Name: Seleniivibrio woodruffii S4
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 23885

Type strain:

Species: Seleniivibrio woodruffii

Strain Designation: S4

Culture col. no.: DSM 24984, ATCC BAA-2290

Strain history: <- M. Häggblom, Rutgers, State Univ. New Jersey, New Brunswick, USA; S4 <- I. Rauschenbach {2011}

NCBI tax ID(s): 1078050 (species)

SI-ID 402850

DSM 24984

Section

Seleniivibrio woodruffii S4 is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from activated sludge from a wastewater treatment plant.

Gram-negative
motile
rod-shaped
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	*Deferribacterota*
	Class	*Deferribacteres*
	Order	*Deferribacterales*
	Family	*Deferribacteraceae*
	Genus	*Seleniivibrio*
	Species	**Seleniivibrio woodruffii**
	Full Scientific Name (LPSN)	Seleniivibrio woodruffii Rauschenbach et al. 2013

Information on morphological and physiological properties Morphology

[Ref.: #30746]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.981

[Ref.: #30746]	Cell length	1.5 µm

[Ref.: #30746]	Cell width	0.15 µm

[Ref.: #30746]	Cell shape	rod-shaped

[Ref.: #30746]	Motility	yes
[Ref.: #69480]	Motility	yes Confidence in %93.041

[Ref.: #30746]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #21277]

Culture medium

SELENIIVIBRIO MEDIUM (ARSENATE) (DSMZ Medium 503d)

[Ref.: #21277]

Culture medium growth

[Ref.: #21277]

Culture medium link

Medium recipe at MediaDive

[Ref.: #21277]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #21277]	growth	30 °C
[Ref.: #30746]	growth	20-37 °C
[Ref.: #30746]	optimum	32.5 °C

[Ref.: #21277]	Temperature range	mesophilic
[Ref.: #30746]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #30746]			optimum	7
[Ref.: #30746]			growth	6.8-7.4

Information on physiology and metabolism Physiology and metabolism

[Ref.: #21277]	Oxygen tolerance	anaerobe
[Ref.: #30746]	Oxygen tolerance	anaerobe
[Ref.: #69480]	Oxygen tolerance	anaerobe Confidence in %100

[Ref.: #30746]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.694

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #30746]		NaCl		growth	0-0.58	%
[Ref.: #30746]		NaCl		optimum	0.116	%

	Metabolite utilization	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #30746]		acetate ChEBI	+	carbon source

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	ethanol fermentation	100	2 of 2
[Ref.: #66794]	C4 and CAM-carbon fixation	100	8 of 8
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	hydrogen production	100	5 of 5
[Ref.: #66794]	acetoin degradation	100	3 of 3
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	lipid A 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]	ubiquinone biosynthesis	85.71	6 of 7
[Ref.: #66794]	heme metabolism	85.71	12 of 14
[Ref.: #66794]	reductive acetyl coenzyme A pathway	85.71	6 of 7
[Ref.: #66794]	1,4-dihydroxy-6-naphthoate biosynthesis	83.33	5 of 6
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	threonine metabolism	80	8 of 10
[Ref.: #66794]	vitamin B12 metabolism	79.41	27 of 34
[Ref.: #66794]	glutamate and glutamine metabolism	78.57	22 of 28
[Ref.: #66794]	photosynthesis	78.57	11 of 14
[Ref.: #66794]	valine metabolism	77.78	7 of 9
[Ref.: #66794]	nitrate assimilation	77.78	7 of 9
[Ref.: #66794]	d-mannose degradation	77.78	7 of 9
[Ref.: #66794]	vitamin B1 metabolism	76.92	10 of 13
[Ref.: #66794]	phenylalanine metabolism	76.92	10 of 13
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	NAD metabolism	72.22	13 of 18
[Ref.: #66794]	citric acid cycle	71.43	10 of 14
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	leucine metabolism	69.23	9 of 13
[Ref.: #66794]	aspartate and asparagine metabolism	66.67	6 of 9
[Ref.: #66794]	serine metabolism	66.67	6 of 9
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	selenocysteine biosynthesis	66.67	4 of 6
[Ref.: #66794]	flavin biosynthesis	66.67	10 of 15
[Ref.: #66794]	CO2 fixation in Crenarchaeota	66.67	6 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	66.67	6 of 9
[Ref.: #66794]	pyrimidine metabolism	66.67	30 of 45
[Ref.: #66794]	formaldehyde oxidation	66.67	2 of 3
[Ref.: #66794]	purine metabolism	65.96	62 of 94
[Ref.: #66794]	tetrahydrofolate metabolism	64.29	9 of 14
[Ref.: #66794]	proline metabolism	63.64	7 of 11
[Ref.: #66794]	vitamin B6 metabolism	63.64	7 of 11
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	alanine metabolism	62.07	18 of 29
[Ref.: #66794]	sulfate reduction	61.54	8 of 13
[Ref.: #66794]	methionine metabolism	61.54	16 of 26
[Ref.: #66794]	starch degradation	60	6 of 10
[Ref.: #66794]	4-hydroxyphenylacetate degradation	60	6 of 10
[Ref.: #66794]	glycogen metabolism	60	3 of 5
[Ref.: #66794]	glycine betaine biosynthesis	60	3 of 5
[Ref.: #66794]	propionate fermentation	60	6 of 10
[Ref.: #66794]	bacilysin biosynthesis	60	3 of 5
[Ref.: #66794]	glycolysis	58.82	10 of 17
[Ref.: #66794]	isoprenoid biosynthesis	57.69	15 of 26
[Ref.: #66794]	oxidative phosphorylation	57.14	52 of 91
[Ref.: #66794]	propanol degradation	57.14	4 of 7
[Ref.: #66794]	cysteine metabolism	55.56	10 of 18
[Ref.: #66794]	non-pathway related	55.26	21 of 38
[Ref.: #66794]	tryptophan metabolism	55.26	21 of 38
[Ref.: #66794]	lipid metabolism	54.84	17 of 31
[Ref.: #66794]	lysine metabolism	54.76	23 of 42
[Ref.: #66794]	pentose phosphate pathway	54.55	6 of 11
[Ref.: #66794]	toluene degradation	50	2 of 4
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	dTDPLrhamnose biosynthesis	50	4 of 8
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	kanosamine biosynthesis II	50	1 of 2
[Ref.: #66794]	tyrosine metabolism	50	7 of 14
[Ref.: #66794]	denitrification	50	1 of 2
[Ref.: #66794]	lactate fermentation	50	2 of 4
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	histidine metabolism	48.28	14 of 29
[Ref.: #66794]	polyamine pathway	47.83	11 of 23
[Ref.: #66794]	arginine metabolism	45.83	11 of 24
[Ref.: #66794]	ethylmalonyl-CoA pathway	40	2 of 5
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	metabolism of amino sugars and derivatives	40	2 of 5
[Ref.: #66794]	Entner Doudoroff pathway	40	4 of 10
[Ref.: #66794]	degradation of hexoses	38.89	7 of 18
[Ref.: #66794]	ketogluconate metabolism	37.5	3 of 8
[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]	phenol degradation	35	7 of 20
[Ref.: #66794]	octane oxidation	33.33	1 of 3
[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]	3-phenylpropionate degradation	33.33	5 of 15
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	33.33	4 of 12
[Ref.: #66794]	cyanate degradation	33.33	1 of 3
[Ref.: #66794]	glycolate and glyoxylate degradation	33.33	2 of 6
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	urea cycle	30.77	4 of 13
[Ref.: #66794]	phenylpropanoid biosynthesis	30.77	4 of 13
[Ref.: #66794]	coenzyme M biosynthesis	30	3 of 10
[Ref.: #66794]	benzoyl-CoA degradation	28.57	2 of 7
[Ref.: #66794]	d-xylose degradation	27.27	3 of 11
[Ref.: #66794]	metabolism of disaccharids	27.27	3 of 11
[Ref.: #66794]	alginate biosynthesis	25	1 of 4
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	degradation of sugar alcohols	25	4 of 16
[Ref.: #66794]	methanogenesis from CO2	25	3 of 12
[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.: #21277]	Sample type/isolated from	activated sludge from a wastewater treatment plant
[Ref.: #21277]	Geographic location (country and/or sea, region)	New Jersey, Verona
[Ref.: #21277]	Country	USA
[Ref.: #21277]	Country ISO 3 Code	USA
[Ref.: #21277]	Continent	North America
[Ref.: #21277]	Geographic location	40.8422°/-74.2350°
* marker position based on {}

Isolation sources categories

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

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence JN107635 (>99% sequence identity) for Seleniivibrio woodruffii subclade from Microbeatlas

Aquatic Samples	650
Soil Samples	153
Animal Samples	66
Plant Samples	24
Total Samples	893

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

[Ref.: #21277]

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.: #21277]	Seleniivibrio woodruffii strain S4 16S ribosomal RNA gene, partial sequence	JN107635	1474	ENA	1078050 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Seleniivibrio woodruffii S4	GCA_007827295	contig	GenBank	1078050 tax ID	*
[Ref.: #66792]	Seleniivibrio woodruffii DSM 24984	GCA_004339245	scaffold	GenBank	1078050 tax ID	*
[Ref.: #66792]	Seleniivibrio woodruffii strain DSM 24984	1078050.3	wgs	PATRIC	1078050 tax ID	*
[Ref.: #66792]	Seleniivibrio woodruffii S4	2602042075	draft	JGI IMG/M	1078050 tax ID	*
[Ref.: #66792]	Seleniivibrio woodruffii DSM 24984	2756170311	draft	JGI IMG/M	1078050 tax ID	*

[Ref.: #21277]	GC-content	47.7 mol%	high performance liquid chromatography (HPLC)
[Ref.: #30746]	GC-content	47.4 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: Seleniivibrio woodruffii DSM 24984 NCBI: GCA_004339245.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Seleniivibrio woodruffii DSM 24984 NCBI: GCA_004339245.1
[Ref.: #69480]	motile	yes	92.441	yes
[Ref.: #69480]	flagellated	no	58.689	no
[Ref.: #69480]	gram-positive	no	99.588	yes
[Ref.: #69480]	anaerobic	yes	99.236	no
[Ref.: #69480]	aerobic	no	98.557	yes
[Ref.: #69480]	halophile	no	96.516	yes
[Ref.: #69480]	spore-forming	no	93.852	yes
[Ref.: #69480]	thermophile	no	83.173	yes
[Ref.: #69480]	glucose-util	no	65.302	no
[Ref.: #69480]	glucose-ferment	no	83.806	no

Availability in culture collections External links

[Ref.: #21277]

Culture collection no.

DSM 24984, ATCC BAA-2290

[Ref.: #87895]

SI-ID 402850

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Seleniivibrio woodruffii gen. nov., sp. nov., a selenate- and arsenate-respiring bacterium in the Deferribacteraceae.	Rauschenbach I, Posternak V, Cantarella P, McConnell J, Starovoytov V, Haggblom MM	Int J Syst Evol Microbiol	10.1099/ijs.0.043547-0	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 )

#21277

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 24984

#30746

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 #27077 (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 )

#87895

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-ID402850.1 )

#27077

IJSEM 3659 2013 ( DOI 10.1099/ijs.0.043547-0 , PubMed 23625257 )

* These data were automatically processed and therefore are not curated

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Seleniivibrio woodruffii DSM 24984

Seleniivibrio woodruffii DSM 24984

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