Strain identifier

BacDive ID: 1681

Type strain: Yes

Species: Serinibacter salmoneus

Strain Designation: Kis4-28

Strain history: <- T. Tamura, NBRC <- T. Iino and T. Iwami, NBRC; Kis4-28

NCBI tax ID(s): 556530 (species)

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General

@ref: 15964

BacDive-ID: 1681

DSM-Number: 21801

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

description: Serinibacter salmoneus Kis4-28 is a mesophilic, Gram-positive, rod-shaped bacterium that was isolated from gut of sillago fish Sillago japonica.

NCBI tax id

  • NCBI tax id: 556530
  • Matching level: species

strain history

  • @ref: 15964
  • history: <- T. Tamura, NBRC <- T. Iino and T. Iwami, NBRC; Kis4-28

doi: 10.13145/bacdive1681.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Beutenbergiaceae
  • genus: Serinibacter
  • species: Serinibacter salmoneus
  • full scientific name: Serinibacter salmoneus Hamada et al. 2009

@ref: 15964

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Beutenbergiaceae

genus: Serinibacter

species: Serinibacter salmoneus

full scientific name: Serinibacter salmoneus Hamada et al. 2009

strain designation: Kis4-28

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
29335positive1.5 µm0.45 µmrod-shapedno
69480positive100

colony morphology

@refcolony colorincubation periodmedium used
19796Deep orange10-14 daysISP 3
19796Beige10-14 daysISP 6
19796Honey yellow10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
19796noISP 3
19796noISP 6
19796noISP 7

pigmentation

  • @ref: 29335
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
15964TRYPTICASE 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
19796ISP 3yesName: ISP 3; 5315 Composition Dog oat flakes 20.0 g/l Trace element solution (5314) 2.5 ml/l Agar 18.0 g/l Preparation: Oat flakes are cooked for 20 minutes, trace element solution and agar are added (in the case of non rolled oat flakes the suspension has to bee filtrated). Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.8 Usage: Maintenance and taxonomy (e.g. SEM As liquid medium for metabolite production) Organisms: All Actinomycetes Trace element solution 5314 Name: Trace element solution 5314; 5314 Composition CaCl2 x H2O 3.0 g/l Fe-III-citrate 1.0 g/l MnSO4 0.2 g/l ZnCl2 0.1 g/l CuSO4 x 5 H2O 0.025 g/l Sodium tetra borate 0.2 g/l CoCl2 x 6 H2O 0.004 g/l Sodium molybdate 0.01 g/l Preparation: Use double destillated water. Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Trace element solution for different media Organisms:
19796ISP 6yesName: ISP 6 (5318) Composition Peptone 15.0 g/l Proteose peptose 5.0 g/l Ferric ammonium citrate 0.5 g/l Sodium glycerophosphate 1.0 g/l Sodium thiosulfate 0.08 g/l Yeast extract 1.0 g/l Agar 15.0 g/l Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigments Organisms: All Actinomycetes
19796ISP 7yesName: ISP 7 (5322) Composition Glycerol 15.0 g/l L-Tyrosine 0.5 g/l L-Asparagine 1.0 g/l K2HPO4 0.5 g/l NaCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Trace element solution 5343 1.0 ml/l Agar 20.0 Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.3 Usage: Production of melanoid pigments Organisms: All Actinomycetes

culture temp

@refgrowthtypetemperaturerange
19796positiveoptimum28mesophilic
15964positivegrowth28mesophilic
29335positivegrowth10-37
29335positiveoptimum28mesophilic

culture pH

@refabilitytypepHPH range
29335positivegrowth06-09alkaliphile
29335positiveoptimum7

Physiology and metabolism

spore formation

@refspore formationconfidence
29335no
69481no95
69480no99.999

halophily

@refsaltgrowthtested relationconcentration
29335NaClpositivegrowth0-10 %
29335NaClpositiveoptimum2.5 %

murein

  • @ref: 15964
  • murein short key: A11.58
  • type: A4alpha L-Lys-L-Ser-L-Glu

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1979662968cellulose-
1979616634raffinose-
1979626546rhamnose-
1979628757fructose-
1979629864mannitol-
1979617268myo-inositol-
1979618222xylose-
1979617992sucrose-
1979622599arabinose-
1979617234glucose-
2933517057cellobiose+carbon source
2933528757fructose+carbon source
2933528260galactose+carbon source
2933517234glucose+carbon source
2933528087glycogen+carbon source
2933517716lactose+carbon source
2933517306maltose+carbon source
2933537684mannose+carbon source
29335506227N-acetylglucosamine+carbon source
2933517992sucrose+carbon source
2933527082trehalose+carbon source
2933518222xylose+carbon source
293354853esculin+hydrolysis
683794853esculin+hydrolysis
6837916199urea-hydrolysis
683795291gelatin+hydrolysis
6837917992sucrose-fermentation
6837928087glycogen-fermentation

enzymes

@refvalueactivityec
29335acid phosphatase+3.1.3.2
29335alpha-galactosidase+3.2.1.22
29335catalase+1.11.1.6
29335pyrazinamidase+3.5.1.B15
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
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
19796+/-----++-+-++/-+/-+/-+/-+/-+/---

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
19796-+--+----++++-+++--

Isolation, sampling and environmental information

isolation

  • @ref: 15964
  • sample type: gut of sillago fish Sillago japonica
  • host species: Sillago japonica
  • geographic location: coast of Tokyo Bay, Kyonan Beach
  • country: Japan
  • origin.country: JPN
  • continent: Asia

isolation source categories

Cat1Cat2Cat3
#Host#Fishes
#Host Body-Site#Gastrointestinal tract#Stomach

taxonmaps

  • @ref: 69479
  • File name: preview.99_13140.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_1152;97_8115;98_9952;99_13140&stattab=map
  • Last taxonomy: Serinibacter
  • 16S sequence: AB455532
  • Sequence Identity:
  • Total samples: 179
  • soil counts: 28
  • aquatic counts: 66
  • animal counts: 77
  • plant counts: 8

Safety information

risk assessment

  • @ref: 15964
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 15964
  • description: Serinibacter salmoneus gene for 16S rRNA, partial sequence
  • accession: AB455532
  • length: 1483
  • database: ena
  • NCBI tax ID: 556530

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Serinibacter salmoneus DSM 21801GCA_002563925contigncbi556530
66792Serinibacter salmoneus strain DSM 21801556530.3wgspatric556530
66792Serinibacter salmoneus DSM 218012627853598draftimg556530

GC content

@refGC-contentmethod
1596470.7high performance liquid chromatography (HPLC)
2933570.7

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno95no
gram-positiveyes89.003yes
anaerobicno98.861no
halophileno79.44no
spore-formingno96.183yes
glucose-utilyes87.866no
thermophileno98.04no
aerobicyes84.189no
motileno89.211yes
flagellatedno97.391yes
glucose-fermentno83.683no

External links

@ref: 15964

culture collection no.: DSM 21801, NBRC 104924

straininfo link

  • @ref: 71328
  • straininfo: 403416

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19628613Serinibacter salmoneus gen. nov., sp. nov., an actinobacterium isolated from the intestinal tract of a fish, and emended descriptions of the families Beutenbergiaceae and Bogoriellaceae.Hamada M, Iino T, Tamura T, Iwami T, Harayama S, Suzuki KInt J Syst Evol Microbiol10.1099/ijs.0.011106-02009Actinobacteria, Actinomycetales/*classification/genetics/*isolation & purification/metabolism, Animals, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/chemistry/metabolism, Fishes/*microbiology, Intestines/*microbiology, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/geneticsMetabolism
Phylogeny25604338Serinibacter tropicus sp. nov., an actinobacterium isolated from the rhizosphere of a mangrove, and emended description of the genus Serinibacter.Hamada M, Shibata C, Nurkanto A, Ratnakomala S, Lisdiyanti P, Tamura T, Suzuki KIInt J Syst Evol Microbiol10.1099/ijs.0.0000682015Actinomycetales/*classification/genetics/isolation & purification, Avicennia/*microbiology, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Indonesia, Islands, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryGenetics
Phylogeny31730034Serinibacter arcticus sp. nov., isolated from a thawing ancient ice wedge.Filippova SN, Surgucheva NA, Detkova EN, Rakitin AL, Beletsky AV, Grouzdev DS, Kolganova TV, Mulyukin ALInt J Syst Evol Microbiol10.1099/ijsem.0.0038482020Actinobacteria/*classification/isolation & purification, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, DNA, Bacterial/genetics, Fatty Acids/chemistry, Glycolipids/chemistry, *Ice, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Siberia, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
15964Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21801)https://www.dsmz.de/collection/catalogue/details/culture/DSM-21801
19796Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM21801.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
29335Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2574728776041
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)
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 updates33211880Nucleic Acids Res. 49: D498-D508 2020
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)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
71328Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID403416.1StrainInfo: A central database for resolving microbial strain identifiers