Ktedonobacter racemifer (DSM 44963, SOSP1-21)

Cell morphology

Multimedia

• @ref:	12216
  multimedia content:	DSM_44963-1.jpg
  multimedia.multimedia content:	https://www.dsmz.de/microorganisms/photos/DSM_44963-1.jpg
  intellectual property rights:	© Leibniz-Institut DSMZ
  manual_annotation:	1

• @ref:	12216
  multimedia content:	DSM_44963.jpg
  multimedia.multimedia content:	https://www.dsmz.de/microorganisms/photos/DSM_44963.jpg
  caption:	Medium 65 pH5.5 28°C
  intellectual property rights:	© Leibniz-Institut DSMZ
  manual_annotation:	1

• @ref:	66793
  multimedia content:	EM_DSM_44963_1.jpg
  multimedia.multimedia content:	EM_DSM_44963_1.jpg
  caption:	electron microscopic image
  intellectual property rights:	© HZI/Manfred Rohde
  manual_annotation:	1

• @ref:	12216
  multimedia content:	DSM_44963-1.jpg
  multimedia.multimedia content:	https://www.dsmz.de/microorganisms/photos/DSM_44963-1.jpg
  caption:	Medium 65 pH5.5 28°C
  intellectual property rights:	Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH
  manual_annotation:	1

Culture medium

@ref	Name	Growth	Medium link	Composition
12216	GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)		Medium recipe at MediaDive	Name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) Composition: Agar 18.0 g/l Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l CaCO3 2.0 g/l Distilled water
12216	ANTIBIOTIC MEDIUM 1 (DSMZ Medium 1532)		Medium recipe at MediaDive	Name: ANTIBIOTIC MEDIUM 1 (DSMZ Medium 1532) Composition: Agar 20.0 g/l Peptone 6.0 g/l Pancreatic digest of casein 4.0 g/l Yeast extract 3.0 g/l Beef extract 1.5 g/l Glucose 1.0 g/l Distilled water
12216	ISP2 MEDIUM (DSMZ Medium 987)		Medium recipe at MediaDive	Name: ISP 2 MEDIUM (DSMZ Medium 987) Composition: Agar 20.0 g/l Malt extract 10.0 g/l Dextrose 4.0 g/l Yeast extract 4.0 g/l Distilled water
12216	ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84)		Medium recipe at MediaDive	Name: ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84) Composition: Agar 20.0 g/l Rolled oats 20.0 g/l ZnSO4 x 7 H2O 0.001 g/l MnCl2 x 4 H2O 0.001 g/l FeSO4 x 7 H2O 0.001 g/l Distilled water

Culture temp

Culture pH

Oxygen tolerance

Nutrition type

Spore formation

Halophily

Observation

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
43418	62968 ChEBI	cellulose	-	hydrolysis
43418	17632 ChEBI	nitrate	-	reduction
43418	28017 ChEBI	starch	+	hydrolysis

Antibiotic resistance

Metabolite production

@ref	Chebi-ID	Metabolite	Production
43418	16136 ChEBI	hydrogen sulfide

Enzymes

@ref	Value	Activity	Ec
43418	catalase	+	1.11.1.6

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions	external links
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	aspartate and asparagine metabolism	100	9 of 9
66794	enterobactin biosynthesis	100	3 of 3
66794	palmitate biosynthesis	100	22 of 22
66794	ppGpp biosynthesis	100	4 of 4
66794	methylglyoxal degradation	100	5 of 5
66794	butanoate fermentation	100	4 of 4
66794	degradation of aromatic, nitrogen containing compounds	100	12 of 12
66794	phenylmercury acetate degradation	100	2 of 2
66794	acetate fermentation	100	4 of 4
66794	starch degradation	100	10 of 10
66794	ethanol fermentation	100	2 of 2
66794	cardiolipin biosynthesis	100	7 of 7
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	ceramide biosynthesis	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	coenzyme A metabolism	100	4 of 4
66794	formaldehyde oxidation	100	3 of 3
66794	glycine betaine biosynthesis	100	5 of 5
66794	vitamin K metabolism	100	5 of 5
66794	phenylacetate degradation (aerobic)	100	5 of 5
66794	kanosamine biosynthesis II	100	2 of 2
66794	glycogen metabolism	100	5 of 5
66794	C4 and CAM-carbon fixation	100	8 of 8
66794	adipate degradation	100	2 of 2
66794	gluconeogenesis	100	8 of 8
66794	folate polyglutamylation	100	1 of 1
66794	cellulose degradation	100	5 of 5
66794	NAD metabolism	94.44	17 of 18
66794	flavin biosynthesis	93.33	14 of 15
66794	leucine metabolism	92.31	12 of 13
66794	Entner Doudoroff pathway	90	9 of 10
66794	threonine metabolism	90	9 of 10
66794	propionate fermentation	90	9 of 10
66794	glutamate and glutamine metabolism	89.29	25 of 28
66794	valine metabolism	88.89	8 of 9
66794	CO2 fixation in Crenarchaeota	88.89	8 of 9
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	degradation of sugar acids	88	22 of 25
66794	citric acid cycle	85.71	12 of 14
66794	ubiquinone biosynthesis	85.71	6 of 7
66794	photosynthesis	85.71	12 of 14
66794	propanol degradation	85.71	6 of 7
66794	phenylalanine metabolism	84.62	11 of 13
66794	tryptophan metabolism	84.21	32 of 38
66794	selenocysteine biosynthesis	83.33	5 of 6
66794	proline metabolism	81.82	9 of 11
66794	degradation of sugar alcohols	81.25	13 of 16
66794	purine metabolism	80.85	76 of 94
66794	gallate degradation	80	4 of 5
66794	ethylmalonyl-CoA pathway	80	4 of 5
66794	hydrogen production	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	factor 420 biosynthesis	80	4 of 5
66794	alanine metabolism	79.31	23 of 29
66794	heme metabolism	78.57	11 of 14
66794	tyrosine metabolism	78.57	11 of 14
66794	d-mannose degradation	77.78	7 of 9
66794	chorismate metabolism	77.78	7 of 9
66794	serine metabolism	77.78	7 of 9
66794	pyrimidine metabolism	75.56	34 of 45
66794	glycogen biosynthesis	75	3 of 4
66794	ketogluconate metabolism	75	6 of 8
66794	sulfopterin metabolism	75	3 of 4
66794	isoleucine metabolism	75	6 of 8
66794	cyclohexanol degradation	75	3 of 4
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	methionine metabolism	73.08	19 of 26
66794	histidine metabolism	72.41	21 of 29
66794	reductive acetyl coenzyme A pathway	71.43	5 of 7
66794	tetrahydrofolate metabolism	71.43	10 of 14
66794	non-pathway related	71.05	27 of 38
66794	arginine metabolism	70.83	17 of 24
66794	glycolysis	70.59	12 of 17
66794	phenol degradation	70	14 of 20
66794	myo-inositol biosynthesis	70	7 of 10
66794	sulfate reduction	69.23	9 of 13
66794	octane oxidation	66.67	2 of 3
66794	degradation of hexoses	66.67	12 of 18
66794	allantoin degradation	66.67	6 of 9
66794	IAA biosynthesis	66.67	2 of 3
66794	glycolate and glyoxylate degradation	66.67	4 of 6
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	cyanate degradation	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	isoprenoid biosynthesis	65.38	17 of 26
66794	oxidative phosphorylation	64.84	59 of 91
66794	lipid metabolism	64.52	20 of 31
66794	pentose phosphate pathway	63.64	7 of 11
66794	d-xylose degradation	63.64	7 of 11
66794	metabolism of disaccharids	63.64	7 of 11
66794	carnitine metabolism	62.5	5 of 8
66794	androgen and estrogen metabolism	62.5	10 of 16
66794	lipoate biosynthesis	60	3 of 5
66794	coenzyme M biosynthesis	60	6 of 10
66794	creatinine degradation	60	3 of 5
66794	lysine metabolism	59.52	25 of 42
66794	bile acid biosynthesis, neutral pathway	58.82	10 of 17
66794	degradation of pentoses	57.14	16 of 28
66794	glutathione metabolism	57.14	8 of 14
66794	4-hydroxymandelate degradation	55.56	5 of 9
66794	cysteine metabolism	55.56	10 of 18
66794	daunorubicin biosynthesis	55.56	5 of 9
66794	cholesterol biosynthesis	54.55	6 of 11
66794	glycine metabolism	50	5 of 10
66794	pantothenate biosynthesis	50	3 of 6
66794	sphingosine metabolism	50	3 of 6
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	4-hydroxyphenylacetate degradation	50	5 of 10
66794	lactate fermentation	50	2 of 4
66794	ascorbate metabolism	50	11 of 22
66794	toluene degradation	50	2 of 4
66794	quinate degradation	50	1 of 2
66794	dTDPLrhamnose biosynthesis	50	4 of 8
66794	biotin biosynthesis	50	2 of 4
66794	carotenoid biosynthesis	50	11 of 22
66794	polyamine pathway	47.83	11 of 23
66794	3-phenylpropionate degradation	46.67	7 of 15
66794	urea cycle	46.15	6 of 13
66794	phenylpropanoid biosynthesis	46.15	6 of 13
66794	vitamin B1 metabolism	46.15	6 of 13
66794	lipid A biosynthesis	44.44	4 of 9
66794	vitamin B12 metabolism	44.12	15 of 34
66794	benzoyl-CoA degradation	42.86	3 of 7
66794	bacilysin biosynthesis	40	2 of 5
66794	metabolism of amino sugars and derivatives	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	3-chlorocatechol degradation	40	2 of 5
66794	D-cycloserine biosynthesis	40	2 of 5
66794	elloramycin biosynthesis	40	2 of 5
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	methanogenesis from CO2	33.33	4 of 12
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	chlorophyll metabolism	33.33	6 of 18
66794	sulfoquinovose degradation	33.33	1 of 3
66794	aclacinomycin biosynthesis	28.57	2 of 7
66794	mevalonate metabolism	28.57	2 of 7
66794	arachidonic acid metabolism	27.78	5 of 18
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	CMP-KDO biosynthesis	25	1 of 4
66794	catecholamine biosynthesis	25	1 of 4
66794	nitrate assimilation	22.22	2 of 9

Isolation source categories

Isolation

Taxonmaps

69479

Global distribution of 16S sequence AM180156 (>99% sequence identity) for Ktedonobacter racemifer subclade from Microbeatlas

Aquatic Samples	371
Soil Samples	3419
Animal Samples	340
Plant Samples	139
Total Samples	4269

Risk assessment

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM17885v1 assembly for Ktedonobacter racemifer DSM 44963 SOSP1-21	scaffold	GCA_000178855	485913.10	648276680	485913	68.01

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20218	Ktedonobacter racemifer gene for 16S rRNA, partial sequence	AB510917	1400		485913
12216	Ktedobacter racemifer partial 16S rRNA gene, strain SOSP1-21	AM180156	1386		485913

GC content

Predictions

Literature

Topic	Title	Authors	Journal	DOI	Year
	Identification of a MarR Subfamily That Regulates Arsenic Resistance Genes.	Yu Y, Chen J, Li Y, Liang J, Xie Z, Feng R, Alwathnani HA, Rosen BP, Grove A, Chen J, Rensing C.	Appl Environ Microbiol	10.1128/aem.01588-21	2021
	Occurrence of vanHAX and Related Genes beyond the Actinobacteria Phylum.	Yushchuk O, Binda E, Fedorenko V, Marinelli F.	Genes (Basel)	10.3390/genes13111960	2022
Enzymology	Reconstructing Genomes of Carbon Monoxide Oxidisers in Volcanic Deposits Including Members of the Class Ktedonobacteria.	Hernandez M, Vera-Gargallo B, Calabi-Floody M, King GM, Conrad R, Tebbe CC.	Microorganisms	10.3390/microorganisms8121880	2020
Metabolism	Comparative structural modeling and docking studies of uricase: possible implication in enzyme supplementation therapy for hyperuricemic disorders.	Beedkar SD, Khobragade CN, Bodade RG, Vinchurkar AS.	Comput Biol Med	10.1016/j.compbiomed.2012.03.001	2012
Genetics	Novel LanT associated lantibiotic clusters identified by genome database mining.	Singh M, Sareen D.	PLoS One	10.1371/journal.pone.0091352	2014
Pathogenicity	Oral Administration of miR-30d from Feces of MS Patients Suppresses MS-like Symptoms in Mice by Expanding Akkermansia muciniphila.	Liu S, Rezende RM, Moreira TG, Tankou SK, Cox LM, Wu M, Song A, Dhang FH, Wei Z, Costamagna G, Weiner HL.	Cell Host Microbe	10.1016/j.chom.2019.10.008	2019
Metabolism	ISC, a Novel Group of Bacterial and Archaeal DNA Transposons That Encode Cas9 Homologs.	Kapitonov VV, Makarova KS, Koonin EV.	J Bacteriol	10.1128/jb.00783-15	2015
	Phylogenetic Distribution and Diversity of Bacterial Pseudo-Orthocaspases Underline Their Putative Role in Photosynthesis.	Klemencic M, Asplund-Samuelsson J, Dolinar M, Funk C.	Front Plant Sci	10.3389/fpls.2019.00293	2019
	Discovery and characterization of ionic liquid-tolerant thermophilic cellulases from a switchgrass-adapted microbial community.	Gladden JM, Park JI, Bergmann J, Reyes-Ortiz V, D'haeseleer P, Quirino BF, Sale KL, Simmons BA, Singer SW.	Biotechnol Biofuels	10.1186/1754-6834-7-15	2014
	Proteorhodopsin genes in giant viruses.	Yutin N, Koonin EV.	Biol Direct	10.1186/1745-6150-7-34	2012
Enzymology	Genome-guided Investigation of Antibiotic Substances produced by Allosalinactinospora lopnorensis CA15-2(T) from Lop Nor region, China.	Huang C, Leung RK, Guo M, Tuo L, Guo L, Yew WW, Lou I, Lee SMY, Sun C.	Sci Rep	10.1038/srep20667	2016
Metabolism	AS3MT-mediated tolerance to arsenic evolved by multiple independent horizontal gene transfers from bacteria to eukaryotes.	Palmgren M, Engstrom K, Hallstrom BM, Wahlberg K, Sondergaard DA, Sall T, Vahter M, Broberg K.	PLoS One	10.1371/journal.pone.0175422	2017
Genetics	Whole-proteome tree of life suggests a deep burst of organism diversity.	Choi J, Kim SH.	Proc Natl Acad Sci U S A	10.1073/pnas.1915766117	2020
Phylogeny	Phylogenetic diversity and environment-specific distributions of glycosyl hydrolase family 10 xylanases in geographically distant soils.	Wang G, Meng K, Luo H, Wang Y, Huang H, Shi P, Yang P, Zhang Z, Yao B.	PLoS One	10.1371/journal.pone.0043480	2012
Enzymology	A novel salt-tolerant chitobiosidase discovered by genetic screening of a metagenomic library derived from chitin-amended agricultural soil.	Cretoiu MS, Berini F, Kielak AM, Marinelli F, van Elsas JD.	Appl Microbiol Biotechnol	10.1007/s00253-015-6639-5	2015
Metabolism	Coordinated Biosynthesis of the Purine Nucleoside Antibiotics Aristeromycin and Coformycin in Actinomycetes.	Xu G, Kong L, Gong R, Xu L, Gao Y, Jiang M, Cai YS, Hong K, Hu Y, Liu P, Deng Z, Price NPJ, Chen W.	Appl Environ Microbiol	10.1128/aem.01860-18	2018
	Structural properties of 2/2 hemoglobins: the group III protein from Helicobacter hepaticus.	Nothnagel HJ, Winer BY, Vuletich DA, Pond MP, Lecomte JT.	IUBMB Life	10.1002/iub.430	2011
Metabolism	Metabolic Adaptation to Sulfur of Hyperthermophilic Palaeococcus pacificus DY20341T from Deep-Sea Hydrothermal Sediments.	Zeng X, Zhang X, Shao Z.	Int J Mol Sci	10.3390/ijms21010368	2020
	Efficient heterologous transformation of Chlamydomonas reinhardtii npq2 mutant with the zeaxanthin epoxidase gene isolated and characterized from Chlorella zofingiensis.	Couso I, Cordero BF, Vargas MA, Rodriguez H.	Mar Drugs	10.3390/md10091955	2012
Genetics	Wide variation in antibiotic resistance proteins identified by functional metagenomic screening of a soil DNA library.	McGarvey KM, Queitsch K, Fields S.	Appl Environ Microbiol	10.1128/aem.06759-11	2012
Metabolism	Structure of an MmyB-like regulator from C. aurantiacus, member of a new transcription factor family linked to antibiotic metabolism in actinomycetes.	Xu Q, van Wezel GP, Chiu HJ, Jaroszewski L, Klock HE, Knuth MW, Miller MD, Lesley SA, Godzik A, Elsliger MA, Deacon AM, Wilson IA.	PLoS One	10.1371/journal.pone.0041359	2012
Metabolism	Pleiotropic control of secondary metabolism and morphological development by KsbC, a butyrolactone autoregulator receptor homologue in Kitasatospora setae.	Aroonsri A, Kitani S, Hashimoto J, Kosone I, Izumikawa M, Komatsu M, Fujita N, Takahashi Y, Shin-ya K, Ikeda H, Nihira T.	Appl Environ Microbiol	10.1128/aem.02355-12	2012
	Novel lipolytic enzymes identified from metagenomic library of deep-sea sediment.	Jeon JH, Kim JT, Lee HS, Kim SJ, Kang SG, Choi SH, Lee JH.	Evid Based Complement Alternat Med	10.1155/2011/271419	2011
Metabolism	Bioactivity-guided genome mining reveals the lomaiviticin biosynthetic gene cluster in Salinispora tropica.	Kersten RD, Lane AL, Nett M, Richter TK, Duggan BM, Dorrestein PC, Moore BS.	Chembiochem	10.1002/cbic.201300147	2013
Metabolism	The Vein Patterning 1 (VEP1) gene family laterally spread through an ecological network.	Tarrio R, Ayala FJ, Rodriguez-Trelles F.	PLoS One	10.1371/journal.pone.0022279	2011
Metabolism	Bacterial biosynthetic gene clusters encoding the anti-cancer haterumalide class of molecules: biogenesis of the broad spectrum antifungal and anti-oomycete compound, oocydin A.	Matilla MA, Stockmann H, Leeper FJ, Salmond GP.	J Biol Chem	10.1074/jbc.m112.401026	2012
Genetics	Genome sequence of the mesophilic Thermotogales bacterium Mesotoga prima MesG1.Ag.4.2 reveals the largest Thermotogales genome to date.	Zhaxybayeva O, Swithers KS, Foght J, Green AG, Bruce D, Detter C, Han S, Teshima H, Han J, Woyke T, Pitluck S, Nolan M, Ivanova N, Pati A, Land ML, Dlutek M, Doolittle WF, Noll KM, Nesbo CL.	Genome Biol Evol	10.1093/gbe/evs059	2012
Enzymology	Highly specific and quick detection of Mycobacterium avium subsp. paratuberculosis in feces and gut tissue of cattle and humans by multiple real-time PCR assays.	Imirzalioglu C, Dahmen H, Hain T, Billion A, Kuenne C, Chakraborty T, Domann E.	J Clin Microbiol	10.1128/jcm.01492-10	2011
Enzymology	The self-sufficient CYP102 family enzyme, Krac9955, from Ktedonobacter racemifer DSM44963 acts as an alkyl- and alkyloxy-benzoic acid hydroxylase.	Maddigan NK, Bell SG	Arch Biochem Biophys	10.1016/j.abb.2016.12.014	2016
Enzymology	Characterisation of two self-sufficient CYP102 family monooxygenases from Ktedonobacter racemifer DSM44963 which have new fatty acid alcohol product profiles.	Munday SD, Maddigan NK, Young RJ, Bell SG	Biochim Biophys Acta	10.1016/j.bbagen.2016.01.023	2016
Genetics	Non-contiguous finished genome sequence and contextual data of the filamentous soil bacterium Ktedonobacter racemifer type strain (SOSP1-21).	Chang YJ, Land M, Hauser L, Chertkov O, Del Rio TG, Nolan M, Copeland A, Tice H, Cheng JF, Lucas S, Han C, Goodwin L, Pitluck S, Ivanova N, Ovchinikova G, Pati A, Chen A, Palaniappan K, Mavromatis K, Liolios K, Brettin T, Fiebig A, Rohde M, Abt B, Goker M, Detter JC, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Lapidus A	Stand Genomic Sci	10.4056/sigs.2114901	2011
Phylogeny	New lineage of filamentous, spore-forming, gram-positive bacteria from soil.	Cavaletti L, Monciardini P, Bamonte R, Schumann P, Rohde M, Sosio M, Donadio S	Appl Environ Microbiol	10.1128/AEM.00132-06	2006
Phylogeny	Reticulibacter mediterranei gen. nov., sp. nov., within the new family Reticulibacteraceae fam. nov., and Ktedonospora formicarum gen. nov., sp. nov., Ktedonobacter robiniae sp. nov., Dictyobacter formicarum sp. nov. and Dictyobacter arantiisoli sp. nov., belonging to the class Ktedonobacteria.	Yabe S, Zheng Y, Wang CM, Sakai Y, Abe K, Yokota A, Donadio S, Cavaletti L, Monciardini P	Int J Syst Evol Microbiol	10.1099/ijsem.0.004883	2021
Phylogeny	Dictyobacter aurantiacus gen. nov., sp. nov., a member of the family Ktedonobacteraceae, isolated from soil, and emended description of the genus Thermosporothrix.	Yabe S, Sakai Y, Abe K, Yokota A, Take A, Matsumoto A, Sugiharto A, Susilowati D, Hamada M, Nara K, Made Sudiana I, Otsuka S	Int J Syst Evol Microbiol	10.1099/ijsem.0.001985	2017
Phylogeny	Thermosporothrix hazakensis gen. nov., sp. nov., isolated from compost, description of Thermosporotrichaceae fam. nov. within the class Ktedonobacteria Cavaletti et al. 2007 and emended description of the class Ktedonobacteria.	Yabe S, Aiba Y, Sakai Y, Hazaka M, Yokota A	Int J Syst Evol Microbiol	10.1099/ijs.0.018069-0	2009