Name: Caldithrix abyssi LF13
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 18090

Type strain:

Species: Caldithrix abyssi

Strain Designation: LF13

Culture col. no.: DSM 13497, VKM B-2286

Strain history: <- M. L. Miroshnichenko, Russian Academy of Sciences, Inst. of Microbiology, Moscow, Russia; LF13 <- M. L. Miroshnichenko

NCBI tax ID(s): 880073 (strain), 187145 (species)

SI-ID 100576

DSM 13497, VKM B-2286

Special Collections

DSMZ

Section

Caldithrix abyssi LF13 is an anaerobe, Gram-negative bacterium that was isolated from deep-sea hot vent.

Gram-negative
anaerobe
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	*Calditrichota*
	Class	*Calditrichia*
	Order	*Calditrichales*
	Family	*Calditrichaceae*
	Genus	*Caldithrix*
	Species	**Caldithrix abyssi**
	Full Scientific Name (LPSN)	Caldithrix abyssi Miroshnichenko et al. 2003

Information on morphological and physiological properties Morphology

[Ref.: #69480]	Gram stain	negative Confidence in %93.689

Multimedia content

[Ref.: #66793]

Caption:

electron microscopic image

[Ref.: #66793]

Intellectual property rights:

Information on culture and growth conditions Culture and growth conditions

[Ref.: #5067]

Culture medium

CALDITHRIX MEDIUM (DSMZ Medium 946a)

[Ref.: #5067]

Culture medium growth

[Ref.: #5067]

Culture medium link

Medium recipe at MediaDive

[Ref.: #5067]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #5067]			growth	60 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #5067]

Oxygen tolerance

anaerobe

[Ref.: #69481]

Ability of spore formation

no Confidence in %100

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	cellulose degradation	100	5 of 5
[Ref.: #66794]	CMP-KDO biosynthesis	100	4 of 4
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	teichoic acid biosynthesis	100	1 of 1
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	hydrogen production	100	5 of 5
[Ref.: #66794]	glycogen metabolism	100	5 of 5
[Ref.: #66794]	glycolate and glyoxylate degradation	100	6 of 6
[Ref.: #66794]	kanosamine biosynthesis II	100	2 of 2
[Ref.: #66794]	C4 and CAM-carbon fixation	100	8 of 8
[Ref.: #66794]	valine metabolism	100	9 of 9
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	lipoate biosynthesis	100	5 of 5
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	dolichol and dolichyl phosphate biosynthesis	100	2 of 2
[Ref.: #66794]	starch degradation	100	10 of 10
[Ref.: #66794]	adipate degradation	100	2 of 2
[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]	serine metabolism	88.89	8 of 9
[Ref.: #66794]	lipid A biosynthesis	88.89	8 of 9
[Ref.: #66794]	NAD metabolism	88.89	16 of 18
[Ref.: #66794]	aspartate and asparagine metabolism	88.89	8 of 9
[Ref.: #66794]	gluconeogenesis	87.5	7 of 8
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	87.5	7 of 8
[Ref.: #66794]	isoleucine metabolism	87.5	7 of 8
[Ref.: #66794]	reductive acetyl coenzyme A pathway	85.71	6 of 7
[Ref.: #66794]	ubiquinone biosynthesis	85.71	6 of 7
[Ref.: #66794]	tetrahydrofolate metabolism	85.71	12 of 14
[Ref.: #66794]	phenylalanine metabolism	84.62	11 of 13
[Ref.: #66794]	methionine metabolism	84.62	22 of 26
[Ref.: #66794]	pyrimidine metabolism	84.44	38 of 45
[Ref.: #66794]	1,4-dihydroxy-6-naphthoate biosynthesis	83.33	5 of 6
[Ref.: #66794]	alanine metabolism	82.76	24 of 29
[Ref.: #66794]	propionate fermentation	80	8 of 10
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	photosynthesis	78.57	11 of 14
[Ref.: #66794]	glutamate and glutamine metabolism	78.57	22 of 28
[Ref.: #66794]	molybdenum cofactor biosynthesis	77.78	7 of 9
[Ref.: #66794]	d-mannose degradation	77.78	7 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	77.78	7 of 9
[Ref.: #66794]	purine metabolism	76.6	72 of 94
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	lipid metabolism	74.19	23 of 31
[Ref.: #66794]	flavin biosynthesis	73.33	11 of 15
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	lysine metabolism	71.43	30 of 42
[Ref.: #66794]	citric acid cycle	71.43	10 of 14
[Ref.: #66794]	leucine metabolism	69.23	9 of 13
[Ref.: #66794]	histidine metabolism	68.97	20 of 29
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	formaldehyde oxidation	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]	selenocysteine biosynthesis	66.67	4 of 6
[Ref.: #66794]	polyamine pathway	65.22	15 of 23
[Ref.: #66794]	glycolysis	64.71	11 of 17
[Ref.: #66794]	heme metabolism	64.29	9 of 14
[Ref.: #66794]	d-xylose degradation	63.64	7 of 11
[Ref.: #66794]	tryptophan metabolism	63.16	24 of 38
[Ref.: #66794]	glycine betaine biosynthesis	60	3 of 5
[Ref.: #66794]	metabolism of amino sugars and derivatives	60	3 of 5
[Ref.: #66794]	Entner Doudoroff pathway	60	6 of 10
[Ref.: #66794]	myo-inositol biosynthesis	60	6 of 10
[Ref.: #66794]	non-pathway related	57.89	22 of 38
[Ref.: #66794]	nitrate assimilation	55.56	5 of 9
[Ref.: #66794]	cysteine metabolism	55.56	10 of 18
[Ref.: #66794]	proline metabolism	54.55	6 of 11
[Ref.: #66794]	pentose phosphate pathway	54.55	6 of 11
[Ref.: #66794]	urea cycle	53.85	7 of 13
[Ref.: #66794]	oxidative phosphorylation	51.65	47 of 91
[Ref.: #66794]	coenzyme M biosynthesis	50	5 of 10
[Ref.: #66794]	glutathione metabolism	50	7 of 14
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	dTDPLrhamnose biosynthesis	50	4 of 8
[Ref.: #66794]	lactate fermentation	50	2 of 4
[Ref.: #66794]	biotin biosynthesis	50	2 of 4
[Ref.: #66794]	tyrosine metabolism	50	7 of 14
[Ref.: #66794]	denitrification	50	1 of 2
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	50	6 of 12
[Ref.: #66794]	isoprenoid biosynthesis	50	13 of 26
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	mannosylglycerate biosynthesis	50	1 of 2
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	arginine metabolism	45.83	11 of 24
[Ref.: #66794]	metabolism of disaccharids	45.45	5 of 11
[Ref.: #66794]	mevalonate metabolism	42.86	3 of 7
[Ref.: #66794]	propanol degradation	42.86	3 of 7
[Ref.: #66794]	ethylmalonyl-CoA pathway	40	2 of 5
[Ref.: #66794]	glycine metabolism	40	4 of 10
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	creatinine degradation	40	2 of 5
[Ref.: #66794]	factor 420 biosynthesis	40	2 of 5
[Ref.: #66794]	degradation of hexoses	38.89	7 of 18
[Ref.: #66794]	arachidonic acid metabolism	38.89	7 of 18
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	38.46	5 of 13
[Ref.: #66794]	vitamin B1 metabolism	38.46	5 of 13
[Ref.: #66794]	androgen and estrogen metabolism	37.5	6 of 16
[Ref.: #66794]	degradation of sugar alcohols	37.5	6 of 16
[Ref.: #66794]	ketogluconate metabolism	37.5	3 of 8
[Ref.: #66794]	vitamin B6 metabolism	36.36	4 of 11
[Ref.: #66794]	cholesterol biosynthesis	36.36	4 of 11
[Ref.: #66794]	degradation of pentoses	35.71	10 of 28
[Ref.: #66794]	methanogenesis from CO2	33.33	4 of 12
[Ref.: #66794]	pantothenate biosynthesis	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]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	sulfate reduction	30.77	4 of 13
[Ref.: #66794]	phenol degradation	30	6 of 20
[Ref.: #66794]	benzoyl-CoA degradation	28.57	2 of 7
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	ascorbate metabolism	27.27	6 of 22
[Ref.: #66794]	3-phenylpropionate degradation	26.67	4 of 15
[Ref.: #66794]	catecholamine biosynthesis	25	1 of 4
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	chlorophyll metabolism	22.22	4 of 18
		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.: #5067]	Sample type/isolated from	deep-sea hot vent
[Ref.: #5067]	Geographic location (country and/or sea, region)	Mid-Atlantic Ridge, Logatchev hydrothermal field
[Ref.: #5067]	Geographic location	14.7500°/-44.9833°
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Hydrothermal vent
#Environmental	#Aquatic	#Marine
#Condition	#Thermophilic (>45°C)	-

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AJ430587 (>99% sequence identity) for Caldithrix abyssi subclade from Microbeatlas

Aquatic Samples	665
Soil Samples	55
Animal Samples	10
Plant Samples	4
Total Samples	734

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

[Ref.: #5067]

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.: #5067]	Caldothrix abyssi 16S rRNA gene, strain LF13T	AJ430587	1504	GenBank ENA	880073 tax ID

Genome sequence information:

Only first 5 entries are displayed. Click here to see all.

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Caldithrix abyssi DSM 13497 strain TH-08apr19-15	880073.23	wgs	PATRIC	880073 tax ID	*
[Ref.: #66792]	Caldithrix abyssi DSM 13497	GCA_000241815	chromosome	GenBank ENA	880073 tax ID	*
[Ref.: #66792]	Caldithrix abyssi DSM 13497	880073.11	complete	PATRIC	880073 tax ID	*
[Ref.: #66792]	Caldithrix abyssi DSM 13497	880073.4	wgs	PATRIC	880073 tax ID	*
[Ref.: #66792]	Caldithrix abyssi LF13, DSM 13497	2561511127	draft	JGI IMG/M	880073 tax ID	*
[Ref.: #66792]	Caldithrix abyssi LF13, DSM 13497	2718218154	complete	JGI IMG/M	880073 tax ID	*

[Ref.: #5067]

GC-content

42.5 mol%

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

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Caldithrix abyssi DSM 13497 LF13 NCBI: GCA_001886815.1
[Ref.: #69481]	spore-forming	spore-formingⓘ	no	100	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Caldithrix abyssi DSM 13497 LF13 NCBI: GCA_001886815.1
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	93.689	no
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	59.048	no
[Ref.: #69480]	aerobic	aerobicⓘ	no	59.904	no
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	78.984	no
[Ref.: #69480]	thermophilic	thermophileⓘ	yes	53.96	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	yes	58.031	no

Availability in culture collections External links

[Ref.: #5067]

Culture collection no.

DSM 13497, VKM B-2286

[Ref.: #87078]

SI-ID 100576

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Caldithrix abyssi gen. nov., sp. nov., a nitrate-reducing, thermophilic, anaerobic bacterium isolated from a Mid-Atlantic Ridge hydrothermal vent, represents a novel bacterial lineage.	Miroshnichenko ML, Kostrikina NA, Chernyh NA, Pimenov NV, Tourova TP, Antipov AN, Spring S, Stackebrandt E, Bonch-Osmolovskaya EA	Int J Syst Evol Microbiol	10.1099/ijs.0.02390-0	2003	*

References

#5067

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 13497

#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) .

#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 )

#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 )

#87078

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-ID100576.1 )

* These data were automatically processed and therefore are not curated

Change proposal

You found an error in BacDive? Please tell us about it!

Note that changes will be reviewed and judged. If your changes are legitimate, changes will occur within the next BacDive update. Only proposed changes supported by the according reference will be reviewed. The BacDive team reserves the right to reject proposed changes.

Search for species Caldithrix abyssi in external resources:
SILVA
BRENDA
PANGAEA
GBIF

Caldithrix abyssi DSM 13497 LF13

Caldithrix abyssi DSM 13497 LF13

Change proposal

Change proposal