Strain identifier

BacDive ID: 3928

Type strain: Yes

Species: Kytococcus sedentarius

Strain Designation: 541, 54

Strain history: CIP <- 1981, CCM <- C.F. ZoBell: strain 54

NCBI tax ID(s): 478801 (strain), 1276 (species)

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General

@ref: 8775

BacDive-ID: 3928

DSM-Number: 20547

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

description: Kytococcus sedentarius 541 is an aerobe, mesophilic bacterium that was isolated from seawater.

NCBI tax id

NCBI tax idMatching level
1276species
478801strain

strain history

@refhistory
8775<- CCM <- C.E. ZoBell, 541
67770CIP 81.72 <-- CCM 314 <-- C. E. ZoBell 541.
122531CIP <- 1981, CCM <- C.F. ZoBell: strain 54

doi: 10.13145/bacdive3928.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Kytococcaceae
  • genus: Kytococcus
  • species: Kytococcus sedentarius
  • full scientific name: Kytococcus sedentarius (ZoBell and Upham 1944) Stackebrandt et al. 1995

  • synonyms

    • @ref: 20215
    • synonym: Micrococcus sedentarius

@ref: 8775

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Kytococcaceae

genus: Kytococcus

species: Kytococcus sedentarius

full scientific name: Kytococcus sedentarius (ZoBell and Upham 1944) Stackebrandt et al. 1995 emend. Nouioui et al. 2018

strain designation: 541, 54

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no93.348
69480100positive
122531nopositivecoccus-shaped

colony morphology

@refcolony colorincubation periodmedium used
18758Cream10-14 days5006
18758Cream10-14 days5425
18758Cream10-14 days5428
18758Cream10-14 days5530
18758Cream10-14 daysISP 2
122531

multicellular morphology

@refforms multicellular complexmedium name
18758noISP 2
18758no5006
18758no5425
18758no5428
18758no5530

multimedia

  • @ref: 66793
  • multimedia content: EM_DSM_20547_1.jpg
  • caption: electron microscopic image
  • intellectual property rights: © HZI/Manfred Rohde

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8775BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)yeshttps://mediadive.dsmz.de/medium/514Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water
18758ISP 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
187585006yesMedium: 5006 Name: Composition (g/l) Sucrose 3,0 Dextrin 15,0 Meat extract 1,0 Yeast extract 2,0 Tryptone soy broth (Oxoid) 5,0 NaCl 0,5 K2HPO4 0,5 MgSO4 x 7 H2O 0,5 FeSO4 x 7 H2O 0,01 Agar 20,0 Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7,3 Usage: Maintenance Organisms: All Actinomycetes
187585425yesName: Brain Heart Infusion (BHI) Agar; 5425 Composition: Calf brain infusion 200.0 g/l Beef heart infusion 250.0 g/l Casein (meat) peptone 10.0 g/l Glucose 2.0 g/l NaCl 5.0 g/l Na2HPO4 2.5 g/l Agar 15.0 g/l Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.4 Usage: Maintenance and revitalization Organisms: Dermatophilus congolensis, Nocardia brasieliensis, N. asteroides, Rhodococcus equi, R. fascians, R. rhodochrous, Streptomyces thermoviol aceus subsp. apingens, Coryneform species
187585428yes
187585530yes
37626MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
122531CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
18758positiveoptimum28mesophilic
8775positivegrowth30mesophilic
37626positivegrowth30mesophilic
51333positivegrowth28-37mesophilic
67770positivegrowth28mesophilic
122531positivegrowth22-37
122531nogrowth10psychrophilic
122531nogrowth41thermophilic
122531nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
51333aerobe
122531obligate aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.999

murein

  • @ref: 8775
  • murein short key: A11.43
  • type: A4alpha L-Lys-D-Glu2

observation

  • @ref: 67770
  • observation: quinones: MK-8, MK-9, MK-10

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371gluconate-builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371turanose-builds acid from32528
68371gentiobiose-builds acid from28066
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose-builds acid from27082
68371sucrose-builds acid from17992
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371maltose-builds acid from17306
68371cellobiose-builds acid from17057
68371salicin-builds acid from17814
68371esculin-builds acid from4853
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
68371N-acetylglucosamine-builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol-builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371D-mannose-builds acid from16024
68371D-fructose-builds acid from15824
68371D-glucose-builds acid from17634
68371D-galactose-builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose-builds acid from65327
68371D-ribose-builds acid from16988
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754
68368gelatin+hydrolysis5291
68368tryptophan-energy source27897
68368urea+hydrolysis16199
68368citrate+assimilation16947
68368ornithine+degradation18257
68368lysine+degradation25094
68368arginine+hydrolysis29016
122531hippurate-hydrolysis606565
122531nitrate-reduction17632
122531nitrite-reduction16301
68379nitrate-reduction17632
68379esculin-hydrolysis4853
68379D-glucose-fermentation17634
68379D-ribose-fermentation16988
68379D-xylose-fermentation65327
68379D-mannitol-fermentation16899
68379maltose-fermentation17306
68379lactose-fermentation17716
68379sucrose-fermentation17992
68379glycogen-fermentation28087
68375urea-hydrolysis16199
68375arginine-hydrolysis29016
68375ornithine-degradation18257
68375esculin-hydrolysis4853
68375D-glucose-fermentation17634
68375D-fructose-fermentation15824
68375D-mannose-fermentation16024
68375maltose-fermentation17306
68375lactose-fermentation17716
68375trehalose-fermentation27082
68375D-mannitol-fermentation16899
68375raffinose-fermentation16634
68375D-ribose-fermentation16988
68375cellobiose-fermentation17057
68375nitrate-reduction17632
68375sucrose-fermentation17992
68375N-acetylglucosamine-fermentation59640
68375turanose-fermentation32528
68375arabinose-fermentation22599
68378D-glucose-builds acid from17634
68378D-fructose-builds acid from15824
68378D-mannose-builds acid from16024
68378maltose-builds acid from17306
68378lactose-builds acid from17716
68378trehalose-builds acid from27082
68378D-mannitol-builds acid from16899
68378xylitol-builds acid from17151
68378melibiose-builds acid from28053
68378nitrate-reduction17632
68378raffinose-builds acid from16634
68378D-xylose-builds acid from65327
68378sucrose-builds acid from17992
68378methyl alpha-D-glucopyranoside-builds acid from320061
68378N-acetylglucosamine-builds acid from59640
68378arginine-hydrolysis29016
68378urea-hydrolysis16199

antibiotic resistance

@refmetaboliteis antibioticis sensitiveChEBIsensitivity conc.
68378lysostaphinyesyes
68375novobiocinyesyes283681.8 µg

metabolite production

@refChebi-IDmetaboliteproduction
6837815688acetoinno
6837515688acetoinno
6836815688acetoinno
6836835581indoleno
6836816136hydrogen sulfideno
12253135581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
6837815688acetoin-
6837515688acetoin-
6836815688acetoin-
6836835581indole-
12253115688acetoin-

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
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382alkaline phosphatase+3.1.3.1
68378urease-3.5.1.5
68378arginine dihydrolase-3.5.3.6
68378alkaline phosphatase-3.1.3.1
68375beta-glucuronidase-3.2.1.31
68375pyrrolidonyl arylamidase-3.4.19.3
68375alkaline phosphatase-3.1.3.1
68375L-arginine arylamidase-
68375beta-galactosidase-3.2.1.23
68375beta-glucosidase-3.2.1.21
68375ornithine decarboxylase-4.1.1.17
68375arginine dihydrolase-3.5.3.6
68375urease-3.5.1.5
68379catalase+1.11.1.6
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
68379pyrrolidonyl arylamidase-3.4.19.3
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
122531oxidase-
122531beta-galactosidase-3.2.1.23
122531alcohol dehydrogenase-1.1.1.1
122531gelatinase+/-
122531amylase-
122531DNase-
122531caseinase+3.4.21.50
122531catalase+1.11.1.6
122531coagulase-
122531tween esterase-
122531gamma-glutamyltransferase+2.3.2.2
122531lecithinase-
122531lipase-
122531lysine decarboxylase-4.1.1.18
122531ornithine decarboxylase-4.1.1.17
122531phenylalanine ammonia-lyase-4.3.1.24
122531protease-
122531urease-3.5.1.5

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYGControlCAT
18758------+--+---------
51333-+-+--+---+---------+

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
18758+-+-++---+---------
51333++--+-----+---+-----
122531+---+-+--++---+-----

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
18758-++++-+---+

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
122531-------------------------------------------------

API ID32STA

@refUREADH ArgODCESCGLUFRUMNEMALLACTREMANRAFRIBCELNITVPbeta GALArgAPALPyrANOVOSACNAGTURARAbeta GUR
51333--------------------------

API STA

@refGLUFRUMNEMALLACTREMANXLTMELNITPALVPRAFXYLSACMDGNAGADHURELSTR
51333--------------------

Isolation, sampling and environmental information

isolation

@refsample type
8775seawater
67770Seawater
122531Environment, Sea water

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic
  • Cat3: #Marine

taxonmaps

  • @ref: 69479
  • File name: preview.99_2534.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_1364;97_1620;98_1971;99_2534&stattab=map
  • Last taxonomy: Kytococcus sedentarius subclade
  • 16S sequence: X87755
  • Sequence Identity:
  • Total samples: 14110
  • soil counts: 1034
  • aquatic counts: 1669
  • animal counts: 11122
  • plant counts: 285

Safety information

risk assessment

@refbiosafety levelbiosafety level commentpathogenicity human
187581Risk group (German classification)
87751Risk group (German classification)yes, in single cases
1225311Risk group (French classification)

Sequence information

16S sequences

  • @ref: 8775
  • description: M.sedentarius 16S rRNA gene
  • accession: X87755
  • length: 1480
  • database: ena
  • NCBI tax ID: 1276

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Kytococcus sedentarius DSM 20547GCA_000023925completencbi478801
66792Kytococcus sedentarius DSM 20547478801.5completepatric478801
66792Kytococcus sedentarius strain FDAARGOS_10611276.16completepatric1276
66792Kytococcus sedentarius strain NCTC110401276.6wgspatric1276
66792Kytococcus sedentarius NCTC 110402839721034draftimg1276
66792Kytococcus sedentarius 541, DSM 20547644736380completeimg478801
67770Kytococcus sedentarius NCTC11040GCA_900452405contigncbi1276

GC content

@refGC-contentmethod
877569.3
6777069.3thermal denaturation, midpoint method (Tm)
6777071.63genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno91.273no
flagellatedno97.252no
gram-positiveyes94.524no
anaerobicno99.392no
aerobicyes89.76yes
halophileyes50.558no
spore-formingno92.169no
thermophileno96.661yes
glucose-utilyes86.633no
glucose-fermentno89.85yes

External links

@ref: 8775

culture collection no.: CCUG 33030, DSM 20547, ATCC 14392, CCM 314, JCM 11482, BCRC 17469, CECT 4619, CIP 81.72, IAM 13003, IFO 15357, IMSNU 21324, LMG 14228, NBRC 15357, NCIMB 13236, NCIMB 14423, NCMB 555, NCTC 11040, VKM Ac-2222, VKM B-1316, VKM B-1824, NCIMB 555

straininfo link

  • @ref: 73438
  • straininfo: 125623

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19541443Kytococcus aerolatus sp. nov., isolated from indoor air in a room colonized with moulds.Kampfer P, Martin K, Schafer J, Schumann PSyst Appl Microbiol10.1016/j.syapm.2009.05.0042009Actinomycetales/chemistry/*classification/genetics/*isolation & purification, *Air Microbiology, Bacterial Typing Techniques, Cell Wall/chemistry, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Lysine/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/analysis, Phylogeny, Pigments, Biological/biosynthesis, RNA, Ribosomal, 16S/genetics, Ribose/analysis, Sequence Analysis, DNA, Vitamin K 2/analysis, Xylose/analysisGenetics
Phylogeny21075908Calidifontibacter indicus gen. nov., sp. nov., a member of the family Dermacoccaceae isolated from a hot spring, and emended description of the family Dermacoccaceae.Ruckmani A, Kaur I, Schumann P, Klenk HP, Mayilraj SInt J Syst Evol Microbiol10.1099/ijs.0.025593-02010Actinomycetales/*classification/genetics/*isolation & purification/physiology, Amino Acids/analysis, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Hot Springs/*microbiology, India, Molecular Sequence Data, Phospholipids/analysis, Phylogeny, Pigments, Biological/metabolism, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analysisGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8775Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20547)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20547
18758Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM20547.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
37626Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/11237
51333Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 33030)https://www.ccug.se/strain?id=33030
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
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68368Automatically annotated from API 20E
68371Automatically annotated from API 50CH acid
68375Automatically annotated from API ID32STA
68378Automatically annotated from API STA
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
73438Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID125623.1StrainInfo: A central database for resolving microbial strain identifiers
122531Curators of the CIPCollection of Institut Pasteur (CIP 81.72)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%2081.72