Strain identifier

BacDive ID: 3902

Type strain: Yes

Species: Brachybacterium faecium

Strain Designation: 6-10

Strain history: CIP <- 1990, NCIB <- H.E. Schefferle: strain 6-10, Arthrobacter sp.

NCBI tax ID(s): 446465 (strain), 43669 (species)

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General

@ref: 1836

BacDive-ID: 3902

DSM-Number: 4810

keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-positive

description: Brachybacterium faecium 6-10 is a mesophilic, Gram-positive bacterium that was isolated from poultry deep litter.

NCBI tax id

NCBI tax idMatching level
446465strain
43669species

strain history

@refhistory
1836<- NCIB <- H.E. Schefferle, 6-10
67770CCM 4372 <-- IFO 14762 <-- NCIB 9860 <-- H. E. Schefferle 6-10.
119224CIP <- 1990, NCIB <- H.E. Schefferle: strain 6-10, Arthrobacter sp.

doi: 10.13145/bacdive3902.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Dermabacteraceae
  • genus: Brachybacterium
  • species: Brachybacterium faecium
  • full scientific name: Brachybacterium faecium Collins et al. 1988

@ref: 1836

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Dermabacteraceae

genus: Brachybacterium

species: Brachybacterium faecium

full scientific name: Brachybacterium faecium Collins et al. 1988 emend. Nouioui et al. 2018

strain designation: 6-10

type strain: yes

Morphology

cell morphology

@refgram stainconfidencemotility
69480positive100
6948091.325no

colony morphology

@refcolony colorincubation periodmedium used
20197Light ivory (1015)10-14 daysISP 2
20197Light ivory (1015)10-14 daysISP 4
20197Light ivory (1015)10-14 daysISP 5

multicellular morphology

@refforms multicellular complexmedium name
20197noISP 2
20197noISP 4
20197noISP 5

multimedia

  • @ref: 66793
  • multimedia content: EM_DSM_4810_1.jpg
  • caption: electron microscopic image
  • intellectual property rights: © HZI/Manfred Rohde

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
1836TRYPTICASE 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
20197ISP 2yesName: ISP 2 / Yeast Malt Agar (5265); 5265 Composition Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l Agar 15.0 g/l Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.0 Usage: Maintenance and Taxonomy Organisms: All Actinomycetes
20197ISP 4yesName: ISP 4; DSM 547 Solution I: Difco soluble starch, 10.0 g. Make a paste of the starch with a small amount of cold distilled water and bring to a volume of 500 ml. Solution II: CaCO3 2.0 g K2HPO4 (anhydrous) 1.0 g MgSO4 x 7 H2O 1.0 g NaCl 1.0 g (NH4)2SO4 2.0 g Distilled water 500.0 ml Trace salt solution (see below) 1.0 ml The pH should be between 7.0 and 7.4. Do not adjust if it is within this range. Mix solutions I and II together. Add 20.0 g agar. Liquify agar by steaming at 100°C for 10 to 20 min. Trace element solution: FeSO4 x 7 H2O 0.1 g MnCl2 x 4 H2O 0.1 g ZnSO4 x 7 H2O 0.1 g Distilled water 100.0 ml
20197ISP 5yesName: ISP 5 (5323) Composition L-Asparagine 1.0 g/l Glycerol 10.0 g/l K2HPO4 1.0 g/l Salt solution (see preparation) 1.0 ml/l Agar 20.0 g/l Preparation: Salt solution 1.0 g FeSO4 x 7 H2O 1.0 g MnCl2 x 4 H2O 1.0 g ZNSO4 x 7 H2O in 100 ml water Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.2 Usage: Maintenance and taxonomy Organisms: All Actinomycetes
40603MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
119224CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
20197positiveoptimum28mesophilic
1836positivegrowth30mesophilic
40603positivegrowth30mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.927

halophily

  • @ref: 20197
  • salt: NaCl
  • growth: positive
  • tested relation: maximum
  • concentration: 7.5 %

murein

  • @ref: 1836
  • murein short key: A31.02
  • type: A4gamma m-Dpm-D-Glu2; alpha-carboxyl group of D-Glu substituted by glycine

observation

  • @ref: 67770
  • observation: quinones: MK-7, MK-8

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2019717234glucose+
2019722599arabinose+
2019717992sucrose+
2019718222xylose+
2019717268myo-inositol+
2019729864mannitol+/-
2019728757fructose+/-
2019726546rhamnose+
2019716634raffinose+
2019762968cellulose+
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816199urea-hydrolysis
6836816947citrate-assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis
683794853esculin-hydrolysis
6837916199urea-hydrolysis
6837917634D-glucose+fermentation
6837916988D-ribose+fermentation
6837965327D-xylose-fermentation
6837917306maltose-fermentation
6837917716lactose+fermentation
6837917992sucrose+fermentation
6837928087glycogen-fermentation

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinno
6836835581indoleno
6836816136hydrogen sulfideno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
6836815688acetoin-
6836835581indole-

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase+3.2.1.24
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase+3.2.1.23
68382alpha-galactosidase+3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase-3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase+3.4.11.3
68382valine arylamidase+
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase+3.1.3.1
68379urease-3.5.1.5
68379beta-glucosidase-3.2.1.21
68379N-acetyl-beta-glucosaminidase-3.2.1.52
68379alpha-glucosidase+3.2.1.20
68379beta-galactosidase+3.2.1.23
68379beta-glucuronidase+3.2.1.31
68379alkaline phosphatase-3.1.3.1
68379pyrrolidonyl arylamidase+3.4.19.3
68379pyrazinamidase+3.5.1.B15
68368gelatinase-
68368tryptophan deaminase-4.1.99.1
68368urease-3.5.1.5
68368ornithine decarboxylase-4.1.1.17
68368lysine decarboxylase-4.1.1.18
68368arginine dihydrolase-3.5.3.6
68368beta-galactosidase+3.2.1.23

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
20197+/-++-+++---+/-++-+/--++-

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
20197+++-+++---+++-+-++-

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
20197+----------

Isolation, sampling and environmental information

isolation

@refsample type
1836poultry deep litter
67770Poultry deep litter
119224Other, Poultry, deep litter

isolation source categories

Cat1Cat2Cat3
#Engineered#Waste
#Host#Birds
#Host#Other#Decomposing animal

taxonmaps

  • @ref: 69479
  • File name: preview.99_2257.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_1217;97_1443;98_1761;99_2257&stattab=map
  • Last taxonomy: Brachybacterium faecium
  • 16S sequence: X83810
  • Sequence Identity:
  • Total samples: 1227
  • soil counts: 60
  • aquatic counts: 66
  • animal counts: 1056
  • plant counts: 45

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
18361Risk group (German classification)
201971
1192241Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218B.faecium 16S rRNA geneX838101480ena446465
1836B.faecium 16S ribosomal RNA geneX910321513ena446465

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Brachybacterium faecium DSM 4810GCA_000023405completencbi446465
66792Brachybacterium faecium DSM 4810446465.5completepatric446465
66792Brachybacterium faecium 6-10, DSM 4810644736331completeimg446465

GC content

@refGC-contentmethod
183669.4thermal denaturation, midpoint method (Tm)
6777072.1high performance liquid chromatography (HPLC)
6777072.05genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno82no
motileno92.071no
flagellatedno97.702no
gram-positiveyes92.343no
anaerobicno99.565no
aerobicyes88.427no
halophileno52.404no
spore-formingno87.32no
thermophileno99.052yes
glucose-utilyes89.791yes
glucose-fermentno65.704no

External links

@ref: 1836

culture collection no.: DSM 4810, ATCC 43885, IMET 11352, NCIB 9860, JCM 11609, CCM 4372, CCUG 32293, CCUG 50351, CIP 103333, IAM 14581, IFO 14762, IMSNU 21277, KCCM 40244, LMG 19847, NBRC 14762, NCIMB 9860, VKM Ac-1423

straininfo link

  • @ref: 73412
  • straininfo: 92763

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny18768630Devriesea agamarum gen. nov., sp. nov., a novel actinobacterium associated with dermatitis and septicaemia in agamid lizards.Martel A, Pasmans F, Hellebuyck T, Haesebrouck F, Vandamme PInt J Syst Evol Microbiol10.1099/ijs.0.65478-02008Actinomycetales/*classification/genetics/*isolation & purification/physiology, Aerobiosis, Animals, Base Composition, Catalase/metabolism, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Dermatitis/microbiology/*veterinary, Fatty Acids/analysis, Genes, rRNA, Lizards/*microbiology, Locomotion, Molecular Sequence Data, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sepsis/microbiology/*veterinary, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Temperature, Vitamin K 2/analysisGenetics
Phylogeny21216918Brachybacterium saurashtrense sp. nov., a halotolerant root-associated bacterium with plant growth-promoting potential.Gontia I, Kavita K, Schmid M, Hartmann A, Jha BInt J Syst Evol Microbiol10.1099/ijs.0.023176-02011Actinomycetales/*classification/genetics/*isolation & purification/metabolism, Base Composition, Chenopodiaceae/growth & development/*microbiology, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/metabolism, Molecular Sequence Data, Phylogeny, Plant Roots/*microbiology, RNA, Ribosomal, 16S/genetics, Sodium Chloride/*metabolismMetabolism
Genetics21304631Complete genome sequence of Brachybacterium faecium type strain (Schefferle 6-10).Lapidus A, Pukall R, Labuttii K, Copeland A, Del Rio TG, Nolan M, Chen F, Lucas S, Tice H, Cheng JF, Bruce D, Goodwin L, Pitluck S, Rohde M, Goker M, Pati A, Ivanova N, Mavrommatis K, Chen A, Palaniappan K, D'haeseleer P, Chain P, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HPStand Genomic Sci10.4056/sigs.4922009
Phylogeny24944333Brachybacterium ginsengisoli sp. nov., isolated from soil of a ginseng field.Hoang VA, Kim YJ, Nguyen NL, Yang DCInt J Syst Evol Microbiol10.1099/ijs.0.058388-02014Actinomycetales/*classification/genetics/isolation & purification, Base Composition, Cell Wall/chemistry, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Panax/*microbiology, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryGenetics
Phylogeny26311250Brachybacterium hainanense sp. nov., isolated from noni (Morinda citrifolia L.) branch.Liu Y, Zhai L, Yao S, Cao Y, Cao Y, Zhang X, Su J, Ge Y, Zhao R, Cheng CInt J Syst Evol Microbiol10.1099/ijsem.0.0005592015Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Glycolipids/chemistry, Morinda/*microbiology, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/chemistryTranscriptome
Phylogeny27514821Brachybacterium aquaticum sp. nov., a novel actinobacterium isolated from seawater.Kaur G, Kumar N, Mual P, Kumar A, Kumar RM, Mayilraj SInt J Syst Evol Microbiol10.1099/ijsem.0.0014142016Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, India, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
1836Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 4810)https://www.dsmz.de/collection/catalogue/details/culture/DSM-4810
20197Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM4810.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
40603Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/15119
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
66793Mukherjee et al.10.1038/nbt.3886GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life 35: 676-683 201728604660
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68368Automatically annotated from API 20E
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
73412Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID92763.1StrainInfo: A central database for resolving microbial strain identifiers
119224Curators of the CIPCollection of Institut Pasteur (CIP 103333)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103333