Strain identifier

BacDive ID: 133018

Type strain: Yes

Species: Brevibacterium sediminis

Strain Designation: FXJ8.269

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

NCBI tax ID(s): 1857024 (species)

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General

@ref: 24806

BacDive-ID: 133018

DSM-Number: 102229

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

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

NCBI tax id

  • NCBI tax id: 1857024
  • Matching level: species

strain history

@refhistory
24806<- Y. Huang, Chinese Acad. Sci. (CAS), Beijing; strain FXJ8.269
67770CGMCC 1.15472 <-- Y. Huang; Inst. of Microbiol., CAS, China; FXJ8.269.

doi: 10.13145/bacdive133018.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Brevibacteriaceae
  • genus: Brevibacterium
  • species: Brevibacterium sediminis
  • full scientific name: Brevibacterium sediminis Chen et al. 2016

@ref: 24806

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Brevibacteriaceae

genus: Brevibacterium

species: Brevibacterium sediminis

full scientific name: Brevibacterium sediminis Chen et al. 2016

strain designation: FXJ8.269

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
25089positive0.7-1.2 µm0.4-0.5 µmrod-shapedno
69480positive100

colony morphology

  • @ref: 25089
  • colony size: 1.5-5.0 mm
  • colony color: pale yellow
  • colony shape: circular
  • incubation period: 3 days
  • medium used: NA (Nutrient Agar)

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
25089NA (Nutrient Agar)yes
24806TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yeshttps://mediadive.dsmz.de/medium/92Name: 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

@refgrowthtypetemperaturerange
25089positivegrowth8.0-37.0
25089positiveoptimum25.0-28.0mesophilic
24806positivegrowth28mesophilic
67770positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
25089positivegrowth5.0-11.0alkaliphile
25089positiveoptimum7.0-8.0

Physiology and metabolism

spore formation

@refspore formationconfidence
25089no
69480no99.993

halophily

@refsaltgrowthtested relationconcentration
25089NaClpositivegrowth0.0-20.0 %(w/v)
25089NaCloptimum3.3 %(w/v)

murein

  • @ref: 25089
  • murein short key: A31
  • type: A1gamma m-Dpm-direct

observation

  • @ref: 67770
  • observation: quinones: MK-8(H2)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
25089167632-oxobutanoate-carbon source
2508918333D-arabitol-carbon source
2508915824D-fructose-carbon source
2508912936D-galactose-carbon source
250898391D-gluconate-carbon source
2508914314D-glucose 6-phosphate-carbon source
2508915748D-glucuronate-carbon source
2508916523D-serine-carbon source
2508923652dextrin-carbon source
2508916537galactarate-carbon source
2508917754glycerol-carbon source
2508970744glycine-proline-carbon source
2508930849L-arabinose-builds acid from
2508929991L-aspartate-carbon source
2508928053melibiose-builds acid from
2508974611methyl (R)-lactate-carbon source
2508951850methyl pyruvate-carbon source
25089506227N-acetylglucosamine-carbon source
2508935418n-acetylneuraminate-carbon source
2508927897tryptophan-energy source
2508917521(-)-quinic acid+carbon source
2508915588D-malate+carbon source
2508916651(S)-lactate+carbon source
2508915589L-malate+carbon source
25089645522-hydroxybutyrate+carbon source
25089309162-oxoglutarate+carbon source
25089370543-hydroxybutyrate+carbon source
25089181014-hydroxyphenylacetic acid+carbon source
2508930089acetate+carbon source
2508913705acetoacetate+carbon source
2508917925alpha-D-glucose+carbon source
2508973706bromosuccinate+carbon source
2508916947citrate+carbon source
2508978697D-fructose 6-phosphate+carbon source
2508915895D-galactonic acid lactone+carbon source
2508918024D-galacturonic acid+carbon source
2508917634D-glucose+builds acid from
2508916899D-mannitol+carbon source
2508917992sucrose+carbon source
2508915740formate+carbon source
2508916865gamma-aminobutyric acid+carbon source
2508932323glucuronamide+carbon source
2508917596inosine+carbon source
2508917268myo-inositol+carbon source
2508916977L-alanine+carbon source
2508916467L-arginine+carbon source
2508929985L-glutamate+carbon source
2508915971L-histidine+carbon source
2508918183L-pyroglutamic acid+carbon source
2508962345L-rhamnose+carbon source
2508962345L-rhamnose+builds acid from
2508917115L-serine+carbon source
2508917632nitrate+reduction
2508917272propionate+carbon source
2508953423tween 40+carbon source

antibiotic resistance

@refChEBImetaboliteis antibioticis resistant
25089161680aztreonamyesyes
2508932735guanidinium chlorideyesyes
2508948607lithium chlorideyesyes
25089100147nalidixic acidyesyes
2508975229sodium bromateyesyes
2508964103sodium butyrateyesyes
2508975228sodium lactateyesyes

metabolite production

@refChebi-IDmetaboliteproduction
2508916136hydrogen sulfideno
2508935581indoleno
2508915688acetoinyes

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
2508915688acetoin+
2508935581indole-

enzymes

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

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountrycontinentlatitudelongitudeenrichment cultureenrichment culture durationenrichment culture temperature
24806deep-sea sedimentCarlsberg Ridge (63.65731° E 3.71069° N, depth of 3690 m)Indian OceanAsia3.710763.6573
25089deep-sea sediment (depth of 3690 m)Oatmeal agar (ISP3)14-105 days28
67770Deep-sea sediment at the Carlsberg Ridge (63.65731° E 3.71069° N, at a depth of 3,690 m)3.7106963.6573

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Environmental#Aquatic#Sediment

taxonmaps

  • @ref: 69479
  • File name: preview.99_4584.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15817;96_81;97_619;98_713;99_4584&stattab=map
  • Last taxonomy: Brevibacterium
  • 16S sequence: KX356313
  • Sequence Identity:
  • Total samples: 2870
  • soil counts: 309
  • aquatic counts: 309
  • animal counts: 2183
  • plant counts: 69

Safety information

risk assessment

  • @ref: 24806
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 24806
  • description: Brevibacterium sediminis strain CGMCC 1.15472 16S ribosomal RNA gene, partial sequence
  • accession: KX356313
  • length: 1489
  • database: ena
  • NCBI tax ID: 1857024

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Brevibacterium sediminis CGMCC 1.15472GCA_014643055contigncbi1857024
66792Brevibacterium sediminis FXJ8.269GCA_013623905contigncbi1857024
66792Brevibacterium sediminis strain CGMCC 1.154721857024.4wgspatric1857024

GC content

  • @ref: 25089
  • GC-content: 64.2
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno85no
motileno92.406yes
gram-positiveyes89.838yes
anaerobicno99.5no
aerobicyes95.162no
halophileyes64.333no
spore-formingno91.296no
glucose-utilyes89.224yes
flagellatedno97.335no
thermophileno99.041no
glucose-fermentno92.823no

External links

@ref: 24806

culture collection no.: DSM 102229, CGMCC 1.15472, JCM 32488

straininfo link

  • @ref: 91292
  • straininfo: 406792

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny27654846Brevibacterium 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 YInt J Syst Evol Microbiol10.1099/ijsem.0.0015062016Bacterial Typing Techniques, Base Composition, Brevibacterium/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/microbiology, Indian Ocean, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny33649904Brevibacterium renqingii sp. nov., isolated from the Daqu of Baijiu.Yan Y, Xing X, Sun Z, Li J, Hao S, Xu JArch Microbiol10.1007/s00203-021-02212-x2021Bacterial Typing Techniques, Base Composition/genetics, *Brevibacterium/classification/genetics/isolation & purification, DNA, Bacterial/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Fermentation, Fermented Foods/*microbiology, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNATranscriptome

Reference

@idauthorstitledoi/urlcataloguejournalpubmed
20215Parte, 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 DSMZ10.1099/ijsem.0.004332
24806Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-102229Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 102229)
25089P. 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 Ridges10.1099/ijsem.0.001506IJSEM 66: 5268-5274 201627654846
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
69479João 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 betahttps://microbeatlas.org/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
91292Reimer, 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 identifiers10.60712/SI-ID406792.1