Name: Halodesulfovibrio aestuarii DSM 17919
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 4161

Type strain:

Species: Halodesulfovibrio aestuarii

Culture col. no.: DSM 17919, ATCC 29578, NCIMB 9335, Sylt 3

Strain history: <- NCIMB <- J. R. Postgate <- K. Stüven, Inst. Allg. Botanik, Univ. Hamburg; Sylt 3

NCBI tax ID(s): 126333 (species)

SI-ID 39595

ATCC 29578, NCIB 9335, NCIMB 9335, DSM 17919

Special Collections

Other strains from Halodesulfovibrio aestuarii

Section

When using BacDive for research please cite our paper

Halodesulfovibrio aestuarii DSM 17919 is an anaerobe, mesophilic, vibrio-shaped bacterium that was isolated from shoal mud.

vibrio-shaped
anaerobe
mesophilic
16S sequence
Bacteria
genome sequence

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

	Last LPSN update	09-12-2024 (DD-MM-YYYY)
	Domain	*Bacteria*
	Phylum	*Pseudomonadota*
	Class	*Deltaproteobacteria*
	Order	*Desulfovibrionales*
	Family	*Desulfovibrionaceae*
	Genus	*Halodesulfovibrio*
	Species	**Halodesulfovibrio aestuarii**
	Full Scientific Name (LPSN)	Halodesulfovibrio aestuarii (Postgate and Campbell 1966) Shivani et al. 2017

	Synonym	Desulfovibrio acrylicus
	Synonym	Desulfovibrio desulfuricans subsp. aestuarii

Information on morphological and physiological properties Morphology

[Ref.: #125438]	Gram stain	negative Confidence in %96.983
[Ref.: #125439]	Gram stain	negative Confidence in %100

[Ref.: #25150]	Cell length	1.5-4.0 µm

[Ref.: #25150]	Cell width	0.5-0.8 µm

[Ref.: #25150]	Cell shape	vibrio-shaped

Information on culture and growth conditions Culture and growth conditions

[Ref.: #7246]

Culture medium

HALODESULFOVIBRIO (POSTGATE) MEDIUM (DSMZ Medium 163)

[Ref.: #7246]

Culture medium growth

[Ref.: #7246]

Culture medium link

Medium recipe at MediaDive

[Ref.: #7246]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #7246]	growth	30 °C
[Ref.: #25150]	optimum	30.0-36.0 °C
[Ref.: #25150]	growth	10.0-40.0 °C

	pH	Kind of pH		pH
[Ref.: #25150]			optimum	7.5
[Ref.: #25150]			growth	6.5-8.5

Information on physiology and metabolism Physiology and metabolism

[Ref.: #7246]	Oxygen tolerance	anaerobe
[Ref.: #25150]	Oxygen tolerance	obligate anaerobe
[Ref.: #125439]	Oxygen tolerance	obligate aerobe Confidence in %92.7

[Ref.: #125438]	Ability of spore formation	no Confidence in %90.216
[Ref.: #125439]	Ability of spore formation	no Confidence in %99.9

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #25150]		NaCl		optimum	2	%
[Ref.: #25150]		NaCl		growth	1.0-4.0	%(w/v)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #25150]	acetate ChEBI	+	electron donor
[Ref.: #25150]	aspartate ChEBI	+	electron donor
[Ref.: #25150]	benzoate ChEBI	+	electron donor
[Ref.: #25150]	cellobiose ChEBI	-	growth
[Ref.: #25150]	cysteine ChEBI	-	electron donor
[Ref.: #25150]	D-fructose ChEBI	-	growth
[Ref.: #25150]	D-galactose ChEBI	+	growth
[Ref.: #25150]	D-glucose ChEBI	+	growth
[Ref.: #25150]	D-mannitol ChEBI	+	growth
[Ref.: #25150]	D-mannose ChEBI	-	growth
[Ref.: #25150]	D-sorbitol ChEBI	-	growth
[Ref.: #25150]	formate ChEBI	+	growth
[Ref.: #25150]	fumarate ChEBI	+	growth
[Ref.: #25150]	gelatin ChEBI	-	hydrolysis
[Ref.: #25150]	glycerol ChEBI	+	electron donor
[Ref.: #25150]	lactate ChEBI	+	growth
[Ref.: #25150]	lactose ChEBI	+	growth
[Ref.: #25150]	malate ChEBI	+	growth
[Ref.: #25150]	pyruvate ChEBI	+	growth
[Ref.: #25150]	serine ChEBI	+	electron donor
[Ref.: #25150]	starch ChEBI	+	growth
[Ref.: #25150]	succinate ChEBI	+	growth
[Ref.: #25150]	sulfite ChEBI	+	electron acceptor
[Ref.: #25150]	tryptophan ChEBI	-	energy source
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #25150]		indole ChEBI	no

	Physiological tests	Metabolite	Indole test
[Ref.: #25150]		indole ChEBI	-

	Enzyme	Enzyme activity	EC number
[Ref.: #25150]	catalase	+	1.11.1.6
[Ref.: #25150]	cytochrome oxidase	-	1.9.3.1
[Ref.: #25150]	tryptophan deaminase	-	4.1.99.1

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #7246]	Sample type/isolated from	shoal mud
[Ref.: #7246]	Country	Germany
[Ref.: #7246]	Country ISO 3 Code	DEU
[Ref.: #7246]	Continent	Europe
* marker position based on {}

Isolation sources categories

#Environmental

#Terrestrial

#Mud (Sludge)

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence FJ655909 (>99% sequence identity) for Halodesulfovibrio from Microbeatlas

Aquatic Samples	28
Soil Samples	2
Animal Samples
Plant Samples
Total Samples	30

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

[Ref.: #7246]

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.: #7246]	Desulfovibrio desulfuricans subsp. aestuarii 16S ribosomal RNA gene, partial sequence	FJ655909	1501	GenBank ENA	126333 tax ID

Genome sequence information:

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

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Halodesulfovibrio aestuarii DSM 17919 = ATCC 29578	GCA_000384815	contig	GenBank ENA	1121444 tax ID	*
[Ref.: #66792]	Halodesulfovibrio aestuarii DSM 17919	GCA_900142115	scaffold	GenBank ENA	126333 tax ID	*
[Ref.: #66792]	Desulfovibrio desulfuricans strain DSM 17919	876.10	wgs	PATRIC	876 tax ID	*
[Ref.: #66792]	Desulfovibrio desulfuricans subsp. aestuarii DSM 17919 = ATCC 29578	1121444.3	wgs	PATRIC	1121444 tax ID	*
[Ref.: #66792]	Desulfovibrio desulfuricans aestuarii DSM 17919	2585428154	draft	JGI IMG/M	876 tax ID	*
[Ref.: #66792]	Halodesulfovibrio aestuarii aestuarii ATCC 29578	2518645586	draft	JGI IMG/M	1121444 tax ID	*

[Ref.: #25150]	GC-content	45.1 mol%	genome sequence analysis
[Ref.: #7246]	GC-content	45.1 mol%	sequence analysis
[Ref.: #7246]	GC-content	46.7 mol%	high performance liquid chromatography (HPLC)

Data predicted using genome information as a basis Genome-based predictions

	Model	Trait	Prediction	Confidence in %	In training data
	Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Halodesulfovibrio aestuarii DSM 17919 NCBI: GCA_900142115.1
[Ref.: #125438]	gram-positive	gram-positiveⓘ	no	96.983	no
[Ref.: #125438]	anaerobic	anaerobicⓘ	yes	83.231	yes
[Ref.: #125438]	aerobic	aerobicⓘ	no	90.168	yes
[Ref.: #125438]	spore-forming	spore-formingⓘ	no	90.216	no
[Ref.: #125438]	thermophile	thermophilicⓘ	no	92.164	yes
[Ref.: #125438]	motile2+	flagellatedⓘ	yes	73.416	no

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Halodesulfovibrio aestuarii DSM 17919 NCBI: GCA_900142115
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	obligate aerobe	92.7
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	negative	100
[Ref.: #125439]	BacteriaNet	motilityⓘ	yes	85.9
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	no	99.9

Availability in culture collections External links

[Ref.: #7246]

Culture collection no.

DSM 17919, ATCC 29578, NCIMB 9335, Sylt 3

[Ref.: #73662]

SI-ID 39595

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Halodesulfovibrio spirochaetisodalis gen. nov. sp. nov. and reclassification of four Desulfovibrio spp.	Shivani Y, Subhash Y, Sasikala C, Ramana CV	Int J Syst Evol Microbiol	10.1099/ijsem.0.001574	2017	*

References

#7246

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 17919

#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 )

#25150

Y. S. Shivani, Y.,Sasikala, C.,Ramana, C. V.: Halodesulfovibrio spirochaetisodalis gen. nov. sp. nov. and reclassification of four Desulfovibrio spp. IJSEM 67: 87 - 93 2017 ( DOI 10.1099/ijsem.0.001574 , PubMed 27902290 )

#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) .

#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 .

#73662

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-ID39595.1 )

#125438

Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )

#125439

Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .

* These data were automatically processed and therefore are not curated

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