Name: Carboxydocella sporoproducens Kar
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 17980

Type strain:

Species: Carboxydocella sporoproducens

Strain Designation: Kar

Culture col. no.: DSM 16521, VKM B-2358

Strain history: <- T. V. Slepova, Russian Academy of Sciences, Inst. of Microbiology, Moscow, Russia; Kar <- T. V. Slepova {2004}

NCBI tax ID(s): 1121270 (strain), 285110 (species)

SI-ID 290963

DSM 16521, VKM B-2358

Section

Carboxydocella sporoproducens Kar is an anaerobe, spore-forming, thermophilic bacterium that was isolated from hot spring of Karymskoe Lake.

Gram-positive
motile
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	*Eubacteriales*
	Family	"Carboxydocellaceae"
	Genus	*Carboxydocella*
	Species	**Carboxydocella sporoproducens**
	Full Scientific Name (LPSN)	Carboxydocella sporoproducens Slepova et al. 2006

Information on morphological and physiological properties Morphology

[Ref.: #31646]	Gram stain	positive
[Ref.: #69480]	Gram stain	positive Confidence in %99.999

[Ref.: #31646]	Cell length	01-06 µm

[Ref.: #31646]	Cell width	0.5 µm

[Ref.: #31646]	Cell shape	rod-shaped

[Ref.: #31646]	Motility	yes
[Ref.: #69480]	Motility	yes Confidence in %90.097

[Ref.: #31646]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #6386]

Culture medium

CARBOXYDOTHERMUS MEDIUM (HETEROTROPH) (DSMZ Medium 508)

[Ref.: #6386]

Culture medium growth

[Ref.: #6386]

Culture medium link

Medium recipe at MediaDive

[Ref.: #6386]

Culture medium composition

expand / minimize

[Ref.: #6386]

Culture medium

CARBOXYDOTHERMUS MEDIUM (DSMZ Medium 507)

[Ref.: #6386]

Culture medium growth

[Ref.: #6386]

Culture medium link

Medium recipe at MediaDive

[Ref.: #6386]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #6386]	growth	60 °C
[Ref.: #31646]	growth	50-70 °C
[Ref.: #31646]	optimum	60 °C

[Ref.: #6386]	Temperature range	thermophilic
[Ref.: #31646]	Temperature range	thermophilic
[Ref.: #69480]	Temperature range	thermophilic Confidence in %99.999

	pH	Kind of pH		pH
[Ref.: #31646]			optimum	06-08
[Ref.: #31646]			growth	06-08

Information on physiology and metabolism Physiology and metabolism

[Ref.: #6386]	Oxygen tolerance	anaerobe
[Ref.: #31646]	Oxygen tolerance	anaerobe
[Ref.: #69480]	Oxygen tolerance	anaerobe Confidence in %99.659

[Ref.: #31646]	Ability of spore formation	yes
[Ref.: #69481]	Ability of spore formation	yes Confidence in %100
[Ref.: #69480]	Ability of spore formation	yes Confidence in %99.999

[Ref.: #31646]

Observation

aggregates in chains

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	reductive acetyl coenzyme A pathway	100	7 of 7
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	glycogen metabolism	100	5 of 5
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	palmitate biosynthesis	90.91	20 of 22
[Ref.: #66794]	threonine metabolism	90	9 of 10
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	isoleucine metabolism	87.5	7 of 8
[Ref.: #66794]	tetrahydrofolate metabolism	85.71	12 of 14
[Ref.: #66794]	ubiquinone biosynthesis	85.71	6 of 7
[Ref.: #66794]	glycolate and glyoxylate degradation	83.33	5 of 6
[Ref.: #66794]	vitamin B12 metabolism	82.35	28 of 34
[Ref.: #66794]	propionate fermentation	80	8 of 10
[Ref.: #66794]	starch degradation	80	8 of 10
[Ref.: #66794]	cellulose degradation	80	4 of 5
[Ref.: #66794]	hydrogen production	80	4 of 5
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	methylglyoxal degradation	80	4 of 5
[Ref.: #66794]	photosynthesis	78.57	11 of 14
[Ref.: #66794]	heme metabolism	78.57	11 of 14
[Ref.: #66794]	valine metabolism	77.78	7 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	77.78	7 of 9
[Ref.: #66794]	leucine metabolism	76.92	10 of 13
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	sulfopterin metabolism	75	3 of 4
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	pyrimidine metabolism	73.33	33 of 45
[Ref.: #66794]	glutamate and glutamine metabolism	71.43	20 of 28
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	glycolysis	70.59	12 of 17
[Ref.: #66794]	phenylalanine metabolism	69.23	9 of 13
[Ref.: #66794]	alanine metabolism	68.97	20 of 29
[Ref.: #66794]	molybdenum cofactor biosynthesis	66.67	6 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	66.67	6 of 9
[Ref.: #66794]	enterobactin biosynthesis	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	serine metabolism	66.67	6 of 9
[Ref.: #66794]	selenocysteine biosynthesis	66.67	4 of 6
[Ref.: #66794]	d-mannose degradation	66.67	6 of 9
[Ref.: #66794]	formaldehyde oxidation	66.67	2 of 3
[Ref.: #66794]	flavin biosynthesis	66.67	10 of 15
[Ref.: #66794]	NAD metabolism	66.67	12 of 18
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	methionine metabolism	65.38	17 of 26
[Ref.: #66794]	proline metabolism	63.64	7 of 11
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	C4 and CAM-carbon fixation	62.5	5 of 8
[Ref.: #66794]	purine metabolism	61.7	58 of 94
[Ref.: #66794]	isoprenoid biosynthesis	61.54	16 of 26
[Ref.: #66794]	oxidative phosphorylation	60.44	55 of 91
[Ref.: #66794]	factor 420 biosynthesis	60	3 of 5
[Ref.: #66794]	lipoate biosynthesis	60	3 of 5
[Ref.: #66794]	glycine betaine biosynthesis	60	3 of 5
[Ref.: #66794]	histidine metabolism	58.62	17 of 29
[Ref.: #66794]	lipid metabolism	58.06	18 of 31
[Ref.: #66794]	citric acid cycle	57.14	8 of 14
[Ref.: #66794]	nitrate assimilation	55.56	5 of 9
[Ref.: #66794]	vitamin B1 metabolism	53.85	7 of 13
[Ref.: #66794]	urea cycle	53.85	7 of 13
[Ref.: #66794]	non-pathway related	52.63	20 of 38
[Ref.: #66794]	gluconeogenesis	50	4 of 8
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	1,4-dihydroxy-6-naphthoate biosynthesis	50	3 of 6
[Ref.: #66794]	ketogluconate metabolism	50	4 of 8
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	glutathione metabolism	50	7 of 14
[Ref.: #66794]	arginine metabolism	50	12 of 24
[Ref.: #66794]	suberin monomers biosynthesis	50	1 of 2
[Ref.: #66794]	lactate fermentation	50	2 of 4
[Ref.: #66794]	mannosylglycerate biosynthesis	50	1 of 2
[Ref.: #66794]	toluene degradation	50	2 of 4
[Ref.: #66794]	cysteine metabolism	50	9 of 18
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	sulfate reduction	46.15	6 of 13
[Ref.: #66794]	metabolism of disaccharids	45.45	5 of 11
[Ref.: #66794]	benzoyl-CoA degradation	42.86	3 of 7
[Ref.: #66794]	propanol degradation	42.86	3 of 7
[Ref.: #66794]	tyrosine metabolism	42.86	6 of 14
[Ref.: #66794]	tryptophan metabolism	42.11	16 of 38
[Ref.: #66794]	phenylacetate degradation (aerobic)	40	2 of 5
[Ref.: #66794]	Entner Doudoroff pathway	40	4 of 10
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	O-antigen biosynthesis	40	2 of 5
[Ref.: #66794]	metabolism of amino sugars and derivatives	40	2 of 5
[Ref.: #66794]	3-chlorocatechol degradation	40	2 of 5
[Ref.: #66794]	polyamine pathway	39.13	9 of 23
[Ref.: #66794]	degradation of hexoses	38.89	7 of 18
[Ref.: #66794]	dTDPLrhamnose biosynthesis	37.5	3 of 8
[Ref.: #66794]	pentose phosphate pathway	36.36	4 of 11
[Ref.: #66794]	lysine metabolism	35.71	15 of 42
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	lipid A biosynthesis	33.33	3 of 9
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	cyanate degradation	33.33	1 of 3
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	33.33	4 of 12
[Ref.: #66794]	pantothenate biosynthesis	33.33	2 of 6
[Ref.: #66794]	coenzyme M biosynthesis	30	3 of 10
[Ref.: #66794]	4-hydroxyphenylacetate degradation	30	3 of 10
[Ref.: #66794]	degradation of pentoses	28.57	8 of 28
[Ref.: #66794]	d-xylose degradation	27.27	3 of 11
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	3-phenylpropionate degradation	26.67	4 of 15
[Ref.: #66794]	CMP-KDO biosynthesis	25	1 of 4
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	methanogenesis from CO2	25	3 of 12
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	23.08	3 of 13
		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.: #6386]	Sample type/isolated from	hot spring of Karymskoe Lake
[Ref.: #6386]	Geographic location (country and/or sea, region)	Kamchatka Peninsula
[Ref.: #6386]	Country	Russia
[Ref.: #6386]	Country ISO 3 Code	RUS
[Ref.: #6386]	Continent	Asia
* marker position based on {}

Isolation sources categories

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

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AY673988 (>99% sequence identity) for Carboxydocella from Microbeatlas

Aquatic Samples
Soil Samples
Animal Samples	1
Plant Samples
Total Samples	1

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

[Ref.: #6386]

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.: #6386]	Carboxydocella sporoproducens strain Kar 16S ribosomal RNA gene, partial sequence	AY673988	1418	ENA	285110 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Carboxydocella sporoproducens DSM 16521	GCA_900167165	contig	GenBank	1121270 tax ID	*
[Ref.: #66792]	Carboxydocella sporoproducens DSM 16521 strain DSM 16521	1121270.4	wgs	PATRIC	1121270 tax ID	*
[Ref.: #66792]	Carboxydocella sporoproducens DSM 16521	2568526009	draft	JGI IMG/M	1121270 tax ID	*

[Ref.: #6386]

GC-content

49.5 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: Carboxydocella sporoproducens DSM 16521 strain DSM 16521 PATRIC: 1121270.4
[Ref.: #69481]	spore-forming	yes	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Carboxydocella sporoproducens DSM 16521 strain DSM 16521 PATRIC: 1121270.4
[Ref.: #69480]	motile	yes	88.637	yes
[Ref.: #69480]	flagellated	no	83.231	no
[Ref.: #69480]	gram-positive	no	85.936	no
[Ref.: #69480]	anaerobic	yes	99.125	no
[Ref.: #69480]	aerobic	no	96.744	yes
[Ref.: #69480]	halophile	no	94.323	no
[Ref.: #69480]	spore-forming	yes	90.507	no
[Ref.: #69480]	thermophile	yes	99.614	yes
[Ref.: #69480]	glucose-util	yes	75.805	no
[Ref.: #69480]	glucose-ferment	no	79.521	no

Availability in culture collections External links

[Ref.: #6386]

Culture collection no.

DSM 16521, VKM B-2358

[Ref.: #86967]

SI-ID 290963

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Carboxydocella sporoproducens sp. nov., a novel anaerobic CO-utilizing/H2-producing thermophilic bacterium from a Kamchatka hot spring.	Slepova TV, Sokolova TG, Lysenko AM, Tourova TP, Kolganova TV, Kamzolkina OV, Karpov GA, Bonch-Osmolovskaya EA	Int J Syst Evol Microbiol	10.1099/ijs.0.63961-0	2006	*

References

#6386

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 16521

#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 )

#31646

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 #27929 (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 )

#86967

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-ID290963.1 )

#27929

IJSEM 797 2006 ( DOI 10.1099/ijs.0.63961-0 , PubMed 16585697 )

* These data were automatically processed and therefore are not curated

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Carboxydocella sporoproducens DSM 16521 strain DSM 16521

Carboxydocella sporoproducens DSM 16521 strain DSM 16521

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