species)

SI-ID 408151

DSM 102911

Section

Desulfocucumis palustris NAW-5 is an obligate anaerobe, spore-forming, Gram-negative bacterium that was isolated from marsh soil.

Gram-negative
motile
rod-shaped
spore-forming
obligate anaerobe
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	*Bacillota*
	Class	*Clostridia*
	Order	*Eubacteriales*
	Family	*Peptococcaceae*
	Genus	*Desulfocucumis*
	Species	**Desulfocucumis palustris**
	Full Scientific Name (LPSN)	Desulfocucumis palustris Watanabe et al. 2017

Information on morphological and physiological properties Morphology

[Ref.: #43451]	Gram stain	negative

[Ref.: #43451]	Cell length	3-4 µm

[Ref.: #43451]	Cell width	1 µm

[Ref.: #43451]	Cell shape	rod-shaped

[Ref.: #43451]	Motility	yes

[Ref.: #43451]	Flagellum arrangement	peritrichous

[Ref.: #43451]	Colony color	pale brown
[Ref.: #43451]	Cultivation medium used	Basal medium

Information on culture and growth conditions Culture and growth conditions

[Ref.: #43451]

Culture medium

Basal medium

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Culture medium growth

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Culture medium

PELOTOMACULUM MEDIUM (DSMZ Medium 960)

[Ref.: #42960]

Culture medium growth

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Culture medium link

Medium recipe at MediaDive

[Ref.: #42960]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #42960]	growth	28 °C
[Ref.: #43451]	growth	18-48 °C
[Ref.: #43451]	optimum	32-37 °C

[Ref.: #42960]	Temperature range	mesophilic
[Ref.: #43451]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #43451]			optimum	6.2-7.3
[Ref.: #43451]			growth	5.8-8.4

Information on physiology and metabolism Physiology and metabolism

[Ref.: #43451]

Oxygen tolerance

obligate anaerobe

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Ability of spore formation

yes

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Halophily / tolerance level

non-halophilic

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #43451]		NaCl		growth	0-2.1	%
[Ref.: #43451]		NaCl		optimum	0	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #43451]	acetate ChEBI	+	assimilation
[Ref.: #43451]	benzoate ChEBI	+	assimilation
[Ref.: #43451]	butyrate ChEBI	+	assimilation
[Ref.: #43451]	elemental sulfur ChEBI	+	electron acceptor
[Ref.: #43451]	ferric iron ChEBI	-	electron acceptor
[Ref.: #43451]	formate ChEBI	+	assimilation
[Ref.: #43451]	fumarate ChEBI	+	assimilation
[Ref.: #43451]	glucose ChEBI	-	assimilation
[Ref.: #43451]	isobutyrate ChEBI	+	assimilation
[Ref.: #43451]	lactate ChEBI	+	assimilation
[Ref.: #43451]	nitrate ChEBI	-	electron acceptor
[Ref.: #43451]	nitrite ChEBI	-	electron acceptor
[Ref.: #43451]	propionate ChEBI	+	assimilation
[Ref.: #43451]	pyruvate ChEBI	+	assimilation
[Ref.: #43451]	sulfate ChEBI	+	electron acceptor
[Ref.: #43451]	sulfite ChEBI	-	electron acceptor
[Ref.: #43451]	thiosulfate ChEBI	+	electron acceptor
	Only first 10 entries are displayed. Click here to see all.

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	aspartate and asparagine metabolism	100	9 of 9
[Ref.: #66794]	glycogen metabolism	100	5 of 5
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	propanol degradation	85.71	6 of 7
[Ref.: #66794]	reductive acetyl coenzyme A pathway	85.71	6 of 7
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	83.33	10 of 12
[Ref.: #66794]	glycine betaine biosynthesis	80	4 of 5
[Ref.: #66794]	propionate fermentation	80	8 of 10
[Ref.: #66794]	cellulose degradation	80	4 of 5
[Ref.: #66794]	glutamate and glutamine metabolism	78.57	22 of 28
[Ref.: #66794]	CO2 fixation in Crenarchaeota	77.78	7 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	77.78	7 of 9
[Ref.: #66794]	d-mannose degradation	77.78	7 of 9
[Ref.: #66794]	glycolysis	76.47	13 of 17
[Ref.: #66794]	alanine metabolism	75.86	22 of 29
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	sulfopterin metabolism	75	3 of 4
[Ref.: #66794]	coenzyme A metabolism	75	3 of 4
[Ref.: #66794]	biotin biosynthesis	75	3 of 4
[Ref.: #66794]	dTDPLrhamnose biosynthesis	75	6 of 8
[Ref.: #66794]	ketogluconate metabolism	75	6 of 8
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	peptidoglycan biosynthesis	73.33	11 of 15
[Ref.: #66794]	photosynthesis	71.43	10 of 14
[Ref.: #66794]	starch degradation	70	7 of 10
[Ref.: #66794]	threonine metabolism	70	7 of 10
[Ref.: #66794]	vitamin B1 metabolism	69.23	9 of 13
[Ref.: #66794]	degradation of sugar alcohols	68.75	11 of 16
[Ref.: #66794]	oxidative phosphorylation	67.03	61 of 91
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	formaldehyde oxidation	66.67	2 of 3
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	IAA biosynthesis	66.67	2 of 3
[Ref.: #66794]	enterobactin biosynthesis	66.67	2 of 3
[Ref.: #66794]	valine metabolism	66.67	6 of 9
[Ref.: #66794]	selenocysteine biosynthesis	66.67	4 of 6
[Ref.: #66794]	NAD metabolism	66.67	12 of 18
[Ref.: #66794]	serine metabolism	66.67	6 of 9
[Ref.: #66794]	methane metabolism	66.67	2 of 3
[Ref.: #66794]	citric acid cycle	64.29	9 of 14
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	pyrimidine metabolism	62.22	28 of 45
[Ref.: #66794]	leucine metabolism	61.54	8 of 13
[Ref.: #66794]	sulfate reduction	61.54	8 of 13
[Ref.: #66794]	phenylalanine metabolism	61.54	8 of 13
[Ref.: #66794]	hydrogen production	60	3 of 5
[Ref.: #66794]	Entner Doudoroff pathway	60	6 of 10
[Ref.: #66794]	phenylacetate degradation (aerobic)	60	3 of 5
[Ref.: #66794]	factor 420 biosynthesis	60	3 of 5
[Ref.: #66794]	non-pathway related	57.89	22 of 38
[Ref.: #66794]	lysine metabolism	57.14	24 of 42
[Ref.: #66794]	ubiquinone biosynthesis	57.14	4 of 7
[Ref.: #66794]	chorismate metabolism	55.56	5 of 9
[Ref.: #66794]	pentose phosphate pathway	54.55	6 of 11
[Ref.: #66794]	purine metabolism	51.06	48 of 94
[Ref.: #66794]	suberin monomers biosynthesis	50	1 of 2
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	tetrahydrofolate metabolism	50	7 of 14
[Ref.: #66794]	toluene degradation	50	2 of 4
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	coenzyme M biosynthesis	50	5 of 10
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	lipid metabolism	48.39	15 of 31
[Ref.: #66794]	flavin biosynthesis	46.67	7 of 15
[Ref.: #66794]	urea cycle	46.15	6 of 13
[Ref.: #66794]	proline metabolism	45.45	5 of 11
[Ref.: #66794]	lipid A biosynthesis	44.44	4 of 9
[Ref.: #66794]	nitrate assimilation	44.44	4 of 9
[Ref.: #66794]	vitamin B12 metabolism	44.12	15 of 34
[Ref.: #66794]	polyamine pathway	43.48	10 of 23
[Ref.: #66794]	cardiolipin biosynthesis	42.86	3 of 7
[Ref.: #66794]	benzoyl-CoA degradation	42.86	3 of 7
[Ref.: #66794]	glycine metabolism	40	4 of 10
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	metabolism of amino sugars and derivatives	40	2 of 5
[Ref.: #66794]	vitamin K metabolism	40	2 of 5
[Ref.: #66794]	cysteine metabolism	38.89	7 of 18
[Ref.: #66794]	gluconeogenesis	37.5	3 of 8
[Ref.: #66794]	vitamin B6 metabolism	36.36	4 of 11
[Ref.: #66794]	ascorbate metabolism	36.36	8 of 22
[Ref.: #66794]	glutathione metabolism	35.71	5 of 14
[Ref.: #66794]	degradation of pentoses	35.71	10 of 28
[Ref.: #66794]	methionine metabolism	34.62	9 of 26
[Ref.: #66794]	histidine metabolism	34.48	10 of 29
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	cyanate degradation	33.33	1 of 3
[Ref.: #66794]	glycolate and glyoxylate degradation	33.33	2 of 6
[Ref.: #66794]	pantothenate biosynthesis	33.33	2 of 6
[Ref.: #66794]	tryptophan metabolism	31.58	12 of 38
[Ref.: #66794]	isoprenoid biosynthesis	30.77	8 of 26
[Ref.: #66794]	4-hydroxyphenylacetate degradation	30	3 of 10
[Ref.: #66794]	arginine metabolism	29.17	7 of 24
[Ref.: #66794]	tyrosine metabolism	28.57	4 of 14
[Ref.: #66794]	degradation of hexoses	27.78	5 of 18
[Ref.: #66794]	d-xylose degradation	27.27	3 of 11
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	metabolism of disaccharids	27.27	3 of 11
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	C4 and CAM-carbon fixation	25	2 of 8
[Ref.: #66794]	carnitine metabolism	25	2 of 8
[Ref.: #66794]	vitamin E metabolism	25	1 of 4
[Ref.: #66794]	methanogenesis from CO2	25	3 of 12
[Ref.: #66794]	CMP-KDO biosynthesis	25	1 of 4
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	23.53	4 of 17
[Ref.: #66794]	4-hydroxymandelate degradation	22.22	2 of 9
[Ref.: #66794]	heme metabolism	21.43	3 of 14
		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.: #42960]	Sample type/isolated from	marsh soil
[Ref.: #42960]	Geographic location (country and/or sea, region)	Hokkaido Prefectural Natural Park, Nopporo Forest Park
[Ref.: #42960]	Country	Japan
[Ref.: #42960]	Country ISO 3 Code	JPN
[Ref.: #42960]	Continent	Asia

[Ref.: #43451]	Sample type/isolated from	Marsh soil from Nopporo Forest Park
[Ref.: #43451]	Geographic location (country and/or sea, region)	Sapporo, Hokkaido
[Ref.: #43451]	Country	Japan
[Ref.: #43451]	Country ISO 3 Code	JPN
[Ref.: #43451]	Continent	Asia
[Ref.: #43451]	Geographic location	43.0680°/141.5190°
* marker position based on {}

Isolation sources categories

#Environmental	#Terrestrial	#Soil
#Environmental	#Terrestrial	#Tidal flat
#Environmental	#Terrestrial	#Wetland (Swamp)

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence LC183909 (>99% sequence identity) for Desulfocucumis palustris subclade from Microbeatlas

Aquatic Samples	7
Soil Samples	2
Animal Samples
Plant Samples	4
Total Samples	13

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

[Ref.: #42960]

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.: #42960]	Desulfocucumis palustris gene for 16S ribosomal RNA, partial sequence, strain: NAW-5	LC183909	1442	ENA	1898651 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Desulfocucumis palustris NAW-5	GCA_002933875	contig	GenBank	1898651 tax ID	*
[Ref.: #66792]	Desulfocucumis palustris NAW-5	2788500037	draft	JGI IMG/M	1898651 tax ID	*

[Ref.: #42960]

GC-content

46.6 mol%

high performance liquid chromatography (HPLC)

Availability in culture collections External links

[Ref.: #42960]

Culture collection no.

DSM 102911, NBRC 112242

[Ref.: #96651]

SI-ID 408151

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Desulfocucumis palustris gen. nov., sp. nov., a mesophilic sulfate reducer belonging to Desulfotomaculum subcluster Ig.	Watanabe M, Kojima H, Fukui M	Int J Syst Evol Microbiol	10.1099/ijsem.0.002005	2017	*

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 )

#42960

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 102911

#43451

Miho Watanabe, Hisaya Kojima, Manabu Fukui: Desulfocucumis palustris gen. nov., sp. nov., a mesophilic sulfate reducer belonging to Desulfotomaculum subcluster Ig. IJSEM 67: 2679 - 2682 2017 ( DOI 10.1099/ijsem.0.002005 , PubMed 28786781 )

#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 .

#96651

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-ID408151.1 )

* These data were automatically processed and therefore are not curated

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