Name: Desulfohalobium retbaense HR100
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 4043

Type strain:

Species: Desulfohalobium retbaense

Strain Designation: HR100, HR₁₀₀

Culture col. no.: DSM 5692, JCM 16813, ATCC 49708

Strain history: DSM 5692 <-- J.-L. Garcia HR₁₀₀.

NCBI tax ID(s): 485915 (strain), 45663 (species)

SI-ID 47983

DSM 5692, ATCC 49708, JCM 16813

Section

Desulfohalobium retbaense HR100 is an anaerobe, mesophilic, Gram-negative bacterium that forms circular colonies and was isolated from saline sediment.

colony-forming
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	*Pseudomonadota*
	Class	*Deltaproteobacteria*
	Order	*Desulfovibrionales*
	Family	*Desulfohalobiaceae*
	Genus	*Desulfohalobium*
	Species	**Desulfohalobium retbaense**
	Full Scientific Name (LPSN)	Desulfohalobium retbaense Ollivier et al. 1991

Information on morphological and physiological properties Morphology

[Ref.: #43365]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.999

[Ref.: #43365]	Cell length	1-3 µm

[Ref.: #43365]	Cell width	0.7-0.9 µm

[Ref.: #43365]	Cell shape	rod-shaped

[Ref.: #43365]	Motility	yes
[Ref.: #69480]	Motility	yes Confidence in %92.213

[Ref.: #43365]	Flagellum arrangement	polar

[Ref.: #43365]	Colony shape	circular
[Ref.: #43365]	Incubation period	30 days

Multimedia content

[Ref.: #66793]

Caption:

electron microscopic image

[Ref.: #66793]

Intellectual property rights:

Information on culture and growth conditions Culture and growth conditions

[Ref.: #2289]

Culture medium

DESULFOHALOBIUM MEDIUM (DSMZ Medium 499)

[Ref.: #2289]

Culture medium growth

[Ref.: #2289]

Culture medium link

Medium recipe at MediaDive

[Ref.: #2289]

Culture medium composition

expand / minimize

[Ref.: #43365]

Culture medium growth

[Ref.: #43365]

Culture medium composition

expand / minimize

[Ref.: #43365]

Culture medium growth

[Ref.: #43365]

Culture medium composition

expand / minimize

	Kind of temperature		Temperature
[Ref.: #2289]		growth	35 °C
[Ref.: #43365]	no	growth	45-52 °C
[Ref.: #43365]		optimum	37-40 °C
[Ref.: #67770]		growth	35 °C

[Ref.: #2289]	Temperature range	mesophilic
[Ref.: #43365]	Temperature range	thermophilic
[Ref.: #67770]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #43365]			optimum	6.5-7
[Ref.: #43365]			growth	5.5-8

Information on physiology and metabolism Physiology and metabolism

[Ref.: #2289]	Oxygen tolerance	anaerobe
[Ref.: #43365]	Oxygen tolerance	obligate anaerobe
[Ref.: #69480]	Oxygen tolerance	anaerobe Confidence in %99.999

[Ref.: #43365]	Ability of spore formation	no
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.993

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #43365]		NaCl		growth	5-24	%
[Ref.: #43365]		NaCl		optimum	10	%

[Ref.: #43365]

Observation

NaCl and MgCl2 are required for growth

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #43365]	choline ChEBI	-	assimilation
[Ref.: #43365]	elemental sulfur ChEBI	+	electron acceptor
[Ref.: #43365]	ethanol ChEBI	+/-	oxidation
[Ref.: #43365]	fructose ChEBI	-	assimilation
[Ref.: #43365]	fumarate ChEBI	-	assimilation
[Ref.: #43365]	glucose ChEBI	-	assimilation
[Ref.: #43365]	glycerol ChEBI	-	assimilation
[Ref.: #43365]	lactate ChEBI	+/-	oxidation
[Ref.: #43365]	malate ChEBI	-	assimilation
[Ref.: #43365]	pyruvate ChEBI	+	fermentation
[Ref.: #43365]	pyruvate ChEBI	+/-	oxidation
[Ref.: #43365]	succinate ChEBI	-	assimilation
[Ref.: #43365]	sulfate ChEBI	+	electron acceptor
[Ref.: #43365]	sulfite ChEBI	+	electron acceptor
[Ref.: #43365]	thiosulfate ChEBI	+	electron acceptor
[Ref.: #43365]	yeast extract	-	assimilation
	Only first 10 entries are displayed. Click here to see all.

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	1,4-dihydroxy-6-naphthoate biosynthesis	100	6 of 6
[Ref.: #66794]	reductive acetyl coenzyme A pathway	100	7 of 7
[Ref.: #66794]	chorismate metabolism	100	9 of 9
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	glycogen metabolism	100	5 of 5
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	hydrogen production	100	5 of 5
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	starch degradation	90	9 of 10
[Ref.: #66794]	lipid A biosynthesis	88.89	8 of 9
[Ref.: #66794]	valine metabolism	88.89	8 of 9
[Ref.: #66794]	isoleucine metabolism	87.5	7 of 8
[Ref.: #66794]	ubiquinone biosynthesis	85.71	6 of 7
[Ref.: #66794]	pentose phosphate pathway	81.82	9 of 11
[Ref.: #66794]	lipoate biosynthesis	80	4 of 5
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	photosynthesis	78.57	11 of 14
[Ref.: #66794]	tetrahydrofolate metabolism	78.57	11 of 14
[Ref.: #66794]	aspartate and asparagine metabolism	77.78	7 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	77.78	7 of 9
[Ref.: #66794]	nitrate assimilation	77.78	7 of 9
[Ref.: #66794]	vitamin B1 metabolism	76.92	10 of 13
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	ppGpp biosynthesis	75	3 of 4
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	flavin biosynthesis	73.33	11 of 15
[Ref.: #66794]	metabolism of disaccharids	72.73	8 of 11
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	glycolysis	70.59	12 of 17
[Ref.: #66794]	threonine metabolism	70	7 of 10
[Ref.: #66794]	phenylalanine metabolism	69.23	9 of 13
[Ref.: #66794]	purine metabolism	69.15	65 of 94
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	formaldehyde oxidation	66.67	2 of 3
[Ref.: #66794]	serine metabolism	66.67	6 of 9
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	selenocysteine biosynthesis	66.67	4 of 6
[Ref.: #66794]	NAD metabolism	66.67	12 of 18
[Ref.: #66794]	methionine metabolism	65.38	17 of 26
[Ref.: #66794]	isoprenoid biosynthesis	65.38	17 of 26
[Ref.: #66794]	oxidative phosphorylation	64.84	59 of 91
[Ref.: #66794]	heme metabolism	64.29	9 of 14
[Ref.: #66794]	glutamate and glutamine metabolism	64.29	18 of 28
[Ref.: #66794]	proline metabolism	63.64	7 of 11
[Ref.: #66794]	non-pathway related	63.16	24 of 38
[Ref.: #66794]	C4 and CAM-carbon fixation	62.5	5 of 8
[Ref.: #66794]	pyrimidine metabolism	62.22	28 of 45
[Ref.: #66794]	alanine metabolism	62.07	18 of 29
[Ref.: #66794]	cellulose degradation	60	3 of 5
[Ref.: #66794]	factor 420 biosynthesis	60	3 of 5
[Ref.: #66794]	citric acid cycle	57.14	8 of 14
[Ref.: #66794]	propanol degradation	57.14	4 of 7
[Ref.: #66794]	d-mannose degradation	55.56	5 of 9
[Ref.: #66794]	vitamin B6 metabolism	54.55	6 of 11
[Ref.: #66794]	leucine metabolism	53.85	7 of 13
[Ref.: #66794]	sulfate reduction	53.85	7 of 13
[Ref.: #66794]	lysine metabolism	52.38	22 of 42
[Ref.: #66794]	lipid metabolism	51.61	16 of 31
[Ref.: #66794]	myo-inositol biosynthesis	50	5 of 10
[Ref.: #66794]	denitrification	50	1 of 2
[Ref.: #66794]	degradation of sugar alcohols	50	8 of 16
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	glycolate and glyoxylate degradation	50	3 of 6
[Ref.: #66794]	gluconeogenesis	50	4 of 8
[Ref.: #66794]	Entner Doudoroff pathway	50	5 of 10
[Ref.: #66794]	suberin monomers biosynthesis	50	1 of 2
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	adipate degradation	50	1 of 2
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	lactate fermentation	50	2 of 4
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	histidine metabolism	48.28	14 of 29
[Ref.: #66794]	tryptophan metabolism	47.37	18 of 38
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	46.15	6 of 13
[Ref.: #66794]	arginine metabolism	45.83	11 of 24
[Ref.: #66794]	CO2 fixation in Crenarchaeota	44.44	4 of 9
[Ref.: #66794]	cysteine metabolism	44.44	8 of 18
[Ref.: #66794]	glutathione metabolism	42.86	6 of 14
[Ref.: #66794]	tyrosine metabolism	42.86	6 of 14
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	metabolism of amino sugars and derivatives	40	2 of 5
[Ref.: #66794]	degradation of hexoses	38.89	7 of 18
[Ref.: #66794]	ketogluconate metabolism	37.5	3 of 8
[Ref.: #66794]	dTDPLrhamnose biosynthesis	37.5	3 of 8
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	33.33	4 of 12
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	sulfoquinovose degradation	33.33	1 of 3
[Ref.: #66794]	cyanate degradation	33.33	1 of 3
[Ref.: #66794]	methanogenesis from CO2	33.33	4 of 12
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	pantothenate biosynthesis	33.33	2 of 6
[Ref.: #66794]	degradation of pentoses	32.14	9 of 28
[Ref.: #66794]	urea cycle	30.77	4 of 13
[Ref.: #66794]	coenzyme M biosynthesis	30	3 of 10
[Ref.: #66794]	d-xylose degradation	27.27	3 of 11
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	vitamin E metabolism	25	1 of 4
[Ref.: #66794]	carnitine metabolism	25	2 of 8
[Ref.: #66794]	vitamin B12 metabolism	23.53	8 of 34
[Ref.: #66794]	ascorbate metabolism	22.73	5 of 22
[Ref.: #66794]	polyamine pathway	21.74	5 of 23
		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.: #2289]	Sample type/isolated from	saline sediment
[Ref.: #2289]	Geographic location (country and/or sea, region)	Retba Lake
[Ref.: #2289]	Country	Senegal
[Ref.: #2289]	Country ISO 3 Code	SEN
[Ref.: #2289]	Continent	Africa

[Ref.: #43365]	Sample type/isolated from	sediments of Retba Lake, a pink hypersaline Lake
[Ref.: #43365]	Geographic location (country and/or sea, region)	Senegal, Retba Lake
[Ref.: #43365]	Country	Senegal
[Ref.: #43365]	Country ISO 3 Code	SEN
[Ref.: #43365]	Continent	Africa
[Ref.: #43365]	Geographic location	14.0000°/-17.0000°

[Ref.: #67770]	Sample type/isolated from	Sediments from a hypersaline lake
[Ref.: #67770]	Geographic location (country and/or sea, region)	Ratba Lake, near Dakar
[Ref.: #67770]	Country	Senegal
[Ref.: #67770]	Country ISO 3 Code	SEN
[Ref.: #67770]	Continent	Africa
* marker position based on {}

Isolation sources categories

#Condition	#Saline	-
#Environmental	#Aquatic	#Lake (large)
#Environmental	#Aquatic	#Sediment

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence X99235 (>99% sequence identity) for Desulfohalobium retbaense subclade from Microbeatlas

Aquatic Samples	494
Soil Samples	46
Animal Samples	65
Plant Samples	10
Total Samples	615

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

[Ref.: #2289]

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.: #20218]	D.retbaense 16S rRNA gene	X99235	1506	ENA	485915 tax ID	*
[Ref.: #20218]	Desulfohalobium retbaense 16S ribosomal RNA gene	U48244	1548	ENA	485915 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Desulfohalobium retbaense DSM 5692	GCA_000024325	complete	GenBank	485915 tax ID	*
[Ref.: #66792]	Desulfohalobium retbaense DSM 5692	485915.10	plasmid	PATRIC	485915 tax ID	*
[Ref.: #66792]	Desulfohalobium retbaense DSM 5692	485915.5	complete	PATRIC	485915 tax ID	*
[Ref.: #66792]	Desulfohalobium retbaense HR100, DSM 5692	644736349	complete	JGI IMG/M	485915 tax ID	*

[Ref.: #2289]	GC-content	57.1 mol%
[Ref.: #43365]	GC-content	56.9-57.3 mol%	high performance liquid chromatography (HPLC)
[Ref.: #67770]	GC-content	57.1 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 GenomeNet Sporulation v. 1 based on: Desulfohalobium retbaense DSM 5692 DSM 5692 NCBI: GCA_000024325.1
[Ref.: #69481]	spore-forming	no	58	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Desulfohalobium retbaense DSM 5692 DSM 5692 NCBI: GCA_000024325.1
[Ref.: #69480]	motile	yes	88.029	no
[Ref.: #69480]	flagellated	yes	53.857	yes
[Ref.: #69480]	gram-positive	no	99.165	yes
[Ref.: #69480]	anaerobic	yes	99.269	no
[Ref.: #69480]	aerobic	no	98.043	yes
[Ref.: #69480]	halophile	yes	75.671	no
[Ref.: #69480]	spore-forming	no	96.354	yes
[Ref.: #69480]	thermophile	no	63.744	no
[Ref.: #69480]	glucose-util	no	66.319	yes
[Ref.: #69480]	glucose-ferment	no	85.529	no

Availability in culture collections External links

[Ref.: #2289]

Culture collection no.

DSM 5692, JCM 16813, ATCC 49708

[Ref.: #73548]

SI-ID 47983

Literature:

Topic	Title	Authors	Journal	DOI	Year
Metabolism	A novel signal transduction protein: Combination of solute binding and tandem PAS-like sensor domains in one polypeptide chain.	Wu R, Wilton R, Cuff ME, Endres M, Babnigg G, Edirisinghe JN, Henry CS, Joachimiak A, Schiffer M, Pokkuluri PR	Protein Sci	10.1002/pro.3134	2017	*
Phylogeny	Desulfohalobium utahense sp. nov., a moderately halophilic, sulfate-reducing bacterium isolated from Great Salt Lake.	Jakobsen TF, Kjeldsen KU, Ingvorsen K	Int J Syst Evol Microbiol	10.1099/ijs.0.64323-0	2006	*

References

#2289

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 5692

#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 )

#43365

B. Olliver, C. E. Hatchikian, G. Prensier, J. Guezennec, J. L. Garcia: Desulfohalobium retbaense gen. nov., sp. nov., a Halophilic Sulfate-Reducing Bacterium from Sediments of a Hypersaline Lake in Senegal. IJSB 41: 74 - 81 1991 ( DOI 10.1099/00207713-41-1-74 )

#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) .

#66793

Mukherjee et al.: GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life. 35: 676 - 683 2017 ( DOI 10.1038/nbt.3886 , PubMed 28604660 )

#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 )

#73548

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-ID47983.1 )

* These data were automatically processed and therefore are not curated

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Desulfohalobium retbaense DSM 5692 DSM 5692

Desulfohalobium retbaense DSM 5692 DSM 5692

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