Desulfurobacterium indicum (DSM 101677, MCCC 1A01868, K6013)

Name: Desulfurobacterium indicum (DSM 101677, MCCC 1A01868, K6013)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 140298

Type strain

Strain Designation K6013

Culture col. no. DSM 101677 MCCC 1A01868 K6013

NCBI tax ID(s) 1914305

Special Collections DSMZ Literature strains

History <- K. Alain, IUEM, Univ. Brest, Plouzané, France; K6013 <- J. Cao

Links

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

Gram-negative motile rod-shaped anaerobe chemolithoautotroph genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 405611

DSM 101677

@ref 20215

Last LPSN update 2026-02-09 11:33:34

Domain Bacteria

Phylum Aquificota

Class Aquificia

Order Desulfurobacteriales

Family Desulfurobacteriaceae

Genus Desulfurobacterium

Species Desulfurobacterium indicum

Full scientific name Desulfurobacterium indicum Cao et al. 2017

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility	Confidence
43270	negative	0.9-2.2 µm	0.4-0.6 µm	rod-shaped
125439	negative					99.8

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
42905	DESULFUROBACTERIUM INDICUM MEDIUM (DSMZ Medium 829d)		Medium recipe at MediaDive	Name: DESULFUROBACTERIUM INDICUM MEDIUM (DSMZ Medium 829d) Composition: Sea Salt 29.4118 g/l Sulfur 9.80392 g/l MES [2-(N-morpholino) ethane sulfonic acid] 1.91176 g/l Na2S x 9 H2O 0.490196 g/l Na2CO3 0.490196 g/l KH2PO4 0.343137 g/l NH4Cl 0.294118 g/l Na-acetate 0.156863 g/l MgSO4 x 7 H2O 0.0294118 g/l Nitrilotriacetic acid 0.0147059 g/l NaCl 0.00980392 g/l MnSO4 x H2O 0.00490196 g/l ZnSO4 x 7 H2O 0.00176471 g/l CoSO4 x 7 H2O 0.00176471 g/l FeSO4 x 7 H2O 0.000980392 g/l CaCl2 x 2 H2O 0.000980392 g/l Sodium resazurin 0.000490196 g/l NiCl2 x 6 H2O 0.000294118 g/l AlK(SO4)2 x 12 H2O 0.000196078 g/l H3BO3 9.80392e-05 g/l Na2MoO4 x 2 H2O 9.80392e-05 g/l CuSO4 x 5 H2O 9.80392e-05 g/l Pyridoxine hydrochloride 9.80392e-05 g/l Riboflavin 4.90196e-05 g/l Thiamine HCl 4.90196e-05 g/l (DL)-alpha-Lipoic acid 4.90196e-05 g/l Calcium D-(+)-pantothenate 4.90196e-05 g/l p-Aminobenzoic acid 4.90196e-05 g/l Nicotinic acid 4.90196e-05 g/l Biotin 1.96078e-05 g/l Folic acid 1.96078e-05 g/l Na2WO4 x 2 H2O 3.92157e-06 g/l Na2SeO3 x 5 H2O 2.94118e-06 g/l Vitamin B12 9.80392e-07 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
42905	positive	growth	65
43270	positive	optimum	65
43270	positive	growth	40-75

Culture pH

@ref	Ability	Type	PH
43270	positive	optimum	6
43270	positive	growth	5-8

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
43270	anaerobe
125439	anaerobe	99.5

Nutrition type

43270

Typechemolithoautotroph

Spore formation

@ref	Spore formation	Confidence
125439		99.9

Halophily

@ref	Salt	Growth	Tested relation	Concentration
43270	NaCl	positive	growth	1.0-4.5 %
43270	NaCl	positive	optimum	2.5 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
43270	16526 ChEBI	carbon dioxide	+	carbon source
43270	18276 ChEBI	dihydrogen	+	electron donor
43270	15379 ChEBI	dioxygen	-	electron acceptor
43270	33403 ChEBI	elemental sulfur	+	electron acceptor
43270	17632 ChEBI	nitrate	+	electron acceptor
43270	16301 ChEBI	nitrite	-	electron acceptor
43270		peptone	-	growth
43270	16189 ChEBI	sulfate	-	electron acceptor
43270	17359 ChEBI	sulfite	-	electron acceptor
43270	16094 ChEBI	thiosulfate	+	electron acceptor
43270		yeast extract	-	growth

Metabolite production

@ref	Chebi-ID	Metabolite	Production
43270	28938 ChEBI	ammonium
43270	16136 ChEBI	hydrogen sulfide

Pathway annotation

Computationally determined by

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

Fatty acid profile

Metadata FA analysis

@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

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Condition	#Sulfuric	-
#Condition	#Thermophilic (>45°C)	-
#Environmental	#Aquatic	#Hydrothermal vent

Isolation

@ref	Sample type	Geographic location	Country	Latitude	Longitude	Sampling date
42905	sulfide sample from a high-temperature hydrothermal vent	Indian Ocean, JL-Dive94-S01 site at a depth of 2771 m	International waters	-38.3	50.0833 -38.3/50.0833
43270	deep-sea sulfide sample	hydrothermal area in the Indian Ocean		-38	50 -38/50	2015-01

Taxonmaps

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

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
42905	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	IMG accession	NCBI tax ID	Score
66792	ASM196898v1 assembly for Desulfurobacterium indicum K6013	contig	GCA_001968985	2832468384	1914305	65.14

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
42905	Desulfurobacterium indicum strain K6013 16S ribosomal RNA gene, partial sequence	KT750866	1517		1914305

GC content

@ref	GC-content (mol%)	Method
43270	38.2	genome sequence analysis
42905	38.2	sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Desulfurobacterium indicum K6013
NCBI: GCA_001968985

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	99.90	no
125439	motility	BacteriaNetⓘ	no	69.30	no
125439	gram_stain	BacteriaNetⓘ	negative	99.80	no
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	99.50	no

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 .
#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 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Desulfurobacterium indicum (DSM 101677, MCCC 1A01868, K6013)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Nutrition type

Spore formation

Halophily

Metabolite utilization

Metabolite production

Pathway annotation

Fatty acid profile

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_001968985

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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