Brachymonas denitrificans (DSM 15123, JCM 9216, CCUG 45365)

Name: Brachymonas denitrificans (DSM 15123, JCM 9216, CCUG 45365)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 2908

Type strain

Strain Designation AS-P1

Culture col. no. DSM 15123 JCM 9216 CCUG 45365 AS-P1 CGMCC 1.7100

NCBI tax ID(s) 1121117 28220

Special Collections DSMZ CCUG JCM

History <- JCM <- A. Hiraishi; AS-P1 A. Hiraishi AS-P1.

Links

Brachymonas denitrificans AS-P1 is an aerobe, mesophilic prokaryote that was isolated from soybean curd waste sludge.

aerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 65713

JCM 9216,DSM 15123,CCUG 45365

@ref 20215

Last LPSN update 2026-02-09 11:18:23

Domain Bacteria

Phylum Pseudomonadota

Class Betaproteobacteria

Order Burkholderiales

Family Comamonadaceae

Genus Brachymonas

Species Brachymonas denitrificans

Full scientific name Brachymonas denitrificans Hiraishi et al. 1995

BacDive ID	Other strains from **Brachymonas denitrificans** (9)	Type strain
151961	B. denitrificans
152138	B. denitrificans CCUG 45880
152139	B. denitrificans CCUG 45881
152140	B. denitrificans CCUG 45882
152141	B. denitrificans CCUG 45883
152142	B. denitrificans CCUG 45884
152143	B. denitrificans CCUG 45885
166019	B. denitrificans JCM 9217
166020	B. denitrificans JCM 9218

Morphology

Cell morphology

@ref	Gram stain	Confidence
125438	negative	98.5
125439	negative	99.2

Colony morphology

56744

Incubation period3 days

Multimedia

@ref:	66793
multimedia content:	EM_DSM_15123_1.jpg
multimedia.multimedia content:	EM_DSM_15123_1.jpg
caption:	electron microscopic image
intellectual property rights:	© HZI/Manfred Rohde
manual_annotation:	1

@ref:	66793
multimedia content:	EM_DSM_15123_2.jpg
multimedia.multimedia content:	EM_DSM_15123_2.jpg
caption:	electron microscopic image
intellectual property rights:	© HZI/Manfred Rohde
manual_annotation:	1

@ref:	66793
multimedia content:	EM_DSM_15123_3.jpg
multimedia.multimedia content:	EM_DSM_15123_3.jpg
caption:	electron microscopic image
intellectual property rights:	© HZI/Manfred Rohde
manual_annotation:	1

@ref:	66793
multimedia content:	EM_DSM_15123_4.jpg
multimedia.multimedia content:	EM_DSM_15123_4.jpg
caption:	electron microscopic image
intellectual property rights:	© HZI/Manfred Rohde
manual_annotation:	1

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
5622	NUTRIENT AGAR (DSMZ Medium 1)		Medium recipe at MediaDive	Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
5622	positive	growth	30	mesophilic
56744	positive	growth	30
67770	positive	growth	30	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
56744	aerobe
125439	obligate aerobe	98.3

Spore formation

@ref	Spore formation	Confidence
125438		93.101
125439		98

Observation

67770

Observationquinones: Q-8, RQ-8

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	adipate degradation	100	2 of 2
66794	biotin biosynthesis	100	4 of 4
66794	palmitate biosynthesis	100	22 of 22
66794	valine metabolism	100	9 of 9
66794	ppGpp biosynthesis	100	4 of 4
66794	L-lactaldehyde degradation	100	3 of 3
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	formaldehyde oxidation	100	3 of 3
66794	denitrification	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
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	ceramide biosynthesis	100	1 of 1
66794	chorismate metabolism	88.89	8 of 9
66794	CO2 fixation in Crenarchaeota	88.89	8 of 9
66794	NAD metabolism	88.89	16 of 18
66794	C4 and CAM-carbon fixation	87.5	7 of 8
66794	photosynthesis	85.71	12 of 14
66794	ubiquinone biosynthesis	85.71	6 of 7
66794	heme metabolism	85.71	12 of 14
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	peptidoglycan biosynthesis	80	12 of 15
66794	methylglyoxal degradation	80	4 of 5
66794	glycine betaine biosynthesis	80	4 of 5
66794	threonine metabolism	80	8 of 10
66794	tetrahydrofolate metabolism	78.57	11 of 14
66794	lipid A biosynthesis	77.78	7 of 9
66794	molybdenum cofactor biosynthesis	77.78	7 of 9
66794	phenylalanine metabolism	76.92	10 of 13
66794	sulfopterin metabolism	75	3 of 4
66794	isoleucine metabolism	75	6 of 8
66794	butanoate fermentation	75	3 of 4
66794	acetate fermentation	75	3 of 4
66794	gluconeogenesis	75	6 of 8
66794	CMP-KDO biosynthesis	75	3 of 4
66794	proline metabolism	72.73	8 of 11
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	tyrosine metabolism	71.43	10 of 14
66794	propanol degradation	71.43	5 of 7
66794	glutamate and glutamine metabolism	71.43	20 of 28
66794	purine metabolism	71.28	67 of 94
66794	vitamin B12 metabolism	70.59	24 of 34
66794	propionate fermentation	70	7 of 10
66794	methionine metabolism	69.23	18 of 26
66794	leucine metabolism	69.23	9 of 13
66794	aspartate and asparagine metabolism	66.67	6 of 9
66794	selenocysteine biosynthesis	66.67	4 of 6
66794	acetoin degradation	66.67	2 of 3
66794	cyanate degradation	66.67	2 of 3
66794	octane oxidation	66.67	2 of 3
66794	d-mannose degradation	66.67	6 of 9
66794	serine metabolism	66.67	6 of 9
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	cysteine metabolism	66.67	12 of 18
66794	alanine metabolism	65.52	19 of 29
66794	citric acid cycle	64.29	9 of 14
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	sulfate reduction	61.54	8 of 13
66794	flavin biosynthesis	60	9 of 15
66794	gallate degradation	60	3 of 5
66794	glycolysis	58.82	10 of 17
66794	non-pathway related	57.89	22 of 38
66794	tryptophan metabolism	57.89	22 of 38
66794	pyrimidine metabolism	57.78	26 of 45
66794	lysine metabolism	57.14	24 of 42
66794	histidine metabolism	55.17	16 of 29
66794	oxidative phosphorylation	54.95	50 of 91
66794	lipid metabolism	54.84	17 of 31
66794	3-phenylpropionate degradation	53.33	8 of 15
66794	ethanol fermentation	50	1 of 2
66794	dTDPLrhamnose biosynthesis	50	4 of 8
66794	kanosamine biosynthesis II	50	1 of 2
66794	quinate degradation	50	1 of 2
66794	glycolate and glyoxylate degradation	50	3 of 6
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	Entner Doudoroff pathway	50	5 of 10
66794	suberin monomers biosynthesis	50	1 of 2
66794	cyclohexanol degradation	50	2 of 4
66794	phenol degradation	50	10 of 20
66794	ketogluconate metabolism	50	4 of 8
66794	glutathione metabolism	50	7 of 14
66794	coenzyme A metabolism	50	2 of 4
66794	urea cycle	46.15	6 of 13
66794	vitamin B1 metabolism	46.15	6 of 13
66794	vitamin B6 metabolism	45.45	5 of 11
66794	nitrate assimilation	44.44	4 of 9
66794	isoprenoid biosynthesis	42.31	11 of 26
66794	glycine metabolism	40	4 of 10
66794	phenylacetate degradation (aerobic)	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	3-chlorocatechol degradation	40	2 of 5
66794	lipoate biosynthesis	40	2 of 5
66794	androgen and estrogen metabolism	37.5	6 of 16
66794	arginine metabolism	37.5	9 of 24
66794	pentose phosphate pathway	36.36	4 of 11
66794	IAA biosynthesis	33.33	1 of 3
66794	enterobactin biosynthesis	33.33	1 of 3
66794	degradation of aromatic, nitrogen containing compounds	33.33	4 of 12
66794	arachidonic acid metabolism	33.33	6 of 18
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	pantothenate biosynthesis	33.33	2 of 6
66794	degradation of pentoses	32.14	9 of 28
66794	phenylpropanoid biosynthesis	30.77	4 of 13
66794	polyamine pathway	30.43	7 of 23
66794	coenzyme M 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	cholesterol biosynthesis	27.27	3 of 11
66794	ascorbate metabolism	27.27	6 of 22
66794	d-xylose degradation	27.27	3 of 11
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	carotenoid biosynthesis	27.27	6 of 22
66794	metabolism of disaccharids	27.27	3 of 11
66794	catecholamine biosynthesis	25	1 of 4
66794	glycogen biosynthesis	25	1 of 4
66794	lactate fermentation	25	1 of 4
66794	degradation of sugar alcohols	25	4 of 16
66794	degradation of hexoses	22.22	4 of 18

Fatty acid profile

Metadata FA analysis

@ref

56744

Fatty acid	Percentage	ECL
C16:1 ω7c	41.7	15.819
C16:0	24	16
C18:1 ω7c /12t/9t	15.8	17.824
C12:0	9	12
C12:0 3OH	1.9	13.455
C18:2 ω6,9c/C18:0 ANTE	1.8	17.724
C10:0 3OH	1.4	11.423
C18:0	0.7	18
C16:0 2OH	0.7	17.233
Unidentified	0.6	9.979
Unidentified	0.5	18.073
C14:0	0.4	14
C19:0 CYCLO ω9c	0.4	18.87
Unidentified	0.4	10.459
C18:1 ω9c	0.4	17.769
C17:0	0.3	17

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Food production	#Food
#Engineered	#Waste	#Solid plant waste
#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Host Body-Site	#Plant	#Fruit (Seed)

Isolation

@ref	Sample type	Country	Country ISO 3 Code	Continent
5622	soybean curd waste sludge	Japan	JPN	Asia
56744	Sludge,soybean curd waste
67770	Soybean curd waste sludge

Taxonmaps

69479

Global distribution of 16S sequence D14320 (>99% sequence identity) for Brachymonas denitrificans subclade from Microbeatlas

Aquatic Samples	1459
Soil Samples	132
Animal Samples	598
Plant Samples	36
Total Samples	2225

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
5622	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	IMG-taxon 2599185145 annotated assembly for Brachymonas denitrificans DSM 15123	scaffold	GCA_900110225	1121117.3	2599185145	1121117	73.79

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
5622	Brachymonas denitrificans gene for 16S rRNA	D14320	1452		28220

GC content

@ref	GC-content (mol%)	Method
5622	64.9	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Brachymonas denitrificans DSM 15123
NCBI: GCA_900110225

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	98.00	no
125439	motility	BacteriaNetⓘ	yes	87.00	no
125439	gram_stain	BacteriaNetⓘ	negative	99.20	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	98.30	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Brachymonas denitrificans DSM 15123
PATRIC: 1121117.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.50	no
125438	anaerobic	anaerobicⓘ	no	94.09	yes
125438	spore-forming	spore-formingⓘ	no	93.10	no
125438	aerobic	aerobicⓘ	yes	78.05	yes
125438	thermophilic	thermophileⓘ	no	95.47	yes
125438	flagellated	motile2+ⓘ	no	77.03	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Metabolism	Poly-beta-hydroxybutyrate-accumulating bacteria protect gnotobiotic Artemia franciscana from pathogenic Vibrio campbellii.	Halet D, Defoirdt T, Van Damme P, Vervaeren H, Forrez I, Van de Wiele T, Boon N, Sorgeloos P, Bossier P, Verstraete W	FEMS Microbiol Ecol	10.1111/j.1574-6941.2007.00305.x	2007
Phylogeny	Brachymonas chironomi sp. nov., isolated from a chironomid egg mass, and emended description of the genus Brachymonas.	Halpern M, Shaked T, Schumann P	Int J Syst Evol Microbiol	10.1099/ijs.0.007211-0	2009

References

#5622	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 15123
#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 )
#56744	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 45365
#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 )
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#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 .
#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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Brachymonas denitrificans (DSM 15123, JCM 9216, CCUG 45365)

Name and taxonomic classification