Name: Calderihabitans maritimus KKC1
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 24651

Type strain:

Species: Calderihabitans maritimus

Strain Designation: KKC1

Culture col. no.: DSM 26464, NBRC 109353

Strain history: <- Y. Yoneda, Kyoto Univ., Lab. of Marine Microbiol., Japan; KKC1 <- Y. Yoneda {2012}

NCBI tax ID(s): 1246530 (species)

SI-ID 404300

DSM 26464

Section

Calderihabitans maritimus KKC1 is an anaerobe, spore-forming, thermophilic bacterium that was isolated from marine sediment core of an undersea caldera.

Gram-negative
rod-shaped
spore-forming
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	*Bacillota*
	Class	*Clostridia*
	Order	*Thermoanaerobacterales*
	Family	*Thermoanaerobacteraceae*
	Genus	*Calderihabitans*
	Species	**Calderihabitans maritimus**
	Full Scientific Name (LPSN)	Calderihabitans maritimus Yoneda et al. 2013

Information on morphological and physiological properties Morphology

[Ref.: #31040]	Gram stain	negative
[Ref.: #69480]	Gram stain	positive Confidence in %99.139

[Ref.: #31040]	Cell length	2 µm

[Ref.: #31040]	Cell shape	rod-shaped

[Ref.: #31040]	Motility	no
[Ref.: #69480]	Motility	yes Confidence in %94.724

Information on culture and growth conditions Culture and growth conditions

[Ref.: #21276]

Culture medium

CALDERIHABITANS MEDIUM (DSMZ Medium 1508)

[Ref.: #21276]

Culture medium growth

[Ref.: #21276]

Culture medium link

Medium recipe at MediaDive

[Ref.: #21276]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #21276]	growth	65 °C
[Ref.: #31040]	growth	55-68 °C
[Ref.: #31040]	optimum	65 °C

[Ref.: #21276]	Temperature range	thermophilic
[Ref.: #31040]	Temperature range	thermophilic
[Ref.: #69480]	Temperature range	thermophilic Confidence in %100

	pH	Kind of pH		pH
[Ref.: #31040]			optimum	7.25
[Ref.: #31040]			growth	5.2-9.2

Information on physiology and metabolism Physiology and metabolism

[Ref.: #21276]	Oxygen tolerance	anaerobe
[Ref.: #31040]	Oxygen tolerance	anaerobe
[Ref.: #69480]	Oxygen tolerance	anaerobe Confidence in %98.845

[Ref.: #31040]	Ability of spore formation	yes
[Ref.: #69481]	Ability of spore formation	yes Confidence in %96
[Ref.: #69480]	Ability of spore formation	yes Confidence in %100

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #31040]		NaCl		growth	0.8-14	%
[Ref.: #31040]		NaCl		optimum	2.46	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #31040]	fructose ChEBI	+	carbon source
[Ref.: #31040]	glucose ChEBI	+	carbon source
[Ref.: #31040]	lactate ChEBI	+	carbon source
[Ref.: #31040]	mannose ChEBI	+	carbon source
[Ref.: #31040]	pyruvate ChEBI	+	carbon source

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	reductive acetyl coenzyme A pathway	100	7 of 7
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	isoleucine metabolism	100	8 of 8
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	hydrogen production	100	5 of 5
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	aspartate and asparagine metabolism	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]	tetrahydrofolate metabolism	85.71	12 of 14
[Ref.: #66794]	ubiquinone biosynthesis	85.71	6 of 7
[Ref.: #66794]	selenocysteine biosynthesis	83.33	5 of 6
[Ref.: #66794]	glycolate and glyoxylate degradation	83.33	5 of 6
[Ref.: #66794]	alanine metabolism	82.76	24 of 29
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	methylglyoxal degradation	80	4 of 5
[Ref.: #66794]	propionate fermentation	80	8 of 10
[Ref.: #66794]	cellulose degradation	80	4 of 5
[Ref.: #66794]	glycogen metabolism	80	4 of 5
[Ref.: #66794]	phenylacetate degradation (aerobic)	80	4 of 5
[Ref.: #66794]	photosynthesis	78.57	11 of 14
[Ref.: #66794]	heme metabolism	78.57	11 of 14
[Ref.: #66794]	glutamate and glutamine metabolism	78.57	22 of 28
[Ref.: #66794]	valine metabolism	77.78	7 of 9
[Ref.: #66794]	NAD metabolism	77.78	14 of 18
[Ref.: #66794]	serine metabolism	77.78	7 of 9
[Ref.: #66794]	leucine metabolism	76.92	10 of 13
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	C4 and CAM-carbon fixation	75	6 of 8
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	citric acid cycle	71.43	10 of 14
[Ref.: #66794]	glycolysis	70.59	12 of 17
[Ref.: #66794]	coenzyme M biosynthesis	70	7 of 10
[Ref.: #66794]	threonine metabolism	70	7 of 10
[Ref.: #66794]	phenylalanine metabolism	69.23	9 of 13
[Ref.: #66794]	urea cycle	69.23	9 of 13
[Ref.: #66794]	vitamin B1 metabolism	69.23	9 of 13
[Ref.: #66794]	pyrimidine metabolism	68.89	31 of 45
[Ref.: #66794]	purine metabolism	68.09	64 of 94
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	formaldehyde oxidation	66.67	2 of 3
[Ref.: #66794]	CO2 fixation in Crenarchaeota	66.67	6 of 9
[Ref.: #66794]	d-mannose degradation	66.67	6 of 9
[Ref.: #66794]	methane metabolism	66.67	2 of 3
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	molybdenum cofactor biosynthesis	66.67	6 of 9
[Ref.: #66794]	nitrate assimilation	66.67	6 of 9
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	flavin biosynthesis	66.67	10 of 15
[Ref.: #66794]	methionine metabolism	65.38	17 of 26
[Ref.: #66794]	oxidative phosphorylation	62.64	57 of 91
[Ref.: #66794]	dTDPLrhamnose biosynthesis	62.5	5 of 8
[Ref.: #66794]	degradation of sugar alcohols	62.5	10 of 16
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	gluconeogenesis	62.5	5 of 8
[Ref.: #66794]	isoprenoid biosynthesis	61.54	16 of 26
[Ref.: #66794]	lipid metabolism	61.29	19 of 31
[Ref.: #66794]	phenol degradation	60	12 of 20
[Ref.: #66794]	myo-inositol biosynthesis	60	6 of 10
[Ref.: #66794]	propanol degradation	57.14	4 of 7
[Ref.: #66794]	histidine metabolism	55.17	16 of 29
[Ref.: #66794]	arginine metabolism	54.17	13 of 24
[Ref.: #66794]	non-pathway related	52.63	20 of 38
[Ref.: #66794]	tryptophan metabolism	52.63	20 of 38
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	Entner Doudoroff pathway	50	5 of 10
[Ref.: #66794]	sulfopterin metabolism	50	2 of 4
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	1,4-dihydroxy-6-naphthoate biosynthesis	50	3 of 6
[Ref.: #66794]	denitrification	50	1 of 2
[Ref.: #66794]	lactate fermentation	50	2 of 4
[Ref.: #66794]	starch degradation	50	5 of 10
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	50	6 of 12
[Ref.: #66794]	lysine metabolism	50	21 of 42
[Ref.: #66794]	cysteine metabolism	50	9 of 18
[Ref.: #66794]	ketogluconate metabolism	50	4 of 8
[Ref.: #66794]	polyamine pathway	47.83	11 of 23
[Ref.: #66794]	sulfate reduction	46.15	6 of 13
[Ref.: #66794]	metabolism of disaccharids	45.45	5 of 11
[Ref.: #66794]	proline metabolism	45.45	5 of 11
[Ref.: #66794]	degradation of hexoses	44.44	8 of 18
[Ref.: #66794]	benzoyl-CoA degradation	42.86	3 of 7
[Ref.: #66794]	tyrosine metabolism	42.86	6 of 14
[Ref.: #66794]	glycine metabolism	40	4 of 10
[Ref.: #66794]	3-chlorocatechol degradation	40	2 of 5
[Ref.: #66794]	metabolism of amino sugars and derivatives	40	2 of 5
[Ref.: #66794]	glycine betaine biosynthesis	40	2 of 5
[Ref.: #66794]	3-phenylpropionate degradation	40	6 of 15
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	pentose phosphate pathway	36.36	4 of 11
[Ref.: #66794]	vitamin B6 metabolism	36.36	4 of 11
[Ref.: #66794]	degradation of sugar acids	36	9 of 25
[Ref.: #66794]	cyanate degradation	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	allantoin degradation	33.33	3 of 9
[Ref.: #66794]	lipid A biosynthesis	33.33	3 of 9
[Ref.: #66794]	methanogenesis from CO2	33.33	4 of 12
[Ref.: #66794]	ascorbate metabolism	31.82	7 of 22
[Ref.: #66794]	4-hydroxyphenylacetate degradation	30	3 of 10
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	29.41	5 of 17
[Ref.: #66794]	degradation of pentoses	28.57	8 of 28
[Ref.: #66794]	glutathione metabolism	28.57	4 of 14
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	androgen and estrogen metabolism	25	4 of 16
[Ref.: #66794]	CMP-KDO biosynthesis	25	1 of 4
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	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.: #21276]	Sample type/isolated from	marine sediment core of an undersea caldera
[Ref.: #21276]	Geographic location (country and/or sea, region)	Kagoshima Prefecture, southern coast of Kyushu Island, Kikai caldera
[Ref.: #21276]	Country	Japan
[Ref.: #21276]	Country ISO 3 Code	JPN
[Ref.: #21276]	Continent	Asia
* marker position based on {}

Isolation sources categories

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

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AB758274 (>99% sequence identity) for Calderihabitans maritimus subclade from Microbeatlas

Aquatic Samples	73
Soil Samples	9
Animal Samples	9
Plant Samples	31
Total Samples	122

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

[Ref.: #21276]

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.: #21276]	Calderihabitans maritimus gene for 16S ribosomal RNA, partial sequence	AB758274	1503	ENA	1246530 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Calderihabitans maritimus KKC1	GCA_002207765	scaffold	GenBank	1246530 tax ID	*
[Ref.: #66792]	Calderihabitans maritimus KKC1	2788499958	draft	JGI IMG/M	1246530 tax ID	*

[Ref.: #21276]	GC-content	50.6 mol%	high performance liquid chromatography (HPLC)
[Ref.: #31040]	GC-content	50.6 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: Calderihabitans maritimus KKC1 NCBI: GCA_002207765.1
[Ref.: #69481]	spore-forming	yes	96	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Calderihabitans maritimus KKC1 NCBI: GCA_002207765.1
[Ref.: #69480]	flagellated	no	91.814	yes
[Ref.: #69480]	gram-positive	no	91.807	yes
[Ref.: #69480]	anaerobic	yes	98.413	no
[Ref.: #69480]	aerobic	no	95.394	yes
[Ref.: #69480]	halophile	no	93.8	no
[Ref.: #69480]	spore-forming	yes	92.728	yes
[Ref.: #69480]	thermophile	yes	100	no
[Ref.: #69480]	glucose-util	yes	80.128	no
[Ref.: #69480]	motile	yes	64.619	yes
[Ref.: #69480]	glucose-ferment	no	85.037	no

Availability in culture collections External links

[Ref.: #21276]

Culture collection no.

DSM 26464, NBRC 109353

[Ref.: #88491]

SI-ID 404300

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	A thermophilic, hydrogenogenic and carboxydotrophic bacterium, Calderihabitans maritimus gen. nov., sp. nov., from a marine sediment core of an undersea caldera.	Yoneda Y, Yoshida T, Yasuda H, Imada C, Sako Y	Int J Syst Evol Microbiol	10.1099/ijs.0.050468-0	2013	*

References

#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 )

#21276

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 26464

#31040

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 #27370 (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 )

#88491

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-ID404300.1 )

#27370

IJSEM 3602 2013 ( DOI 10.1099/ijs.0.050468-0 , PubMed 23606483 )

* These data were automatically processed and therefore are not curated

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