Strain identifier

BacDive ID: 3932

Type strain: Yes

Species: Branchiibius hedensis

Strain Designation: 29717

Strain history: <- A. Arisawa, Mercian Corporation, Iwata, Japan; 29717 <- S. Sugimoto

NCBI tax ID(s): 672460 (species)

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General

@ref: 16629

BacDive-ID: 3932

DSM-Number: 22951

keywords: genome sequence, 16S sequence, Bacteria, mesophilic

description: Branchiibius hedensis 29717 is a mesophilic bacterium that was isolated from branchia of a Japanese codling, Physiculus japonicus.

NCBI tax id

  • NCBI tax id: 672460
  • Matching level: species

strain history

  • @ref: 16629
  • history: <- A. Arisawa, Mercian Corporation, Iwata, Japan; 29717 <- S. Sugimoto

doi: 10.13145/bacdive3932.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Dermacoccaceae
  • genus: Branchiibius
  • species: Branchiibius hedensis
  • full scientific name: Branchiibius hedensis Sugimoto et al. 2011

@ref: 16629

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Dermacoccaceae

genus: Branchiibius

species: Branchiibius hedensis

full scientific name: Branchiibius hedensis Sugimoto et al. 2011

strain designation: 29717

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480no94.425
69480100positive

colony morphology

@refcolony colormedium used
69232Light ivory (1015)ISP 7
69232Oyster white (1013)ISP 2
69232Oyster white (1013)ISP 3
69232Oyster white (1013)ISP 4
69232Oyster white (1013)ISP 5
69232Oyster white (1013)suter with tyrosine
69232Oyster white (1013)suter without tyrosine

multicellular morphology

@refforms multicellular complexcomplex namemedium name
69232noAerial myceliumISP 2
69232noAerial myceliumISP 3
69232noAerial myceliumISP 4
69232noAerial myceliumISP 5
69232noAerial myceliumISP 7
69232noAerial myceliumsuter with tyrosine
69232noAerial myceliumsuter without tyrosine

pigmentation

@refproductionname
69232noMelanin
69232nosoluble pigment

Culture and growth conditions

culture medium

  • @ref: 16629
  • name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/92
  • composition: 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: 16629
  • growth: positive
  • type: growth
  • temperature: 28
  • range: mesophilic

Physiology and metabolism

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.689

halophily

  • @ref: 69232
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-2.5 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6923222599arabinose+growth
6923262968cellulose+growth
6923228757fructose+growth
6923217234glucose+growth
6923217268inositol+/-growth
6923237684mannose+/-growth
6923216634raffinose+/-growth
6923226546rhamnose+/-growth
6923217992sucrose+growth
6923218222xylose+/-growth
6837917632nitrate-reduction
683794853esculin+hydrolysis
6837916199urea+hydrolysis
683795291gelatin+hydrolysis
6837917634D-glucose-fermentation
6837916988D-ribose-fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol-fermentation
6837917306maltose-fermentation
6837917716lactose-fermentation
6837917992sucrose-fermentation
6837928087glycogen-fermentation

enzymes

@refvalueactivityec
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
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
68379gelatinase+
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

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
69232-+++--+-+++--------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
69232+++++++++++/-+/-++++++/-+/-

Isolation, sampling and environmental information

isolation

  • @ref: 16629
  • sample type: branchia of a Japanese codling, Physiculus japonicus
  • host species: Physiculus japonicus
  • geographic location: Shizuoka prefecture, Suruga Bay, Heda
  • country: Japan
  • origin.country: JPN
  • continent: Asia

isolation source categories

Cat1Cat2Cat3
#Host#Fishes
#Host Body-Site#Oral cavity and airways#Airways

taxonmaps

  • @ref: 69479
  • File name: preview.99_53367.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_23888;97_29888;98_38211;99_53367&stattab=map
  • Last taxonomy: Branchiibius
  • 16S sequence: AB520822
  • Sequence Identity:
  • Total samples: 1843
  • soil counts: 151
  • aquatic counts: 355
  • animal counts: 1282
  • plant counts: 55

Safety information

risk assessment

  • @ref: 16629
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 16629
  • description: Branchiibius hedensis gene for 16S ribosomal RNA, partial sequence
  • accession: AB520822
  • length: 1524
  • database: ena
  • NCBI tax ID: 672460

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Branchiibius hedensis DSM 22951GCA_900108585contigncbi672460
66792Branchiibius hedensis DSM 22951GCA_003149195contigncbi672460
66792Branchiibius hedensis strain DSM 22951672460.4wgspatric672460
66792Branchiibius hedensis strain DSM 22951672460.3wgspatric672460
66792Branchiibius hedensis DSM 229512634166369draftimg672460

GC content

  • @ref: 16629
  • GC-content: 68
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno80no
gram-positiveyes92.64no
anaerobicno98.794no
halophileno95.387no
spore-formingno82.68no
glucose-utilyes90.205yes
thermophileno99.227yes
flagellatedno98.341no
motileno95.206no
aerobicyes88.619no
glucose-fermentno91.085yes

External links

@ref: 16629

culture collection no.: DSM 22951, NBRC 106121, Mer 29717

straininfo link

  • @ref: 73442
  • straininfo: 405955

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny20562243Branchiibius hedensis gen. nov., sp. nov., an actinobacterium isolated from a Japanese codling (Physiculus japonicus).Sugimoto S, Kato T, Ito M, Sakata N, Tsuchida T, Matsumoto A, Takahashi YInt J Syst Evol Microbiol10.1099/ijs.0.023648-02010Actinomycetales/*classification/genetics/*isolation & purification/metabolism, Animals, Base Composition, DNA, Bacterial/genetics, Fatty Acids/metabolism, Gadiformes/*microbiology, Japan, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/geneticsMetabolism
Phylogeny21940130Branchiibius cervicis sp. nov., a novel species isolated from patients with atopic dermatitis.Tomida J, Sakamoto D, Sugita T, Fujiwara N, Naka T, Hamada M, Morita Y, Kawamura YSyst Appl Microbiol10.1016/j.syapm.2011.08.0032011Actinomycetales/chemistry/*classification/genetics/*isolation & purification/pathogenicity, Actinomycetales Infections/microbiology, Adolescent, Adult, Base Composition, Cell Wall/chemistry, Chromatography, High Pressure Liquid, DNA, Bacterial/genetics, Dermatitis, Atopic/*microbiology, Fatty Acids/chemistry, Female, Genes, Bacterial, Genes, rRNA, Humans, Male, Neck/microbiology, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Ribotyping, Vitamin K 2/chemistry, Young AdultPathogenicity
Phylogeny28920829Allobranchiibius huperziae gen. nov., sp. nov., a member of Dermacoccaceae isolated from the root of a medicinal plant Huperzia serrata (Thunb.).Ai MJ, Sun Y, Sun HM, Liu HY, Yu LY, Zhang YQInt J Syst Evol Microbiol10.1099/ijsem.0.0022842017Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Glycolipids/chemistry, Huperzia/*microbiology, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, Plant Roots/*microbiology, Plants, Medicinal/microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNATranscriptome

Reference

@idauthorscataloguedoi/urltitle
16629Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22951)https://www.dsmz.de/collection/catalogue/details/culture/DSM-22951
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
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)
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
69232Wink, J.https://cdn.dsmz.de/wink/DSM%2022951.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
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)
73442Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID405955.1StrainInfo: A central database for resolving microbial strain identifiers