Caldisphaera lagunensis (DSM 15908, ANMR 0165, JCM 11604)

Name: Caldisphaera lagunensis (DSM 15908, ANMR 0165, JCM 11604)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 2090

Type strain

Strain Designation IC-154

Culture col. no. DSM 15908 ANMR 0165 JCM 11604 MCC-UPLB 1331 IC-154

NCBI tax ID(s) 1056495 200415

Special Collections DSMZ JCM Literature strains

History <- T. Itoh, JCM; IC-154 <- T. Itoh and P. C. Sanchez {1996} T. Itoh and P. C. Sanchez IC-154.

Links

Caldisphaera lagunensis IC-154 is an anaerobe, chemoorganotroph, thermophilic prokaryote that was isolated from an acidic hot spring.

coccus-shaped anaerobe chemoorganotroph thermophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 111750

JCM 11604,DSM 15908

@ref 20215

Last LPSN update 2025-12-16 09:47:15

Domain Thermoproteati

Phylum Thermoproteota

Class Thermoprotei

Order Acidilobales

Family Acidilobaceae

Genus Caldisphaera

Species Caldisphaera lagunensis

Full scientific name Caldisphaera lagunensis Itoh et al. 2003

BacDive ID	Other strains from **Caldisphaera lagunensis** (1)	Type strain
161176	C. lagunensis JCM 11605, ANMR 0174, MCC-UPLB 1332

Morphology

Cell morphology

@ref	Cell length	Cell shape	Motility	Gram stain	Confidence
23168	0.8-1.1 µm	coccus-shaped
125439				negative	92.1

Multimedia

@ref:	66793
multimedia content:	EM_DSM_15908_1.jpg
multimedia.multimedia content:	EM_DSM_15908_1.jpg
caption:	electron microscopic image
intellectual property rights:	© HZI/Manfred Rohde
manual_annotation:	1

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
6178	CALDISPHAERA MEDIUM (DSMZ Medium 991)		Medium recipe at MediaDive	Name: CALDISPHAERA MEDIUM (DSMZ Medium 991) Composition: Sulfur 9.8912 g/l Trisodium citrate x 2 H2O 2.90801 g/l (NH4)2SO4 1.28586 g/l Na2S x 9 H2O 0.49456 g/l Yeast extract 0.49456 g/l KH2PO4 0.276954 g/l MgSO4 x 7 H2O 0.24728 g/l CaCl2 x 2 H2O 0.0692384 g/l FeCl3 x 6 H2O 0.0197824 g/l Na2B4O7 x 10 H2O 0.00445104 g/l MnCl2 x 4 H2O 0.00178042 g/l Sodium resazurin 0.00049456 g/l ZnSO4 x 7 H2O 0.000217606 g/l Pyridoxine hydrochloride 9.8912e-05 g/l (DL)-alpha-Lipoic acid 4.9456e-05 g/l CuCl2 x 2 H2O 4.9456e-05 g/l Thiamine HCl 4.9456e-05 g/l Calcium D-(+)-pantothenate 4.9456e-05 g/l p-Aminobenzoic acid 4.9456e-05 g/l Nicotinic acid 4.9456e-05 g/l Riboflavin 4.9456e-05 g/l Na2MoO4 x 2 H2O 2.96736e-05 g/l VOSO4 x 2 H2O 2.96736e-05 g/l Folic acid 1.97824e-05 g/l Biotin 1.97824e-05 g/l CoSO4 x 7 H2O 9.8912e-06 g/l Vitamin B12 9.8912e-07 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
6178	positive	growth	75	thermophilic
23168	negative	growth	40
23168	negative	growth	82
23168	positive	maximum	80	hyperthermophilic
23168	positive	minimum	45	thermophilic
23168	positive	optimum	70-78	thermophilic
67770	positive	growth	75	thermophilic

Culture pH

@ref	Ability	Type	PH	PH range
23168	positive	optimum	3.5-4.0
23168	positive	growth	2.3-5.4	acidophile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
6178	anaerobe
23168	anaerobe

Nutrition type

23168

Typechemoorganotroph

Spore formation

@ref	Spore formation	Confidence
125438		92.193

Halophily

@ref	Salt	Growth	Tested relation	Concentration
23168	NaCl	positive	growth	<1.5 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
23168	30089 ChEBI	acetate	-	carbon source
23168	30089 ChEBI	acetate	-	energy source
23168	17968 ChEBI	butyrate	-	carbon source
23168	17968 ChEBI	butyrate	-	energy source
23168		casamino acids	+	carbon source
23168		casamino acids	+	energy source
23168	16947 ChEBI	citrate	-	carbon source
23168	16947 ChEBI	citrate	-	energy source
23168	17108 ChEBI	D-arabinose	-	carbon source
23168	17108 ChEBI	D-arabinose	-	energy source
23168	15824 ChEBI	D-fructose	-	carbon source
23168	15824 ChEBI	D-fructose	-	energy source
23168	12936 ChEBI	D-galactose	-	carbon source
23168	12936 ChEBI	D-galactose	-	energy source
23168	17634 ChEBI	D-glucose	-	carbon source
23168	17634 ChEBI	D-glucose	-	energy source
23168	16988 ChEBI	D-ribose	-	carbon source
23168	16988 ChEBI	D-ribose	-	energy source
23168	65327 ChEBI	D-xylose	-	carbon source
23168	65327 ChEBI	D-xylose	-	energy source
23168	16397 ChEBI	formamide	-	carbon source
23168	16397 ChEBI	formamide	-	energy source
23168	15740 ChEBI	formate	-	carbon source
23168	15740 ChEBI	formate	-	energy source
23168	29806 ChEBI	fumarate	-	carbon source
23168	29806 ChEBI	fumarate	-	energy source
23168	5291 ChEBI	gelatin	+	carbon source
23168	5291 ChEBI	gelatin	+	energy source
23168	28087 ChEBI	glycogen	+	carbon source
23168	28087 ChEBI	glycogen	+	energy source
23168	15589 ChEBI	L-malate	-	carbon source
23168	15589 ChEBI	L-malate	-	energy source
23168	24996 ChEBI	lactate	-	carbon source
23168	24996 ChEBI	lactate	-	energy source
23168	17716 ChEBI	lactose	-	carbon source
23168	17716 ChEBI	lactose	-	energy source
23168	17306 ChEBI	maltose	-	carbon source
23168	17306 ChEBI	maltose	-	energy source
23168	37684 ChEBI	mannose	-	carbon source
23168	37684 ChEBI	mannose	-	energy source
23168	17790 ChEBI	methanol	-	carbon source
23168	17790 ChEBI	methanol	-	energy source
23168	16830 ChEBI	methylamine	-	carbon source
23168	16830 ChEBI	methylamine	-	energy source
23168		peptone	+	carbon source
23168		peptone	+	energy source
23168	17272 ChEBI	propionate	-	carbon source
23168	17272 ChEBI	propionate	-	energy source
23168	15361 ChEBI	pyruvate	-	carbon source
23168	15361 ChEBI	pyruvate	-	energy source
23168	28017 ChEBI	starch	+	carbon source
23168	28017 ChEBI	starch	+	energy source
23168	30031 ChEBI	succinate	-	carbon source
23168	30031 ChEBI	succinate	-	energy source
23168	17992 ChEBI	sucrose	-	carbon source
23168	17992 ChEBI	sucrose	-	energy source
23168	18139 ChEBI	trimethylamine	-	carbon source
23168	18139 ChEBI	trimethylamine	-	energy source
23168		yeast extract	+	carbon source
23168		yeast extract	+	energy source

Antibiotic resistance

@ref	ChEBI	Metabolite
23168	17698	chloramphenicol
23168	48923	erythromycin
23168	6104	kanamycin
23168	28368	novobiocin
23168	28077	rifampicin
23168	17076	streptomycin
23168	28001	vancomycin

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	aspartate and asparagine metabolism	100	9 of 9
66794	ribulose monophosphate pathway	100	2 of 2
66794	glycogen metabolism	100	5 of 5
66794	adipate degradation	100	2 of 2
66794	L-lactaldehyde degradation	100	3 of 3
66794	propanol degradation	100	7 of 7
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	suberin monomers biosynthesis	100	2 of 2
66794	valine metabolism	100	9 of 9
66794	flavin biosynthesis	93.33	14 of 15
66794	chorismate metabolism	88.89	8 of 9
66794	starch degradation	80	8 of 10
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	molybdenum cofactor biosynthesis	77.78	7 of 9
66794	palmitate biosynthesis	77.27	17 of 22
66794	acetate fermentation	75	3 of 4
66794	coenzyme A metabolism	75	3 of 4
66794	glutamate and glutamine metabolism	75	21 of 28
66794	glycogen biosynthesis	75	3 of 4
66794	CMP-KDO biosynthesis	75	3 of 4
66794	methionine metabolism	73.08	19 of 26
66794	citric acid cycle	71.43	10 of 14
66794	photosynthesis	71.43	10 of 14
66794	threonine metabolism	70	7 of 10
66794	serine metabolism	66.67	6 of 9
66794	acetoin degradation	66.67	2 of 3
66794	pantothenate biosynthesis	66.67	4 of 6
66794	glycolate and glyoxylate degradation	66.67	4 of 6
66794	formaldehyde oxidation	66.67	2 of 3
66794	enterobactin biosynthesis	66.67	2 of 3
66794	d-mannose degradation	66.67	6 of 9
66794	alanine metabolism	65.52	19 of 29
66794	glycolysis	64.71	11 of 17
66794	heme metabolism	64.29	9 of 14
66794	pentose phosphate pathway	63.64	7 of 11
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	C4 and CAM-carbon fixation	62.5	5 of 8
66794	vitamin B1 metabolism	61.54	8 of 13
66794	lipid metabolism	61.29	19 of 31
66794	NAD metabolism	61.11	11 of 18
66794	propionate fermentation	60	6 of 10
66794	creatinine degradation	60	3 of 5
66794	methylglyoxal degradation	60	3 of 5
66794	reductive acetyl coenzyme A pathway	57.14	4 of 7
66794	lysine metabolism	57.14	24 of 42
66794	cysteine metabolism	55.56	10 of 18
66794	pyrimidine metabolism	55.56	25 of 45
66794	phenylalanine metabolism	53.85	7 of 13
66794	polyamine pathway	52.17	12 of 23
66794	ethanol fermentation	50	1 of 2
66794	tryptophan metabolism	50	19 of 38
66794	kanosamine biosynthesis II	50	1 of 2
66794	gluconeogenesis	50	4 of 8
66794	phenylmercury acetate degradation	50	1 of 2
66794	butanoate fermentation	50	2 of 4
66794	cis-vaccenate biosynthesis	50	1 of 2
66794	selenocysteine biosynthesis	50	3 of 6
66794	CDP-diacylglycerol biosynthesis	50	1 of 2
66794	glycine metabolism	50	5 of 10
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	mannosylglycerate biosynthesis	50	1 of 2
66794	ketogluconate metabolism	50	4 of 8
66794	purine metabolism	48.94	46 of 94
66794	ubiquinone biosynthesis	42.86	3 of 7
66794	benzoyl-CoA degradation	42.86	3 of 7
66794	mevalonate metabolism	42.86	3 of 7
66794	oxidative phosphorylation	41.76	38 of 91
66794	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
66794	arginine metabolism	41.67	10 of 24
66794	hydrogen production	40	2 of 5
66794	coenzyme M biosynthesis	40	4 of 10
66794	3-chlorocatechol degradation	40	2 of 5
66794	lipoate biosynthesis	40	2 of 5
66794	Entner Doudoroff pathway	40	4 of 10
66794	phenylacetate degradation (aerobic)	40	2 of 5
66794	degradation of hexoses	38.89	7 of 18
66794	sulfate reduction	38.46	5 of 13
66794	urea cycle	38.46	5 of 13
66794	isoprenoid biosynthesis	38.46	10 of 26
66794	d-xylose degradation	36.36	4 of 11
66794	proline metabolism	36.36	4 of 11
66794	dolichyl-diphosphooligosaccharide biosynthesis	36.36	4 of 11
66794	degradation of pentoses	35.71	10 of 28
66794	tyrosine metabolism	35.71	5 of 14
66794	histidine metabolism	34.48	10 of 29
66794	non-pathway related	34.21	13 of 38
66794	sulfoquinovose degradation	33.33	1 of 3
66794	octane oxidation	33.33	1 of 3
66794	peptidoglycan biosynthesis	33.33	5 of 15
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	cyanate degradation	33.33	1 of 3
66794	lipid A biosynthesis	33.33	3 of 9
66794	IAA biosynthesis	33.33	1 of 3
66794	leucine metabolism	30.77	4 of 13
66794	4-hydroxyphenylacetate degradation	30	3 of 10
66794	tetrahydrofolate metabolism	28.57	4 of 14
66794	glutathione metabolism	28.57	4 of 14
66794	metabolism of disaccharids	27.27	3 of 11
66794	vitamin B12 metabolism	26.47	9 of 34
66794	lactate fermentation	25	1 of 4
66794	biotin biosynthesis	25	1 of 4
66794	cyclohexanol degradation	25	1 of 4
66794	toluene degradation	25	1 of 4
66794	carnitine metabolism	25	2 of 8
66794	ppGpp biosynthesis	25	1 of 4
66794	phenol degradation	25	5 of 20
66794	degradation of sugar acids	24	6 of 25
66794	ascorbate metabolism	22.73	5 of 22
66794	nitrate assimilation	22.22	2 of 9

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Thermal spring
#Condition	#Acidic	-
#Condition	#Thermophilic (>45°C)	-

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
6178	an acidic hot spring	Mt. Maquiling	Philippines	PHL	Asia
23168	a hot spring on Mt Maquiling	Laguna
67770	Acidic hot spring at Mt. Maquiling		Philippines	PHL	Asia

Taxonmaps

69479

Global distribution of 16S sequence AB087499 (>99% sequence identity) for Caldisphaera lagunensis subclade from Microbeatlas

Aquatic Samples	248
Soil Samples	9
Animal Samples
Plant Samples
Total Samples	257

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
6178	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	ASM31779v1 assembly for Caldisphaera lagunensis DSM 15908	complete	GCA_000317795	1056495.6	2510065009	1056495	95.5

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
6178	Caldisphaera lagunensis gene for 16S rRNA, partial sequence	AB087499	1466		1056495

GC content

@ref	GC-content (mol%)	Method
6178	31
23168	30.7	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: Caldisphaera lagunensis DSM 15908
IMG: 2510065009

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	80.60	no
125439	gram_stain	BacteriaNetⓘ	negative	92.10	no
125439	motility	BacteriaNetⓘ	yes	65.00	no
125439	spore_formation	BacteriaNetⓘ	yes	52.50	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Caldisphaera lagunensis DSM 15908 DSM 15908
NCBI: GCA_000317795.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	76.20	no
125438	anaerobic	anaerobicⓘ	yes	66.70	no
125438	aerobic	aerobicⓘ	no	82.25	yes
125438	spore-forming	spore-formingⓘ	no	92.19	no
125438	thermophilic	thermophileⓘ	yes	77.96	no
125438	flagellated	motile2+ⓘ	no	88.50	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Phenotype-driven assessment of the ancestral trajectory of sulfur biooxidation in the thermoacidophilic archaea Sulfolobaceae.	Willard DJ, H Manesh MJ, Bing RG, Alexander BH, Kelly RM.	mBio	10.1128/mbio.01033-24	2024
Phylogeny	Identification of Microbial Dark Matter in Antarctic Environments.	Bowman JS.	Front Microbiol	10.3389/fmicb.2018.03165	2018
Genetics	Deconstruction of archaeal genome depict strategic consensus in core pathways coding sequence assembly.	Pal A, Banerjee R, Mondal UK, Mukhopadhyay S, Bothra AK.	PLoS One	10.1371/journal.pone.0118245	2015
	Phylogeny and Taxonomy of Archaea: A Comparison of the Whole-Genome-Based CVTree Approach with 16S rRNA Sequence Analysis.	Zuo G, Xu Z, Hao B.	Life (Basel)	10.3390/life5010949	2015
Genetics	METABOLIC: high-throughput profiling of microbial genomes for functional traits, metabolism, biogeochemistry, and community-scale functional networks.	Zhou Z, Tran PQ, Breister AM, Liu Y, Kieft K, Cowley ES, Karaoz U, Anantharaman K.	Microbiome	10.1186/s40168-021-01213-8	2022
Enzymology	Candidatus Nitrosocaldus cavascurensis, an Ammonia Oxidizing, Extremely Thermophilic Archaeon with a Highly Mobile Genome.	Abby SS, Melcher M, Kerou M, Krupovic M, Stieglmeier M, Rossel C, Pfeifer K, Schleper C.	Front Microbiol	10.3389/fmicb.2018.00028	2018
Genetics	Dark matter in archaeal genomes: a rich source of novel mobile elements, defense systems and secretory complexes.	Makarova KS, Wolf YI, Forterre P, Prangishvili D, Krupovic M, Koonin EV.	Extremophiles	10.1007/s00792-014-0672-7	2014
Metabolism	The archaeal Ced system imports DNA.	van Wolferen M, Wagner A, van der Does C, Albers SV.	Proc Natl Acad Sci U S A	10.1073/pnas.1513740113	2016
Metabolism	Carbon source preference in chemosynthetic hot spring communities.	Urschel MR, Kubo MD, Hoehler TM, Peters JW, Boyd ES.	Appl Environ Microbiol	10.1128/aem.00511-15	2015
Genetics	Proteomics and comparative genomics of Nitrososphaera viennensis reveal the core genome and adaptations of archaeal ammonia oxidizers.	Kerou M, Offre P, Valledor L, Abby SS, Melcher M, Nagler M, Weckwerth W, Schleper C.	Proc Natl Acad Sci U S A	10.1073/pnas.1601212113	2016
Phylogeny	Kocuria subflava sp. nov., isolated from marine sediment from the Indian Ocean.	Jiang Z, Zhang WH, Yuan CG, Chen JY, Cao LX, Park DJ, Xiao M, Kim CJ, Li WJ.	Antonie Van Leeuwenhoek	10.1007/s10482-015-0587-z	2015
Phylogeny	Caldisphaera lagunensis gen. nov., sp. nov., a novel thermoacidophilic crenarchaeote isolated from a hot spring at Mt Maquiling, Philippines.	Itoh T, Suzuki K, Sanchez PC, Nakase T	Int J Syst Evol Microbiol	10.1099/ijs.0.02580-0	2003

References

#6178	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 15908
#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 )
#23168	T. Itoh, K. Suzuki, P. C. Sanchez, T. Nakase: Caldisphaera lagunensis gen. nov., sp. nov., a novel thermoacidophilic crenarchaeote isolated from a hot spring at Mt Maquiling, Philippines. IJSEM 53: 1149 - 1154 2003 ( DOI 10.1099/ijs.0.02580-0 , PubMed 12892143 )
#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 )
#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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Caldisphaera lagunensis (DSM 15908, ANMR 0165, JCM 11604)

Name and taxonomic classification

Morphology

Cell morphology

Multimedia

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Nutrition type

Spore formation

Halophily

Metabolite utilization

Antibiotic resistance

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000317795

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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