Brevibacterium sediminis (DSM 102229, CGMCC 1.15472, FXJ8.269)

Name: Brevibacterium sediminis (DSM 102229, CGMCC 1.15472, FXJ8.269)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 133018

Type strain

Strain Designation FXJ8.269

Culture col. no. DSM 102229 CGMCC 1.15472 FXJ8.269 JCM 32488

NCBI tax ID(s) 1857024

Special Collections DSMZ JCM Literature strains

History DSMZ <- Y. Huang, Chinese Acad. Sci. (CAS), Beijing; strain FXJ8.269 JCM <-- CGMCC 1.15472 <-- Y. Huang; Inst. of Microbiol., CAS, China; FXJ8.269.

Links

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

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

Name and taxonomic classification

SI-ID 406792

DSM 102229

@ref 20215

Last LPSN update 2026-05-29 08:37:59

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Micrococcales

Family Brevibacteriaceae

Genus Brevibacterium

Species Brevibacterium sediminis

Full scientific name Brevibacterium sediminis Chen et al. 2016

BacDive ID	Other strains from **Brevibacterium sediminis** (2)	Type strain
133017	B. sediminis FXJ8.128, DSM 102228, CGMCC 1.15471
133019	B. sediminis FXJ8.309, DSM 102230, CGMCC 1.15473

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility	Confidence
25089	positive	0.7-1.2 µm	0.4-0.5 µm	rod-shaped
125438	positive					91.504

Colony morphology

@ref	Colony size	Colony color	Colony shape	Incubation period	Medium used
25089	1.5-5.0 mm	pale yellow	circular	3 days	NA (Nutrient Agar)

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
25089	NA (Nutrient Agar)
24806	TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)		Medium recipe at MediaDive	Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
24806	positive	growth	28
25089	positive	growth	8.0-37.0
25089	positive	optimum	25.0-28.0
67770	positive	growth	28

Culture pH

@ref	Ability	Type	PH	PH range
25089	positive	optimum	7.0-8.0
25089	positive	growth	5.0-11.0	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125438	aerobe	90.686
125439	obligate aerobe	93.713

Spore formation

@ref	Spore formation	Confidence
25089
125439		93.813

Halophily

@ref	Salt	Growth	Tested relation	Concentration
25089	NaCl	positive	growth	0.0-20.0 %(w/v)
25089	NaCl		optimum	3.3 %(w/v)

Murein

@ref	Murein short key	Type
25089	A31	A1gamma m-Dpm-direct

Observation

67770

Observationquinones: MK-8(H₂)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
25089	16651 ChEBI	(S)-lactate	+	carbon source
25089	64552 ChEBI	2-hydroxybutyrate	+	carbon source
25089	16763 ChEBI	2-oxobutanoate	-	carbon source
25089	30916 ChEBI	2-oxoglutarate	+	carbon source
25089	37054 ChEBI	3-hydroxybutyrate	+	carbon source
25089	18101 ChEBI	4-hydroxyphenylacetic acid	+	carbon source
25089	30089 ChEBI	acetate	+	carbon source
25089	13705 ChEBI	acetoacetate	+	carbon source
25089	17925 ChEBI	alpha-D-glucose	+	carbon source
25089	73706 ChEBI	bromosuccinate	+	carbon source
25089	16947 ChEBI	citrate	+	carbon source
25089	18333 ChEBI	D-arabitol	-	carbon source
25089	15824 ChEBI	D-fructose	-	carbon source
25089	78697 ChEBI	D-fructose 6-phosphate	+	carbon source
25089	15895 ChEBI	D-galactonic acid lactone	+	carbon source
25089	12936 ChEBI	D-galactose	-	carbon source
25089	18024 ChEBI	D-galacturonic acid	+	carbon source
25089	8391 ChEBI	D-gluconate	-	carbon source
25089	17634 ChEBI	D-glucose	+	builds acid from
25089	14314 ChEBI	D-glucose 6-phosphate	-	carbon source
25089	15748 ChEBI	D-glucuronate	-	carbon source
25089	15588 ChEBI	D-malate	+	carbon source
25089	16899 ChEBI	D-mannitol	+	carbon source
25089	16523 ChEBI	D-serine	-	carbon source
25089	23652 ChEBI	dextrin	-	carbon source
25089	15740 ChEBI	formate	+	carbon source
25089	16537 ChEBI	galactarate	-	carbon source
25089	16865 ChEBI	gamma-aminobutyric acid	+	carbon source
25089	32323 ChEBI	glucuronamide	+	carbon source
25089	17754 ChEBI	glycerol	-	carbon source
25089	70744 ChEBI	glycine-proline	-	carbon source
25089	17596 ChEBI	inosine	+	carbon source
25089	16977 ChEBI	L-alanine	+	carbon source
25089	30849 ChEBI	L-arabinose	-	builds acid from
25089	16467 ChEBI	L-arginine	+	carbon source
25089	29991 ChEBI	L-aspartate	-	carbon source
25089	29985 ChEBI	L-glutamate	+	carbon source
25089	15971 ChEBI	L-histidine	+	carbon source
25089	15589 ChEBI	L-malate	+	carbon source
25089	18183 ChEBI	L-pyroglutamic acid	+	carbon source
25089	62345 ChEBI	L-rhamnose	+	carbon source
25089	62345 ChEBI	L-rhamnose	+	builds acid from
25089	17115 ChEBI	L-serine	+	carbon source
25089	28053 ChEBI	melibiose	-	builds acid from
25089	74611 ChEBI	methyl (R)-lactate	-	carbon source
25089	51850 ChEBI	methyl pyruvate	-	carbon source
25089	17268 ChEBI	myo-inositol	+	carbon source
25089	506227 ChEBI	N-acetylglucosamine	-	carbon source
25089	35418 ChEBI	n-acetylneuraminate	-	carbon source
25089	17632 ChEBI	nitrate	+	reduction
25089	17272 ChEBI	propionate	+	carbon source
25089	26490 ChEBI	quinate	+	carbon source
25089	17992 ChEBI	sucrose	+	carbon source
25089	27897 ChEBI	tryptophan	-	energy source
25089	53423 ChEBI	tween 40	+	carbon source

Antibiotic resistance

@ref	ChEBI	Metabolite
25089	161680	aztreonam
25089	32735	guanidinium chloride
25089	48607	lithium chloride
25089	100147	nalidixic acid
25089	75229	sodium bromate
25089	64103	sodium butyrate
25089	75228	sodium lactate

Metabolite production

@ref	Chebi-ID	Metabolite
25089	15688 ChEBI	acetoin
25089	16136 ChEBI	hydrogen sulfide
25089	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test	Indole test
25089	15688 ChEBI	acetoin	+
25089	35581 ChEBI	indole		-

Enzymes

@ref	Value	Activity	Ec
25089	acid phosphatase	+	3.1.3.2
25089	alkaline phosphatase	+	3.1.3.1
25089	catalase	+	1.11.1.6
25089	cytochrome oxidase	+	1.9.3.1
25089	esterase (C 4)	+
25089	esterase Lipase (C 8)	+
25089	leucine arylamidase	+	3.4.11.1
25089	lipase (C 14)	+
25089	naphthol-AS-BI-phosphohydrolase	+
25089	tryptophan deaminase	-	4.1.99.1
25089	urease	-	3.5.1.5
25089	valine arylamidase	+

Isolation, sampling and environmental information

Isolation source categories

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

Isolation

@ref	Sample type	Geographic location	Country	Continent	Latitude	Longitude	Enrichment culture	Enrichment culture duration	Enrichment culture temperature
24806	deep-sea sediment	Carlsberg Ridge (63.65731° E 3.71069° N, depth of 3690 m)	Indian Ocean	Asia	3.7107	63.6573 3.7107/63.6573
25089	deep-sea sediment (depth of 3690 m)						Oatmeal agar (ISP3)	14-105 days	28
67770	Deep-sea sediment at the Carlsberg Ridge (63.65731° E 3.71069° N, at a depth of 3,690 m)				3.71069	63.6573 3.71069/63.6573

Taxonmaps

69479

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

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
24806	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	ASM1362390v1 assembly for Brevibacterium sediminis FXJ8.269	contig	GCA_013623905	1857024.3	8073540522	1857024	67.61
66792	ASM1464305v1 assembly for Brevibacterium sediminis CGMCC 1.15472	contig	GCA_014643055	1857024.4	8073412100	1857024	66.72

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
24806	Brevibacterium sediminis strain CGMCC 1.15472 16S ribosomal RNA gene, partial sequence	KX356313	1489		1857024
124043	Brevibacterium sediminis strain CGMCC 1.15472 16S ribosomal RNA gene, partial sequence.	MN894560	981		1857024

GC content

@ref	GC-content (mol%)	Method
25089	64.2	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: ASM1362390v1 assembly for Brevibacterium sediminis FXJ8.269
NCBI: GCA_013623905

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	93.71	no
125439	motility	BacteriaNetⓘ	no	67.00	no
125439	gram_stain	BacteriaNetⓘ	positive	81.77	no
125439	spore_formation	BacteriaNetⓘ	no	93.81	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Brevibacterium sediminis strain CGMCC 1.15472
PATRIC: 1857024.4

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	91.50	yes
125438	anaerobic	anaerobicⓘ	no	97.94	no
125438	spore-forming	spore-formingⓘ	no	76.40	yes
125438	aerobic	aerobicⓘ	yes	90.69	no
125438	thermophilic	thermophileⓘ	no	95.50	no
125438	flagellated	motile2+ⓘ	no	89.60	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Identification, characterization, and genome sequencing of Brevibacterium sediminis MG-1 isolate with growth-promoting properties.	Lutfullin MT, Lutfullina GF, Pudova DS, Akosah YA, Shagimardanova EI, Vologin SG, Sharipova MR, Mardanova AM.	3 Biotech	10.1007/s13205-022-03392-z	2022
Genetics	Draft genome sequence of a new carotenoid-producing strain Brevibacterium sp. XU54, isolated from radioactive soil in Xinjiang, China.	Zhang Z, Huang C, Du B, Xie C, Jiang L, Tang S, Xu X.	3 Biotech	10.1007/s13205-022-03366-1	2022
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 .
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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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Brevibacterium sediminis (DSM 102229, CGMCC 1.15472, FXJ8.269)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Murein

Observation

Metabolite utilization

Antibiotic resistance

Metabolite production

Metabolite tests

Enzymes

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_013623905

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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