Name: Bradymonas sediminis FA350
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 131340

Type strain:

Species: Bradymonas sediminis

Strain Designation: FA350

Culture col. no.: DSM 28820, CICC 10904

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

NCBI tax ID(s): 1548548 (species)

SI-ID 397639

DSM 28820

Section

Bradymonas sediminis FA350 is a mesophilic, Gram-negative bacterium that was isolated from coastal marine sediment.

Gram-negative
mesophilic
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	*Deltaproteobacteria*
	Order	*Bradymonadales*
	Family	*Bradymonadaceae*
	Genus	*Bradymonas*
	Species	**Bradymonas sediminis**
	Full Scientific Name (LPSN)	Bradymonas sediminis Wang et al. 2015

Information on morphological and physiological properties Morphology

[Ref.: #69480]	Gram stain	negative Confidence in %99.997

Multimedia content

[Ref.: #22567]

Intellectual property rights:

Information on culture and growth conditions Culture and growth conditions

[Ref.: #22567]

Culture medium

BRADYMONAS SEDIMINIS MEDIUM (DSMZ Medium 1588)

[Ref.: #22567]

Culture medium growth

[Ref.: #22567]

Culture medium link

Medium recipe at MediaDive

[Ref.: #22567]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #22567]			growth	28 °C

[Ref.: #22567]

Temperature range

mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.98

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	reductive acetyl coenzyme A pathway	100	7 of 7
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	denitrification	100	2 of 2
[Ref.: #66794]	teichoic acid biosynthesis	100	1 of 1
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	enterobactin biosynthesis	100	3 of 3
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	aspartate and asparagine metabolism	100	9 of 9
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	butanoate fermentation	100	4 of 4
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	vitamin K metabolism	100	5 of 5
[Ref.: #66794]	lipoate biosynthesis	100	5 of 5
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	NAD metabolism	88.89	16 of 18
[Ref.: #66794]	gluconeogenesis	87.5	7 of 8
[Ref.: #66794]	C4 and CAM-carbon fixation	87.5	7 of 8
[Ref.: #66794]	photosynthesis	85.71	12 of 14
[Ref.: #66794]	pentose phosphate pathway	81.82	9 of 11
[Ref.: #66794]	glycine betaine biosynthesis	80	4 of 5
[Ref.: #66794]	threonine metabolism	80	8 of 10
[Ref.: #66794]	glycogen metabolism	80	4 of 5
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	propionate fermentation	80	8 of 10
[Ref.: #66794]	glutamate and glutamine metabolism	78.57	22 of 28
[Ref.: #66794]	tetrahydrofolate metabolism	78.57	11 of 14
[Ref.: #66794]	d-mannose degradation	77.78	7 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	77.78	7 of 9
[Ref.: #66794]	palmitate biosynthesis	77.27	17 of 22
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	ppGpp biosynthesis	75	3 of 4
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	methionine metabolism	73.08	19 of 26
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	heme metabolism	71.43	10 of 14
[Ref.: #66794]	glutathione metabolism	71.43	10 of 14
[Ref.: #66794]	citric acid cycle	71.43	10 of 14
[Ref.: #66794]	propanol degradation	71.43	5 of 7
[Ref.: #66794]	glycolysis	70.59	12 of 17
[Ref.: #66794]	starch degradation	70	7 of 10
[Ref.: #66794]	phenylalanine metabolism	69.23	9 of 13
[Ref.: #66794]	vitamin B1 metabolism	69.23	9 of 13
[Ref.: #66794]	purine metabolism	69.15	65 of 94
[Ref.: #66794]	lysine metabolism	69.05	29 of 42
[Ref.: #66794]	non-pathway related	68.42	26 of 38
[Ref.: #66794]	lipid metabolism	67.74	21 of 31
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	serine metabolism	66.67	6 of 9
[Ref.: #66794]	flavin biosynthesis	66.67	10 of 15
[Ref.: #66794]	valine metabolism	66.67	6 of 9
[Ref.: #66794]	cysteine metabolism	66.67	12 of 18
[Ref.: #66794]	CO2 fixation in Crenarchaeota	66.67	6 of 9
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	tryptophan metabolism	65.79	25 of 38
[Ref.: #66794]	alanine metabolism	65.52	19 of 29
[Ref.: #66794]	tyrosine metabolism	64.29	9 of 14
[Ref.: #66794]	metabolism of disaccharids	63.64	7 of 11
[Ref.: #66794]	proline metabolism	63.64	7 of 11
[Ref.: #66794]	ketogluconate metabolism	62.5	5 of 8
[Ref.: #66794]	isoleucine metabolism	62.5	5 of 8
[Ref.: #66794]	pyrimidine metabolism	62.22	28 of 45
[Ref.: #66794]	leucine metabolism	61.54	8 of 13
[Ref.: #66794]	Entner Doudoroff pathway	60	6 of 10
[Ref.: #66794]	myo-inositol biosynthesis	60	6 of 10
[Ref.: #66794]	carotenoid biosynthesis	59.09	13 of 22
[Ref.: #66794]	arginine metabolism	58.33	14 of 24
[Ref.: #66794]	ubiquinone biosynthesis	57.14	4 of 7
[Ref.: #66794]	lipid A biosynthesis	55.56	5 of 9
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	54.55	6 of 11
[Ref.: #66794]	vitamin B6 metabolism	54.55	6 of 11
[Ref.: #66794]	urea cycle	53.85	7 of 13
[Ref.: #66794]	histidine metabolism	51.72	15 of 29
[Ref.: #66794]	cis-vaccenate biosynthesis	50	1 of 2
[Ref.: #66794]	kanosamine biosynthesis II	50	1 of 2
[Ref.: #66794]	dTDPLrhamnose biosynthesis	50	4 of 8
[Ref.: #66794]	lactate fermentation	50	2 of 4
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	catecholamine biosynthesis	50	2 of 4
[Ref.: #66794]	biotin biosynthesis	50	2 of 4
[Ref.: #66794]	sphingosine metabolism	50	3 of 6
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	oxidative phosphorylation	49.45	45 of 91
[Ref.: #66794]	allantoin degradation	44.44	4 of 9
[Ref.: #66794]	daunorubicin biosynthesis	44.44	4 of 9
[Ref.: #66794]	nitrate assimilation	44.44	4 of 9
[Ref.: #66794]	mevalonate metabolism	42.86	3 of 7
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
[Ref.: #66794]	hydrogen production	40	2 of 5
[Ref.: #66794]	factor 420 biosynthesis	40	2 of 5
[Ref.: #66794]	phenylacetate degradation (aerobic)	40	2 of 5
[Ref.: #66794]	coenzyme M biosynthesis	40	4 of 10
[Ref.: #66794]	isoprenoid biosynthesis	38.46	10 of 26
[Ref.: #66794]	sulfate reduction	38.46	5 of 13
[Ref.: #66794]	cholesterol biosynthesis	36.36	4 of 11
[Ref.: #66794]	ascorbate metabolism	36.36	8 of 22
[Ref.: #66794]	polyamine pathway	34.78	8 of 23
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	methane metabolism	33.33	1 of 3
[Ref.: #66794]	cyanate degradation	33.33	1 of 3
[Ref.: #66794]	pantothenate biosynthesis	33.33	2 of 6
[Ref.: #66794]	arachidonic acid metabolism	33.33	6 of 18
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	selenocysteine biosynthesis	33.33	2 of 6
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	degradation of sugar alcohols	31.25	5 of 16
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	29.41	5 of 17
[Ref.: #66794]	degradation of pentoses	28.57	8 of 28
[Ref.: #66794]	benzoyl-CoA degradation	28.57	2 of 7
[Ref.: #66794]	degradation of hexoses	27.78	5 of 18
[Ref.: #66794]	3-phenylpropionate degradation	26.67	4 of 15
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	androgen and estrogen metabolism	25	4 of 16
[Ref.: #66794]	CMP-KDO biosynthesis	25	1 of 4
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	23.08	3 of 13
[Ref.: #66794]	chlorophyll metabolism	22.22	4 of 18
[Ref.: #66794]	4-hydroxymandelate degradation	22.22	2 of 9
		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.: #22567]	Sample type/isolated from	coastal marine sediment
[Ref.: #22567]	Geographic location (country and/or sea, region)	Weihai, Xiaoshi Island (37° 31' 36'' N 122° 00' 58'' E)
[Ref.: #22567]	Country	China
[Ref.: #22567]	Country ISO 3 Code	CHN
[Ref.: #22567]	Continent	Asia
[Ref.: #22567]	Geographic location	37.5267°/122.0160°
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Marine
#Environmental	#Aquatic	#Sediment

What are isolation sources categories?

[Ref.: #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

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

[Ref.: #22567]

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.: #22567]	Bradymonas sediminis strain FA350 16S ribosomal RNA gene, partial sequence	KM034744	1461	ENA	1548548 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Bradymonas sediminis FA350	GCA_003258315	complete	GenBank	1548548 tax ID	*
[Ref.: #66792]	Bradymonas sediminis DSM 28820	GCA_004362595	scaffold	GenBank	1548548 tax ID	*
[Ref.: #66792]	Bradymonas sediminis strain DSM 28820	1548548.14	wgs	PATRIC	1548548 tax ID	*
[Ref.: #66792]	Bradymonas sediminis DSM 28820	2770939511	draft	JGI IMG/M	1548548 tax ID	*
[Ref.: #66792]	Bradymonas sediminis FA350	2839912435	complete	JGI IMG/M	1548548 tax ID	*

[Ref.: #22567]

GC-content

44.6 mol%

fluorimetric

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Bradymonas sediminis FA350 NCBI: GCA_003258315.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Bradymonas sediminis FA350 NCBI: GCA_003258315.1
[Ref.: #69480]	flagellated	no	93.342	no
[Ref.: #69480]	gram-positive	no	96.463	no
[Ref.: #69480]	anaerobic	no	98.726	no
[Ref.: #69480]	aerobic	yes	62.496	no
[Ref.: #69480]	halophile	no	57.68	no
[Ref.: #69480]	spore-forming	no	86.439	no
[Ref.: #69480]	glucose-util	yes	71.915	no
[Ref.: #69480]	thermophile	no	93.861	no
[Ref.: #69480]	motile	no	62.446	no
[Ref.: #69480]	glucose-ferment	no	92.165	no

Availability in culture collections External links

[Ref.: #22567]

Culture collection no.

DSM 28820, CICC 10904

[Ref.: #89781]

SI-ID 397639

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 .

#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 )

#89781

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-ID397639.1 )

* These data were automatically processed and therefore are not curated

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