Name: Thermophagus xiamenensis HS1
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 17817

Type strain:

Species: Thermophagus xiamenensis

Strain Designation: HS1

Culture col. no.: DSM 19012, CGMCCC 1.5071

Strain history: <- X. Xu, Third Inst. Oceanography, State Oceanic Administration, Xiamen, China; HS1 <- X. Liu and X. Zhang {2006}

NCBI tax ID(s): 385682 (species)

SI-ID 396897

DSM 19012

Section

Thermophagus xiamenensis HS1 is an anaerobe, thermophilic, Gram-negative bacterium that was isolated from sediment from an offshore hot spring.

Gram-negative
motile
rod-shaped
anaerobe
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	*Bacteroidota*
	Class	*Bacteroidia*
	Order	*Bacteroidales*
	Family	*Marinilabiliaceae*
	Genus	*Thermophagus*
	Species	**Thermophagus xiamenensis**
	Full Scientific Name (LPSN)	Thermophagus xiamenensis Gao et al. 2013

Information on morphological and physiological properties Morphology

[Ref.: #30552]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.998

[Ref.: #30552]	Cell length	7 µm

[Ref.: #30552]	Cell width	0.25 µm

[Ref.: #30552]	Cell shape	rod-shaped

[Ref.: #30552]	Motility	yes

[Ref.: #30552]

Pigment production

Information on culture and growth conditions Culture and growth conditions

[Ref.: #7830]

Culture medium

ANAEROBIC SEAWATER (SWM) MEDIUM (DSMZ Medium 504)

[Ref.: #7830]

Culture medium growth

[Ref.: #7830]

Culture medium link

Medium recipe at MediaDive

[Ref.: #7830]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #7830]	growth	55 °C
[Ref.: #30552]	growth	35-55 °C
[Ref.: #30552]	optimum	50 °C

[Ref.: #7830]	Temperature range	thermophilic
[Ref.: #30552]	Temperature range	thermophilic

	pH	Kind of pH		pH
[Ref.: #30552]			optimum	7
[Ref.: #30552]			growth	5.5-8

Information on physiology and metabolism Physiology and metabolism

[Ref.: #7830]	Oxygen tolerance	anaerobe
[Ref.: #30552]	Oxygen tolerance	anaerobe
[Ref.: #69480]	Oxygen tolerance	anaerobe Confidence in %95.472

[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.911

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #30552]		NaCl		growth	01-08	%
[Ref.: #30552]		NaCl		optimum	3	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #30552]	arabinose ChEBI	+	carbon source
[Ref.: #30552]	cellobiose ChEBI	+	carbon source
[Ref.: #30552]	fructose ChEBI	+	carbon source
[Ref.: #30552]	galactose ChEBI	+	carbon source
[Ref.: #30552]	glucose ChEBI	+	carbon source
[Ref.: #30552]	lactose ChEBI	+	carbon source
[Ref.: #30552]	maltose ChEBI	+	carbon source
[Ref.: #30552]	mannose ChEBI	+	carbon source
[Ref.: #30552]	rhamnose ChEBI	+	carbon source
[Ref.: #30552]	sucrose ChEBI	+	carbon source
[Ref.: #30552]	trehalose ChEBI	+	carbon source
[Ref.: #30552]	xylose ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #30552]		catalase	+	1.11.1.6
[Ref.: #30552]		gelatinase	+

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	vitamin K metabolism	100	5 of 5
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	glycogen metabolism	100	5 of 5
[Ref.: #66794]	lipoate biosynthesis	100	5 of 5
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	starch degradation	100	10 of 10
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	C4 and CAM-carbon fixation	100	8 of 8
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	tetrahydrofolate metabolism	92.86	13 of 14
[Ref.: #66794]	lipid A biosynthesis	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	serine metabolism	88.89	8 of 9
[Ref.: #66794]	valine metabolism	88.89	8 of 9
[Ref.: #66794]	propanol degradation	85.71	6 of 7
[Ref.: #66794]	vitamin B1 metabolism	84.62	11 of 13
[Ref.: #66794]	NAD metabolism	83.33	15 of 18
[Ref.: #66794]	degradation of sugar alcohols	81.25	13 of 16
[Ref.: #66794]	hydrogen production	80	4 of 5
[Ref.: #66794]	threonine metabolism	80	8 of 10
[Ref.: #66794]	cellulose degradation	80	4 of 5
[Ref.: #66794]	Entner Doudoroff pathway	80	8 of 10
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	citric acid cycle	78.57	11 of 14
[Ref.: #66794]	heme metabolism	78.57	11 of 14
[Ref.: #66794]	d-mannose degradation	77.78	7 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	77.78	7 of 9
[Ref.: #66794]	biotin biosynthesis	75	3 of 4
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	glutamate and glutamine metabolism	75	21 of 28
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	flavin biosynthesis	73.33	11 of 15
[Ref.: #66794]	vitamin B6 metabolism	72.73	8 of 11
[Ref.: #66794]	pentose phosphate pathway	72.73	8 of 11
[Ref.: #66794]	alanine metabolism	72.41	21 of 29
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	reductive acetyl coenzyme A pathway	71.43	5 of 7
[Ref.: #66794]	photosynthesis	71.43	10 of 14
[Ref.: #66794]	pyrimidine metabolism	71.11	32 of 45
[Ref.: #66794]	lipid metabolism	70.97	22 of 31
[Ref.: #66794]	propionate fermentation	70	7 of 10
[Ref.: #66794]	purine metabolism	69.15	65 of 94
[Ref.: #66794]	formaldehyde oxidation	66.67	2 of 3
[Ref.: #66794]	degradation of hexoses	66.67	12 of 18
[Ref.: #66794]	enterobactin biosynthesis	66.67	2 of 3
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	CO2 fixation in Crenarchaeota	66.67	6 of 9
[Ref.: #66794]	UDP-GlcNAc biosynthesis	66.67	2 of 3
[Ref.: #66794]	polyamine pathway	65.22	15 of 23
[Ref.: #66794]	glycolysis	64.71	11 of 17
[Ref.: #66794]	proline metabolism	63.64	7 of 11
[Ref.: #66794]	d-xylose degradation	63.64	7 of 11
[Ref.: #66794]	dTDPLrhamnose biosynthesis	62.5	5 of 8
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	isoprenoid biosynthesis	61.54	16 of 26
[Ref.: #66794]	leucine metabolism	61.54	8 of 13
[Ref.: #66794]	phenylalanine metabolism	61.54	8 of 13
[Ref.: #66794]	phenylacetate degradation (aerobic)	60	3 of 5
[Ref.: #66794]	coenzyme M biosynthesis	60	6 of 10
[Ref.: #66794]	non-pathway related	57.89	22 of 38
[Ref.: #66794]	methionine metabolism	57.69	15 of 26
[Ref.: #66794]	ubiquinone biosynthesis	57.14	4 of 7
[Ref.: #66794]	lysine metabolism	57.14	24 of 42
[Ref.: #66794]	cysteine metabolism	55.56	10 of 18
[Ref.: #66794]	sulfate reduction	53.85	7 of 13
[Ref.: #66794]	tryptophan metabolism	52.63	20 of 38
[Ref.: #66794]	myo-inositol biosynthesis	50	5 of 10
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	50	6 of 12
[Ref.: #66794]	kanosamine biosynthesis II	50	1 of 2
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	selenocysteine biosynthesis	50	3 of 6
[Ref.: #66794]	dolichol and dolichyl phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	glycolate and glyoxylate degradation	50	3 of 6
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	toluene degradation	50	2 of 4
[Ref.: #66794]	glutathione metabolism	50	7 of 14
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	histidine metabolism	48.28	14 of 29
[Ref.: #66794]	oxidative phosphorylation	47.25	43 of 91
[Ref.: #66794]	degradation of pentoses	46.43	13 of 28
[Ref.: #66794]	metabolism of disaccharids	45.45	5 of 11
[Ref.: #66794]	degradation of sugar acids	44	11 of 25
[Ref.: #66794]	arginine metabolism	41.67	10 of 24
[Ref.: #66794]	ethylmalonyl-CoA pathway	40	2 of 5
[Ref.: #66794]	glycine metabolism	40	4 of 10
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	metabolism of amino sugars and derivatives	40	2 of 5
[Ref.: #66794]	phenylpropanoid biosynthesis	38.46	5 of 13
[Ref.: #66794]	urea cycle	38.46	5 of 13
[Ref.: #66794]	ketogluconate metabolism	37.5	3 of 8
[Ref.: #66794]	ascorbate metabolism	36.36	8 of 22
[Ref.: #66794]	tyrosine metabolism	35.71	5 of 14
[Ref.: #66794]	vitamin B12 metabolism	35.29	12 of 34
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	L-lactaldehyde degradation	33.33	1 of 3
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	molybdenum cofactor biosynthesis	33.33	3 of 9
[Ref.: #66794]	nitrate assimilation	33.33	3 of 9
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	mevalonate metabolism	28.57	2 of 7
[Ref.: #66794]	arachidonic acid metabolism	27.78	5 of 18
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	carnitine metabolism	25	2 of 8
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	23.08	3 of 13
[Ref.: #66794]	allantoin 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.: #7830]	Sample type/isolated from	sediment from an offshore hot spring
[Ref.: #7830]	Geographic location (country and/or sea, region)	Xiamen
[Ref.: #7830]	Country	China
[Ref.: #7830]	Country ISO 3 Code	CHN
[Ref.: #7830]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Sediment
#Environmental	#Aquatic	#Thermal spring
#Condition	#Thermophilic (>45°C)	-

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence DQ517535 (>99% sequence identity) for Thermophagus xiamenensis subclade from Microbeatlas

Aquatic Samples	597
Soil Samples	162
Animal Samples	550
Plant Samples	36
Total Samples	1345

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

[Ref.: #7830]

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.: #7830]	Thermophagus xiamenensis strain HS1 16S ribosomal RNA gene, partial sequence	DQ517535	1488	ENA	385682 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Thermophagus xiamenensis HS1	GCA_000220155	contig	GenBank	385682 tax ID	*
[Ref.: #66792]	Thermophagus xiamenensis DSM 19012	GCA_900112795	scaffold	GenBank	385682 tax ID	*
[Ref.: #66792]	Thermophagus xiamenensis strain DSM 19012	385682.7	wgs	PATRIC	385682 tax ID	*
[Ref.: #66792]	Thermophagus xiamenensis HS1	2515154052	draft	JGI IMG/M	385682 tax ID	*
[Ref.: #66792]	Thermophagus xiamenensis DSM 19012	2693429893	draft	JGI IMG/M	385682 tax ID	*

[Ref.: #7830]	GC-content	38.7 mol%	high performance liquid chromatography (HPLC)
[Ref.: #30552]	GC-content	38.7 mol%

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: Thermophagus xiamenensis strain DSM 19012 PATRIC: 385682.4
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Thermophagus xiamenensis DSM 19012 NCBI: GCA_900112795.1
[Ref.: #69480]	flagellated	no	97.109	no
[Ref.: #69480]	gram-positive	no	97.226	yes
[Ref.: #69480]	anaerobic	yes	93.585	yes
[Ref.: #69480]	aerobic	no	93.777	yes
[Ref.: #69480]	halophile	no	53.505	no
[Ref.: #69480]	spore-forming	no	94.286	no
[Ref.: #69480]	glucose-ferment	yes	51.123	no
[Ref.: #69480]	thermophile	no	87.809	no
[Ref.: #69480]	glucose-util	yes	88.341	yes
[Ref.: #69480]	motile	no	70.246	yes

Availability in culture collections External links

[Ref.: #7830]

Culture collection no.

DSM 19012, CGMCCC 1.5071

[Ref.: #86808]

SI-ID 396897

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Thermophagus xiamenensis gen. nov., sp. nov., a moderately thermophilic and strictly anaerobic bacterium isolated from hot spring sediment.	Gao ZM, Liu X, Zhang XY, Ruan LW	Int J Syst Evol Microbiol	10.1099/ijs.0.038547-0	2012	*

References

#7830

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 19012

#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 )

#30552

Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #26883 (see below)

#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 .

#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 )

#86808

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-ID396897.1 )

#26883

IJSEM 109 2013 ( DOI 10.1099/ijs.0.038547-0 , PubMed 22345138 )

* These data were automatically processed and therefore are not curated

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Thermophagus xiamenensis strain DSM 19012

Thermophagus xiamenensis DSM 19012

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