Name: Thermosediminibacter oceani JW/IW-1228P
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 18013

Type strain:

Species: Thermosediminibacter oceani

Strain Designation: JW/IW-1228P

Culture col. no.: DSM 16646, ATCC BAA-1034

Strain history: <- J. Wiegel, Univ. Georgia <- Y.-J. Lee; JW/IW-1228P {2003}

NCBI tax ID(s): 555079 (strain), 291990 (species)

SI-ID 291138

ATCC BAA-1034, DSM 16646

Special Collections

DSMZ

Section

Thermosediminibacter oceani JW/IW-1228P is an anaerobe bacterium that was isolated from core sample of deep sea sediment.

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	*Bacillota*
	Class	*Clostridia*
	Order	*Thermosediminibacterales*
	Family	*Thermosediminibacteraceae*
	Genus	*Thermosediminibacter*
	Species	**Thermosediminibacter oceani**
	Full Scientific Name (LPSN)	Thermosediminibacter oceani Lee et al. 2006

Information on morphological and physiological properties Morphology

Multimedia content

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Caption:

electron microscopic image

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Intellectual property rights:

Information on culture and growth conditions Culture and growth conditions

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Culture medium

THERMOTOGA ELFII MEDIUM (DSMZ Medium 664)

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Culture medium growth

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Culture medium link

Medium recipe at MediaDive

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Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #6547]			growth	68 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #6547]	Oxygen tolerance	anaerobe
[Ref.: #69480]	Oxygen tolerance	anaerobe Confidence in %92.848

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	aminopropanol phosphate biosynthesis	100	2 of 2
[Ref.: #66794]	reductive acetyl coenzyme A pathway	100	7 of 7
[Ref.: #66794]	C4 and CAM-carbon fixation	100	8 of 8
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	palmitate biosynthesis	95.45	21 of 22
[Ref.: #66794]	threonine metabolism	90	9 of 10
[Ref.: #66794]	aspartate and asparagine metabolism	88.89	8 of 9
[Ref.: #66794]	d-mannose degradation	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	vitamin B12 metabolism	88.24	30 of 34
[Ref.: #66794]	degradation of sugar alcohols	87.5	14 of 16
[Ref.: #66794]	propanol degradation	85.71	6 of 7
[Ref.: #66794]	ubiquinone biosynthesis	85.71	6 of 7
[Ref.: #66794]	cellulose degradation	80	4 of 5
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	flavin biosynthesis	80	12 of 15
[Ref.: #66794]	photosynthesis	78.57	11 of 14
[Ref.: #66794]	vitamin B1 metabolism	76.92	10 of 13
[Ref.: #66794]	phenylalanine metabolism	76.92	10 of 13
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	ketogluconate metabolism	75	6 of 8
[Ref.: #66794]	sulfopterin metabolism	75	3 of 4
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	pentose phosphate pathway	72.73	8 of 11
[Ref.: #66794]	NAD metabolism	72.22	13 of 18
[Ref.: #66794]	heme metabolism	71.43	10 of 14
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	Entner Doudoroff pathway	70	7 of 10
[Ref.: #66794]	purine metabolism	67.02	63 of 94
[Ref.: #66794]	glycolate and glyoxylate degradation	66.67	4 of 6
[Ref.: #66794]	serine metabolism	66.67	6 of 9
[Ref.: #66794]	formaldehyde oxidation	66.67	2 of 3
[Ref.: #66794]	methane metabolism	66.67	2 of 3
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	selenocysteine biosynthesis	66.67	4 of 6
[Ref.: #66794]	molybdenum cofactor biosynthesis	66.67	6 of 9
[Ref.: #66794]	methionine metabolism	65.38	17 of 26
[Ref.: #66794]	glycolysis	64.71	11 of 17
[Ref.: #66794]	pyrimidine metabolism	64.44	29 of 45
[Ref.: #66794]	non-pathway related	63.16	24 of 38
[Ref.: #66794]	oxidative phosphorylation	62.64	57 of 91
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	isoleucine metabolism	62.5	5 of 8
[Ref.: #66794]	alanine metabolism	62.07	18 of 29
[Ref.: #66794]	urea cycle	61.54	8 of 13
[Ref.: #66794]	glycogen metabolism	60	3 of 5
[Ref.: #66794]	propionate fermentation	60	6 of 10
[Ref.: #66794]	metabolism of amino sugars and derivatives	60	3 of 5
[Ref.: #66794]	factor 420 biosynthesis	60	3 of 5
[Ref.: #66794]	tetrahydrofolate metabolism	57.14	8 of 14
[Ref.: #66794]	glutamate and glutamine metabolism	57.14	16 of 28
[Ref.: #66794]	cysteine metabolism	55.56	10 of 18
[Ref.: #66794]	vitamin B6 metabolism	54.55	6 of 11
[Ref.: #66794]	isoprenoid biosynthesis	53.85	14 of 26
[Ref.: #66794]	CMP-KDO biosynthesis	50	2 of 4
[Ref.: #66794]	adipate degradation	50	1 of 2
[Ref.: #66794]	myo-inositol biosynthesis	50	5 of 10
[Ref.: #66794]	cis-vaccenate biosynthesis	50	1 of 2
[Ref.: #66794]	glutathione metabolism	50	7 of 14
[Ref.: #66794]	dolichol and dolichyl phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	lactate fermentation	50	2 of 4
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	starch degradation	50	5 of 10
[Ref.: #66794]	biotin biosynthesis	50	2 of 4
[Ref.: #66794]	polyamine pathway	47.83	11 of 23
[Ref.: #66794]	arginine metabolism	45.83	11 of 24
[Ref.: #66794]	proline metabolism	45.45	5 of 11
[Ref.: #66794]	lysine metabolism	45.24	19 of 42
[Ref.: #66794]	histidine metabolism	44.83	13 of 29
[Ref.: #66794]	tryptophan metabolism	44.74	17 of 38
[Ref.: #66794]	lipid A biosynthesis	44.44	4 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	44.44	4 of 9
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
[Ref.: #66794]	glycine metabolism	40	4 of 10
[Ref.: #66794]	methylglyoxal degradation	40	2 of 5
[Ref.: #66794]	hydrogen production	40	2 of 5
[Ref.: #66794]	lipoate biosynthesis	40	2 of 5
[Ref.: #66794]	phenol degradation	40	8 of 20
[Ref.: #66794]	degradation of pentoses	39.29	11 of 28
[Ref.: #66794]	degradation of hexoses	38.89	7 of 18
[Ref.: #66794]	metabolism of disaccharids	36.36	4 of 11
[Ref.: #66794]	tyrosine metabolism	35.71	5 of 14
[Ref.: #66794]	citric acid cycle	35.71	5 of 14
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	valine metabolism	33.33	3 of 9
[Ref.: #66794]	3-phenylpropionate degradation	33.33	5 of 15
[Ref.: #66794]	cyanate degradation	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	nitrate assimilation	33.33	3 of 9
[Ref.: #66794]	leucine metabolism	30.77	4 of 13
[Ref.: #66794]	4-hydroxyphenylacetate degradation	30	3 of 10
[Ref.: #66794]	coenzyme M biosynthesis	30	3 of 10
[Ref.: #66794]	lipid metabolism	29.03	9 of 31
[Ref.: #66794]	degradation of sugar acids	28	7 of 25
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	methanogenesis from CO2	25	3 of 12
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	sulfate reduction	23.08	3 of 13
[Ref.: #66794]	4-hydroxymandelate degradation	22.22	2 of 9
		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.: #6547]	Sample type/isolated from	core sample of deep sea sediment
[Ref.: #6547]	Geographic location (country and/or sea, region)	Peru Margin
[Ref.: #6547]	Country	Peru
[Ref.: #6547]	Country ISO 3 Code	PER
[Ref.: #6547]	Continent	Middle and South America
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Marine
#Environmental	#Terrestrial	#Core sample
#Environmental	#Terrestrial	#Sediment

What are isolation sources categories?

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Global distribution of 16S sequence AY703478 (>99% sequence identity) for Thermosediminibacter oceani subclade from Microbeatlas

Aquatic Samples	198
Soil Samples	113
Animal Samples	379
Plant Samples	10
Total Samples	700

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

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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.: #6547]	Thermosediminibacter oceani 16S ribosomal RNA gene, partial sequence	AY703478	1386	GenBank ENA	291990 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Thermosediminibacter oceani DSM 16646	GCA_000144645	complete	GenBank ENA	555079 tax ID	*
[Ref.: #66792]	Thermosediminibacter oceani DSM 16646	555079.3	complete	PATRIC	555079 tax ID	*
[Ref.: #66792]	Thermosediminibacter oceani JW/IW-1228P, DSM 16646	648028061	complete	JGI IMG/M	555079 tax ID	*

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GC-content

50 mol%

high performance liquid chromatography (HPLC)

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

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Thermosediminibacter oceani DSM 16646 DSM 16646 NCBI: GCA_000144645.1
[Ref.: #69480]	gram-positive	gram-positiveⓘ	yes	52.737	no
[Ref.: #69480]	anaerobic	anaerobicⓘ	yes	92.848	yes
[Ref.: #69480]	aerobic	aerobicⓘ	no	96.674	yes
[Ref.: #69480]	spore-forming	spore-formingⓘ	yes	50.52	no
[Ref.: #69480]	thermophilic	thermophileⓘ	yes	74.176	no
[Ref.: #69480]	flagellated	motile2+ⓘ	yes	72.775	no

Availability in culture collections External links

[Ref.: #6547]

Culture collection no.

DSM 16646, ATCC BAA-1034

[Ref.: #87000]

SI-ID 291138

Literature:

Topic	Title	Authors	Journal	DOI	Year
Genetics	Complete genome sequence of Thermosediminibacter oceani type strain (JW/IW-1228P).	Pitluck S, Yasawong M, Munk C, Nolan M, Lapidus A, Lucas S, Glavina Del Rio T, Tice H, Cheng JF, Bruce D, Detter C, Tapia R, Han C, Goodwin L, Liolios K, Ivanova N, Mavromatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Rohde M, Spring S, Sikorski J, Goker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP	Stand Genomic Sci	10.4056/sigs.1133078	2010	*
Phylogeny	Caldanaerovirga acetigignens gen. nov., sp. nov., an anaerobic xylanolytic, alkalithermophilic bacterium isolated from Trego Hot Spring, Nevada, USA.	Wagner ID, Ahmed S, Zhao W, Zhang CL, Romanek CS, Rohde M, Wiegel J	Int J Syst Evol Microbiol	10.1099/ijs.0.005207-0	2009	*
Phylogeny	Thermovorax subterraneus, gen. nov., sp. nov., a thermophilic hydrogen-producing bacterium isolated from geothermally active underground mine.	Makinen AE, Kaksonen AH, Puhakka JA	Extremophiles	10.1007/s00792-009-0235-5	2009	*
Phylogeny	Thermosediminibacter oceani gen. nov., sp. nov. and Thermosediminibacter litoriperuensis sp. nov., new anaerobic thermophilic bacteria isolated from Peru Margin.	Lee YJ, Wagner ID, Brice ME, Kevbrin VV, Mills GL, Romanek CS, Wiegel J	Extremophiles	10.1007/s00792-005-0453-4	2005	*

References

#6547

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 16646

#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 )

#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) .

#66793

Mukherjee et al.: GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life. 35: 676 - 683 2017 ( DOI 10.1038/nbt.3886 , PubMed 28604660 )

#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 .

#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) .

#87000

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-ID291138.1 )

* These data were automatically processed and therefore are not curated

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Thermosediminibacter oceani DSM 16646 DSM 16646

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