Bradymonas sediminis (DSM 28820, CICC 10904, FA350)

Name: Bradymonas sediminis (DSM 28820, CICC 10904, FA350)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 131340

Type strain

Strain Designation FA350

Culture col. no. DSM 28820 CICC 10904 FA350

NCBI tax ID(s) 1548548

Special Collections DSMZ

History DSMZ <- Z.-J. Du, Shandong University at Weihai; FA350 <- Q.-Q. Liu, College of Marine Science, Shandong University at Weihai, PR China

Links

Bradymonas sediminis FA350 is a bacterium that was isolated from coastal marine sediment.

genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 397639

DSM 28820

@ref 20215

Last LPSN update 2026-05-29 08:37:35

Domain Bacteria

Phylum Pseudomonadota

Class Deltaproteobacteria

Order Bradymonadales

Family Bradymonadaceae

Genus Bradymonas

Species Bradymonas sediminis

Full scientific name Bradymonas sediminis Wang et al. 2015

Morphology

Multimedia

@ref:	22567
multimedia content:	DSM_28820.jpg
multimedia.multimedia content:	https://www.dsmz.de/microorganisms/photos/DSM_28820.jpg
intellectual property rights:	© Leibniz-Institut DSMZ
manual_annotation:	1

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
22567	BRADYMONAS SEDIMINIS MEDIUM (DSMZ Medium 1588)		Medium recipe at MediaDive	Name: BRADYMONAS SEDIMINIS MEDIUM (DSMZ Medium 1588) Composition: Agar 19.0 g/l Peptone 10.0 g/l NaCl 5.0 g/l Meat extract 3.0 g/l D(+)-Trehalose 1.0 g/l Tap water Natural sea water

Culture temp

@ref	Growth	Type	Temperature (°C)
22567	positive	growth	28

Physiology and metabolism

Spore formation

@ref	Spore formation	Confidence
125439		93.218

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	reductive acetyl coenzyme A pathway	100	7 of 7
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	denitrification	100	2 of 2
66794	teichoic acid biosynthesis	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	enterobactin biosynthesis	100	3 of 3
66794	adipate degradation	100	2 of 2
66794	sulfopterin metabolism	100	4 of 4
66794	aspartate and asparagine metabolism	100	9 of 9
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	butanoate fermentation	100	4 of 4
66794	methylglyoxal degradation	100	5 of 5
66794	folate polyglutamylation	100	1 of 1
66794	vitamin K metabolism	100	5 of 5
66794	lipoate biosynthesis	100	5 of 5
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	formaldehyde oxidation	100	3 of 3
66794	coenzyme A metabolism	100	4 of 4
66794	chorismate metabolism	88.89	8 of 9
66794	NAD metabolism	88.89	16 of 18
66794	gluconeogenesis	87.5	7 of 8
66794	C4 and CAM-carbon fixation	87.5	7 of 8
66794	photosynthesis	85.71	12 of 14
66794	pentose phosphate pathway	81.82	9 of 11
66794	glycine betaine biosynthesis	80	4 of 5
66794	threonine metabolism	80	8 of 10
66794	glycogen metabolism	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	propionate fermentation	80	8 of 10
66794	glutamate and glutamine metabolism	78.57	22 of 28
66794	tetrahydrofolate metabolism	78.57	11 of 14
66794	d-mannose degradation	77.78	7 of 9
66794	molybdenum cofactor biosynthesis	77.78	7 of 9
66794	palmitate biosynthesis	77.27	17 of 22
66794	glycogen biosynthesis	75	3 of 4
66794	ppGpp biosynthesis	75	3 of 4
66794	acetate fermentation	75	3 of 4
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	methionine metabolism	73.08	19 of 26
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	heme metabolism	71.43	10 of 14
66794	glutathione metabolism	71.43	10 of 14
66794	citric acid cycle	71.43	10 of 14
66794	propanol degradation	71.43	5 of 7
66794	glycolysis	70.59	12 of 17
66794	starch degradation	70	7 of 10
66794	phenylalanine metabolism	69.23	9 of 13
66794	vitamin B1 metabolism	69.23	9 of 13
66794	purine metabolism	69.15	65 of 94
66794	lysine metabolism	69.05	29 of 42
66794	non-pathway related	68.42	26 of 38
66794	lipid metabolism	67.74	21 of 31
66794	octane oxidation	66.67	2 of 3
66794	serine metabolism	66.67	6 of 9
66794	flavin biosynthesis	66.67	10 of 15
66794	valine metabolism	66.67	6 of 9
66794	cysteine metabolism	66.67	12 of 18
66794	CO2 fixation in Crenarchaeota	66.67	6 of 9
66794	acetoin degradation	66.67	2 of 3
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	tryptophan metabolism	65.79	25 of 38
66794	alanine metabolism	65.52	19 of 29
66794	tyrosine metabolism	64.29	9 of 14
66794	metabolism of disaccharids	63.64	7 of 11
66794	proline metabolism	63.64	7 of 11
66794	ketogluconate metabolism	62.5	5 of 8
66794	isoleucine metabolism	62.5	5 of 8
66794	pyrimidine metabolism	62.22	28 of 45
66794	leucine metabolism	61.54	8 of 13
66794	Entner Doudoroff pathway	60	6 of 10
66794	myo-inositol biosynthesis	60	6 of 10
66794	carotenoid biosynthesis	59.09	13 of 22
66794	arginine metabolism	58.33	14 of 24
66794	ubiquinone biosynthesis	57.14	4 of 7
66794	lipid A biosynthesis	55.56	5 of 9
66794	dolichyl-diphosphooligosaccharide biosynthesis	54.55	6 of 11
66794	vitamin B6 metabolism	54.55	6 of 11
66794	urea cycle	53.85	7 of 13
66794	histidine metabolism	51.72	15 of 29
66794	cis-vaccenate biosynthesis	50	1 of 2
66794	kanosamine biosynthesis II	50	1 of 2
66794	dTDPLrhamnose biosynthesis	50	4 of 8
66794	lactate fermentation	50	2 of 4
66794	ethanol fermentation	50	1 of 2
66794	glycine metabolism	50	5 of 10
66794	catecholamine biosynthesis	50	2 of 4
66794	biotin biosynthesis	50	2 of 4
66794	sphingosine metabolism	50	3 of 6
66794	phenylmercury acetate degradation	50	1 of 2
66794	oxidative phosphorylation	49.45	45 of 91
66794	allantoin degradation	44.44	4 of 9
66794	daunorubicin biosynthesis	44.44	4 of 9
66794	nitrate assimilation	44.44	4 of 9
66794	mevalonate metabolism	42.86	3 of 7
66794	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
66794	hydrogen production	40	2 of 5
66794	factor 420 biosynthesis	40	2 of 5
66794	phenylacetate degradation (aerobic)	40	2 of 5
66794	coenzyme M biosynthesis	40	4 of 10
66794	isoprenoid biosynthesis	38.46	10 of 26
66794	sulfate reduction	38.46	5 of 13
66794	cholesterol biosynthesis	36.36	4 of 11
66794	ascorbate metabolism	36.36	8 of 22
66794	polyamine pathway	34.78	8 of 23
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	methane metabolism	33.33	1 of 3
66794	cyanate degradation	33.33	1 of 3
66794	pantothenate biosynthesis	33.33	2 of 6
66794	arachidonic acid metabolism	33.33	6 of 18
66794	IAA biosynthesis	33.33	1 of 3
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	degradation of sugar alcohols	31.25	5 of 16
66794	bile acid biosynthesis, neutral pathway	29.41	5 of 17
66794	degradation of pentoses	28.57	8 of 28
66794	benzoyl-CoA degradation	28.57	2 of 7
66794	degradation of hexoses	27.78	5 of 18
66794	3-phenylpropionate degradation	26.67	4 of 15
66794	cyclohexanol degradation	25	1 of 4
66794	androgen and estrogen metabolism	25	4 of 16
66794	CMP-KDO biosynthesis	25	1 of 4
66794	toluene degradation	25	1 of 4
66794	phosphatidylethanolamine bioynthesis	23.08	3 of 13
66794	chlorophyll metabolism	22.22	4 of 18
66794	4-hydroxymandelate degradation	22.22	2 of 9

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Marine
#Environmental	#Aquatic	#Sediment

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude
22567	coastal marine sediment	Weihai, Xiaoshi Island (37° 31' 36'' N 122° 00' 58'' E)	China	CHN	Asia	37.5267	122.016 37.5267/122.016

Taxonmaps

69479

Global distribution of 16S sequence KM034744 (>99% sequence identity) for Bradymonas sediminis subclade from Microbeatlas

Aquatic Samples	565
Soil Samples	143
Animal Samples	506
Plant Samples	30
Total Samples	1244

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
22567	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM325831v1 assembly for Bradymonas sediminis FA350	complete	GCA_003258315	1548548.3	2839912435	1548548	91.6
66792	ASM436259v1 assembly for Bradymonas sediminis DSM 28820	scaffold	GCA_004362595	1548548.14	2770939511	1548548	67.81

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
22567	Bradymonas sediminis strain FA350 16S ribosomal RNA gene, partial sequence	KM034744	1461		1548548

GC content

@ref	GC-content (mol%)	Method
22567	44.6	fluorimetric

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM436259v1 assembly for Bradymonas sediminis DSM 28820
BV-BRC: 1548548.14

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	82.79	no
125439	gram_stain	BacteriaNetⓘ	negative	81.04	no
125439	motility	BacteriaNetⓘ	yes	40.97	no
125439	spore_formation	BacteriaNetⓘ	no	93.22	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Bradymonas sediminis FA350
NCBI: GCA_003258315.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	84.40	no
125438	anaerobic	anaerobicⓘ	no	92.87	no
125438	aerobic	aerobicⓘ	yes	71.15	no
125438	spore-forming	spore-formingⓘ	no	77.51	no
125438	thermophilic	thermophileⓘ	no	88.72	no
125438	flagellated	motile2+ⓘ	yes	51.17	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Microvenator marinus gen. nov., sp. nov., isolated from marine sediment, and description of Microvenatoraceae fam. nov. and Lujinxingiaceae fam. nov.	Wang S, Chen GJ, Du ZJ	Int J Syst Evol Microbiol	10.1099/ijsem.0.005380	2022
Phylogeny	Persicimonas caeni gen. nov., sp. nov., the Representative of a Novel Wide-Ranging Predatory Taxon in Bradymonadales.	Wang S, Mu D, Du ZJ	Front Microbiol	10.3389/fmicb.2020.00698	2020
Phylogeny	Lujinxingia litoralis gen. nov., sp. nov. and Lujinxingia sediminis sp. nov., two new representatives in the order Bradymonadales.	Guo LY, Li CM, Wang S, Mu DS, Du ZJ	Int J Syst Evol Microbiol	10.1099/ijsem.0.003556	2019
Phylogeny	Bradymonas sediminis gen. nov., sp. nov., isolated from coastal sediment, and description of Bradymonadaceae fam. nov. and Bradymonadales ord. nov.	Wang ZJ, Liu QQ, Zhao LH, Du ZJ, Chen GJ	Int J Syst Evol Microbiol	10.1099/ijs.0.000135	2015

References

#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 )
#22567	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 28820
#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 )
#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 )

Content

About us

Bradymonas sediminis (DSM 28820, CICC 10904, FA350)

Name and taxonomic classification

Morphology

Multimedia

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Spore formation

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_003258315

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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