Name: Brachymonas denitrificans AS-P1
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 2908

Type strain:

Species: Brachymonas denitrificans

Strain Designation: AS-P1

Culture col. no.: DSM 15123, JCM 9216, CCUG 45365, CGMCC 1.7100

Strain history: A. Hiraishi AS-P1.

NCBI tax ID(s): 1121117 (strain), 28220 (species)

SI-ID 65713

JCM 9216, DSM 15123, CCUG 45365

Special Collections

Other strains from Brachymonas denitrificans

Section

Brachymonas denitrificans AS-P1 is an aerobe, Gram-negative bacterium that was isolated from soybean curd waste sludge.

Gram-negative
aerobe
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	*Pseudomonadota*
	Class	*Betaproteobacteria*
	Order	*Burkholderiales*
	Family	*Comamonadaceae*
	Genus	*Brachymonas*
	Species	**Brachymonas denitrificans**
	Full Scientific Name (LPSN)	Brachymonas denitrificans Hiraishi et al. 1995

Information on morphological and physiological properties Morphology

[Ref.: #69480]	Gram stain	negative Confidence in %98.5

[Ref.: #56744]

Incubation period

3 days

Multimedia content

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Caption:

electron microscopic image

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Intellectual property rights:

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electron microscopic image

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Intellectual property rights:

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electron microscopic image

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Intellectual property rights:

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electron microscopic image

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Intellectual property rights:

Information on culture and growth conditions Culture and growth conditions

[Ref.: #5622]

Culture medium

NUTRIENT AGAR (DSMZ Medium 1)

[Ref.: #5622]

Culture medium growth

[Ref.: #5622]

Culture medium link

Medium recipe at MediaDive

[Ref.: #5622]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #5622]	growth	30 °C
[Ref.: #56744]	growth	30 °C
[Ref.: #67770]	growth	30 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #56744]

Oxygen tolerance

aerobe

[Ref.: #69480]	Ability of spore formation	no Confidence in %93.101
[Ref.: #69481]	Ability of spore formation	no Confidence in %100

[Ref.: #67770]

Observation

quinones: Q-8, RQ-8

Fatty acid profile

Metadata FA analysis

Reference

[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

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	valine metabolism	100	9 of 9
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	denitrification	100	2 of 2
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	ceramide biosynthesis	100	1 of 1
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	88.89	8 of 9
[Ref.: #66794]	NAD metabolism	88.89	16 of 18
[Ref.: #66794]	C4 and CAM-carbon fixation	87.5	7 of 8
[Ref.: #66794]	photosynthesis	85.71	12 of 14
[Ref.: #66794]	ubiquinone biosynthesis	85.71	6 of 7
[Ref.: #66794]	heme metabolism	85.71	12 of 14
[Ref.: #66794]	reductive acetyl coenzyme A pathway	85.71	6 of 7
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	methylglyoxal degradation	80	4 of 5
[Ref.: #66794]	glycine betaine biosynthesis	80	4 of 5
[Ref.: #66794]	threonine metabolism	80	8 of 10
[Ref.: #66794]	tetrahydrofolate metabolism	78.57	11 of 14
[Ref.: #66794]	lipid A biosynthesis	77.78	7 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	77.78	7 of 9
[Ref.: #66794]	phenylalanine metabolism	76.92	10 of 13
[Ref.: #66794]	sulfopterin metabolism	75	3 of 4
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	butanoate fermentation	75	3 of 4
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	gluconeogenesis	75	6 of 8
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	proline metabolism	72.73	8 of 11
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	tyrosine metabolism	71.43	10 of 14
[Ref.: #66794]	propanol degradation	71.43	5 of 7
[Ref.: #66794]	glutamate and glutamine metabolism	71.43	20 of 28
[Ref.: #66794]	purine metabolism	71.28	67 of 94
[Ref.: #66794]	vitamin B12 metabolism	70.59	24 of 34
[Ref.: #66794]	propionate fermentation	70	7 of 10
[Ref.: #66794]	methionine metabolism	69.23	18 of 26
[Ref.: #66794]	leucine metabolism	69.23	9 of 13
[Ref.: #66794]	aspartate and asparagine metabolism	66.67	6 of 9
[Ref.: #66794]	selenocysteine biosynthesis	66.67	4 of 6
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	d-mannose degradation	66.67	6 of 9
[Ref.: #66794]	serine metabolism	66.67	6 of 9
[Ref.: #66794]	acetyl CoA biosynthesis	66.67	2 of 3
[Ref.: #66794]	cysteine metabolism	66.67	12 of 18
[Ref.: #66794]	alanine metabolism	65.52	19 of 29
[Ref.: #66794]	citric acid cycle	64.29	9 of 14
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	sulfate reduction	61.54	8 of 13
[Ref.: #66794]	flavin biosynthesis	60	9 of 15
[Ref.: #66794]	gallate degradation	60	3 of 5
[Ref.: #66794]	glycolysis	58.82	10 of 17
[Ref.: #66794]	non-pathway related	57.89	22 of 38
[Ref.: #66794]	tryptophan metabolism	57.89	22 of 38
[Ref.: #66794]	pyrimidine metabolism	57.78	26 of 45
[Ref.: #66794]	lysine metabolism	57.14	24 of 42
[Ref.: #66794]	histidine metabolism	55.17	16 of 29
[Ref.: #66794]	oxidative phosphorylation	54.95	50 of 91
[Ref.: #66794]	lipid metabolism	54.84	17 of 31
[Ref.: #66794]	3-phenylpropionate degradation	53.33	8 of 15
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	dTDPLrhamnose biosynthesis	50	4 of 8
[Ref.: #66794]	kanosamine biosynthesis II	50	1 of 2
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	glycolate and glyoxylate degradation	50	3 of 6
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	Entner Doudoroff pathway	50	5 of 10
[Ref.: #66794]	suberin monomers biosynthesis	50	1 of 2
[Ref.: #66794]	cyclohexanol degradation	50	2 of 4
[Ref.: #66794]	phenol degradation	50	10 of 20
[Ref.: #66794]	ketogluconate metabolism	50	4 of 8
[Ref.: #66794]	glutathione metabolism	50	7 of 14
[Ref.: #66794]	coenzyme A metabolism	50	2 of 4
[Ref.: #66794]	urea cycle	46.15	6 of 13
[Ref.: #66794]	vitamin B1 metabolism	46.15	6 of 13
[Ref.: #66794]	vitamin B6 metabolism	45.45	5 of 11
[Ref.: #66794]	nitrate assimilation	44.44	4 of 9
[Ref.: #66794]	isoprenoid biosynthesis	42.31	11 of 26
[Ref.: #66794]	glycine metabolism	40	4 of 10
[Ref.: #66794]	phenylacetate degradation (aerobic)	40	2 of 5
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	3-chlorocatechol degradation	40	2 of 5
[Ref.: #66794]	lipoate biosynthesis	40	2 of 5
[Ref.: #66794]	androgen and estrogen metabolism	37.5	6 of 16
[Ref.: #66794]	arginine metabolism	37.5	9 of 24
[Ref.: #66794]	pentose phosphate pathway	36.36	4 of 11
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	33.33	4 of 12
[Ref.: #66794]	arachidonic acid metabolism	33.33	6 of 18
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	pantothenate biosynthesis	33.33	2 of 6
[Ref.: #66794]	degradation of pentoses	32.14	9 of 28
[Ref.: #66794]	phenylpropanoid biosynthesis	30.77	4 of 13
[Ref.: #66794]	polyamine pathway	30.43	7 of 23
[Ref.: #66794]	coenzyme M biosynthesis	30	3 of 10
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	29.41	5 of 17
[Ref.: #66794]	benzoyl-CoA degradation	28.57	2 of 7
[Ref.: #66794]	cholesterol biosynthesis	27.27	3 of 11
[Ref.: #66794]	ascorbate metabolism	27.27	6 of 22
[Ref.: #66794]	d-xylose degradation	27.27	3 of 11
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	carotenoid biosynthesis	27.27	6 of 22
[Ref.: #66794]	metabolism of disaccharids	27.27	3 of 11
[Ref.: #66794]	catecholamine biosynthesis	25	1 of 4
[Ref.: #66794]	glycogen biosynthesis	25	1 of 4
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	degradation of sugar alcohols	25	4 of 16
[Ref.: #66794]	degradation of hexoses	22.22	4 of 18
		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.: #5622]	Sample type/isolated from	soybean curd waste sludge
[Ref.: #5622]	Country	Japan
[Ref.: #5622]	Country ISO 3 Code	JPN
[Ref.: #5622]	Continent	Asia

[Ref.: #56744]	Sample type/isolated from	Sludge,soybean curd waste

[Ref.: #67770]	Sample type/isolated from	Soybean curd waste sludge
* marker position based on {}

Isolation sources categories

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

What are isolation sources categories?

[Ref.: #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

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

[Ref.: #5622]

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.: #5622]	Brachymonas denitrificans gene for 16S rRNA	D14320	1452	GenBank ENA	28220 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Brachymonas denitrificans DSM 15123	GCA_900110225	scaffold	GenBank ENA	1121117 tax ID
[Ref.: #66792]	Brachymonas denitrificans DSM 15123	1121117.3	wgs	PATRIC	1121117 tax ID	*
[Ref.: #66792]	Brachymonas denitrificans DSM 15123	2599185145	draft	JGI IMG/M	1121117 tax ID	*

[Ref.: #5622]

GC-content

64.9 mol%

high performance liquid chromatography (HPLC)

Data predicted using genome information as a basis Genome-based predictions

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Brachymonas denitrificans DSM 15123 DSM 15123 NCBI: GCA_900110225.1
[Ref.: #69481]	spore-forming	spore-formingⓘ	no	100	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Brachymonas denitrificans DSM 15123 PATRIC: 1121117.3
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	98.5	no
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	94.09	yes
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	93.101	no
[Ref.: #69480]	aerobic	aerobicⓘ	yes	78.053	yes
[Ref.: #69480]	thermophilic	thermophileⓘ	no	95.471	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	no	77.031	no

Availability in culture collections External links

[Ref.: #5622]

Culture collection no.

DSM 15123, JCM 9216, CCUG 45365, CGMCC 1.7100

[Ref.: #72431]

SI-ID 65713

Literature:

Topic	Title	Authors	Journal	DOI	Year
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	*
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	*

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

#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 )

#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 .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#72431

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-ID65713.1 )

* These data were automatically processed and therefore are not curated

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Brachymonas denitrificans DSM 15123 DSM 15123

Brachymonas denitrificans DSM 15123

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