Name: Pseudodesulfovibrio indicus J2
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 132642

Type strain:

Species: Pseudodesulfovibrio indicus

Strain Designation: J2

Culture col. no.: DSM 101483, MCCC 1A01867

Strain history: <- K. Alain, IUEM, Univ. Brest, Plouzané, France; J2 <- J. Cao {2015}

NCBI tax ID(s): 1716143 (species)

SI-ID 396767

DSM 101483

Section

Pseudodesulfovibrio indicus J2 is an anaerobe, Gram-negative, motile bacterium that was isolated from deep-sea serpentinized peridotite.

Gram-negative
motile
vibrio-shaped
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	*Pseudomonadota*
	Class	*Deltaproteobacteria*
	Order	*Desulfovibrionales*
	Family	*Desulfovibrionaceae*
	Genus	*Pseudodesulfovibrio*
	Species	**Pseudodesulfovibrio indicus**
	Full Scientific Name (LPSN)	Pseudodesulfovibrio indicus Cao et al. 2016

Information on morphological and physiological properties Morphology

[Ref.: #24938]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.989

[Ref.: #24938]	Cell length	2.0-6.0 µm

[Ref.: #24938]	Cell width	0.5 µm

[Ref.: #24938]	Cell shape	vibrio-shaped

[Ref.: #24938]	Motility	yes
[Ref.: #69480]	Motility	yes Confidence in %97.67

[Ref.: #24938]

Cultivation medium used

TRM

Information on culture and growth conditions Culture and growth conditions

[Ref.: #24938]

Culture medium

TRM

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Culture medium growth

[Ref.: #24431]

Culture medium

DESULFOBACTER SP. MEDIUM (LACTATE) (DSMZ Medium 195c)

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Culture medium growth

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Culture medium link

Medium recipe at MediaDive

[Ref.: #24431]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #24431]	growth	35 °C
[Ref.: #24938]	growth	9-40 °C
[Ref.: #24938]	optimum	30-35 °C

[Ref.: #24431]	Temperature range	mesophilic
[Ref.: #24938]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #24938]			optimum	6.5-7.0
[Ref.: #24938]			growth	5.0-8.0

Information on physiology and metabolism Physiology and metabolism

[Ref.: #24938]	Oxygen tolerance	anaerobe
[Ref.: #69480]	Oxygen tolerance	anaerobe Confidence in %99.473

[Ref.: #69481]	Ability of spore formation	no Confidence in %94
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.918

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #24938]		NaCl		growth	0.2-6.0	%
[Ref.: #24938]		NaCl		optimum	2.5	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #24938]	acetate ChEBI	-	electron donor
[Ref.: #24938]	alanine ChEBI	-	electron donor
[Ref.: #24938]	elemental sulfur ChEBI	-	electron acceptor
[Ref.: #24938]	ethanol ChEBI	-	electron donor
[Ref.: #24938]	formate ChEBI	+	energy source
[Ref.: #24938]	formate ChEBI	+	electron donor
[Ref.: #24938]	fumarate ChEBI	-	electron donor
[Ref.: #24938]	fumarate ChEBI	-	fermentation
[Ref.: #24938]	fumarate ChEBI	+	electron acceptor
[Ref.: #24938]	lactate ChEBI	+	energy source
[Ref.: #24938]	lactate ChEBI	+	fermentation
[Ref.: #24938]	malate ChEBI	-	fermentation
[Ref.: #24938]	malate ChEBI	+	energy source
[Ref.: #24938]	malate ChEBI	+	electron donor
[Ref.: #24938]	nitrate ChEBI	+	electron acceptor
[Ref.: #24938]	nitrite ChEBI	-	electron acceptor
[Ref.: #24938]	propionate ChEBI	-	electron donor
[Ref.: #24938]	pyruvate ChEBI	+	energy source
[Ref.: #24938]	pyruvate ChEBI	+	fermentation
[Ref.: #24938]	sulfate ChEBI	+	electron acceptor
[Ref.: #24938]	sulfite ChEBI	+	electron acceptor
[Ref.: #24938]	thiosulfate ChEBI	+	electron acceptor
	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.: #24431]	Sample type/isolated from	deep-sea serpentinized peridotite
[Ref.: #24431]	Geographic location (country and/or sea, region)	27° 88' S, 63° 53' E; site 30I-TVG05 at a depth of 3173 m
[Ref.: #24431]	Country	Indian Ocean
[Ref.: #24431]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Marine
#Environmental	#Terrestrial	#Geologic

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence KT750867 (>99% sequence identity) for Pseudodesulfovibrio indicus subclade from Microbeatlas

Aquatic Samples	55
Soil Samples	7
Animal Samples	8
Plant Samples	1
Total Samples	71

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

[Ref.: #24431]

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.: #24431]	Pseudodesulfovibrio indicus strain J2 16S ribosomal RNA gene, partial sequence	KT750867	1491	ENA	1716143 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]	Pseudodesulfovibrio indicus DSM 101483	GCA_004365595	scaffold	GenBank	1716143 tax ID	*
[Ref.: #66792]	Pseudodesulfovibrio indicus J2	GCA_001563225	complete	GenBank	1716143 tax ID	*
[Ref.: #66792]	Pseudodesulfovibrio indicus strain DSM 101483	1716143.16	wgs	PATRIC	1716143 tax ID	*
[Ref.: #66792]	Pseudodesulfovibrio indicus J2	2651869878	complete	JGI IMG/M	1716143 tax ID	*
[Ref.: #66792]	Pseudodesulfovibrio indicus J2	2687453294	complete	JGI IMG/M	1716143 tax ID	*
[Ref.: #66792]	Pseudodesulfovibrio indicus DSM 101483	2784746795	draft	JGI IMG/M	1716143 tax ID	*

[Ref.: #24938]	GC-content	63.5 mol%	genome sequence analysis
[Ref.: #24431]	GC-content	63.5 mol%	sequence analysis

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: Pseudodesulfovibrio indicus J2 NCBI: GCA_001563225.1
[Ref.: #69481]	spore-forming	no	94	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Pseudodesulfovibrio indicus J2 NCBI: GCA_001563225.1
[Ref.: #69480]	flagellated	yes	57.818	no
[Ref.: #69480]	gram-positive	no	99.034	yes
[Ref.: #69480]	anaerobic	yes	97.252	yes
[Ref.: #69480]	aerobic	no	98.014	no
[Ref.: #69480]	halophile	no	69.505	no
[Ref.: #69480]	spore-forming	no	93.854	no
[Ref.: #69480]	thermophile	no	96.429	yes
[Ref.: #69480]	glucose-util	no	69.469	no
[Ref.: #69480]	motile	yes	90.452	yes
[Ref.: #69480]	glucose-ferment	no	83.663	no

Availability in culture collections External links

[Ref.: #24431]

Culture collection no.

DSM 101483, MCCC 1A01867

[Ref.: #90955]

SI-ID 396767

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Pseudodesulfovibrio indicus gen. nov., sp. nov., a piezophilic sulfate-reducing bacterium from the Indian Ocean and reclassification of four species of the genus Desulfovibrio.	Cao J, Gayet N, Zeng X, Shao Z, Jebbar M, Alain K	Int J Syst Evol Microbiol	10.1099/ijsem.0.001286	2016	*

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 )

#24431

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 101483

#24938

J. G. Cao, Nicolas,Zeng, Xiang,Shao, Zongze,Jebbar, Mohamed,Alain, Karine: Pseudodesulfovibrio indicus gen. nov., sp. nov., a piezophilic sulfate-reducing bacterium from the Indian Ocean and reclassification of four species of the genus Desulfovibrio. IJSEM 66: 3904 - 3911 2016 ( DOI 10.1099/ijsem.0.001286 , PubMed 27392787 )

#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 .

#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 )

#90955

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-ID396767.1 )

* These data were automatically processed and therefore are not curated

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