Alkalithermobacter thermoalcaliphilus (DSM 7309, ATCC 51508, CIP 105528)

Name: Alkalithermobacter thermoalcaliphilus (DSM 7309, ATCC 51508, CIP 105528)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 2774

Type strain

Strain Designation JW/YL23-2

Culture col. no. DSM 7309 ATCC 51508 CIP 105528 JW/YL23-2

NCBI tax ID(s) 29346

Special Collections DSMZ CIP

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

Links

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

anaerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 46154

ATCC 51508,DSM 7309,CIP 105528

@ref 20215

Last LPSN update 2026-05-29 08:25:33

Domain Bacteria

Phylum Bacillota

Class Clostridia

Order Eubacteriales

Family Tepidibacteraceae

Genus Alkalithermobacter

Species Alkalithermobacter thermoalcaliphilus

Full scientific name Alkalithermobacter thermoalcaliphilus corrig. (Li et al. 1994) Bello et al. 2024

Synonyms (2)

Alkalithermobacter thermoalcaliphilum
Clostridium thermoalcaliphilum

Morphology

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
3111	ALKALITHERMOBACTER MEDIUM (DSMZ Medium 616)		Medium recipe at MediaDive	Name: ALKALITHERMOBACTER MEDIUM (DSMZ Medium 616) Composition: Tryptone 10.0 g/l Na2CO3 5.3 g/l Yeast extract 5.0 g/l D-Glucose 3.0 g/l Na2HPO4 x 2 H2O 0.36 g/l Na2S x 9 H2O 0.2 g/l L-Cysteine HCl x H2O 0.2 g/l KCl 0.08 g/l Sodium resazurin 0.0005 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
3111	positive	growth	50

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
3111	anaerobe
125438	anaerobe	94.275
125439	obligate anaerobe	97.321

Murein

@ref	Murein short key	Type
3111	A21.04	A4ß L-Orn-D-Asp

Pathway annotation

Computationally determined by

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

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Waste	#Sewage sludge

Isolation

@ref	Sample type	Country	Country ISO 3 Code	Continent
3111	sewage sludge	USA	USA	North America

Taxonmaps

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

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
3111	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	Clostridium thermoalcaliphilum JW/YL23-2	complete			2711768657	29349	91.3
66792	ASM202929v1 assembly for Alkalithermobacter paradoxus DSM 7309	contig	GCA_002029295	29349.3	2833455180	29349	67.56

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
3111	Clostridium thermoalcaliphilum partial 16S rRNA gene, type strain DSM 7309T, clone 1	FR749953	1581		29349
3111	Clostridium thermoalcaliphilum partial 16S rRNA gene, type strain DSM 7309T, clone 2	FR749954	1546		29349

GC content

@ref	GC-content (mol%)	Method
3111	32.0	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: ASM202929v1 assembly for Alkalithermobacter paradoxus DSM 7309
BV-BRC: 29349.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate anaerobe	97.32	no
125439	gram_stain	BacteriaNetⓘ	positive	62.88	no
125439	motility	BacteriaNetⓘ	yes	56.18	no
125439	spore_formation	BacteriaNetⓘ	no	74.89	no

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	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	69.24	no
125438	anaerobic	anaerobicⓘ	yes	94.28	yes
125438	spore-forming	spore-formingⓘ	yes	70.44	no
125438	aerobic	aerobicⓘ	no	98.50	no
125438	thermophilic	thermophileⓘ	yes	55.41	yes
125438	flagellated	motile2+ⓘ	yes	73.61	no

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 .
#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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Alkalithermobacter thermoalcaliphilus (DSM 7309, ATCC 51508, CIP 105528)

Name and taxonomic classification

Morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Murein

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_002029295

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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