Kosmotoga pacifica (DSM 26965, JCM 19180, MCCC 1A00641)

Name: Kosmotoga pacifica (DSM 26965, JCM 19180, MCCC 1A00641)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 131351

Type strain

Strain Designation SLHLJ1

Culture col. no. DSM 26965 JCM 19180 MCCC 1A00641 UBOCC 3254 SLHLJ1

NCBI tax ID(s) 1330330

Special Collections DSMZ JCM

History <- K. Alain and S. L'Haridon, IUEM, Univ. Brest, Plouzané, France; SLHLJ1 <- S. L'Haridon {2012} S. L'Haridon SLHLJ1.

Links

Kosmotoga pacifica SLHLJ1 is an anaerobe, thermophilic prokaryote that was isolated from hydrothermal sediment mixed with fragments of inactive sulphide chimneys, depth of 2891 m.

anaerobe thermophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 399984

JCM 19180,DSM 26965

@ref 20215

Last LPSN update 2026-02-09 11:31:26

Domain Bacteria

Phylum Thermotogota

Class Thermotogae

Order Kosmotogales

Family Kosmotogaceae

Genus Kosmotoga

Species Kosmotoga pacifica

Full scientific name Kosmotoga pacifica L'Haridon et al. 2016

Morphology

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
22578	METHANOCALDOCOCCUS MEDIUM (DSMZ Medium 282)		Medium recipe at MediaDive	Name: METHANOCALDOCOCCUS MEDIUM (DSMZ Medium 282; with strain-specific modifications) Composition: MgCl2 x 6 H2O 4.05138 g/l Yeast extract 2.96443 g/l Maltose 2.47036 g/l NaHCO3 0.988142 g/l Na2S x 9 H2O 0.494071 g/l L-Cysteine HCl x H2O 0.494071 g/l KCl 0.326087 g/l NH4Cl 0.247036 g/l K2HPO4 0.13834 g/l MgSO4 x 7 H2O 0.0296443 g/l Nitrilotriacetic acid 0.0148221 g/l Fe(NH4)2(SO4)2 x 6 H2O 0.00988142 g/l NaCl 0.00988142 g/l MnSO4 x H2O 0.00494071 g/l ZnSO4 x 7 H2O 0.00177866 g/l CoSO4 x 7 H2O 0.00177866 g/l FeSO4 x 7 H2O 0.000988142 g/l CaCl2 x 2 H2O 0.000988142 g/l Sodium resazurin 0.000494071 g/l NiCl2 x 6 H2O 0.000296443 g/l AlK(SO4)2 x 12 H2O 0.000197628 g/l CuSO4 x 5 H2O 9.88142e-05 g/l H3BO3 9.88142e-05 g/l Na2MoO4 x 2 H2O 9.88142e-05 g/l Pyridoxine hydrochloride 9.88142e-05 g/l (DL)-alpha-Lipoic acid 4.94071e-05 g/l p-Aminobenzoic acid 4.94071e-05 g/l Riboflavin 4.94071e-05 g/l Thiamine HCl 4.94071e-05 g/l Nicotinic acid 4.94071e-05 g/l Calcium D-(+)-pantothenate 4.94071e-05 g/l Biotin 1.97628e-05 g/l Folic acid 1.97628e-05 g/l Na2WO4 x 2 H2O 3.95257e-06 g/l Na2SeO3 x 5 H2O 2.96443e-06 g/l Vitamin B12 9.88142e-07 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
22578	positive	growth	70	thermophilic
67770	positive	growth	70	thermophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
22578	anaerobe
125439	anaerobe	90.9

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	cellulose degradation	100	5 of 5
66794	C4 and CAM-carbon fixation	100	8 of 8
66794	glycogen metabolism	100	5 of 5
66794	coenzyme A metabolism	100	4 of 4
66794	sulfopterin metabolism	100	4 of 4
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	folate polyglutamylation	100	1 of 1
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	suberin monomers biosynthesis	100	2 of 2
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	palmitate biosynthesis	95.45	21 of 22
66794	d-mannose degradation	88.89	8 of 9
66794	gluconeogenesis	87.5	7 of 8
66794	peptidoglycan biosynthesis	86.67	13 of 15
66794	starch degradation	80	8 of 10
66794	methylglyoxal degradation	80	4 of 5
66794	glycine betaine biosynthesis	80	4 of 5
66794	photosynthesis	78.57	11 of 14
66794	glycolysis	76.47	13 of 17
66794	butanoate fermentation	75	3 of 4
66794	acetate fermentation	75	3 of 4
66794	glycogen biosynthesis	75	3 of 4
66794	ppGpp biosynthesis	75	3 of 4
66794	pyrimidine metabolism	73.33	33 of 45
66794	propanol degradation	71.43	5 of 7
66794	degradation of sugar alcohols	68.75	11 of 16
66794	purine metabolism	68.09	64 of 94
66794	glutamate and glutamine metabolism	67.86	19 of 28
66794	serine metabolism	66.67	6 of 9
66794	molybdenum cofactor biosynthesis	66.67	6 of 9
66794	enterobactin biosynthesis	66.67	2 of 3
66794	octane oxidation	66.67	2 of 3
66794	NAD metabolism	66.67	12 of 18
66794	glycolate and glyoxylate degradation	66.67	4 of 6
66794	acetoin degradation	66.67	2 of 3
66794	formaldehyde oxidation	66.67	2 of 3
66794	aspartate and asparagine metabolism	66.67	6 of 9
66794	alanine metabolism	65.52	19 of 29
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	dTDPLrhamnose biosynthesis	62.5	5 of 8
66794	isoleucine metabolism	62.5	5 of 8
66794	phenylalanine metabolism	61.54	8 of 13
66794	degradation of hexoses	61.11	11 of 18
66794	hydrogen production	60	3 of 5
66794	metabolism of amino sugars and derivatives	60	3 of 5
66794	myo-inositol biosynthesis	60	6 of 10
66794	propionate fermentation	60	6 of 10
66794	oxidative phosphorylation	59.34	54 of 91
66794	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
66794	reductive acetyl coenzyme A pathway	57.14	4 of 7
66794	CO2 fixation in Crenarchaeota	55.56	5 of 9
66794	pentose phosphate pathway	54.55	6 of 11
66794	isoprenoid biosynthesis	53.85	14 of 26
66794	urea cycle	53.85	7 of 13
66794	non-pathway related	52.63	20 of 38
66794	ethanol fermentation	50	1 of 2
66794	adipate degradation	50	1 of 2
66794	degradation of pentoses	50	14 of 28
66794	threonine metabolism	50	5 of 10
66794	coenzyme M biosynthesis	50	5 of 10
66794	Entner Doudoroff pathway	50	5 of 10
66794	lactate fermentation	50	2 of 4
66794	kanosamine biosynthesis II	50	1 of 2
66794	glycine metabolism	50	5 of 10
66794	cis-vaccenate biosynthesis	50	1 of 2
66794	biotin biosynthesis	50	2 of 4
66794	tetrahydrofolate metabolism	50	7 of 14
66794	ketogluconate metabolism	50	4 of 8
66794	lysine metabolism	47.62	20 of 42
66794	flavin biosynthesis	46.67	7 of 15
66794	methionine metabolism	46.15	12 of 26
66794	metabolism of disaccharids	45.45	5 of 11
66794	d-xylose degradation	45.45	5 of 11
66794	proline metabolism	45.45	5 of 11
66794	cysteine metabolism	44.44	8 of 18
66794	lipid A biosynthesis	44.44	4 of 9
66794	ubiquinone biosynthesis	42.86	3 of 7
66794	cardiolipin biosynthesis	42.86	3 of 7
66794	citric acid cycle	42.86	6 of 14
66794	tryptophan metabolism	42.11	16 of 38
66794	phenylacetate degradation (aerobic)	40	2 of 5
66794	factor 420 biosynthesis	40	2 of 5
66794	lipid metabolism	38.71	12 of 31
66794	leucine metabolism	38.46	5 of 13
66794	vitamin B1 metabolism	38.46	5 of 13
66794	histidine metabolism	37.93	11 of 29
66794	vitamin B6 metabolism	36.36	4 of 11
66794	valine metabolism	33.33	3 of 9
66794	nitrate assimilation	33.33	3 of 9
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	pantothenate biosynthesis	33.33	2 of 6
66794	IAA biosynthesis	33.33	1 of 3
66794	sphingosine metabolism	33.33	2 of 6
66794	arachidonic acid metabolism	33.33	6 of 18
66794	cyanate degradation	33.33	1 of 3
66794	L-lactaldehyde degradation	33.33	1 of 3
66794	ascorbate metabolism	31.82	7 of 22
66794	arginine metabolism	29.17	7 of 24
66794	glutathione metabolism	28.57	4 of 14
66794	tyrosine metabolism	28.57	4 of 14
66794	cyclohexanol degradation	25	1 of 4
66794	toluene degradation	25	1 of 4
66794	carnitine metabolism	25	2 of 8
66794	CMP-KDO biosynthesis	25	1 of 4
66794	degradation of sugar acids	24	6 of 25
66794	sulfate reduction	23.08	3 of 13
66794	phosphatidylethanolamine bioynthesis	23.08	3 of 13
66794	phenylpropanoid biosynthesis	23.08	3 of 13
66794	polyamine pathway	21.74	5 of 23
66794	heme metabolism	21.43	3 of 14

Isolation, sampling and environmental information

Isolation source categories

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

Isolation

@ref	Sample type	Geographic location	Country	Latitude	Longitude
22578	hydrothermal sediment mixed with fragments of inactive sulphide chimneys, depth of 2891 m	Pacific Ocean, East Pacific Rise (site DY115-22VI-S019-TGV13)	International waters	-3.9667	-102.917 -3.9667/-102.917
67770	Sediment of an active hydrothermal vent on the East Pacific Rise

Taxonmaps

69479

Global distribution of 16S sequence KC119212 (>99% sequence identity) for Kosmotoga pacifica subclade from Microbeatlas

Aquatic Samples	18
Soil Samples
Animal Samples	3
Plant Samples	1
Total Samples	22

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
22578	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM102702v1 assembly for Kosmotoga pacifica SLHLJ1	complete	GCA_001027025	1330330.3	2645727976	1330330	98.62

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
22578	Kosmotoga pacifica strain SLHLJ1 16S ribosomal RNA gene, partial sequence	KC119212	1501		1330330

GC content

@ref	GC-content (mol%)	Method
22578	42.5	sequence analysis
67770	43.7	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Kosmotoga pacifica strain SLHLJ1
PATRIC: 1330330.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	83.90	no
125439	motility	BacteriaNetⓘ	no	72.90	no
125439	gram_stain	BacteriaNetⓘ	negative	83.40	no
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	90.90	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Kosmotoga pacifica SLHLJ1
NCBI: GCA_001027025.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	66.97	no
125438	anaerobic	anaerobicⓘ	yes	88.81	yes
125438	aerobic	aerobicⓘ	no	94.59	yes
125438	spore-forming	spore-formingⓘ	no	79.50	no
125438	thermophilic	thermophileⓘ	yes	68.81	yes
125438	flagellated	motile2+ⓘ	no	65.95	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Global Association between Thermophilicity and Vancomycin Susceptibility in Bacteria.	Roy C, Alam M, Mandal S, Haldar PK, Bhattacharya S, Mukherjee T, Roy R, Rameez MJ, Misra AK, Chakraborty R, Nanda AK, Mukhopadhyay SK, Ghosh W.	Front Microbiol	10.3389/fmicb.2016.00412	2016
Enzymology	Structural elements determining the transglycosylating activity of glycoside hydrolase family 57 glycogen branching enzymes.	Xiang G, Leemhuis H, van der Maarel MJEC.	Proteins	10.1002/prot.26200	2022
Metabolism	Time-restricted feeding ameliorates non-alcoholic fatty liver disease through modulating hepatic nicotinamide metabolism via gut microbiota remodeling.	Feng R, Yang W, Feng W, Huang X, Cen M, Peng G, Wu W, Wang Z, Jing Y, Long T, Liu Y, Li Z, Chang G, Huang K.	Gut Microbes	10.1080/19490976.2024.2390164	2024
Metabolism	Identification of Thermotoga maritima MSB8 GH57 alpha-amylase AmyC as a glycogen-branching enzyme with high hydrolytic activity.	Zhang X, Leemhuis H, Janecek S, Martinovicova M, Pijning T, van der Maarel MJEC.	Appl Microbiol Biotechnol	10.1007/s00253-019-09938-1	2019
Metabolism	Genome-Resolved Metagenomics and Detailed Geochemical Speciation Analyses Yield New Insights into Microbial Mercury Cycling in Geothermal Springs.	Gionfriddo CM, Stott MB, Power JF, Ogorek JM, Krabbenhoft DP, Wick R, Holt K, Chen LX, Thomas BC, Banfield JF, Moreau JW.	Appl Environ Microbiol	10.1128/aem.00176-20	2020
Genetics	Phylogenetic distribution, biogeography and the effects of land management upon bacterial non-specific Acid phosphatase Gene diversity and abundance.	Neal AL, Blackwell M, Akkari E, Guyomar C, Clark I, Hirsch PR.	Plant Soil	10.1007/s11104-017-3301-2	2018
Genetics	Expanded Phylogenetic Diversity and Metabolic Flexibility of Mercury-Methylating Microorganisms.	McDaniel EA, Peterson BD, Stevens SLR, Tran PQ, Anantharaman K, McMahon KD.	mSystems	10.1128/msystems.00299-20	2020
Transcriptome	Genomic insights into temperature-dependent transcriptional responses of Kosmotoga olearia, a deep-biosphere bacterium that can grow from 20 to 79 °C.	Pollo SMJ, Adebusuyi AA, Straub TJ, Foght JM, Zhaxybayeva O, Nesbo CL.	Extremophiles	10.1007/s00792-017-0956-9	2017
Genetics	Complete genome sequence and whole-genome phylogeny of Kosmotoga pacifica type strain SLHLJ1(T) from an East Pacific hydrothermal sediment.	Jiang L, L'Haridon S, Jebbar M, Xu H, Alain K, Shao Z	Stand Genomic Sci	10.1186/s40793-016-0214-2	2017
Phylogeny	Kosmotoga pacifica sp. nov., a thermophilic chemoorganoheterotrophic bacterium isolated from an East Pacific hydrothermal sediment.	L'Haridon S, Jiang L, Alain K, Chalopin M, Rouxel O, Beauverger M, Xu H, Shao Z, Jebbar M	Extremophiles	10.1007/s00792-013-0596-7	2013

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 )
#22578	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 26965
#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 )
#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 .
#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 .
#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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Kosmotoga pacifica (DSM 26965, JCM 19180, MCCC 1A00641)

Name and taxonomic classification

Morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_001027025

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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