Name: Alkalithermobacter thermoalcaliphilus JW/YL23-2
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 2774

Type strain:

Species: Alkalithermobacter thermoalcaliphilus

Strain Designation: JW/YL23-2

Culture col. no.: DSM 7309, ATCC 51508, CIP 105528

Strain history: <- Y. Li and J. Wiegel, Department of Microbiology, University of Georgia, Athens, USA; JW/YL23-2 (Clostridium thermoalcaliphilum)

NCBI tax ID(s): 29349 (species)

SI-ID 46154

ATCC 51508, DSM 7309, CIP 105528

Special Collections

DSMZ
CIP

Section

When using BacDive for research please cite our paper

Alkalithermobacter thermoalcaliphilus JW/YL23-2 is an anaerobe, thermophilic bacterium that was isolated from sewage sludge.

anaerobe
thermophilic
16S sequence
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	09-12-2024 (DD-MM-YYYY)
	Domain	*Bacteria*
	Phylum	*Bacillota*
	Class	*Clostridia*
	Order	*Eubacteriales*
	Family	*Tepidibacteraceae*
	Genus	*Alkalithermobacter*
	Species	**Alkalithermobacter thermoalcaliphilus**
	Full Scientific Name (LPSN)	Alkalithermobacter thermoalcaliphilus corrig. (Li et al. 1994) Bello et al. 2024

	Synonym	Alkalithermobacter thermoalcaliphilum
	Synonym	Clostridium thermoalcaliphilum

Information on culture and growth conditions Culture and growth conditions

[Ref.: #3111]

Culture medium

ALKALITHERMOBACTER MEDIUM (DSMZ Medium 616)

[Ref.: #3111]

Culture medium growth

[Ref.: #3111]

Culture medium link

Medium recipe provided by DSMZ

	Temperatures	Kind of temperature		Temperature
[Ref.: #3111]			growth	50 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #3111]	Oxygen tolerance	anaerobe
[Ref.: #125438]	Oxygen tolerance	anaerobe Confidence in %94.275
[Ref.: #125439]	Oxygen tolerance	anaerobe Confidence in %98.3

[Ref.: #3111]	Murein short key	A21.04
[Ref.: #3111]	Murein types	A4ß L-Orn-D-Asp

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	aminopropanol phosphate biosynthesis	100	2 of 2
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	88.89	8 of 9
[Ref.: #66794]	C4 and CAM-carbon fixation	87.5	7 of 8
[Ref.: #66794]	gluconeogenesis	87.5	7 of 8
[Ref.: #66794]	urea cycle	84.62	11 of 13
[Ref.: #66794]	glycine betaine biosynthesis	80	4 of 5
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	hydrogen production	80	4 of 5
[Ref.: #66794]	glycogen metabolism	80	4 of 5
[Ref.: #66794]	heme metabolism	78.57	11 of 14
[Ref.: #66794]	photosynthesis	78.57	11 of 14
[Ref.: #66794]	tetrahydrofolate metabolism	78.57	11 of 14
[Ref.: #66794]	vitamin B1 metabolism	76.92	10 of 13
[Ref.: #66794]	purine metabolism	76.6	72 of 94
[Ref.: #66794]	butanoate fermentation	75	3 of 4
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	biotin biosynthesis	75	3 of 4
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	pyrimidine metabolism	73.33	33 of 45
[Ref.: #66794]	flavin biosynthesis	73.33	11 of 15
[Ref.: #66794]	alanine metabolism	72.41	21 of 29
[Ref.: #66794]	threonine metabolism	70	7 of 10
[Ref.: #66794]	starch degradation	70	7 of 10
[Ref.: #66794]	phenylalanine metabolism	69.23	9 of 13
[Ref.: #66794]	glutamate and glutamine metabolism	67.86	19 of 28
[Ref.: #66794]	CO2 fixation in Crenarchaeota	66.67	6 of 9
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	formaldehyde oxidation	66.67	2 of 3
[Ref.: #66794]	selenocysteine biosynthesis	66.67	4 of 6
[Ref.: #66794]	NAD metabolism	66.67	12 of 18
[Ref.: #66794]	glycolysis	64.71	11 of 17
[Ref.: #66794]	cysteine metabolism	61.11	11 of 18
[Ref.: #66794]	propionate fermentation	60	6 of 10
[Ref.: #66794]	methionine metabolism	57.69	15 of 26
[Ref.: #66794]	propanol degradation	57.14	4 of 7
[Ref.: #66794]	serine metabolism	55.56	5 of 9
[Ref.: #66794]	d-mannose degradation	55.56	5 of 9
[Ref.: #66794]	oxidative phosphorylation	54.95	50 of 91
[Ref.: #66794]	sulfate reduction	53.85	7 of 13
[Ref.: #66794]	tryptophan metabolism	52.63	20 of 38
[Ref.: #66794]	lipid metabolism	51.61	16 of 31
[Ref.: #66794]	suberin monomers biosynthesis	50	1 of 2
[Ref.: #66794]	acetate fermentation	50	2 of 4
[Ref.: #66794]	isoleucine metabolism	50	4 of 8
[Ref.: #66794]	CMP-KDO biosynthesis	50	2 of 4
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	ketogluconate metabolism	50	4 of 8
[Ref.: #66794]	citric acid cycle	50	7 of 14
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	sulfopterin metabolism	50	2 of 4
[Ref.: #66794]	histidine metabolism	48.28	14 of 29
[Ref.: #66794]	lysine metabolism	47.62	20 of 42
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	46.15	6 of 13
[Ref.: #66794]	isoprenoid biosynthesis	46.15	12 of 26
[Ref.: #66794]	metabolism of disaccharids	45.45	5 of 11
[Ref.: #66794]	nitrate assimilation	44.44	4 of 9
[Ref.: #66794]	vitamin B12 metabolism	44.12	15 of 34
[Ref.: #66794]	cardiolipin biosynthesis	42.86	3 of 7
[Ref.: #66794]	arginine metabolism	41.67	10 of 24
[Ref.: #66794]	factor 420 biosynthesis	40	2 of 5
[Ref.: #66794]	cellulose degradation	40	2 of 5
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	metabolism of amino sugars and derivatives	40	2 of 5
[Ref.: #66794]	methylglyoxal degradation	40	2 of 5
[Ref.: #66794]	non-pathway related	39.47	15 of 38
[Ref.: #66794]	proline metabolism	36.36	4 of 11
[Ref.: #66794]	d-xylose degradation	36.36	4 of 11
[Ref.: #66794]	pentose phosphate pathway	36.36	4 of 11
[Ref.: #66794]	degradation of pentoses	35.71	10 of 28
[Ref.: #66794]	polyamine pathway	34.78	8 of 23
[Ref.: #66794]	molybdenum cofactor biosynthesis	33.33	3 of 9
[Ref.: #66794]	lipid A biosynthesis	33.33	3 of 9
[Ref.: #66794]	cyanate degradation	33.33	1 of 3
[Ref.: #66794]	glycolate and glyoxylate degradation	33.33	2 of 6
[Ref.: #66794]	octane oxidation	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	1,4-dihydroxy-6-naphthoate biosynthesis	33.33	2 of 6
[Ref.: #66794]	valine metabolism	33.33	3 of 9
[Ref.: #66794]	degradation of sugar alcohols	31.25	5 of 16
[Ref.: #66794]	leucine metabolism	30.77	4 of 13
[Ref.: #66794]	myo-inositol biosynthesis	30	3 of 10
[Ref.: #66794]	glycine metabolism	30	3 of 10
[Ref.: #66794]	coenzyme M biosynthesis	30	3 of 10
[Ref.: #66794]	reductive acetyl coenzyme A pathway	28.57	2 of 7
[Ref.: #66794]	glutathione metabolism	28.57	4 of 14
[Ref.: #66794]	benzoyl-CoA degradation	28.57	2 of 7
[Ref.: #66794]	degradation of hexoses	27.78	5 of 18
[Ref.: #66794]	vitamin B6 metabolism	27.27	3 of 11
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	25	3 of 12
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	tyrosine metabolism	21.43	3 of 14
		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.: #3111]	Sample type/isolated from	sewage sludge
[Ref.: #3111]	Country	USA
[Ref.: #3111]	Country ISO 3 Code	USA
[Ref.: #3111]	Continent	North America
* marker position based on {}

Isolation sources categories

#Engineered

#Waste

#Sewage sludge

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence FR749954 (>99% sequence identity) for [Clostridium] thermoalcaliphilum subclade from Microbeatlas

Aquatic Samples	156
Soil Samples	101
Animal Samples	155
Plant Samples	10
Total Samples	422

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

[Ref.: #3111]

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.: #3111]	Clostridium thermoalcaliphilum partial 16S rRNA gene, type strain DSM 7309T, clone 1	FR749953	1581	GenBank ENA	29349 tax ID
[Ref.: #3111]	Clostridium thermoalcaliphilum partial 16S rRNA gene, type strain DSM 7309T, clone 2	FR749954	1546	GenBank ENA	29349 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	[Clostridium] thermoalcaliphilum DSM 7309	GCA_002029295	contig	GenBank ENA	29349 tax ID	*
[Ref.: #66792]	[Clostridium] thermoalcaliphilum strain DSM 7309	29349.3	wgs	PATRIC	29349 tax ID	*
[Ref.: #66792]	Clostridium thermoalcaliphilum DSM 7309	2833455180	draft	JGI IMG/M	29349 tax ID	*
[Ref.: #66792]	Clostridium thermoalcaliphilum JW/YL23-2	2711768657	draft	JGI IMG/M	29349 tax ID	*

[Ref.: #3111]

GC-content

32.0 mol%

high performance liquid chromatography (HPLC)

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

	Model	Trait	Prediction	Confidence in %	In training data
	Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: [Clostridium] thermoalcaliphilum strain DSM 7309 PATRIC: 29349.3
[Ref.: #125438]	gram-positive	gram-positiveⓘ	yes	69.238	no
[Ref.: #125438]	anaerobic	anaerobicⓘ	yes	94.275	yes
[Ref.: #125438]	spore-forming	spore-formingⓘ	yes	70.441	no
[Ref.: #125438]	aerobic	aerobicⓘ	no	98.499	no
[Ref.: #125438]	thermophile	thermophilicⓘ	yes	55.408	yes
[Ref.: #125438]	motile2+	flagellatedⓘ	yes	73.61	no

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: [Clostridium] thermoalcaliphilum DSM 7309 NCBI: GCA_002029295
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	no	59.9
[Ref.: #125439]	BacteriaNet	motilityⓘ	yes	65.2
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	positive	80.5
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	anaerobe	98.3

Availability in culture collections External links

[Ref.: #3111]

Culture collection no.

DSM 7309, ATCC 51508, CIP 105528

[Ref.: #72304]

SI-ID 46154

Literature:

Topic	Title	Authors	Journal	DOI	Year
Genetics	First Insights into the Genome Sequence of the Alkaliphilic Thermotolerant Bacterium Clostridium thermoalcaliphilum JW/YL23-2(T).	Poehlein A, Berg A, Welsing G, Daniel R	Genome Announc	10.1128/genomeA.00368-17	2017	*
Phylogeny	Clostridium thermoalcaliphilum sp. nov., an anaerobic and thermotolerant facultative alkaliphile.	Li Y, Engle M, Weiss N, Mandelco L, Wiegel J	Int J Syst Bacteriol	10.1099/00207713-44-1-111	1994	*

References

#3111

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 7309

#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) .

#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 .

#72304

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-ID46154.1 )

#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 .

* These data were automatically processed and therefore are not curated

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[Clostridium] thermoalcaliphilum strain DSM 7309

[Clostridium] thermoalcaliphilum DSM 7309

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