Bergeriella denitrificans (DSM 17675, ATCC 14686, CCUG 2155)

Name: Bergeriella denitrificans (DSM 17675, ATCC 14686, CCUG 2155)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 10446

Type strain

Strain Designation M37

Culture col. no. DSM 17675 ATCC 14686 CCUG 2155 IAM 14975 NCTC 10295 4 more

NCBI tax ID(s) 1349758 494

Special Collections DSMZ CCUG JCM CIP

Links

Bergeriella denitrificans M37 is an obligate aerobe, mesophilic, Gram-negative prokaryote that was isolated from oral mucosa of rat.

Gram-negative coccus-shaped obligate aerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 389283

ATCC 14686,CCUG 2155,NCTC 10295,CIP 72.16,IAM 14975,DSM 17675,NBRC 102155,JCM 21446,CNCTC 6141

@ref 20215

Last LPSN update 2025-12-16 09:49:20

Domain Pseudomonadati

Phylum Pseudomonadota

Class Betaproteobacteria

Order Neisseriales

Family Neisseriaceae

Genus Bergeriella

Species Bergeriella denitrificans

Full scientific name Bergeriella denitrificans (Berger 1962) Xie and Yokota 2005

Synonyms (1)

Neisseria denitrificans

BacDive ID	Other strains from **Bergeriella denitrificans** (1)	Type strain
143106	B. denitrificans CCUG 17229

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Motility
118892	negative	coccus-shaped
125438	negative

Colony morphology

118892

Hemolysis ability1

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
7117	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
36044	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)
118892	CIP Medium 6	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
7117	positive	growth	37	mesophilic
36044	positive	growth	37	mesophilic
67770	positive	growth	37	mesophilic
118892	positive	growth	22-45

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
118892	obligate aerobe
125439	microaerophile

Spore formation

@ref	Spore formation	Confidence
125438		91.87
125439		96.6

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68381	40585 ChEBI	alpha-cyclodextrin	-	builds acid from	from API rID32STR
68381	29016 ChEBI	arginine	-	hydrolysis	from API rID32STR
68381	18333 ChEBI	D-arabitol	-	builds acid from	from API rID32STR
118892	15824 ChEBI	D-fructose	+	degradation
118892	17634 ChEBI	D-glucose	+	degradation
68381	16899 ChEBI	D-mannitol	-	builds acid from	from API rID32STR
68381	16988 ChEBI	D-ribose	-	builds acid from	from API rID32STR
68381	16443 ChEBI	D-tagatose	-	builds acid from	from API rID32STR
68381	28087 ChEBI	glycogen	-	builds acid from	from API rID32STR
68381	606565 ChEBI	hippurate	+	hydrolysis	from API rID32STR
68381	30849 ChEBI	L-arabinose	-	builds acid from	from API rID32STR
68381	17716 ChEBI	lactose	-	builds acid from	from API rID32STR
118892	17716 ChEBI	lactose	+	degradation
68381	17306 ChEBI	maltose	-	builds acid from	from API rID32STR
118892	17306 ChEBI	maltose	+	degradation
68381	6731 ChEBI	melezitose	-	builds acid from	from API rID32STR
68381	28053 ChEBI	melibiose	-	builds acid from	from API rID32STR
68381	320055 ChEBI	methyl beta-D-glucopyranoside	-	builds acid from	from API rID32STR
118892	17632 ChEBI	nitrate	-	reduction
118892	16301 ChEBI	nitrite	+	reduction
68381	27941 ChEBI	pullulan	-	builds acid from	from API rID32STR
68381	16634 ChEBI	raffinose	-	builds acid from	from API rID32STR
68381	30911 ChEBI	sorbitol	-	builds acid from	from API rID32STR
68381	17992 ChEBI	sucrose	-	builds acid from	from API rID32STR
118892	17992 ChEBI	sucrose	+	degradation
68381	27082 ChEBI	trehalose	-	builds acid from	from API rID32STR
118892	35020 ChEBI	tributyrin	-	hydrolysis
68381	16199 ChEBI	urea	+	hydrolysis	from API rID32STR

Antibiotic resistance

@ref	Metabolite	Is antibiotic	Is sensitive	Is resistant
118892	0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)

Metabolite production

@ref	Chebi-ID	Metabolite	Production
68381	15688 ChEBI	acetoin		from API rID32STR
118892		polysaccharides

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test
68381	15688 ChEBI	acetoin	-	from API rID32STR

Enzymes

@ref	Value	Activity
68381	Alanyl-Phenylalanyl-Proline arylamidase	-	from API rID32STR
118892	alcohol dehydrogenase	-
68381	alkaline phosphatase	+	from API rID32STR
68381	alpha-galactosidase	-	from API rID32STR
68381	arginine dihydrolase	-	from API rID32STR
68381	beta-galactosidase	-	from API rID32STR
118892	beta-galactosidase	-
68381	beta-glucosidase	-	from API rID32STR
68381	beta-glucuronidase	-	from API rID32STR
68381	beta-mannosidase	-	from API rID32STR
118892	catalase	+
118892	DNase	-
118892	gamma-glutamyltransferase	-
68381	glycyl tryptophan arylamidase	-	from API rID32STR
118892	lysine decarboxylase	-
68381	N-acetyl-beta-glucosaminidase	-	from API rID32STR
118892	ornithine decarboxylase	-
118892	oxidase	+
68381	pyrrolidonyl arylamidase	-	from API rID32STR
68381	urease	+	from API rID32STR
118892	urease	+

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	suberin monomers biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	ppGpp biosynthesis	100	4 of 4
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	denitrification	100	2 of 2
66794	vitamin B1 metabolism	100	13 of 13
66794	pentose phosphate pathway	100	11 of 11
66794	coenzyme A metabolism	100	4 of 4
66794	ubiquinone biosynthesis	100	7 of 7
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	formaldehyde oxidation	100	3 of 3
66794	folate polyglutamylation	100	1 of 1
66794	teichoic acid biosynthesis	100	1 of 1
66794	L-lactaldehyde degradation	100	3 of 3
66794	ribulose monophosphate pathway	100	2 of 2
66794	palmitate biosynthesis	95.45	21 of 22
66794	valine metabolism	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	lipid A biosynthesis	88.89	8 of 9
66794	isoleucine metabolism	87.5	7 of 8
66794	propanol degradation	85.71	6 of 7
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	photosynthesis	85.71	12 of 14
66794	proline metabolism	81.82	9 of 11
66794	threonine metabolism	80	8 of 10
66794	peptidoglycan biosynthesis	80	12 of 15
66794	methylglyoxal degradation	80	4 of 5
66794	heme metabolism	78.57	11 of 14
66794	tetrahydrofolate metabolism	78.57	11 of 14
66794	citric acid cycle	78.57	11 of 14
66794	phenylalanine metabolism	76.92	10 of 13
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	CMP-KDO biosynthesis	75	3 of 4
66794	sulfopterin metabolism	75	3 of 4
66794	gluconeogenesis	75	6 of 8
66794	C4 and CAM-carbon fixation	75	6 of 8
66794	glycogen biosynthesis	75	3 of 4
66794	alanine metabolism	72.41	21 of 29
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	propionate fermentation	70	7 of 10
66794	purine metabolism	68.09	64 of 94
66794	glutamate and glutamine metabolism	67.86	19 of 28
66794	octane oxidation	66.67	2 of 3
66794	flavin biosynthesis	66.67	10 of 15
66794	serine metabolism	66.67	6 of 9
66794	acetoin degradation	66.67	2 of 3
66794	aspartate and asparagine metabolism	66.67	6 of 9
66794	NAD metabolism	66.67	12 of 18
66794	CO2 fixation in Crenarchaeota	66.67	6 of 9
66794	d-mannose degradation	66.67	6 of 9
66794	vitamin B6 metabolism	63.64	7 of 11
66794	methionine metabolism	61.54	16 of 26
66794	isoprenoid biosynthesis	61.54	16 of 26
66794	urea cycle	61.54	8 of 13
66794	tryptophan metabolism	60.53	23 of 38
66794	glycogen metabolism	60	3 of 5
66794	gallate degradation	60	3 of 5
66794	3-phenylpropionate degradation	60	9 of 15
66794	Entner Doudoroff pathway	60	6 of 10
66794	vitamin K metabolism	60	3 of 5
66794	hydrogen production	60	3 of 5
66794	non-pathway related	57.89	22 of 38
66794	tyrosine metabolism	57.14	8 of 14
66794	cysteine metabolism	55.56	10 of 18
66794	phenylpropanoid biosynthesis	53.85	7 of 13
66794	leucine metabolism	53.85	7 of 13
66794	glycolysis	52.94	9 of 17
66794	lysine metabolism	52.38	22 of 42
66794	pyrimidine metabolism	51.11	23 of 45
66794	cis-vaccenate biosynthesis	50	1 of 2
66794	ethanol fermentation	50	1 of 2
66794	dolichol and dolichyl phosphate biosynthesis	50	1 of 2
66794	lactate fermentation	50	2 of 4
66794	glycolate and glyoxylate degradation	50	3 of 6
66794	cyclohexanol degradation	50	2 of 4
66794	dTDPLrhamnose biosynthesis	50	4 of 8
66794	butanoate fermentation	50	2 of 4
66794	degradation of aromatic, nitrogen containing compounds	50	6 of 12
66794	quinate degradation	50	1 of 2
66794	starch degradation	50	5 of 10
66794	ketogluconate metabolism	50	4 of 8
66794	glutathione metabolism	50	7 of 14
66794	adipate degradation	50	1 of 2
66794	acetate fermentation	50	2 of 4
66794	histidine metabolism	48.28	14 of 29
66794	degradation of sugar acids	48	12 of 25
66794	sulfate reduction	46.15	6 of 13
66794	arginine metabolism	45.83	11 of 24
66794	lipid metabolism	45.16	14 of 31
66794	oxidative phosphorylation	40.66	37 of 91
66794	glycine metabolism	40	4 of 10
66794	lipoate biosynthesis	40	2 of 5
66794	ethylmalonyl-CoA pathway	40	2 of 5
66794	phosphatidylethanolamine bioynthesis	38.46	5 of 13
66794	degradation of sugar alcohols	37.5	6 of 16
66794	metabolism of disaccharids	36.36	4 of 11
66794	degradation of pentoses	35.71	10 of 28
66794	cyanate degradation	33.33	1 of 3
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	chlorophyll metabolism	33.33	6 of 18
66794	sulfoquinovose degradation	33.33	1 of 3
66794	pantothenate biosynthesis	33.33	2 of 6
66794	4-hydroxymandelate degradation	33.33	3 of 9
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	enterobactin biosynthesis	33.33	1 of 3
66794	IAA biosynthesis	33.33	1 of 3
66794	coenzyme M biosynthesis	30	3 of 10
66794	4-hydroxyphenylacetate degradation	30	3 of 10
66794	phenol degradation	30	6 of 20
66794	degradation of hexoses	27.78	5 of 18
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	carotenoid biosynthesis	27.27	6 of 22
66794	toluene degradation	25	1 of 4
66794	ascorbate metabolism	22.73	5 of 22
66794	molybdenum cofactor biosynthesis	22.22	2 of 9
66794	nitrate assimilation	22.22	2 of 9

API rID32STR

@ref	ADH (Arg)	beta GLU	beta GAR	beta GUR	alpha GAL	PAL	RIB	MAN	SOR	LAC	TRE	RAF	SAC	LARA	DARL	Acid from alpha-cyclodextrinCDEX	Acetoin production (Voges Proskauer test)VP	Alanyl-Phenylalanyl-Proline arylamidaseAPPA	beta GAL	Pyrrolidonyl arylamidasePyrA	N-Acetyl-glucosaminidasebeta NAG	Glycyl-tryptophan arylamidaseGTA	HIP	GLYG	PUL	MAL	MEL	MLZ	Acidification of methyl beta-D-glucopyranosideMbeta DG	TAG	beta MAN	URE
44501	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Mammals	#Muridae (Mouse/Rat)
#Host Body-Site	#Oral cavity and airways	-

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
7117	oral mucosa of rat	Hamburg	Germany	DEU	Europe
44501	Rabbit oral mucosa	Hamburg	Germany	DEU	Europe
67770	Oral mucosa of guinea pig		Germany	DEU	Europe
118892	Animal, Rabbit, oral mucosa	Hamburg	Germany	DEU	Europe

Taxonmaps

69479

Global distribution of 16S sequence AB087265 (>99% sequence identity) for Bergeriella denitrificans subclade from Microbeatlas

Aquatic Samples	192
Soil Samples	5
Animal Samples	484
Plant Samples
Total Samples	681

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
7117	1	Risk group (German classification) According to TRBA 466
118892	1	Risk group (French classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	NCBI tax ID	Score
124043	ASM4783912v1 assembly for Bergeriella denitrificans DSM 17675	complete	GCA_047839125	494	99.2
67770	44738_H02 assembly for Bergeriella denitrificans NCTC10295	contig	GCA_900453875	494	77.93
67770	ASM159218v1 assembly for Bergeriella denitrificans NBRC 102155	contig	GCA_001592185	1349758	0.34

Genome browser: GCA_047839125

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Neisseria denitrificans 16S ribosomal RNA	L06173	1478	494
20218	N.denitrificans 16S ribosomal RNA	M35020	1478	494
7117	Bergeriella denitrificans gene for 16S rRNA, strain: IAM 14975	AB087265	1494	494
124043	Bergeriella denitrificans gene for 16S rRNA, partial sequence, strain: NBRC 102155.	AB681722	1466	494

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Bergeriella denitrificans NBRC 102155
NCBI: GCA_001592185

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	96.60	no
125439	motility	BacteriaNetⓘ	no	87.10	no
125439	gram_stain	BacteriaNetⓘ	positive	80.70	no
125439	oxygen_tolerance	BacteriaNetⓘ	microaerophile	97.60	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Bergeriella denitrificans NBRC 102155
PATRIC: 1349758.6

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	99.50	no
125438	anaerobic	anaerobicⓘ	no	92.63	yes
125438	spore-forming	spore-formingⓘ	no	91.87	no
125438	aerobic	aerobicⓘ	no	50.44	yes
125438	thermophilic	thermophileⓘ	no	97.32	no
125438	flagellated	motile2+ⓘ	no	82.91	no

Literature

References

#7117	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 17675
#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 )
#36044	; Curators of the CIP;
#44501	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 2155
#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 )
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#68381	Automatically annotated from API rID32STR .
#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 .
#118892	Collection of Institut Pasteur ; Curators of the CIP; CIP 72.16
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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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