Name: Brevibacterium sediminis FXJ8.269
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 133018

Type strain:

Species: Brevibacterium sediminis

Strain Designation: FXJ8.269

Culture col. no.: DSM 102229, CGMCC 1.15472, JCM 32488

Strain history: CGMCC 1.15472 <-- Y. Huang; Inst. of Microbiol., CAS, China; FXJ8.269.

NCBI tax ID(s): 1857024 (species)

SI-ID 406792

DSM 102229

Special Collections

Other strains from Brevibacterium sediminis

Section

Brevibacterium sediminis FXJ8.269 is an aerobe, Gram-positive, rod-shaped bacterium that forms circular colonies and was isolated from deep-sea sediment.

colony-forming
Gram-positive
rod-shaped
aerobe
16S sequence
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	09-12-2024 (DD-MM-YYYY)
	Domain	*Bacteria*
	Phylum	*Actinomycetota*
	Class	*Actinomycetes*
	Order	*Micrococcales*
	Family	*Brevibacteriaceae*
	Genus	*Brevibacterium*
	Species	**Brevibacterium sediminis**
	Full Scientific Name (LPSN)	Brevibacterium sediminis Chen et al. 2016

Information on morphological and physiological properties Morphology

[Ref.: #25089]	Gram stain	positive
[Ref.: #69480]	Gram stain	positive Confidence in %91.504

[Ref.: #25089]	Cell length	0.7-1.2 µm

[Ref.: #25089]	Cell width	0.4-0.5 µm

[Ref.: #25089]	Cell shape	rod-shaped

[Ref.: #25089]	Motility	no

[Ref.: #25089]	Colony size	1.5-5.0 mm
[Ref.: #25089]	Colony color	pale yellow
[Ref.: #25089]	Colony shape	circular
[Ref.: #25089]	Incubation period	3 days
[Ref.: #25089]	Cultivation medium used	NA (Nutrient Agar)

Information on culture and growth conditions Culture and growth conditions

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Culture medium

NA (Nutrient Agar)

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Culture medium growth

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Culture medium

TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)

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Culture medium growth

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Culture medium link

Medium recipe at MediaDive

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Culture medium composition

expand / minimize

		Temperature
[Ref.: #24806]	growth	28 °C
[Ref.: #25089]	growth	8.0-37.0 °C
[Ref.: #25089]	optimum	25.0-28.0 °C
[Ref.: #67770]	growth	28 °C

	pH	Kind of pH		pH
[Ref.: #25089]			optimum	7.0-8.0
[Ref.: #25089]			growth	5.0-11.0

Information on physiology and metabolism Physiology and metabolism

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Oxygen tolerance

aerobe Confidence in %90.686

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Ability of spore formation

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #25089]		NaCl		growth	0.0-20.0	%(w/v)
[Ref.: #25089]		NaCl		optimum	3.3	%(w/v)

[Ref.: #25089]	Murein short key	A31
[Ref.: #25089]	Murein types	A1gamma m-Dpm-direct

[Ref.: #67770]

Observation

quinones: MK-8(H₂)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #25089]	(-)-quinic acid ChEBI	+	carbon source
[Ref.: #25089]	(S)-lactate ChEBI	+	carbon source
[Ref.: #25089]	2-hydroxybutyrate ChEBI	+	carbon source
[Ref.: #25089]	2-oxobutanoate ChEBI	-	carbon source
[Ref.: #25089]	2-oxoglutarate ChEBI	+	carbon source
[Ref.: #25089]	3-hydroxybutyrate ChEBI	+	carbon source
[Ref.: #25089]	4-hydroxyphenylacetic acid ChEBI	+	carbon source
[Ref.: #25089]	acetate ChEBI	+	carbon source
[Ref.: #25089]	acetoacetate ChEBI	+	carbon source
[Ref.: #25089]	alpha-D-glucose ChEBI	+	carbon source
[Ref.: #25089]	bromosuccinate ChEBI	+	carbon source
[Ref.: #25089]	citrate ChEBI	+	carbon source
[Ref.: #25089]	D-arabitol ChEBI	-	carbon source
[Ref.: #25089]	D-fructose ChEBI	-	carbon source
[Ref.: #25089]	D-fructose 6-phosphate ChEBI	+	carbon source
[Ref.: #25089]	D-galactonic acid lactone ChEBI	+	carbon source
[Ref.: #25089]	D-galactose ChEBI	-	carbon source
[Ref.: #25089]	D-galacturonic acid ChEBI	+	carbon source
[Ref.: #25089]	D-gluconate ChEBI	-	carbon source
[Ref.: #25089]	D-glucose ChEBI	+	builds acid from
[Ref.: #25089]	D-glucose 6-phosphate ChEBI	-	carbon source
[Ref.: #25089]	D-glucuronate ChEBI	-	carbon source
[Ref.: #25089]	D-malate ChEBI	+	carbon source
[Ref.: #25089]	D-mannitol ChEBI	+	carbon source
[Ref.: #25089]	D-serine ChEBI	-	carbon source
[Ref.: #25089]	dextrin ChEBI	-	carbon source
[Ref.: #25089]	formate ChEBI	+	carbon source
[Ref.: #25089]	galactarate ChEBI	-	carbon source
[Ref.: #25089]	gamma-aminobutyric acid ChEBI	+	carbon source
[Ref.: #25089]	glucuronamide ChEBI	+	carbon source
[Ref.: #25089]	glycerol ChEBI	-	carbon source
[Ref.: #25089]	glycine-proline ChEBI	-	carbon source
[Ref.: #25089]	inosine ChEBI	+	carbon source
[Ref.: #25089]	L-alanine ChEBI	+	carbon source
[Ref.: #25089]	L-arabinose ChEBI	-	builds acid from
[Ref.: #25089]	L-arginine ChEBI	+	carbon source
[Ref.: #25089]	L-aspartate ChEBI	-	carbon source
[Ref.: #25089]	L-glutamate ChEBI	+	carbon source
[Ref.: #25089]	L-histidine ChEBI	+	carbon source
[Ref.: #25089]	L-malate ChEBI	+	carbon source
[Ref.: #25089]	L-pyroglutamic acid ChEBI	+	carbon source
[Ref.: #25089]	L-rhamnose ChEBI	+	carbon source
[Ref.: #25089]	L-rhamnose ChEBI	+	builds acid from
[Ref.: #25089]	L-serine ChEBI	+	carbon source
[Ref.: #25089]	melibiose ChEBI	-	builds acid from
[Ref.: #25089]	methyl (R)-lactate ChEBI	-	carbon source
[Ref.: #25089]	methyl pyruvate ChEBI	-	carbon source
[Ref.: #25089]	myo-inositol ChEBI	+	carbon source
[Ref.: #25089]	N-acetylglucosamine ChEBI	-	carbon source
[Ref.: #25089]	n-acetylneuraminate ChEBI	-	carbon source
[Ref.: #25089]	nitrate ChEBI	+	reduction
[Ref.: #25089]	propionate ChEBI	+	carbon source
[Ref.: #25089]	sucrose ChEBI	+	carbon source
[Ref.: #25089]	tryptophan ChEBI	-	energy source
[Ref.: #25089]	tween 40 ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Antibiotic resistance
[Ref.: #25089]	aztreonam ChEBI	yes
[Ref.: #25089]	guanidinium chloride ChEBI	yes
[Ref.: #25089]	lithium chloride ChEBI	yes
[Ref.: #25089]	nalidixic acid ChEBI	yes
[Ref.: #25089]	sodium bromate ChEBI	yes
[Ref.: #25089]	sodium butyrate ChEBI	yes
[Ref.: #25089]	sodium lactate ChEBI	yes

	Metabolite	Production
[Ref.: #25089]	acetoin ChEBI	yes
[Ref.: #25089]	hydrogen sulfide ChEBI	no
[Ref.: #25089]	indole ChEBI	no

	Physiological tests	Metabolite	Voges-Proskauer-test	Indole test
[Ref.: #25089]		acetoin ChEBI	+
[Ref.: #25089]		indole ChEBI		-

	Enzyme	Enzyme activity	EC number
[Ref.: #25089]	acid phosphatase	+	3.1.3.2
[Ref.: #25089]	alkaline phosphatase	+	3.1.3.1
[Ref.: #25089]	catalase	+	1.11.1.6
[Ref.: #25089]	cytochrome oxidase	+	1.9.3.1
[Ref.: #25089]	esterase (C 4)	+
[Ref.: #25089]	esterase Lipase (C 8)	+
[Ref.: #25089]	leucine arylamidase	+	3.4.11.1
[Ref.: #25089]	lipase (C 14)	+
[Ref.: #25089]	naphthol-AS-BI-phosphohydrolase	+
[Ref.: #25089]	tryptophan deaminase	-	4.1.99.1
[Ref.: #25089]	urease	-	3.5.1.5
[Ref.: #25089]	valine arylamidase	+
	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.: #24806]	Sample type/isolated from	deep-sea sediment
[Ref.: #24806]	Geographic location (country and/or sea, region)	Carlsberg Ridge (63.65731° E 3.71069° N, depth of 3690 m)
[Ref.: #24806]	Country	Indian Ocean
[Ref.: #24806]	Continent	Asia
[Ref.: #24806]	Geographic location	3.7107°/63.6573°

[Ref.: #25089]	Sample type/isolated from	deep-sea sediment (depth of 3690 m)
[Ref.: #25089]	Enrichment culture	Oatmeal agar (ISP3)
[Ref.: #25089]	Enrichment culture duration	14-105 days
[Ref.: #25089]	Enrichment culture temperature	28 ̊C

[Ref.: #67770]	Sample type/isolated from	Deep-sea sediment at the Carlsberg Ridge (63.65731° E 3.71069° N, at a depth of 3,690 m)
[Ref.: #67770]	Geographic location	3.7107°/63.6573°
* marker position based on {}

Isolation sources categories

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

What are isolation sources categories?

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Global distribution of 16S sequence KX356313 (>99% sequence identity) for Brevibacterium from Microbeatlas

Aquatic Samples	309
Soil Samples	309
Animal Samples	2183
Plant Samples	69
Total Samples	2870

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

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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.: #24806]	Brevibacterium sediminis strain CGMCC 1.15472 16S ribosomal RNA gene, partial sequence	KX356313	1489	GenBank ENA	1857024 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Brevibacterium sediminis CGMCC 1.15472	GCA_014643055	contig	GenBank ENA	1857024 tax ID	*
[Ref.: #66792]	Brevibacterium sediminis FXJ8.269	GCA_013623905	contig	GenBank ENA	1857024 tax ID	*
[Ref.: #66792]	Brevibacterium sediminis strain CGMCC 1.15472	1857024.4	wgs	PATRIC	1857024 tax ID	*

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GC-content

64.2 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: Brevibacterium sediminis strain CGMCC 1.15472 PATRIC: 1857024.3
[Ref.: #69481]	spore-forming	spore-formingⓘ	no	85	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Brevibacterium sediminis strain CGMCC 1.15472 PATRIC: 1857024.4
[Ref.: #69480]	gram-positive	gram-positiveⓘ	yes	91.504	yes
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	97.94	no
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	76.395	yes
[Ref.: #69480]	aerobic	aerobicⓘ	yes	90.686	no
[Ref.: #69480]	thermophilic	thermophileⓘ	no	95.5	no
[Ref.: #69480]	flagellated	motile2+ⓘ	no	89.6	no

Availability in culture collections External links

[Ref.: #24806]

Culture collection no.

DSM 102229, CGMCC 1.15472, JCM 32488

[Ref.: #91292]

SI-ID 406792

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Brevibacterium renqingii sp. nov., isolated from the Daqu of Baijiu.	Yan Y, Xing X, Sun Z, Li J, Hao S, Xu J	Arch Microbiol	10.1007/s00203-021-02212-x	2021	*
Phylogeny	Brevibacterium sediminis sp. nov., isolated from deep-sea sediments from the Carlsberg and Southwest Indian Ridges.	Chen P, Zhang L, Wang J, Ruan J, Han X, Huang Y	Int J Syst Evol Microbiol	10.1099/ijsem.0.001506	2016	*

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 )

#24806

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 102229

#25089

P. Z. Chen, L.,Wang, J.,Ruan, J.,Han, X.,Huang, Y.: Brevibacterium sediminis sp. nov., isolated from deep-sea sediments from the Carlsberg and Southwest Indian Ridges. IJSEM 66: 5268 - 5274 2016 ( DOI 10.1099/ijsem.0.001506 , PubMed 27654846 )

#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) .

#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 )

#91292

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-ID406792.1 )

* These data were automatically processed and therefore are not curated

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Brevibacterium sediminis strain CGMCC 1.15472

Brevibacterium sediminis strain CGMCC 1.15472

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