Name: Desulfurobacterium indicum K6013
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 140298

Type strain:

Species: Desulfurobacterium indicum

Strain Designation: K6013

Culture col. no.: DSM 101677, MCCC 1A01868

Strain history: <- K. Alain, IUEM, Univ. Brest, Plouzané, France; K6013 <- J. Cao

NCBI tax ID(s): 1914305 (species)

SI-ID 405611

DSM 101677

Section

Desulfurobacterium indicum K6013 is an anaerobe, chemolithoautotroph, thermophilic bacterium that was isolated from sulfide sample from a high-temperature hydrothermal vent.

Gram-negative
motile
rod-shaped
anaerobe
chemolithoautotroph
thermophilic
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	*Aquificota*
	Class	*Aquificia*
	Order	*Desulfurobacteriales*
	Family	*Desulfurobacteriaceae*
	Genus	*Desulfurobacterium*
	Species	**Desulfurobacterium indicum**
	Full Scientific Name (LPSN)	Desulfurobacterium indicum Cao et al. 2017

Information on morphological and physiological properties Morphology

[Ref.: #43270]	Gram stain	negative

[Ref.: #43270]	Cell length	0.9-2.2 µm

[Ref.: #43270]	Cell width	0.4-0.6 µm

[Ref.: #43270]	Cell shape	rod-shaped

[Ref.: #43270]	Motility	yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #42905]

Culture medium

DESULFUROBACTERIUM INDICUM MEDIUM (DSMZ Medium 829d)

[Ref.: #42905]

Culture medium growth

[Ref.: #42905]

Culture medium link

Medium recipe at MediaDive

[Ref.: #42905]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #42905]	growth	65 °C
[Ref.: #43270]	optimum	65 °C
[Ref.: #43270]	growth	40-75 °C

[Ref.: #42905]	Temperature range	thermophilic
[Ref.: #43270]	Temperature range	thermophilic

	pH	Kind of pH		pH
[Ref.: #43270]			optimum	6
[Ref.: #43270]			growth	5-8

Information on physiology and metabolism Physiology and metabolism

[Ref.: #43270]

Oxygen tolerance

anaerobe

[Ref.: #43270]

Nutrition type

chemolithoautotroph

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #43270]		NaCl		growth	1.0-4.5	%
[Ref.: #43270]		NaCl		optimum	2.5	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #43270]	carbon dioxide ChEBI	+	carbon source
[Ref.: #43270]	dihydrogen ChEBI	+	electron donor
[Ref.: #43270]	dioxygen ChEBI	-	electron acceptor
[Ref.: #43270]	elemental sulfur ChEBI	+	electron acceptor
[Ref.: #43270]	nitrate ChEBI	+	electron acceptor
[Ref.: #43270]	nitrite ChEBI	-	electron acceptor
[Ref.: #43270]	peptone	-	growth
[Ref.: #43270]	sulfate ChEBI	-	electron acceptor
[Ref.: #43270]	sulfite ChEBI	-	electron acceptor
[Ref.: #43270]	thiosulfate ChEBI	+	electron acceptor
[Ref.: #43270]	yeast extract	-	growth
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #43270]		ammonium ChEBI	yes
[Ref.: #43270]		hydrogen sulfide ChEBI	yes

Fatty acid profile

Metadata FA analysis

Reference

[Ref.: #43270]

Fatty acid	Percentage
C18:1ω7c / C18:1ω6c	37.91
C18:0	18.29
C16:0	17.4
C14:0 3OH / C16:1 iso I	8.56
C18:1ω9c	4.84
C18:2ω6,9c / anteiso-C18:0	4.14
C16:1ω7c / C16:1ω6c	2.13
C9:0	1.37

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	hydrogen production	100	5 of 5
[Ref.: #66794]	chorismate metabolism	100	9 of 9
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	cardiolipin biosynthesis	100	7 of 7
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	palmitate biosynthesis	86.36	19 of 22
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	tetrahydrofolate metabolism	78.57	11 of 14
[Ref.: #66794]	photosynthesis	78.57	11 of 14
[Ref.: #66794]	NAD metabolism	77.78	14 of 18
[Ref.: #66794]	lipid A biosynthesis	77.78	7 of 9
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	C4 and CAM-carbon fixation	75	6 of 8
[Ref.: #66794]	ubiquinone biosynthesis	71.43	5 of 7
[Ref.: #66794]	threonine metabolism	70	7 of 10
[Ref.: #66794]	phenylalanine metabolism	69.23	9 of 13
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	aspartate and asparagine metabolism	66.67	6 of 9
[Ref.: #66794]	flavin biosynthesis	66.67	10 of 15
[Ref.: #66794]	formaldehyde oxidation	66.67	2 of 3
[Ref.: #66794]	purine metabolism	64.89	61 of 94
[Ref.: #66794]	pyrimidine metabolism	64.44	29 of 45
[Ref.: #66794]	citric acid cycle	64.29	9 of 14
[Ref.: #66794]	glutamate and glutamine metabolism	64.29	18 of 28
[Ref.: #66794]	heme metabolism	64.29	9 of 14
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	isoleucine metabolism	62.5	5 of 8
[Ref.: #66794]	urea cycle	61.54	8 of 13
[Ref.: #66794]	methylglyoxal degradation	60	3 of 5
[Ref.: #66794]	glycolysis	58.82	10 of 17
[Ref.: #66794]	reductive acetyl coenzyme A pathway	57.14	4 of 7
[Ref.: #66794]	serine metabolism	55.56	5 of 9
[Ref.: #66794]	valine metabolism	55.56	5 of 9
[Ref.: #66794]	alanine metabolism	55.17	16 of 29
[Ref.: #66794]	vitamin B6 metabolism	54.55	6 of 11
[Ref.: #66794]	arginine metabolism	54.17	13 of 24
[Ref.: #66794]	vitamin B1 metabolism	53.85	7 of 13
[Ref.: #66794]	non-pathway related	52.63	20 of 38
[Ref.: #66794]	mannosylglycerate biosynthesis	50	1 of 2
[Ref.: #66794]	denitrification	50	1 of 2
[Ref.: #66794]	1,4-dihydroxy-6-naphthoate biosynthesis	50	3 of 6
[Ref.: #66794]	dTDPLrhamnose biosynthesis	50	4 of 8
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	glycolate and glyoxylate degradation	50	3 of 6
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	adipate degradation	50	1 of 2
[Ref.: #66794]	selenocysteine biosynthesis	50	3 of 6
[Ref.: #66794]	gluconeogenesis	50	4 of 8
[Ref.: #66794]	cis-vaccenate biosynthesis	50	1 of 2
[Ref.: #66794]	coenzyme M biosynthesis	50	5 of 10
[Ref.: #66794]	histidine metabolism	48.28	14 of 29
[Ref.: #66794]	leucine metabolism	46.15	6 of 13
[Ref.: #66794]	isoprenoid biosynthesis	46.15	12 of 26
[Ref.: #66794]	proline metabolism	45.45	5 of 11
[Ref.: #66794]	nitrate assimilation	44.44	4 of 9
[Ref.: #66794]	propanol degradation	42.86	3 of 7
[Ref.: #66794]	lysine metabolism	42.86	18 of 42
[Ref.: #66794]	methionine metabolism	42.31	11 of 26
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
[Ref.: #66794]	oxidative phosphorylation	40.66	37 of 91
[Ref.: #66794]	propionate fermentation	40	4 of 10
[Ref.: #66794]	ethylmalonyl-CoA pathway	40	2 of 5
[Ref.: #66794]	myo-inositol biosynthesis	40	4 of 10
[Ref.: #66794]	glycine metabolism	40	4 of 10
[Ref.: #66794]	cysteine metabolism	38.89	7 of 18
[Ref.: #66794]	degradation of hexoses	38.89	7 of 18
[Ref.: #66794]	sulfate reduction	38.46	5 of 13
[Ref.: #66794]	pentose phosphate pathway	36.36	4 of 11
[Ref.: #66794]	glutathione metabolism	35.71	5 of 14
[Ref.: #66794]	tyrosine metabolism	35.71	5 of 14
[Ref.: #66794]	molybdenum cofactor biosynthesis	33.33	3 of 9
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	d-mannose degradation	33.33	3 of 9
[Ref.: #66794]	cyanate degradation	33.33	1 of 3
[Ref.: #66794]	CO2 fixation in Crenarchaeota	33.33	3 of 9
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	lipid metabolism	32.26	10 of 31
[Ref.: #66794]	tryptophan metabolism	31.58	12 of 38
[Ref.: #66794]	polyamine pathway	30.43	7 of 23
[Ref.: #66794]	degradation of pentoses	28.57	8 of 28
[Ref.: #66794]	vitamin E metabolism	25	1 of 4
[Ref.: #66794]	glycogen biosynthesis	25	1 of 4
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	butanoate fermentation	25	1 of 4
[Ref.: #66794]	phenylpropanoid biosynthesis	23.08	3 of 13
		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.: #42905]	Sample type/isolated from	sulfide sample from a high-temperature hydrothermal vent
[Ref.: #42905]	Geographic location (country and/or sea, region)	Indian Ocean, JL-Dive94-S01 site at a depth of 2771 m
[Ref.: #42905]	Country	International waters
[Ref.: #42905]	Geographic location	-38.3000°/50.0833°

[Ref.: #43270]	Sample type/isolated from	deep-sea sulfide sample
[Ref.: #43270]	Sampling date	2015-01
[Ref.: #43270]	Geographic location (country and/or sea, region)	hydrothermal area in the Indian Ocean
[Ref.: #43270]	Geographic location	-38.0000°/50.0000°
* marker position based on {}

Isolation sources categories

#Condition	#Sulfuric	-
#Condition	#Thermophilic (>45°C)	-
#Environmental	#Aquatic	#Hydrothermal vent

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence KT750866 (>99% sequence identity) for Desulfurobacterium indicum subclade from Microbeatlas

Aquatic Samples	34
Soil Samples	2
Animal Samples	43
Plant Samples
Total Samples	79

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

[Ref.: #42905]

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.: #42905]	Desulfurobacterium indicum strain K6013 16S ribosomal RNA gene, partial sequence	KT750866	1517	ENA	1914305 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Desulfurobacterium indicum K6013	GCA_001968985	contig	GenBank	1914305 tax ID	*
[Ref.: #66792]	Desulfurobacterium indicum K6013	2832468384	draft	JGI IMG/M	1914305 tax ID	*

[Ref.: #43270]	GC-content	38.2 mol%	genome sequence analysis
[Ref.: #42905]	GC-content	38.2 mol%	sequence analysis

Availability in culture collections External links

[Ref.: #42905]

Culture collection no.

DSM 101677, MCCC 1A01868

[Ref.: #96603]

SI-ID 405611

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Desulfurobacterium indicum sp. nov., a thermophilic sulfur-reducing bacterium from the Indian Ocean.	Cao J, Birien T, Gayet N, Huang Z, Shao Z, Jebbar M, Alain K	Int J Syst Evol Microbiol	10.1099/ijsem.0.001837	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 )

#42905

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 101677

#43270

Junwei Cao, Tiphaine Birien, Nicolas Gayet, Zhaobin Huang, Zongze Shao, Mohamed Jebbar and Karine Alain: Desulfurobacterium indicum sp. nov., a thermophilic sulfurreducing bacterium from the Indian Ocean. IJSEM 67: 1665 - 1668 2017 ( DOI 10.1099/ijsem.0.001837 , PubMed 28150576 )

#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 .

#96603

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-ID405611.1 )

* These data were automatically processed and therefore are not curated

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