Nicoletella semolina (DSM 16380, CCUG 43639, CIP 108715)

Name: Nicoletella semolina (DSM 16380, CCUG 43639, CIP 108715)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 11728

Type strain

Strain Designation D1522_98, JF2139, D1522

Culture col. no. DSM 16380 CCUG 43639 CIP 108715 D1522_98 JF2139 1 more

NCBI tax ID(s) 271160

Special Collections DSMZ CCUG CIP

History <- P. Kuhnert; D1522_98 CIP <- 2005, CCUG <- 2000, P. Kuhnert, Berne Univ., Berne, Switzerland: strain D1522

Links

Nicoletella semolina D1522_98 is a microaerophile, Gram-negative, rod-shaped animal pathogen that was isolated from horse trachea.

Gram-negative rod-shaped microaerophile animal pathogen genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 133066

CCUG 43639,DSM 16380,CIP 108715

@ref 20215

Last LPSN update 2026-02-09 11:20:38

Domain Bacteria

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Pasteurellales

Family Pasteurellaceae

Genus Nicoletella

Species Nicoletella semolina

Full scientific name Nicoletella semolina Kuhnert et al. 2005

BacDive ID	Other strains from **Nicoletella semolina** (18)	Type strain
144196	N. semolina CCUG 23468, MCCM 00056
144979	N. semolina CCUG 27342, CG 848/89
145040	N. semolina CCUG 27497, CCUG 25592
146800	N. semolina CCUG 32135
146822	N. semolina CCUG 32179
150320	N. semolina CCUG 39639
150998	N. semolina CCUG 42978
151289	N. semolina CCUG 43638
151290	N. semolina CCUG 43640
151291	N. semolina CCUG 43641
151292	N. semolina CCUG 43642
151293	N. semolina CCUG 43643
151294	N. semolina CCUG 43644
151295	N. semolina CCUG 43645
151296	N. semolina CCUG 43646
151297	N. semolina CCUG 43647
152092	N. semolina CCUG 45728
152518	N. semolina CCUG 46992

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
122556	negative	rod-shaped
125438			95
125438	negative		90

Colony morphology

122556

Hemolysis ability1

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
6417	COLUMBIA BLOOD AGAR (DSMZ Medium 429)	Medium recipe at MediaDive	Name: COLUMBIA BLOOD AGAR (DSMZ Medium 429) Composition: Horse blood 40.0 g/l Columbia agar base
6417	COLUMBIA BLOOD AGAR WITH CHARCOAL (DSMZ Medium 429a)	Medium recipe at MediaDive	Name: COLUMBIA BLOOD AGAR WITH CHARCOAL (DSMZ Medium 429a) Composition: Horse blood 40.0 g/l Activated charcoal 2.0 g/l Columbia agar base
39866	MEDIUM 6 - Columbia agar with 10 % horse blood		Distilled water make up to (1000.000 ml);Columbia agar (39.000 g);Horseblood (100.000 ml)
122556	CIP Medium 6	Medium recipe at CIP
122556	CIP Medium 45	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
6417	positive	growth	37
39866	positive	growth	37

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
6417	microaerophile
125439	microaerophile	95.1

Spore formation

@ref	Spore formation	Confidence
125439		99.5
125438		90.088

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68371	27613 ChEBI	amygdalin	-	builds acid from	from API 50CH acid
68371	18305 ChEBI	arbutin	-	builds acid from	from API 50CH acid
68371	17057 ChEBI	cellobiose	-	builds acid from	from API 50CH acid
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	16024 ChEBI	D-mannose	+	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
68371	16813 ChEBI	galactitol	-	builds acid from	from API 50CH acid
68371	28066 ChEBI	gentiobiose	-	builds acid from	from API 50CH acid
68371	24265 ChEBI	gluconate	-	builds acid from	from API 50CH acid
68371	17754 ChEBI	glycerol	-	builds acid from	from API 50CH acid
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
68371	17716 ChEBI	lactose	-	builds acid from	from API 50CH acid
68371	17306 ChEBI	maltose	+	builds acid from	from API 50CH acid
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
68371	17268 ChEBI	myo-inositol	-	builds acid from	from API 50CH acid
68371	59640 ChEBI	N-acetylglucosamine	+	builds acid from	from API 50CH acid
122556	17632 ChEBI	nitrate	+	reduction
122556	16301 ChEBI	nitrite	-	reduction
68371		Potassium 2-ketogluconate	-	builds acid from	from API 50CH acid
68371	16634 ChEBI	raffinose	-	builds acid from	from API 50CH acid
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
68371	17992 ChEBI	sucrose	+	builds acid from	from API 50CH acid
68371	27082 ChEBI	trehalose	+	builds acid from	from API 50CH acid
68371	32528 ChEBI	turanose	-	builds acid from	from API 50CH acid
68371	17151 ChEBI	xylitol	-	builds acid from	from API 50CH acid

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
122556	alcohol dehydrogenase	-	1.1.1.1
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-galactosidase	-	3.2.1.22	from API zym
68382	alpha-glucosidase	+	3.2.1.20	from API zym
68382	alpha-mannosidase	-	3.2.1.24	from API zym
68382	beta-galactosidase	-	3.2.1.23	from API zym
68382	beta-glucosidase	-	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
122556	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	lipase (C 14)	-		from API zym
122556	lysine decarboxylase	-	4.1.1.18
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
122556	ornithine decarboxylase	-	4.1.1.17
122556	oxidase	+
68382	trypsin	-	3.4.21.4	from API zym
122556	urease	+	3.5.1.5
68382	valine arylamidase	-		from API zym

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	L-lactaldehyde degradation	100	3 of 3
66794	ppGpp biosynthesis	100	4 of 4
66794	vitamin K metabolism	100	5 of 5
66794	metabolism of amino sugars and derivatives	100	5 of 5
66794	gluconeogenesis	100	8 of 8
66794	adipate degradation	100	2 of 2
66794	ubiquinone biosynthesis	100	7 of 7
66794	coenzyme A metabolism	100	4 of 4
66794	biotin biosynthesis	100	4 of 4
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	tetrahydrofolate metabolism	100	14 of 14
66794	folate polyglutamylation	100	1 of 1
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	palmitate biosynthesis	95.45	21 of 22
66794	pentose phosphate pathway	90.91	10 of 11
66794	threonine metabolism	90	9 of 10
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	C4 and CAM-carbon fixation	87.5	7 of 8
66794	photosynthesis	85.71	12 of 14
66794	vitamin B1 metabolism	84.62	11 of 13
66794	Entner Doudoroff pathway	80	8 of 10
66794	peptidoglycan biosynthesis	80	12 of 15
66794	glycogen metabolism	80	4 of 5
66794	methylglyoxal degradation	80	4 of 5
66794	valine metabolism	77.78	7 of 9
66794	lipid A biosynthesis	77.78	7 of 9
66794	phenylalanine metabolism	76.92	10 of 13
66794	acetate fermentation	75	3 of 4
66794	CMP-KDO biosynthesis	75	3 of 4
66794	sulfopterin metabolism	75	3 of 4
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	isoleucine metabolism	75	6 of 8
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	purine metabolism	68.09	64 of 94
66794	enterobactin biosynthesis	66.67	2 of 3
66794	flavin biosynthesis	66.67	10 of 15
66794	serine metabolism	66.67	6 of 9
66794	CO2 fixation in Crenarchaeota	66.67	6 of 9
66794	acetoin degradation	66.67	2 of 3
66794	selenocysteine biosynthesis	66.67	4 of 6
66794	cyanate degradation	66.67	2 of 3
66794	formaldehyde oxidation	66.67	2 of 3
66794	glycolysis	64.71	11 of 17
66794	pyrimidine metabolism	64.44	29 of 45
66794	alanine metabolism	62.07	18 of 29
66794	leucine metabolism	61.54	8 of 13
66794	non-pathway related	57.89	22 of 38
66794	methionine metabolism	57.69	15 of 26
66794	heme metabolism	57.14	8 of 14
66794	degradation of pentoses	57.14	16 of 28
66794	citric acid cycle	57.14	8 of 14
66794	aspartate and asparagine metabolism	55.56	5 of 9
66794	proline metabolism	54.55	6 of 11
66794	isoprenoid biosynthesis	53.85	14 of 26
66794	tryptophan metabolism	52.63	20 of 38
66794	oxidative phosphorylation	51.65	47 of 91
66794	ribulose monophosphate pathway	50	1 of 2
66794	cis-vaccenate biosynthesis	50	1 of 2
66794	ethanol fermentation	50	1 of 2
66794	glycolate and glyoxylate degradation	50	3 of 6
66794	kanosamine biosynthesis II	50	1 of 2
66794	suberin monomers biosynthesis	50	1 of 2
66794	phenylmercury acetate degradation	50	1 of 2
66794	NAD metabolism	50	9 of 18
66794	butanoate fermentation	50	2 of 4
66794	glycogen biosynthesis	50	2 of 4
66794	arginine metabolism	50	12 of 24
66794	ketogluconate metabolism	50	4 of 8
66794	histidine metabolism	48.28	14 of 29
66794	urea cycle	46.15	6 of 13
66794	vitamin B6 metabolism	45.45	5 of 11
66794	lysine metabolism	45.24	19 of 42
66794	lipid metabolism	45.16	14 of 31
66794	nitrate assimilation	44.44	4 of 9
66794	cysteine metabolism	44.44	8 of 18
66794	d-mannose degradation	44.44	4 of 9
66794	degradation of sugar acids	44	11 of 25
66794	degradation of sugar alcohols	43.75	7 of 16
66794	propanol degradation	42.86	3 of 7
66794	glutamate and glutamine metabolism	42.86	12 of 28
66794	tyrosine metabolism	42.86	6 of 14
66794	reductive acetyl coenzyme A pathway	42.86	3 of 7
66794	ascorbate metabolism	40.91	9 of 22
66794	glycine metabolism	40	4 of 10
66794	starch degradation	40	4 of 10
66794	lipoate biosynthesis	40	2 of 5
66794	degradation of hexoses	38.89	7 of 18
66794	metabolism of disaccharids	36.36	4 of 11
66794	sulfoquinovose degradation	33.33	1 of 3
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	octane oxidation	33.33	1 of 3
66794	propionate fermentation	30	3 of 10
66794	myo-inositol biosynthesis	30	3 of 10
66794	coenzyme M biosynthesis	30	3 of 10
66794	d-xylose degradation	27.27	3 of 11
66794	lactate fermentation	25	1 of 4
66794	cyclohexanol degradation	25	1 of 4
66794	dTDPLrhamnose biosynthesis	25	2 of 8
66794	degradation of aromatic, nitrogen containing compounds	25	3 of 12
66794	sulfate reduction	23.08	3 of 13
66794	glutathione metabolism	21.43	3 of 14

API zym

@ref	Control	Alkaline phosphatase	Esterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	Lipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
122556	-	+	+	+	-	+	-	-	-	-	+	+	-	-	-	+	-	-	-	-

API 50CHac

@ref	ControlQ	GLY	ERY	DARA	LARA	RIB	DXYL	LXYL	ADO	MDX	GAL	GLU	FRU	MNE	SBE	RHA	DUL	INO	MAN	SOR	MDM	MDG	NAG	AMY	ARB	ESC	SAL	CEL	MAL	LAC	MEL	SAC	TRE	INU	MLZ	RAF	AMD	GLYG	XLT	GEN	TUR	LYX	TAG	DFUC	LFUC	DARL	LARL	GNT	2KG	5KG
122556	not determinedn.d.	-	-	-	-	-	-	-	-	-	-	+	+	+	-	-	-	-	+	-	-	-	+	-	-	-	-	-	+	-	-	+	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+/-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Mammals	#Equidae (Horse)
#Host Body-Site	#Oral cavity and airways	#Trachea

Isolation

@ref	Sample type	Sampling date	Geographic location	Country	Country ISO 3 Code	Continent	Isolation date
6417	horse trachea		Bern	Switzerland	CHE	Europe
55978	Equine nasal discharge,adult horse,chronic cough	1998	Berne	Switzerland	CHE	Europe
122556	Animal, Horse, nose		Bern	Switzerland	CHE	Europe	1998

Taxonmaps

69479

Global distribution of 16S sequence AY508816 (>99% sequence identity) for Nicoletella semolina subclade from Microbeatlas

Aquatic Samples	339
Soil Samples	284
Animal Samples	13492
Plant Samples	89
Total Samples	14204

Interaction and safety

Risk assessment

@ref	Pathogenicity animal	Biosafety level	Biosafety level comment
6417		2	Risk group (German classification) According to TRBA 466
122556		1	Risk group (French classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM2985217v1 assembly for Nicoletella semolina JF2139	contig	GCA_029852175	271160.4		271160	73.32
66792	ASM434574v1 assembly for Nicoletella semolina DSM 16380	scaffold	GCA_004345745	271160.3	2795385463	271160	73.24

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
6417	Nicoletella semolina strain CCUG 43639 16S ribosomal RNA gene, partial sequence	AY508816	1365		271160

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Nicoletella semolina DSM 16380
NCBI: GCA_004345745

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	99.50	no
125439	motility	BacteriaNetⓘ	no	74.80	no
125439	gram_stain	BacteriaNetⓘ	negative	84.90	no
125439	oxygen_tolerance	BacteriaNetⓘ	microaerophile	95.10	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Nicoletella semolina DSM 16380
NCBI: GCA_004345745.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	90.00	no
125438	anaerobic	anaerobicⓘ	no	92.46	no
125438	aerobic	aerobicⓘ	no	74.88	no
125438	spore-forming	spore-formingⓘ	no	90.09	no
125438	thermophilic	thermophileⓘ	no	96.89	yes
125438	flagellated	motile2+ⓘ	no	95.00	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Nicoletella semolina gen. nov., sp. nov., a new member of Pasteurellaceae isolated from horses with airway disease.	Kuhnert P, Korczak B, Falsen E, Straub R, Hoops A, Boerlin P, Frey J, Mutters R	J Clin Microbiol	10.1128/JCM.42.12.5542-5548.2004	2004

References

#6417	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 16380
#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 )
#39866	; Curators of the CIP;
#55978	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 43639
#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) .
#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 )
#68371	Automatically annotated from API 50CH acid .
#68382	Automatically annotated from API zym .
#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 .
#122556	Collection of Institut Pasteur ; Curators of the CIP; CIP 108715
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Nicoletella semolina (DSM 16380, CCUG 43639, CIP 108715)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Metabolite utilization

Enzymes

Pathway annotation

API zym

API 50CHac

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_029852175

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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