Kyrpidia tusciae (DSM 2912, IFO 15312, NBRC 15312)

Multimedia

• @ref:	66793
  multimedia content:	EM_DSM_2912_1.jpg
  multimedia.multimedia content:	EM_DSM_2912_1.jpg
  caption:	electron microscopic image
  intellectual property rights:	© HZI/Manfred Rohde
  manual_annotation:	1

Culture medium

@ref	Name	Growth	Medium link	Composition
1245	BACILLUS TUSCIAE MEDIUM (DSMZ Medium 369)		Medium recipe at MediaDive	Name: BACILLUS TUSCIAE MEDIUM (DSMZ Medium 369) Composition: Agar 15.0 g/l Na2HPO4 x 2 H2O 4.5 g/l KH2PO4 1.5 g/l NH4Cl 1.0 g/l MgSO4 x 7 H2O 0.2 g/l MnSO4 x H2O 0.01 g/l CaCl2 x 2 H2O 0.01 g/l Ferric ammonium citrate 0.005 g/l H3BO3 0.0009 g/l CoCl2 x 6 H2O 0.0006 g/l ZnSO4 x 7 H2O 0.0003 g/l MnCl2 x 4 H2O 9e-05 g/l Na2MoO4 x 2 H2O 9e-05 g/l NiCl2 x 6 H2O 6e-05 g/l CuCl2 x 2 H2O 3e-05 g/l Distilled water

Culture temp

Oxygen tolerance

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions	external links
66794	gluconeogenesis	100	8 of 8
66794	ppGpp biosynthesis	100	4 of 4
66794	C4 and CAM-carbon fixation	100	8 of 8
66794	cyanate degradation	100	3 of 3
66794	methylglyoxal degradation	100	5 of 5
66794	L-lactaldehyde degradation	100	3 of 3
66794	formaldehyde oxidation	100	3 of 3
66794	valine metabolism	100	9 of 9
66794	glycine betaine biosynthesis	100	5 of 5
66794	biotin biosynthesis	100	4 of 4
66794	palmitate biosynthesis	100	22 of 22
66794	coenzyme A metabolism	100	4 of 4
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	sulfopterin metabolism	100	4 of 4
66794	lipoate biosynthesis	100	5 of 5
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	folate polyglutamylation	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	methane metabolism	100	3 of 3
66794	adipate degradation	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	cardiolipin biosynthesis	100	7 of 7
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	phenylacetate degradation (aerobic)	100	5 of 5
66794	tetrahydrofolate metabolism	92.86	13 of 14
66794	photosynthesis	92.86	13 of 14
66794	threonine metabolism	90	9 of 10
66794	4-hydroxyphenylacetate degradation	90	9 of 10
66794	glutamate and glutamine metabolism	89.29	25 of 28
66794	aspartate and asparagine metabolism	88.89	8 of 9
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	serine metabolism	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	isoleucine metabolism	87.5	7 of 8
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	leucine metabolism	84.62	11 of 13
66794	glycolate and glyoxylate degradation	83.33	5 of 6
66794	vitamin B12 metabolism	82.35	28 of 34
66794	propionate fermentation	80	8 of 10
66794	gallate degradation	80	4 of 5
66794	cellulose degradation	80	4 of 5
66794	phenol degradation	80	16 of 20
66794	flavin biosynthesis	80	12 of 15
66794	peptidoglycan biosynthesis	80	12 of 15
66794	allantoin degradation	77.78	7 of 9
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	phenylalanine metabolism	76.92	10 of 13
66794	vitamin B1 metabolism	76.92	10 of 13
66794	glycogen biosynthesis	75	3 of 4
66794	acetate fermentation	75	3 of 4
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	3-phenylpropionate degradation	73.33	11 of 15
66794	proline metabolism	72.73	8 of 11
66794	pentose phosphate pathway	72.73	8 of 11
66794	NAD metabolism	72.22	13 of 18
66794	glutathione metabolism	71.43	10 of 14
66794	citric acid cycle	71.43	10 of 14
66794	purine metabolism	71.28	67 of 94
66794	pyrimidine metabolism	68.89	31 of 45
66794	androgen and estrogen metabolism	68.75	11 of 16
66794	tryptophan metabolism	68.42	26 of 38
66794	arginine metabolism	66.67	16 of 24
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	d-mannose degradation	66.67	6 of 9
66794	acetoin degradation	66.67	2 of 3
66794	octane oxidation	66.67	2 of 3
66794	alanine metabolism	65.52	19 of 29
66794	methionine metabolism	65.38	17 of 26
66794	heme metabolism	64.29	9 of 14
66794	urea cycle	61.54	8 of 13
66794	sulfate reduction	61.54	8 of 13
66794	oxidative phosphorylation	61.54	56 of 91
66794	arachidonate biosynthesis	60	3 of 5
66794	coenzyme M biosynthesis	60	6 of 10
66794	bacilysin biosynthesis	60	3 of 5
66794	factor 420 biosynthesis	60	3 of 5
66794	glycolysis	58.82	10 of 17
66794	histidine metabolism	58.62	17 of 29
66794	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
66794	isoprenoid biosynthesis	57.69	15 of 26
66794	propanol degradation	57.14	4 of 7
66794	degradation of sugar alcohols	56.25	9 of 16
66794	nitrate assimilation	55.56	5 of 9
66794	cysteine metabolism	55.56	10 of 18
66794	non-pathway related	55.26	21 of 38
66794	lysine metabolism	54.76	23 of 42
66794	pantothenate biosynthesis	50	3 of 6
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	ribulose monophosphate pathway	50	1 of 2
66794	Entner Doudoroff pathway	50	5 of 10
66794	myo-inositol biosynthesis	50	5 of 10
66794	kanosamine biosynthesis II	50	1 of 2
66794	1,4-dihydroxy-6-naphthoate biosynthesis	50	3 of 6
66794	CMP-KDO biosynthesis	50	2 of 4
66794	butanoate fermentation	50	2 of 4
66794	glycine metabolism	50	5 of 10
66794	dolichol and dolichyl phosphate biosynthesis	50	1 of 2
66794	tyrosine metabolism	50	7 of 14
66794	phenylmercury acetate degradation	50	1 of 2
66794	toluene degradation	50	2 of 4
66794	ethanol fermentation	50	1 of 2
66794	ketogluconate metabolism	50	4 of 8
66794	dTDPLrhamnose biosynthesis	50	4 of 8
66794	carnitine metabolism	50	4 of 8
66794	lipid metabolism	48.39	15 of 31
66794	metabolism of disaccharids	45.45	5 of 11
66794	vitamin B6 metabolism	45.45	5 of 11
66794	degradation of hexoses	44.44	8 of 18
66794	benzoyl-CoA degradation	42.86	3 of 7
66794	ubiquinone biosynthesis	42.86	3 of 7
66794	ethylmalonyl-CoA pathway	40	2 of 5
66794	glycogen metabolism	40	2 of 5
66794	creatinine degradation	40	2 of 5
66794	metabolism of amino sugars and derivatives	40	2 of 5
66794	starch degradation	40	4 of 10
66794	3-chlorocatechol degradation	40	2 of 5
66794	hydrogen production	40	2 of 5
66794	polyamine pathway	39.13	9 of 23
66794	d-xylose degradation	36.36	4 of 11
66794	lipid A biosynthesis	33.33	3 of 9
66794	IAA biosynthesis	33.33	1 of 3
66794	enterobactin biosynthesis	33.33	1 of 3
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	sphingosine metabolism	33.33	2 of 6
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	degradation of pentoses	32.14	9 of 28
66794	phosphatidylethanolamine bioynthesis	30.77	4 of 13
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	lactate fermentation	25	1 of 4
66794	cyclohexanol degradation	25	1 of 4
66794	methanogenesis from CO2	25	3 of 12
66794	bile acid biosynthesis, neutral pathway	23.53	4 of 17
66794	4-hydroxymandelate degradation	22.22	2 of 9
66794	arachidonic acid metabolism	22.22	4 of 18

Isolation source categories

Isolation

Taxonmaps

69479

Global distribution of 16S sequence Z26933 (>99% sequence identity) for Kyrpidia tusciae subclade from Microbeatlas

Aquatic Samples	41
Soil Samples	287
Animal Samples	133
Plant Samples	8
Total Samples	469

Risk assessment

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM9290v1 assembly for Kyrpidia tusciae DSM 2912	complete	GCA_000092905	562970.4	646564511	562970	93.72

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20218	Kyrpidia tusciae gene for 16S rRNA, partial sequence, strain: NBRC 15312	AB680831	1465		562970
20218	Kyrpidia tusciae DSM 2912 partial 16S rRNA gene	Z26933	1491		562970
124043	Kyrpidia tusciae DSM 2912 gene for 16S ribosomal RNA, partial sequence.	AB042062	1512		562970

GC content

Predictions

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Prokaryotic Life Associated with Coal-Fire Gas Vents Revealed by Metagenomics.	Kadnikov VV, Mardanov AV, Beletsky AV, Karnachuk OV, Ravin NV.	Biology (Basel)	10.3390/biology12050723	2023
Metabolism	Distribution and preservation of the components of the engulfment. What is beyond representative genomes?	Soto-Avila L, Merce RC, Santos W, Castaneda N, Gutierrez-Rios RM.	PLoS One	10.1371/journal.pone.0246651	2021
Metabolism	Eubacterial SpoVG homologs constitute a new family of site-specific DNA-binding proteins.	Jutras BL, Chenail AM, Rowland CL, Carroll D, Miller MC, Bykowski T, Stevenson B.	PLoS One	10.1371/journal.pone.0066683	2013
	From an extremophilic community to an electroautotrophic production strain: identifying a novel Knallgas bacterium as cathodic biofilm biocatalyst.	Reiner JE, Geiger K, Hackbarth M, Fink M, Lapp CJ, Jung T, Dotsch A, Hugler M, Wagner M, Hille-Reichel A, Wilcke W, Kerzenmacher S, Horn H, Gescher J.	ISME J	10.1038/s41396-020-0595-5	2020
	Origin and evolution of gene families in Bacteria and Archaea.	Collins RE, Merz H, Higgs PG.	BMC Bioinformatics	10.1186/1471-2105-12-s9-s14	2011
Metabolism	Evidence for natural horizontal transfer of the pcpB gene in the evolution of polychlorophenol-degrading sphingomonads.	Tiirola MA, Wang H, Paulin L, Kulomaa MS.	Appl Environ Microbiol	10.1128/aem.68.9.4495-4501.2002	2002
	Inhibitory proteins of Bacillus subtilis interact within the membrane to block intramembrane protease activity.	Mandal S, Soriano A, Erpelding C, Ruffner J, Smith E, Orlando BJ, Kroos L.	J Bacteriol	10.1128/jb.00186-25	2025
	Improving the Cathodic Biofilm Growth Capabilities of Kyrpidia spormannii EA-1 by Undirected Mutagenesis.	Jung T, Hackbarth M, Horn H, Gescher J.	Microorganisms	10.3390/microorganisms9010077	2020
	Insights into the production and evolution of lantibiotics from a computational analysis of peptides associated with the lanthipeptide cyclase domain.	Maheshwari N, Jermiin LS, Cotroneo C, Gordon SV, Shields DC.	R Soc Open Sci	10.1098/rsos.240491	2024
	New-to-nature CO2-dependent acetyl-CoA assimilation enabled by an engineered B12-dependent acyl-CoA mutase.	Schulz-Mirbach H, Wichmann P, Satanowski A, Meusel H, Wu T, Nattermann M, Burgener S, Paczia N, Bar-Even A, Erb TJ.	Nat Commun	10.1038/s41467-024-53762-9	2024
	Thermophilic Chloroflexi Dominate in the Microbial Community Associated with Coal-Fire Gas Vents in the Kuznetsk Coal Basin, Russia.	Kadnikov VV, Mardanov AV, Beletsky AV, Grigoriev MA, Karnachuk OV, Ravin NV.	Microorganisms	10.3390/microorganisms9050948	2021
Genetics	High-quality draft genome sequence of Effusibacillus lacus strain skLN1T, facultative anaerobic spore-former isolated from freshwater lake sediment.	Watanabe M, Tokizawa R, Kojima H, Fukui M.	Stand Genomic Sci	10.1186/s40793-017-0302-y	2017
	New insights into the structures and interactions of bacterial Y-family DNA polymerases.	Timinskas K, Venclovas C.	Nucleic Acids Res	10.1093/nar/gkz198	2019
Enzymology	A widely distributed hydrogenase oxidises atmospheric H2 during bacterial growth.	Islam ZF, Welsh C, Bayly K, Grinter R, Southam G, Gagen EJ, Greening C.	ISME J	10.1038/s41396-020-0713-4	2020
	A Therapeutic Uricase with Reduced Immunogenicity Risk and Improved Development Properties.	Nyborg AC, Ward C, Zacco A, Chacko B, Grinberg L, Geoghegan JC, Bean R, Wendeler M, Bartnik F, O'Connor E, Gruia F, Iyer V, Feng H, Roy V, Berge M, Miner JN, Wilson DM, Zhou D, Nicholson S, Wilker C, Wu CY, Wilson S, Jermutus L, Wu H, Owen DA, Osbourn J, Coats S, Baca M.	PLoS One	10.1371/journal.pone.0167935	2016
Metabolism	Identification and classification of known and putative antimicrobial compounds produced by a wide variety of Bacillales species.	Zhao X, Kuipers OP.	BMC Genomics	10.1186/s12864-016-3224-y	2016
Phylogeny	CVTree3 Web Server for Whole-genome-based and Alignment-free Prokaryotic Phylogeny and Taxonomy.	Zuo G, Hao B.	Genomics Proteomics Bioinformatics	10.1016/j.gpb.2015.08.004	2015
Metabolism	Cultivation and Genomic Analysis of "Candidatus Nitrosocaldus islandicus," an Obligately Thermophilic, Ammonia-Oxidizing Thaumarchaeon from a Hot Spring Biofilm in Graendalur Valley, Iceland.	Daebeler A, Herbold CW, Vierheilig J, Sedlacek CJ, Pjevac P, Albertsen M, Kirkegaard RH, de la Torre JR, Daims H, Wagner M.	Front Microbiol	10.3389/fmicb.2018.00193	2018
Metabolism	Comparative genomics and phylogenomic analyses of lysine riboswitch distributions in bacteria.	Mukherjee S, Barash D, Sengupta S.	PLoS One	10.1371/journal.pone.0184314	2017
Metabolism	Actinobacterial Degradation of 2-Hydroxyisobutyric Acid Proceeds via Acetone and Formyl-CoA by Employing a Thiamine-Dependent Lyase Reaction.	Rohwerder T, Rohde MT, Jehmlich N, Purswani J	Front Microbiol	10.3389/fmicb.2020.00691	2020
Metabolism	Production of 2-Hydroxyisobutyric Acid from Methanol by Methylobacterium extorquens AM1 Expressing (R)-3-Hydroxybutyryl Coenzyme A-Isomerizing Enzymes.	Rohde MT, Tischer S, Harms H, Rohwerder T	Appl Environ Microbiol	10.1128/AEM.02622-16	2017
Metabolism	Thermophilic Coenzyme B12-Dependent Acyl Coenzyme A (CoA) Mutase from Kyrpidia tusciae DSM 2912 Preferentially Catalyzes Isomerization of (R)-3-Hydroxybutyryl-CoA and 2-Hydroxyisobutyryl-CoA.	Weichler MT, Kurteva-Yaneva N, Przybylski D, Schuster J, Muller RH, Harms H, Rohwerder T	Appl Environ Microbiol	10.1128/AEM.00716-15	2015
Genetics	Complete genome sequence of the thermophilic, hydrogen-oxidizing Bacillus tusciae type strain (T2) and reclassification in the new genus, Kyrpidia gen. nov. as Kyrpidia tusciae comb. nov. and emendation of the family Alicyclobacillaceae da Costa and Rainey, 2010.	Klenk HP, Lapidus A, Chertkov O, Copeland A, Del Rio TG, Nolan M, Lucas S, Chen F, Tice H, Cheng JF, Han C, Bruce D, Goodwin L, Pitluck S, Pati A, Ivanova N, Mavromatis K, Daum C, Chen A, Palaniappan K, Chang YJ, Land M, Hauser L, Jeffries CD, Detter JC, Rohde M, Abt B, Pukall R, Goker M, Bristow J, Markowitz V, Hugenholtz P, Eisen JA	Stand Genomic Sci	10.4056/sigs.2144922	2011
	Fodinisporobacter ferrooxydans gen. nov., sp. nov.-A Spore-Forming Ferrous-Oxidizing Bacterium Isolated from a Polymetallic Mine.	Jiang Z, Li X, Liang Z, Tan Z, Zhou N, Liu Y, Liu Z, Yin H, Luo K, Ingsriswang S, Liu S, Jiang C.	Microorganisms	10.3390/microorganisms12050853	2024
Phylogeny	Kyrpidia spormannii sp. nov., a thermophilic, hydrogen-oxidizing, facultative autotroph, isolated from hydrothermal systems at São Miguel Island, and emended description of the genus Kyrpidia.	Reiner JE, Jung T, Lapp CJ, Siedler M, Bunk B, Overmann J, Gescher J.	Int J Syst Evol Microbiol	10.1099/ijsem.0.003037	2018