Name: Ktedonobacter racemifer SOSP1-21
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 17649

Type strain:

Species: Ktedonobacter racemifer

Strain Designation: SOSP1-21

Culture col. no.: DSM 44963

Strain history: <- L. Cavaletti; SOSP1-21 (Ktedobacter racemifer)

NCBI tax ID(s): 485913 (strain), 363277 (species)

SI-ID 296455

NRRL B-41538, DSM 44963

Section

Ktedonobacter racemifer SOSP1-21 is an aerobe, heterotroph, spore-forming bacterium that was isolated from forest soil.

filament-shaped
Gram-positive
spore-forming
aerobe
heterotroph
mesophilic
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	*Chloroflexota*
	Class	*Ktedonobacteria*
	Order	*Ktedonobacterales*
	Family	*Ktedonobacteraceae*
	Genus	*Ktedonobacter*
	Species	**Ktedonobacter racemifer**
	Full Scientific Name (LPSN)	Ktedonobacter racemifer corrig. Cavaletti et al. 2007

Synonym

Ktedobacter racemifer

Information on morphological and physiological properties Morphology

[Ref.: #43418]	Gram stain	positive

[Ref.: #43418]	Cell shape	filament-shaped

[Ref.: #43418]	Motility	no

Multimedia content

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Intellectual property rights:

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Caption:

Medium 65 pH5.5 28°C

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Intellectual property rights:

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Caption:

electron microscopic image

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Intellectual property rights:

Information on culture and growth conditions Culture and growth conditions

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Culture medium

GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)

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Culture medium growth

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Culture medium link

Medium recipe at MediaDive

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Culture medium composition

expand / minimize

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Culture medium

ANTIBIOTIC MEDIUM 1 (DSMZ Medium 1532)

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Culture medium growth

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Culture medium link

Medium recipe at MediaDive

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Culture medium composition

expand / minimize

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Culture medium

ISP2 MEDIUM (DSMZ Medium 987)

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Culture medium growth

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Culture medium link

Medium recipe at MediaDive

[Ref.: #12216]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #12216]			growth	28 °C
[Ref.: #43418]			optimum	28-33 °C

[Ref.: #12216]	Temperature range	mesophilic
[Ref.: #43418]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #43418]			optimum	6
[Ref.: #43418]			growth	4.8-6.8

Information on physiology and metabolism Physiology and metabolism

[Ref.: #43418]

Oxygen tolerance

aerobe

[Ref.: #43418]

Nutrition type

heterotroph

[Ref.: #43418]	Spore description	spherical
[Ref.: #43418]	Type of spore	spore
[Ref.: #43418]	Ability of spore formation	yes

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #43418]		NaCl		growth	0-10	g/L

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Observation

grows under microaerophilic conditions

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #43418]	cellulose ChEBI	-	hydrolysis
[Ref.: #43418]	nitrate ChEBI	-	reduction
[Ref.: #43418]	starch ChEBI	+	hydrolysis

	Metabolite	Antibiotic sensitivity	Concentration
[Ref.: #43418]	apramycin ChEBI	yes	20000	µg/mL
[Ref.: #43418]	novobiocin ChEBI	yes	5000	µg/mL
[Ref.: #43418]	ramoplanin ChEBI	yes	5000	µg/mL

	Metabolite production	Metabolite	Production
[Ref.: #43418]		hydrogen sulfide ChEBI	yes

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #43418]		catalase	+	1.11.1.6

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	aspartate and asparagine metabolism	100	9 of 9
[Ref.: #66794]	enterobactin biosynthesis	100	3 of 3
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	butanoate fermentation	100	4 of 4
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	100	12 of 12
[Ref.: #66794]	phenylmercury acetate degradation	100	2 of 2
[Ref.: #66794]	acetate fermentation	100	4 of 4
[Ref.: #66794]	starch degradation	100	10 of 10
[Ref.: #66794]	ethanol fermentation	100	2 of 2
[Ref.: #66794]	cardiolipin biosynthesis	100	7 of 7
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	ceramide biosynthesis	100	1 of 1
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	glycine betaine biosynthesis	100	5 of 5
[Ref.: #66794]	vitamin K metabolism	100	5 of 5
[Ref.: #66794]	phenylacetate degradation (aerobic)	100	5 of 5
[Ref.: #66794]	kanosamine biosynthesis II	100	2 of 2
[Ref.: #66794]	glycogen metabolism	100	5 of 5
[Ref.: #66794]	C4 and CAM-carbon fixation	100	8 of 8
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	cellulose degradation	100	5 of 5
[Ref.: #66794]	NAD metabolism	94.44	17 of 18
[Ref.: #66794]	flavin biosynthesis	93.33	14 of 15
[Ref.: #66794]	leucine metabolism	92.31	12 of 13
[Ref.: #66794]	Entner Doudoroff pathway	90	9 of 10
[Ref.: #66794]	threonine metabolism	90	9 of 10
[Ref.: #66794]	propionate fermentation	90	9 of 10
[Ref.: #66794]	glutamate and glutamine metabolism	89.29	25 of 28
[Ref.: #66794]	valine metabolism	88.89	8 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	88.89	8 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	88.89	8 of 9
[Ref.: #66794]	degradation of sugar acids	88	22 of 25
[Ref.: #66794]	citric acid cycle	85.71	12 of 14
[Ref.: #66794]	ubiquinone biosynthesis	85.71	6 of 7
[Ref.: #66794]	photosynthesis	85.71	12 of 14
[Ref.: #66794]	propanol degradation	85.71	6 of 7
[Ref.: #66794]	phenylalanine metabolism	84.62	11 of 13
[Ref.: #66794]	tryptophan metabolism	84.21	32 of 38
[Ref.: #66794]	selenocysteine biosynthesis	83.33	5 of 6
[Ref.: #66794]	proline metabolism	81.82	9 of 11
[Ref.: #66794]	degradation of sugar alcohols	81.25	13 of 16
[Ref.: #66794]	purine metabolism	80.85	76 of 94
[Ref.: #66794]	gallate degradation	80	4 of 5
[Ref.: #66794]	ethylmalonyl-CoA pathway	80	4 of 5
[Ref.: #66794]	hydrogen production	80	4 of 5
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	factor 420 biosynthesis	80	4 of 5
[Ref.: #66794]	alanine metabolism	79.31	23 of 29
[Ref.: #66794]	heme metabolism	78.57	11 of 14
[Ref.: #66794]	tyrosine metabolism	78.57	11 of 14
[Ref.: #66794]	d-mannose degradation	77.78	7 of 9
[Ref.: #66794]	chorismate metabolism	77.78	7 of 9
[Ref.: #66794]	serine metabolism	77.78	7 of 9
[Ref.: #66794]	pyrimidine metabolism	75.56	34 of 45
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	ketogluconate metabolism	75	6 of 8
[Ref.: #66794]	sulfopterin metabolism	75	3 of 4
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	cyclohexanol degradation	75	3 of 4
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	methionine metabolism	73.08	19 of 26
[Ref.: #66794]	histidine metabolism	72.41	21 of 29
[Ref.: #66794]	reductive acetyl coenzyme A pathway	71.43	5 of 7
[Ref.: #66794]	tetrahydrofolate metabolism	71.43	10 of 14
[Ref.: #66794]	non-pathway related	71.05	27 of 38
[Ref.: #66794]	arginine metabolism	70.83	17 of 24
[Ref.: #66794]	glycolysis	70.59	12 of 17
[Ref.: #66794]	phenol degradation	70	14 of 20
[Ref.: #66794]	myo-inositol biosynthesis	70	7 of 10
[Ref.: #66794]	sulfate reduction	69.23	9 of 13
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	degradation of hexoses	66.67	12 of 18
[Ref.: #66794]	allantoin degradation	66.67	6 of 9
[Ref.: #66794]	IAA biosynthesis	66.67	2 of 3
[Ref.: #66794]	glycolate and glyoxylate degradation	66.67	4 of 6
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	isoprenoid biosynthesis	65.38	17 of 26
[Ref.: #66794]	oxidative phosphorylation	64.84	59 of 91
[Ref.: #66794]	lipid metabolism	64.52	20 of 31
[Ref.: #66794]	pentose phosphate pathway	63.64	7 of 11
[Ref.: #66794]	d-xylose degradation	63.64	7 of 11
[Ref.: #66794]	metabolism of disaccharids	63.64	7 of 11
[Ref.: #66794]	carnitine metabolism	62.5	5 of 8
[Ref.: #66794]	androgen and estrogen metabolism	62.5	10 of 16
[Ref.: #66794]	lipoate biosynthesis	60	3 of 5
[Ref.: #66794]	coenzyme M biosynthesis	60	6 of 10
[Ref.: #66794]	creatinine degradation	60	3 of 5
[Ref.: #66794]	lysine metabolism	59.52	25 of 42
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	58.82	10 of 17
[Ref.: #66794]	degradation of pentoses	57.14	16 of 28
[Ref.: #66794]	glutathione metabolism	57.14	8 of 14
[Ref.: #66794]	4-hydroxymandelate degradation	55.56	5 of 9
[Ref.: #66794]	cysteine metabolism	55.56	10 of 18
[Ref.: #66794]	daunorubicin biosynthesis	55.56	5 of 9
[Ref.: #66794]	cholesterol biosynthesis	54.55	6 of 11
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	sphingosine metabolism	50	3 of 6
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	4-hydroxyphenylacetate degradation	50	5 of 10
[Ref.: #66794]	lactate fermentation	50	2 of 4
[Ref.: #66794]	ascorbate metabolism	50	11 of 22
[Ref.: #66794]	toluene degradation	50	2 of 4
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	dTDPLrhamnose biosynthesis	50	4 of 8
[Ref.: #66794]	biotin biosynthesis	50	2 of 4
[Ref.: #66794]	carotenoid biosynthesis	50	11 of 22
[Ref.: #66794]	polyamine pathway	47.83	11 of 23
[Ref.: #66794]	3-phenylpropionate degradation	46.67	7 of 15
[Ref.: #66794]	urea cycle	46.15	6 of 13
[Ref.: #66794]	phenylpropanoid biosynthesis	46.15	6 of 13
[Ref.: #66794]	vitamin B1 metabolism	46.15	6 of 13
[Ref.: #66794]	lipid A biosynthesis	44.44	4 of 9
[Ref.: #66794]	vitamin B12 metabolism	44.12	15 of 34
[Ref.: #66794]	benzoyl-CoA degradation	42.86	3 of 7
[Ref.: #66794]	bacilysin biosynthesis	40	2 of 5
[Ref.: #66794]	metabolism of amino sugars and derivatives	40	2 of 5
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	3-chlorocatechol degradation	40	2 of 5
[Ref.: #66794]	D-cycloserine biosynthesis	40	2 of 5
[Ref.: #66794]	elloramycin biosynthesis	40	2 of 5
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	methanogenesis from CO2	33.33	4 of 12
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	chlorophyll metabolism	33.33	6 of 18
[Ref.: #66794]	sulfoquinovose degradation	33.33	1 of 3
[Ref.: #66794]	aclacinomycin biosynthesis	28.57	2 of 7
[Ref.: #66794]	mevalonate metabolism	28.57	2 of 7
[Ref.: #66794]	arachidonic acid metabolism	27.78	5 of 18
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	CMP-KDO biosynthesis	25	1 of 4
[Ref.: #66794]	catecholamine biosynthesis	25	1 of 4
[Ref.: #66794]	nitrate assimilation	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.: #12216]	Sample type/isolated from	forest soil
[Ref.: #12216]	Country	Italy
[Ref.: #12216]	Country ISO 3 Code	ITA
[Ref.: #12216]	Continent	Europe

[Ref.: #43418]	Sample type/isolated from	soil sample of a black locust wood
[Ref.: #43418]	Sampling date	2001-11
[Ref.: #43418]	Geographic location (country and/or sea, region)	Gerenzano, Nothern Italy
[Ref.: #43418]	Country	Italy
[Ref.: #43418]	Country ISO 3 Code	ITA
[Ref.: #43418]	Continent	Europe
[Ref.: #43418]	Geographic location	45.0000°/9.0000°
* marker position based on {}

Isolation sources categories

#Environmental	#Terrestrial	#Forest
#Environmental	#Terrestrial	#Soil
#Host Body Product	#Plant	#Timber
#Host	#Plants	#Tree

What are isolation sources categories?

[Ref.: #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

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

[Ref.: #12216]

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.: #12216]	Ktedobacter racemifer partial 16S rRNA gene, strain SOSP1-21	AM180156	1386	ENA	485913 tax ID
[Ref.: #20218]	Ktedonobacter racemifer gene for 16S rRNA, partial sequence	AB510917	1400	ENA	485913 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Ktedonobacter racemifer DSM 44963 SOSP1-21	GCA_000178855	scaffold	GenBank	485913 tax ID	*
[Ref.: #66792]	Ktedonobacter racemifer DSM 44963 strain SOSP1-21	485913.10	wgs	PATRIC	485913 tax ID	*
[Ref.: #66792]	Ktedonobacter racemifer SOSP1-21, DSM 44963	648276680	complete	JGI IMG/M	485913 tax ID	*

[Ref.: #12216]	GC-content	53.9 mol%
[Ref.: #43418]	GC-content	53.79 mol%	high performance liquid chromatography (HPLC)

Availability in culture collections External links

[Ref.: #12216]

Culture collection no.

DSM 44963

[Ref.: #86640]

SI-ID 296455

Literature:

Only first 10 entries are displayed. Click here to see all.

Topic	Title	Authors	Journal	DOI	Year
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	*
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	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	*
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	*

References

#12216

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 44963

#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 )

#20218

Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )

#43418

Yun-juan Chang, Miriam Land, Loren Hauser, Olga Chertkov, Tijana Glavina Del Rio, Matt Nolan, Alex Copeland, Hope Tice, Jan-Fang Cheng, Susan Lucas, Cliff Han, Lynne Goodwin, Sam Pitluck, Natalia Ivanova, Galina Ovchinikova, Amrita Pati, Amy Chen, Krishna Palaniappan, Konstantinos Mavromatis, Konstantinos Liolios, Thomas Brettin, Anne Fiebig, Manfred Rohde, Birte Abt, Markus Göker, John C. Detter, Tanja Woyke, James Bristow, Jonathan A. Eisen, Victor Markowitz, Philip Hugenholtz, Nikos C. Kyrpides, Hans-Peter Klenk, Alla Lapidus: Non-contiguous finished genome sequence and contextual data of the filamentous soil bacterium Ktedonobacter racemifer type strain (SOSP1-21). Stand Genomic Sci 5: 97 - 111 2011 ( DOI 10.4056/sigs.2114901 , PubMed 22180814 )

#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 .

#86640

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-ID296455.1 )

* These data were automatically processed and therefore are not curated

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