Jonesia denitrificans (DSM 20603, ATCC 14870, CIP 55134)

Cell morphology

Colony morphology

Multicellular morphology

Multimedia

• @ref:	66793
  multimedia content:	EM_DSM_20603_1.jpg
  multimedia.multimedia content:	EM_DSM_20603_1.jpg
  caption:	electron microscopic image
  intellectual property rights:	© HZI/Manfred Rohde
  manual_annotation:	1

Culture medium

@ref	Name	Growth	Medium link	Composition
8951	COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)		Medium recipe at MediaDive	Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base
8951	BHI MEDIUM (DSMZ Medium 215)		Medium recipe at MediaDive	Name: BHI MEDIUM (DSMZ Medium 215) Composition: Brain heart infusion 37.0 g/l Distilled water
18763	ISP 2			Name: ISP 2 / Yeast Malt Agar (5265); 5265 Composition Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l Agar 15.0 g/l Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.0 Usage: Maintenance and Taxonomy Organisms: All Actinomycetes
18763	ISP 3			Name: ISP 3; 5315 Composition Dog oat flakes 20.0 g/l Trace element solution (5314) 2.5 ml/l Agar 18.0 g/l Preparation: Oat flakes are cooked for 20 minutes, trace element solution and agar are added (in the case of non rolled oat flakes the suspension has to bee filtrated). Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.8 Usage: Maintenance and taxonomy (e.g. SEM As liquid medium for metabolite production) Organisms: All Actinomycetes Trace element solution 5314 Name: Trace element solution 5314; 5314 Composition CaCl2 x H2O 3.0 g/l Fe-III-citrate 1.0 g/l MnSO4 0.2 g/l ZnCl2 0.1 g/l CuSO4 x 5 H2O 0.025 g/l Sodium tetra borate 0.2 g/l CoCl2 x 6 H2O 0.004 g/l Sodium molybdate 0.01 g/l Preparation: Use double destillated water. Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Trace element solution for different media Organisms:
18763	ISP 4			Name: ISP 4; DSM 547 Solution I: Difco soluble starch, 10.0 g. Make a paste of the starch with a small amount of cold distilled water and bring to a volume of 500 ml. Solution II: CaCO3 2.0 g K2HPO4 (anhydrous) 1.0 g MgSO4 x 7 H2O 1.0 g NaCl 1.0 g (NH4)2SO4 2.0 g Distilled water 500.0 ml Trace salt solution (see below) 1.0 ml The pH should be between 7.0 and 7.4. Do not adjust if it is within this range. Mix solutions I and II together. Add 20.0 g agar. Liquify agar by steaming at 100°C for 10 to 20 min. Trace element solution: FeSO4 x 7 H2O 0.1 g MnCl2 x 4 H2O 0.1 g ZnSO4 x 7 H2O 0.1 g Distilled water 100.0 ml
18763	ISP 5			Name: ISP 5 (5323) Composition L-Asparagine 1.0 g/l Glycerol 10.0 g/l K2HPO4 1.0 g/l Salt solution (see preparation) 1.0 ml/l Agar 20.0 g/l Preparation: Salt solution 1.0 g FeSO4 x 7 H2O 1.0 g MnCl2 x 4 H2O 1.0 g ZNSO4 x 7 H2O in 100 ml water Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.2 Usage: Maintenance and taxonomy Organisms: All Actinomycetes
37598	MEDIUM 3 - Columbia agar			Columbia agar (39.000 g);distilled water (1000.000 ml)
118898	CIP Medium 72		Medium recipe at CIP
118898	CIP Medium 3		Medium recipe at CIP

Culture temp

Oxygen tolerance

Halophily

Murein

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68371	27613 ChEBI	amygdalin	-	builds acid from	from API 50CH acid
18763	22599 ChEBI	arabinose	-
68371	18305 ChEBI	arbutin	+	builds acid from	from API 50CH acid
68368	29016 ChEBI	arginine	-	hydrolysis	from API 20E
68371	17057 ChEBI	cellobiose	+	builds acid from	from API 50CH acid
18763	62968 ChEBI	cellulose	-
68368	16947 ChEBI	citrate	+	assimilation	from API 20E
68371	17108 ChEBI	D-arabinose	-	builds acid from	from API 50CH acid
68371	18333 ChEBI	D-arabitol	-	builds acid from	from API 50CH acid
68371	15824 ChEBI	D-fructose	+	builds acid from	from API 50CH acid
68371	28847 ChEBI	D-fucose	-	builds acid from	from API 50CH acid
68371	12936 ChEBI	D-galactose	+	builds acid from	from API 50CH acid
68371	17634 ChEBI	D-glucose	+	builds acid from	from API 50CH acid
68371	62318 ChEBI	D-lyxose	-	builds acid from	from API 50CH acid
68371	16899 ChEBI	D-mannitol	-	builds acid from	from API 50CH acid
68371	16988 ChEBI	D-ribose	-	builds acid from	from API 50CH acid
68371	17924 ChEBI	D-sorbitol	-	builds acid from	from API 50CH acid
68371	16443 ChEBI	D-tagatose	-	builds acid from	from API 50CH acid
68371	65327 ChEBI	D-xylose	+	builds acid from	from API 50CH acid
68371	17113 ChEBI	erythritol	-	builds acid from	from API 50CH acid
68371	4853 ChEBI	esculin	+	builds acid from	from API 50CH acid
18763	28757 ChEBI	fructose	-
68371	16813 ChEBI	galactitol	-	builds acid from	from API 50CH acid
68368	5291 ChEBI	gelatin	-	hydrolysis	from API 20E
68371	28066 ChEBI	gentiobiose	+	builds acid from	from API 50CH acid
68371	24265 ChEBI	gluconate	-	builds acid from	from API 50CH acid
18763	17234 ChEBI	glucose	-
68371	28087 ChEBI	glycogen	+	builds acid from	from API 50CH acid
68371	15443 ChEBI	inulin	-	builds acid from	from API 50CH acid
68371	30849 ChEBI	L-arabinose	+	builds acid from	from API 50CH acid
68371	18403 ChEBI	L-arabitol	-	builds acid from	from API 50CH acid
68371	18287 ChEBI	L-fucose	-	builds acid from	from API 50CH acid
68371	62345 ChEBI	L-rhamnose	-	builds acid from	from API 50CH acid
68371	17266 ChEBI	L-sorbose	-	builds acid from	from API 50CH acid
68371	65328 ChEBI	L-xylose	-	builds acid from	from API 50CH acid
68368	25094 ChEBI	lysine	-	degradation	from API 20E
68371	17306 ChEBI	maltose	+	builds acid from	from API 50CH acid
18763	29864 ChEBI	mannitol	-
68371	6731 ChEBI	melezitose	-	builds acid from	from API 50CH acid
68371	28053 ChEBI	melibiose	-	builds acid from	from API 50CH acid
68371	320061 ChEBI	methyl alpha-D-glucopyranoside	-	builds acid from	from API 50CH acid
68371	43943 ChEBI	methyl alpha-D-mannoside	-	builds acid from	from API 50CH acid
68371	74863 ChEBI	methyl beta-D-xylopyranoside	-	builds acid from	from API 50CH acid
18763	17268 ChEBI	myo-inositol	-
68371	17268 ChEBI	myo-inositol	-	builds acid from	from API 50CH acid
68371	59640 ChEBI	N-acetylglucosamine	-	builds acid from	from API 50CH acid
118898	17632 ChEBI	nitrate	+	reduction
118898	16301 ChEBI	nitrite	-	reduction
68368	18257 ChEBI	ornithine	-	degradation	from API 20E
68371	0 ChEBI	Potassium 2-ketogluconate	-	builds acid from	from API 50CH acid
18763	16634 ChEBI	raffinose	-
68371	16634 ChEBI	raffinose	-	builds acid from	from API 50CH acid
18763	26546 ChEBI	rhamnose	-
68371	15963 ChEBI	ribitol	-	builds acid from	from API 50CH acid
68371	17814 ChEBI	salicin	+	builds acid from	from API 50CH acid
68371	28017 ChEBI	starch	+	builds acid from	from API 50CH acid
18763	17992 ChEBI	sucrose	-
68371	17992 ChEBI	sucrose	+	builds acid from	from API 50CH acid
68368	27897 ChEBI	tryptophan	-	energy source	from API 20E
68371	32528 ChEBI	turanose	+	builds acid from	from API 50CH acid
68368	16199 ChEBI	urea	-	hydrolysis	from API 20E
68371	17151 ChEBI	xylitol	-	builds acid from	from API 50CH acid
18763	18222 ChEBI	xylose	-

Metabolite production

@ref	Chebi-ID	Metabolite	Production
68368	15688 ChEBI	acetoin		from API 20E
68368	16136 ChEBI	hydrogen sulfide		from API 20E
118898	35581 ChEBI	indole
68368	35581 ChEBI	indole		from API 20E

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test	Indole test
68368	15688 ChEBI	acetoin	-		from API 20E
68368	35581 ChEBI	indole		-	from API 20E

Enzymes

@ref	Value	Activity	Ec
68382	alkaline phosphatase	-	3.1.3.1	from API zym
68382	alpha-chymotrypsin	-	3.4.21.1	from API zym
68382	alpha-fucosidase	-	3.2.1.51	from API zym
68382	alpha-glucosidase	+	3.2.1.20	from API zym
68382	alpha-mannosidase	-	3.2.1.24	from API zym
68368	arginine dihydrolase	-	3.5.3.6	from API 20E
68368	beta-galactosidase	+	3.2.1.23	from API 20E
68382	beta-glucosidase	+	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
118898	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
68382	esterase (C 4)	-		from API zym
68368	gelatinase	-		from API 20E
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	lipase (C 14)	-		from API zym
68368	lysine decarboxylase	-	4.1.1.18	from API 20E
68382	naphthol-AS-BI-phosphohydrolase	-		from API zym
68368	ornithine decarboxylase	-	4.1.1.17	from API 20E
118898	oxidase	-
68382	trypsin	-	3.4.21.4	from API zym
68368	tryptophan deaminase	-	4.1.99.1	from API 20E
118898	urease	-	3.5.1.5
68368	urease	-	3.5.1.5	from API 20E
68382	valine arylamidase	-		from API zym

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions	external links
66794	cellulose degradation	100	5 of 5
66794	palmitate biosynthesis	100	22 of 22
66794	ppGpp biosynthesis	100	4 of 4
66794	adipate degradation	100	2 of 2
66794	glycogen metabolism	100	5 of 5
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	starch degradation	100	10 of 10
66794	vitamin K metabolism	100	5 of 5
66794	coenzyme A metabolism	100	4 of 4
66794	denitrification	100	2 of 2
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	folate polyglutamylation	100	1 of 1
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	chorismate metabolism	88.89	8 of 9
66794	heme metabolism	85.71	12 of 14
66794	pentose phosphate pathway	81.82	9 of 11
66794	flavin biosynthesis	80	12 of 15
66794	methylglyoxal degradation	80	4 of 5
66794	threonine metabolism	80	8 of 10
66794	photosynthesis	78.57	11 of 14
66794	pyrimidine metabolism	77.78	35 of 45
66794	molybdenum cofactor biosynthesis	77.78	7 of 9
66794	valine metabolism	77.78	7 of 9
66794	acetate fermentation	75	3 of 4
66794	sulfopterin metabolism	75	3 of 4
66794	isoleucine metabolism	75	6 of 8
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	peptidoglycan biosynthesis	73.33	11 of 15
66794	NAD metabolism	72.22	13 of 18
66794	reductive acetyl coenzyme A pathway	71.43	5 of 7
66794	tetrahydrofolate metabolism	71.43	10 of 14
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	Entner Doudoroff pathway	70	7 of 10
66794	phenylalanine metabolism	69.23	9 of 13
66794	vitamin B1 metabolism	69.23	9 of 13
66794	purine metabolism	67.02	63 of 94
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	aspartate and asparagine metabolism	66.67	6 of 9
66794	acetoin degradation	66.67	2 of 3
66794	serine metabolism	66.67	6 of 9
66794	octane oxidation	66.67	2 of 3
66794	glycolate and glyoxylate degradation	66.67	4 of 6
66794	CO2 fixation in Crenarchaeota	66.67	6 of 9
66794	alanine metabolism	65.52	19 of 29
66794	isoprenoid biosynthesis	65.38	17 of 26
66794	glycolysis	64.71	11 of 17
66794	citric acid cycle	64.29	9 of 14
66794	d-xylose degradation	63.64	7 of 11
66794	oxidative phosphorylation	62.64	57 of 91
66794	gluconeogenesis	62.5	5 of 8
66794	degradation of sugar alcohols	62.5	10 of 16
66794	C4 and CAM-carbon fixation	62.5	5 of 8
66794	glutamate and glutamine metabolism	60.71	17 of 28
66794	factor 420 biosynthesis	60	3 of 5
66794	metabolism of amino sugars and derivatives	60	3 of 5
66794	lipid metabolism	58.06	18 of 31
66794	methionine metabolism	57.69	15 of 26
66794	propanol degradation	57.14	4 of 7
66794	cysteine metabolism	55.56	10 of 18
66794	nitrate assimilation	55.56	5 of 9
66794	metabolism of disaccharids	54.55	6 of 11
66794	leucine metabolism	53.85	7 of 13
66794	butanoate fermentation	50	2 of 4
66794	mannosylglycerate biosynthesis	50	1 of 2
66794	ethanol fermentation	50	1 of 2
66794	phenylmercury acetate degradation	50	1 of 2
66794	ketogluconate metabolism	50	4 of 8
66794	suberin monomers biosynthesis	50	1 of 2
66794	glycogen biosynthesis	50	2 of 4
66794	histidine metabolism	48.28	14 of 29
66794	tryptophan metabolism	47.37	18 of 38
66794	degradation of pentoses	46.43	13 of 28
66794	arginine metabolism	45.83	11 of 24
66794	proline metabolism	45.45	5 of 11
66794	vitamin B6 metabolism	45.45	5 of 11
66794	non-pathway related	44.74	17 of 38
66794	lipid A biosynthesis	44.44	4 of 9
66794	d-mannose degradation	44.44	4 of 9
66794	degradation of sugar acids	44	11 of 25
66794	glutathione metabolism	42.86	6 of 14
66794	lysine metabolism	40.48	17 of 42
66794	arachidonate biosynthesis	40	2 of 5
66794	lipoate biosynthesis	40	2 of 5
66794	propionate fermentation	40	4 of 10
66794	glycine metabolism	40	4 of 10
66794	degradation of hexoses	38.89	7 of 18
66794	sulfate reduction	38.46	5 of 13
66794	phenylpropanoid biosynthesis	38.46	5 of 13
66794	tyrosine metabolism	35.71	5 of 14
66794	cyanate degradation	33.33	1 of 3
66794	methane metabolism	33.33	1 of 3
66794	formaldehyde oxidation	33.33	1 of 3
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	pantothenate biosynthesis	33.33	2 of 6
66794	enterobactin biosynthesis	33.33	1 of 3
66794	IAA biosynthesis	33.33	1 of 3
66794	sphingosine metabolism	33.33	2 of 6
66794	sulfoquinovose degradation	33.33	1 of 3
66794	ascorbate metabolism	31.82	7 of 22
66794	urea cycle	30.77	4 of 13
66794	myo-inositol biosynthesis	30	3 of 10
66794	bile acid biosynthesis, neutral pathway	29.41	5 of 17
66794	benzoyl-CoA degradation	28.57	2 of 7
66794	ubiquinone biosynthesis	28.57	2 of 7
66794	mevalonate metabolism	28.57	2 of 7
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	lactate fermentation	25	1 of 4
66794	cyclohexanol degradation	25	1 of 4
66794	carnitine metabolism	25	2 of 8
66794	degradation of aromatic, nitrogen containing compounds	25	3 of 12
66794	dTDPLrhamnose biosynthesis	25	2 of 8
66794	CMP-KDO biosynthesis	25	1 of 4
66794	arachidonic acid metabolism	22.22	4 of 18

Fatty acid profile

Metadata FA analysis
type of FA analysis	whole cell analysis
method/protocol	CCUG
@ref	46273
Fatty acid Percentage ECL C15:0 ANTEISO 49.6 14.711 C16:0 14.7 16 C16:0 iso 8.7 15.626 C17:0 anteiso 4.8 16.722 C15:0 ISO 4.6 14.621 C14:0 4.5 14 C14:0 ISO 3.5 13.618 C15:1 ANTEISO A 3 14.526 C13:0 ANTEISO 2 12.701 C18:2 ω6,9c/C18:0 ANTE 1.8 17.724 C18:1 ω9c 1.3 17.769 C15:0 0.7 15 C18:0 0.4 18 C17:0 iso 0.4 16.629

API 20E

API zym

API 50CHac

Isolation source categories

Isolation

Taxonmaps

69479

Global distribution of 16S sequence X83811 (>99% sequence identity) for Jonesia denitrificans subclade from Microbeatlas

Aquatic Samples	156
Soil Samples	236
Animal Samples	1091
Plant Samples	57
Total Samples	1540

Risk assessment

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
124043	ASM1904846v1 assembly for Jonesia denitrificans FDAARGOS 1440	complete	GCA_019048465	43674.5	8063552596	43674	98.7
66792	45232_G01 assembly for Jonesia denitrificans NCTC10816	complete	GCA_900475835	43674.4	2808606808	43674	98.54
66792	ASM2406v1 assembly for Jonesia denitrificans DSM 20603	complete	GCA_000024065	471856.5	644736376	471856	98.54

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20218	Jonesia denitrificans 16S rRNA gene	X78420	1514		471856
20218	J.denitrificans 16S rRNA gene	X83811	1420		471856

GC content

Predictions

Literature

Topic	Title	Authors	Journal	DOI	Year
Metabolism	Light-inducible carotenoid production controlled by a MarR-type regulator in Corynebacterium glutamicum.	Sumi S, Suzuki Y, Matsuki T, Yamamoto T, Tsuruta Y, Mise K, Kawamura T, Ito Y, Shimada Y, Watanabe E, Watanabe S, Toriyabe M, Takano Shiratori H, Ueda K, Takano H.	Sci Rep	10.1038/s41598-019-49384-7	2019
Stress	Crystal structure of a phosphoribosyl anthranilate isomerase from the hyperthermophilic archaeon Thermococcus kodakaraensis.	Perveen S, Rashid N, Papageorgiou AC.	Acta Crystallogr F Struct Biol Commun	10.1107/s2053230x16015223	2016
Metabolism	Degradation of Granular Starch by the Bacterium Microbacterium aurum Strain B8.A Involves a Modular alpha-Amylase Enzyme System with FNIII and CBM25 Domains.	Valk V, Eeuwema W, Sarian FD, van der Kaaij RM, Dijkhuizen L.	Appl Environ Microbiol	10.1128/aem.01029-15	2015
Genetics	Genomic and proteomic features of mycobacteriophage SWU1 isolated from China soil.	Fan X, Yan J, Xie L, Zeng L, Young RF, Xie J.	Gene	10.1016/j.gene.2015.02.053	2015
Enzymology	Comprehensive Laboratory Evaluation of a Specific Lateral Flow Assay for the Presumptive Identification of Francisella tularensis in Suspicious White Powders and Aerosol Samples.	Pillai SP, DePalma L, Prentice KW, Ramage JG, Chapman C, Sarwar J, Parameswaran N, Petersen J, Yockey B, Young J, Singh A, Pillai CA, Manickam G, Thirunavkkarasu N, Avila JR, Sharma S, Morse SA, Venkateswaran K, Anderson K, Hodge DR.	Health Secur	10.1089/hs.2019.0151	2020
Phylogeny	Highly diverse nirK genes comprise two major clades that harbour ammonium-producing denitrifiers.	Helen D, Kim H, Tytgat B, Anne W.	BMC Genomics	10.1186/s12864-016-2465-0	2016
Metabolism	Cellodextrin utilization by bifidobacterium breve UCC2003.	Pokusaeva K, O'Connell-Motherway M, Zomer A, Macsharry J, Fitzgerald GF, van Sinderen D.	Appl Environ Microbiol	10.1128/aem.01786-10	2011
Metabolism	Discovery of a cytokinin deaminase.	Goble AM, Fan H, Sali A, Raushel FM.	ACS Chem Biol	10.1021/cb200198c	2011
Enzymology	Comprehensive Laboratory Evaluation of a Lateral Flow Assay for the Detection of Yersinia pestis.	Prentice KW, DePalma L, Ramage JG, Sarwar J, Parameswaran N, Petersen J, Yockey B, Young J, Joshi M, Thirunavvukarasu N, Singh A, Chapman C, Avila JR, Pillai CA, Manickam G, Sharma SK, Morse SA, Venkateswaran KV, Anderson K, Hodge DR, Pillai SP.	Health Secur	10.1089/hs.2019.0094	2019
Enzymology	Unexpected abundance of coenzyme F(420)-dependent enzymes in Mycobacterium tuberculosis and other actinobacteria.	Selengut JD, Haft DH.	J Bacteriol	10.1128/jb.00425-10	2010
	In silico characterization of pectate lyase protein sequences from different source organisms.	Dubey AK, Yadav S, Kumar M, Singh VK, Sarangi BK, Yadav D.	Enzyme Res	10.4061/2010/950230	2010
	Identification of putative adhesins of Actinobacillus suis and their homologues in other members of the family Pasteurellaceae.	Bujold AR, MacInnes JI.	BMC Res Notes	10.1186/s13104-015-1659-x	2015
Metabolism	Genomics of aerobic cellulose utilization systems in actinobacteria.	Anderson I, Abt B, Lykidis A, Klenk HP, Kyrpides N, Ivanova N.	PLoS One	10.1371/journal.pone.0039331	2012
Genetics	Characterization of the genome of the polyvalent lytic bacteriophage GTE2, which has potential for biocontrol of Gordonia-, Rhodococcus-, and Nocardia-stabilized foams in activated sludge plants.	Petrovski S, Seviour RJ, Tillett D.	Appl Environ Microbiol	10.1128/aem.00025-11	2011
Enzymology	Comprehensive Laboratory Evaluation of a Highly Specific Lateral Flow Assay for the Presumptive Identification of Bacillus anthracis Spores in Suspicious White Powders and Environmental Samples.	Ramage JG, Prentice KW, DePalma L, Venkateswaran KS, Chivukula S, Chapman C, Bell M, Datta S, Singh A, Hoffmaster A, Sarwar J, Parameswaran N, Joshi M, Thirunavkkarasu N, Krishnan V, Morse S, Avila JR, Sharma S, Estacio PL, Stanker L, Hodge DR, Pillai SP.	Health Secur	10.1089/hs.2016.0041	2016
Metabolism	Environmental Sensing in Actinobacteria: a Comprehensive Survey on the Signaling Capacity of This Phylum.	Huang X, Pinto D, Fritz G, Mascher T.	J Bacteriol	10.1128/jb.00176-15	2015
Metabolism	A mycobacterial phosphoribosyltransferase promotes bacillary survival by inhibiting oxidative stress and autophagy pathways in macrophages and zebrafish.	Mohanty S, Jagannathan L, Ganguli G, Padhi A, Roy D, Alaridah N, Saha P, Nongthomba U, Godaly G, Gopal RK, Banerjee S, Sonawane A.	J Biol Chem	10.1074/jbc.m114.598482	2015
	Annotation of Protein Domains Reveals Remarkable Conservation in the Functional Make up of Proteomes Across Superkingdoms.	Nasir A, Naeem A, Khan MJ, Nicora HD, Caetano-Anolles G.	Genes (Basel)	10.3390/genes2040869	2011
Phylogeny	Bioinformatic characterization of the 4-Toluene Sulfonate Uptake Permease (TSUP) family of transmembrane proteins.	Shlykov MA, Zheng WH, Chen JS, Saier MH.	Biochim Biophys Acta	10.1016/j.bbamem.2011.12.005	2012
Genetics	Developmental biology of Streptomyces from the perspective of 100 actinobacterial genome sequences.	Chandra G, Chater KF.	FEMS Microbiol Rev	10.1111/1574-6976.12047	2014
Phylogeny	Phylogenetic framework and molecular signatures for the main clades of the phylum Actinobacteria.	Gao B, Gupta RS.	Microbiol Mol Biol Rev	10.1128/mmbr.05011-11	2012
	A Novel Loop-Mediated Isothermal Amplification (LAMP) Assay for Detecting Salmonella Ser. Typhimurium in Egg Products.	Hu L, Zhang G.	J AOAC Int	10.1093/jaoacint/qsaf078	2025
	Neutron and high-resolution room-temperature X-ray data collection from crystallized lytic polysaccharide monooxygenase.	Bacik JP, Mekasha S, Forsberg Z, Kovalevsky A, Nix JC, Cuneo MJ, Coates L, Vaaje-Kolstad G, Chen JC, Eijsink VG, Unkefer CJ.	Acta Crystallogr F Struct Biol Commun	10.1107/s2053230x15019743	2015
Phylogeny	Cellular fatty acid composition as an adjunct to the identification of asporogenous, aerobic gram-positive rods.	Bernard KA, Bellefeuille M, Ewan EP.	J Clin Microbiol	10.1128/jcm.29.1.83-89.1991	1991
Phylogeny	Bacteriophage typing of Listeria species.	Loessner MJ, Busse M.	Appl Environ Microbiol	10.1128/aem.56.6.1912-1918.1990	1990
	Evaluation of hybridization characteristics of a cloned pRF106 probe for Listeria monocytogenes detection and development of a nonisotopic colony hybridization assay.	Kim CM, Graves LM, Swaminathan B, Mayer LW, Weaver RE.	Appl Environ Microbiol	10.1128/aem.57.1.289-294.1991	1991
Biotechnology	Rapid confirmation of Listeria monocytogenes isolated from foods by a colony blot assay using a digoxigenin-labeled synthetic oligonucleotide probe.	Kim C, Swaminathan B, Cassaday PK, Mayer LW, Holloway BP.	Appl Environ Microbiol	10.1128/aem.57.6.1609-1614.1991	1991
	Production of prebiotic xylooligosaccharides from arabino- and glucuronoxylan using a two-domain Jonesia denitrificans xylanase from GH10 family.	Vacilotto MM, Sepulchro AGV, Pellegrini VOA, Polikarpov I.	Enzyme Microb Technol	10.1016/j.enzmictec.2021.109743	2021
	1H, 13C, 15N resonance assignment of the apo form of the small, chitin-active lytic polysaccharide monooxygenase JdLPMO10A from Jonesia denitrificans.	Christensen IA, Eijsink VGH, Aachmann FL, Courtade G.	Biomol NMR Assign	10.1007/s12104-020-09986-z	2021
Metabolism	Structural and functional characterization of a small chitin-active lytic polysaccharide monooxygenase domain of a multi-modular chitinase from Jonesia denitrificans.	Mekasha S, Forsberg Z, Dalhus B, Bacik JP, Choudhary S, Schmidt-Dannert C, Vaaje-Kolstad G, Eijsink VG.	FEBS Lett	10.1002/1873-3468.12025	2016
	Neutron and Atomic Resolution X-ray Structures of a Lytic Polysaccharide Monooxygenase Reveal Copper-Mediated Dioxygen Binding and Evidence for N-Terminal Deprotonation.	Bacik JP, Mekasha S, Forsberg Z, Kovalevsky AY, Vaaje-Kolstad G, Eijsink VGH, Nix JC, Coates L, Cuneo MJ, Unkefer CJ, Chen JC.	Biochemistry	10.1021/acs.biochem.7b00019	2017
	Identification and Characterization of a Novel Endo-beta-1,4-Xylanase from Streptomyces sp. T7 and Its Application in Xylo-Oligosaccharide Production.	Li Y, Zhang X, Lu C, Lu P, Yin C, Ye Z, Huang Z.	Molecules	10.3390/molecules27082516	2022
Phylogeny	Phylogenetic diversity and activity screening of cultivable Actinobacteria isolated from marine sponges and associated environments from the western coast of India.	Baig U, Dahanukar N, Shintre N, Holkar K, Pund A, Lele U, Gujarathi T, Patel K, Jakati A, Singh R, Vidwans H, Tamhane V, Deshpande N, Watve M.	Access Microbiol	10.1099/acmi.0.000242	2021
Genetics	Sequence and structure analyses of lytic polysaccharide monooxygenases mined from metagenomic DNA of humus samples around white-rot fungi in Cuc Phuong tropical forest, Vietnam	Truong N, Le T, Nguyen H, Nguyen H, Dao T, Tran T, Tran H, Nguyen D, Nguyen T, Phan T, Do T, Phan N, Ngo T, Vu V.	PeerJ		2024
	Property and Function of a Novel Chitinase Containing Dual Catalytic Domains Capable of Converting Chitin Into N-Acetyl-D-Glucosamine.	Wang C, Chen X, Zhou N, Chen Y, Zhang A, Chen K, Ouyang P.	Front Microbiol	10.3389/fmicb.2022.790301	2022
	Characterization of a novel GH10 alkali-thermostable xylanase from a termite microbiome.	Mon ML, Marrero Diaz de Villegas R, Campos E, Soria MA, Talia PM.	Bioresour Bioprocess	10.1186/s40643-022-00572-w	2022
	Chitin-Active Lytic Polysaccharide Monooxygenases Are Rare in Cellulomonas Species.	Li J, Goddard-Borger ED, Raji O, Saxena H, Solhi L, Mathieu Y, Master ER, Wakarchuk WW, Brumer H.	Appl Environ Microbiol	10.1128/aem.00968-22	2022
Metabolism	A trimodular bacterial enzyme combining hydrolytic activity with oxidative glycosidic bond cleavage efficiently degrades chitin.	Mekasha S, Tuveng TR, Askarian F, Choudhary S, Schmidt-Dannert C, Niebisch A, Modregger J, Vaaje-Kolstad G, Eijsink VGH.	J Biol Chem	10.1074/jbc.ra120.013040	2020
	Complete genome sequence of Rhodothermaceae bacterium RA with cellulolytic and xylanolytic activities.	Liew KJ, Teo SC, Shamsir MS, Sani RK, Chong CS, Chan KG, Goh KM.	3 Biotech	10.1007/s13205-018-1391-z	2018
Cultivation	Evaluation of several modifications of an ecometric technique for assessment of media performance.	Kornacki JL, Gurtler JB, Yan Z, Cooper CM.	J Food Prot	10.4315/0362-028x-66.9.1727	2003
	Same but not alike: Structure, flexibility and energetics of domains in multi-domain proteins are influenced by the presence of other domains.	Vishwanath S, de Brevern AG, Srinivasan N.	PLoS Comput Biol	10.1371/journal.pcbi.1006008	2018
Phylogeny	A taxonomic study of the genus Listeria using sodium dodecyl sulphate-polyacrylamide gel electrophoresis of intracellular proteins.	Finn B, Rowe M.	Electrophoresis	10.1002/elps.1150171025	1996
Phylogeny	Phylogenetic analysis of the genera Cellulomonas, Promicromonospora, and Jonesia and proposal to exclude the genus Jonesia from the family Cellulomonadaceae.	Rainey FA, Weiss N, Stackebrandt E.	Int J Syst Bacteriol	10.1099/00207713-45-4-649	1995
Enzymology	Polymerase chain reaction amplification of the flaA gene for the rapid identification of Listeria spp.	Gray DI, Kroll RG.	Lett Appl Microbiol	10.1111/j.1472-765x.1995.tb00409.x	1995
Enzymology	Molecular characterization of a Xylanase-producing fungus isolated from fouled soil.	Sakthiselvan P, Naveena B, Partha N.	Braz J Microbiol	10.1590/s1517-83822014000400020	2014
Phylogeny	Taxonomy of the genus Listeria.	Rocourt J.	Infection	10.1007/bf01639728	1988
Metabolism	Analyses of fermentation products of Listeria species by frequency-pulsed electron-capture gas-liquid chromatography.	Daneshvar MI, Brooks JB, Malcolm GB, Pine L.	Can J Microbiol	10.1139/m89-131	1989
	Identification of a novel pentatricopeptide repeat subfamily with a C-terminal domain of bacterial origin acquired via ancient horizontal gene transfer.	Manna S, Barth C.	BMC Res Notes	10.1186/1756-0500-6-525	2013
Metabolism	Expression of Surface Protein LapB by a Wide Spectrum of Listeria monocytogenes Serotypes as Demonstrated with Anti-LapB Monoclonal Antibodies.	Boivin T, Elmgren C, Brooks BW, Huang H, Pagotto F, Lin M.	Appl Environ Microbiol	10.1128/aem.01908-16	2016
	Harnessing microbial wealth for lignocellulose biomass valorization through secretomics: a review.	Sethupathy S, Morales GM, Li Y, Wang Y, Jiang J, Sun J, Zhu D.	Biotechnol Biofuels	10.1186/s13068-021-02006-9	2021
Enzymology	Co-occurrence of analogous enzymes determines evolution of a novel (betaalpha)8-isomerase sub-family after non-conserved mutations in flexible loop.	Verduzco-Castro EA, Michalska K, Endres M, Juarez-Vazquez AL, Noda-Garcia L, Chang C, Henry CS, Babnigg G, Joachimiak A, Barona-Gomez F.	Biochem J	10.1042/bj20151271	2016
	Cultivation-independent methods applied to the microbial prospection of oil and gas in soil from a sedimentary basin in Brazil.	Miqueletto PB, Andreote FD, Dias AC, Ferreira JC, Dos Santos Neto EV, de Oliveira VM.	AMB Express	10.1186/2191-0855-1-35	2011
Enzymology	Denitrifying bacteria isolated from terrestrial subsurface sediments exposed to mixed-waste contamination.	Green SJ, Prakash O, Gihring TM, Akob DM, Jasrotia P, Jardine PM, Watson DB, Brown SD, Palumbo AV, Kostka JE.	Appl Environ Microbiol	10.1128/aem.03069-09	2010
Metabolism	Oxygen Activation by Cu LPMOs in Recalcitrant Carbohydrate Polysaccharide Conversion to Monomer Sugars.	Meier KK, Jones SM, Kaper T, Hansson H, Koetsier MJ, Karkehabadi S, Solomon EI, Sandgren M, Kelemen B.	Chem Rev	10.1021/acs.chemrev.7b00421	2018
Genetics	Genome-Based Taxonomic Classification of the Phylum Actinobacteria.	Nouioui I, Carro L, Garcia-Lopez M, Meier-Kolthoff JP, Woyke T, Kyrpides NC, Pukall R, Klenk HP, Goodfellow M, Goker M.	Front Microbiol	10.3389/fmicb.2018.02007	2018
Genetics	Complete genome sequence of Jonesia denitrificans type strain (Prevot 55134).	Pukall R, Gehrich-Schroter G, Lapidus A, Nolan M, Glavina Del Rio T, Lucas S, Chen F, Tice H, Pitluck S, Cheng JF, Copeland A, Saunders E, Brettin T, Detter JC, Bruce D, Goodwin L, Pati A, Ivanova N, Mavromatis K, Ovchinnikova G, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Chain P, Goker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Han C	Stand Genomic Sci	10.4056/sigs.41646	2009
	The Murein Types of Listeria grayi, Listeria murrayi and Listeria denitrificans.	Fiedler F, Seger J	Syst Appl Microbiol	10.1016/S0723-2020(83)80002-2	1983
Phylogeny	Identification of some clinical strains of CDC coryneform group A-3 and A-4 bacteria as Cellulomonas species and proposal of Cellulomonas hominis sp. nov. for some group A-3 strains.	Funke G, Ramos CP, Collins MD.	J Clin Microbiol	10.1128/jcm.33.8.2091-2097.1995	1995
Phylogeny	Jonesia quinghaiensis sp. nov., a new member of the suborder Micrococcineae.	Schumann P, Cui X, Stackebrandt E, Kroppenstedt RM, Xu L, Jiang C.	Int J Syst Evol Microbiol	10.1099/ijs.0.63223-0	2004