Strain identifier

BacDive ID: 7646

Type strain: No

Species: Kocuria rhizophila

Strain history: CIP <- 1953, Y.A. Chabbert, Inst. Pasteur, Paris, France, Micrococcus luteus <- F.D.A USA: strain PCI 1001, Sarcina lutea <- E.R. Squibb & Sons

NCBI tax ID(s): 378753 (strain), 72000 (species)

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General

@ref: 141

BacDive-ID: 7646

DSM-Number: 348

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

description: Kocuria rhizophila DSM 348 is an obligate aerobe, mesophilic bacterium that was isolated from Soil.

NCBI tax id

NCBI tax idMatching level
378753strain
72000species

strain history

@refhistory
141<- ATCC <- FDA, PCI 1001 (Sarcina lutea)
67770IAM 1099 <-- NIHJ <-- ATCC 9341 <-- FDA strain PCI 1001 ("Sarcina lutea") <-- E. R. Squibb & Sons.
122203CIP <- 1953, Y.A. Chabbert, Inst. Pasteur, Paris, France, Micrococcus luteus <- F.D.A USA: strain PCI 1001, Sarcina lutea <- E.R. Squibb & Sons

doi: 10.13145/bacdive7646.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Micrococcaceae
  • genus: Kocuria
  • species: Kocuria rhizophila
  • full scientific name: Kocuria rhizophila Kovács et al. 1999

@ref: 141

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Micrococcaceae

genus: Kocuria

species: Kocuria rhizophila

full scientific name: Kocuria rhizophila Kovács et al. 1999

type strain: no

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no93.877
69480100positive
122203nopositivecoccus-shaped

colony morphology

  • @ref: 122203

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
141NUTRIENT AGAR (DSMZ Medium 1)yeshttps://mediadive.dsmz.de/medium/1Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
36878MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
122203CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
141positivegrowth30mesophilic
36878positivegrowth30mesophilic
67770positivegrowth28mesophilic
122203positivegrowth15-41
122203nogrowth10psychrophilic
122203nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 122203
  • oxygen tolerance: obligate aerobe

antibiogram

@refmediumincubation temperatureincubation timeoxygen conditionPenicillin Goxacillinampicillinticarcillinmezlocillincefalotincefazolincefotaximeaztreonamimipenemtetracyclinechloramphenicolgentamycinamikacinvancomycinerythromycinlincomycinofloxacinnorfloxacincolistinpipemidic acidnitrofurantoinbacitracinpolymyxin bkanamycinneomycindoxycyclineceftriaxoneclindamycinfosfomycinmoxifloxacinlinezolidnystatinquinupristin/dalfopristinteicoplaninpiperacillin/tazobactam
141Mueller-Hinton Agar302aerob>50>50>50>50>50>5044>5024-26>5044-4646-48262630>50502614-16666428202644>50>50>50344804824-26>50
141Mueller-Hinton Agar37>50>50>50>50>505040>5024>50404228303044-464024-2620018-20103812242840-42n.d.n.d.n.d.n.d.n.d.n.d.n.d.n.d.n.d.
141Mueller-Hinton Agar30aerob>50>50>50>50>50>5048>5022>5042463032284844262282210-123810243042-445050>503248044-4624>50
141Mueller-Hinton Agar30aerob>50>50>50>50>50>5048>5022>5042463032284844262282210-123810243042-445050>503248044-4624>50

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.999

compound production

@refcompound
141L sorbosone
1416 aminopenicillanic acid
20216L-sorbosone

murein

  • @ref: 141
  • murein short key: A11.06
  • type: A3alpha L-Lys-L-Ala3

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
122203606565hippurate+hydrolysis
12220317632nitrate-reduction
12220316301nitrite-reduction

metabolite production

@refmetaboliteproductionChebi-ID
67770L-sorbosoneyes
122203indoleno35581

metabolite tests

  • @ref: 122203
  • Chebi-ID: 15688
  • metabolite: acetoin
  • voges-proskauer-test: -

enzymes

@refvalueactivityec
122203oxidase-
122203beta-galactosidase-3.2.1.23
122203alcohol dehydrogenase-1.1.1.1
122203gelatinase+/-
122203amylase-
122203DNase-
122203caseinase+3.4.21.50
122203catalase+1.11.1.6
122203tween esterase-
122203gamma-glutamyltransferase+2.3.2.2
122203lecithinase-
122203lipase-
122203lysine decarboxylase-4.1.1.18
122203ornithine decarboxylase-4.1.1.17
122203protease-
122203tryptophan deaminase-
122203urease+3.5.1.5

Isolation, sampling and environmental information

isolation

@refsample type
67770Soil
122203Environment, Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_685.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_424;97_481;98_552;99_685&stattab=map
  • Last taxonomy: Kocuria
  • 16S sequence: AF542072
  • Sequence Identity:
  • Total samples: 2208
  • soil counts: 69
  • aquatic counts: 275
  • animal counts: 1797
  • plant counts: 67

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
1411Risk group (German classification)
1222031Risk group (French classification)

Sequence information

16S sequences

  • @ref: 67770
  • description: Kocuria rhizophila 16S ribosomal RNA gene, partial sequence
  • accession: AF542072
  • length: 1334
  • database: ena
  • NCBI tax ID: 378753

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Kocuria rhizophila NCTC8340GCA_900637835completencbi72000
66792Kocuria rhizophila DC2201GCA_000010285completencbi378753
66792Kocuria rhizophila DC2201378753.5completepatric378753
66792Kocuria rhizophila strain NCTC834072000.33completepatric72000

GC content

  • @ref: 67770
  • GC-content: 70.4

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno89no
motileno95.14no
flagellatedno98.088no
gram-positiveyes93.441no
anaerobicno99.351no
halophileyes65.516no
spore-formingno94.267no
thermophileno91.359yes
glucose-utilyes89.109no
aerobicyes89.796no
glucose-fermentno78.74no

External links

@ref: 141

culture collection no.: DSM 348, ATCC 9341, PCI 1001, JCM 20050, BCRC 10449, CCM 552, CECT 241, CIP 53.45, CNCTC 5039, IAM 1099, IFO 12708, LMG 8194, LMG 8764, LMG 8789, LMG 8816, NBRC 103217, NBRC 12708, NBRC 3232, NCIMB 8553, NCTC 8340, IMET 10397, NCDO 758

straininfo link

  • @ref: 77090
  • straininfo: 10565

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny12892116Reclassification of ATCC 9341 from Micrococcus luteus to Kocuria rhizophila.Tang JS, Gillevet PMInt J Syst Evol Microbiol10.1099/ijs.0.02372-02003DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Micrococcaceae/*classification/genetics/metabolism, Micrococcus luteus/*classification/genetics/metabolism, Molecular Sequence Data, Phenotype, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Terminology as TopicMetabolism
Genetics18408034Complete genome sequence of the soil actinomycete Kocuria rhizophila.Takarada H, Sekine M, Kosugi H, Matsuo Y, Fujisawa T, Omata S, Kishi E, Shimizu A, Tsukatani N, Tanikawa S, Fujita N, Harayama SJ Bacteriol10.1128/JB.01853-072008DNA, Bacterial/chemistry/genetics, *Genome, Bacterial, Micrococcaceae/classification/*genetics, Models, Biological, Models, Genetic, Molecular Sequence Data, Phylogeny, Sequence Analysis, DNA, *Soil MicrobiologyPhylogeny
Metabolism26886276Polysaccharide-based silver nanoparticles synthesized by Klebsiella oxytoca DSM 29614 cause DNA fragmentation in E. coli cells.Baldi F, Daniele S, Gallo M, Paganelli S, Battistel D, Piccolo O, Faleri C, Puglia AM, Gallo GBiometals10.1007/s10534-016-9918-42016Anti-Bacterial Agents/biosynthesis/*pharmacology, Bioreactors, DNA Fragmentation, Escherichia coli/*drug effects/genetics, Klebsiella oxytoca/*metabolism, *Metal Nanoparticles, Microbial Sensitivity Tests, Polysaccharides, Bacterial/biosynthesis/*pharmacology, Silver/metabolism/*pharmacologyPathogenicity
Enzymology27033169Chemical composition and antimicrobial activity of the essential oils of Onychopetalum amazonicum R.E.Fr.de Lima BR, da Silva FM, Soares ER, de Almeida RA, da Silva Filho FA, Pereira Junior RC, Hernandez Tasco AJ, Salvador MJ, Koolen HH, de Souza AD, Pinheiro MLNat Prod Res10.1080/14786419.2016.11636912016Annonaceae/*chemistry, Anti-Infective Agents/chemistry/*isolation & purification/pharmacology, Azulenes/isolation & purification, Escherichia coli/drug effects, Gas Chromatography-Mass Spectrometry, Microbial Sensitivity Tests, Oils, Volatile/*chemistry/isolation & purification/*pharmacology, Plant Leaves/chemistry, Polycyclic Sesquiterpenes, *Sesquiterpenes/analysis/isolation & purification, Staphylococcus epidermidis/drug effects, Terpenes/isolation & purificationPhylogeny
Pathogenicity28756196Inhibition of bacterial biofilms by carboxymethyl chitosan combined with silver, zinc and copper salts.Goncalves RC, da Silva DP, Signini R, Naves PLFInt J Biol Macromol10.1016/j.ijbiomac.2017.07.0482017Animals, Artemia, Bacteria/*drug effects, Biofilms/*drug effects/growth & development, Chitosan/*analogs & derivatives/chemistry/pharmacology/toxicity, Copper/chemistry, Metals, Heavy/*chemistry, Microbial Sensitivity Tests, Silver/chemistry, Sulfates/chemistry, Zinc/chemistry
29027118Genetic Variation of pln Loci Among Probiotic Lactobacillus plantarum Group Strains with Antioxidant and Cholesterol-Lowering Ability.Devi SM, Halami PMProbiotics Antimicrob Proteins10.1007/s12602-017-9336-02019Anti-Infective Agents/pharmacology, Anticholesteremic Agents/*pharmacology, Antioxidants/*pharmacology, Bacteriocins/genetics, Genetic Variation, Lactobacillus plantarum/*genetics, Probiotics/*pharmacology
29230202Development of a Novel Escherichia coli-Kocuria Shuttle Vector Using the Cryptic pKPAL3 Plasmid from K. palustris IPUFS-1 and Its Utilization in Producing Enantiopure (S)-Styrene Oxide.Toda H, Itoh NFront Microbiol10.3389/fmicb.2017.023132017
Pathogenicity30712459Characterization and mode of action of a potent bio-preservative from food-grade Bacillus licheniformis MCC 2016.Vadakedath N, Halami PMPrep Biochem Biotechnol10.1080/10826068.2019.15661412019Anti-Bacterial Agents/isolation & purification/*pharmacology, Antimicrobial Cationic Peptides/isolation & purification/*pharmacology, Bacillus cereus/drug effects, Bacillus licheniformis/*chemistry, Cell Wall/drug effects, Dose-Response Relationship, Drug, Food Preservatives, Hydrogen-Ion Concentration, Listeria monocytogenes/drug effects, Microbial Sensitivity Tests, Micrococcaceae/drug effects, Molecular Weight, Salmonella typhimurium/drug effects, Spores, Bacterial/drug effects, Staphylococcus aureus/drug effects, TemperatureEnzymology
Phylogeny30941598Characterisation of Two Polyketides from Streptomyces sp. SKH1-2 Isolated from Roots of Musa (ABB) cv. 'Kluai Sao Kratuep Ho'.Kuncharoen N, Fukasawa W, Iwatsuki M, Mori M, Shiomi K, Tanasupawat SInt Microbiol10.1007/s10123-019-00071-72019Anti-Bacterial Agents/*chemistry/isolation & purification/metabolism/*pharmacology, Bacillus subtilis/drug effects/growth & development, Endophytes/chemistry/genetics/isolation & purification/*metabolism, Microbial Sensitivity Tests, Molecular Structure, Musa/microbiology, Phylogeny, Plant Roots/microbiology, Polyketides/*chemistry/isolation & purification/metabolism/*pharmacology, Staphylococcus aureus/drug effects/growth & development, Streptomyces/chemistry/genetics/isolation & purification/*metabolism, ThailandEnzymology
Phylogeny32063893Genome Analysis of Lactobacillus plantarum Isolated From Some Indian Fermented Foods for Bacteriocin Production and Probiotic Marker Genes.Goel A, Halami PM, Tamang JPFront Microbiol10.3389/fmicb.2020.000402020Biotechnology
33569376Comparative Study of the Antimicrobial Activity of Selenium Nanoparticles With Different Surface Chemistry and Structure.Filipovic N, Usjak D, Milenkovic MT, Zheng K, Liverani L, Boccaccini AR, Stevanovic MMFront Bioeng Biotechnol10.3389/fbioe.2020.6246212021
Metabolism33772601In vitro validation studies for adhesion factor and adhesion efficiency of probiotic Bacillus licheniformis MCC 2514 and Bifidobacterium breve NCIM 5671 on HT-29 cell lines.Rohith HS, Halami PMArch Microbiol10.1007/s00203-021-02257-y2021*Antibiosis/physiology, *Bacillus licheniformis/metabolism, *Bacterial Adhesion/physiology, *Bifidobacterium breve/metabolism, HT29 Cells, Humans, Micrococcaceae/physiology, *Probiotics/metabolismPathogenicity
Phylogeny34870574Actinomadura violacea sp. nov., a madurastatin A1-producing strain isolated from lichen in Thailand.Kanchanasin P, Phongsopitanun W, Yuki M, Kudo T, Ohkuma M, Nakashima T, Tanasupawat SInt J Syst Evol Microbiol10.1099/ijsem.0.0051262021Actinomadura/*classification/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Lichens/microbiology, Nucleic Acid Hybridization, Oligopeptides/*biosynthesis, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Thailand, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
141Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 348)https://www.dsmz.de/collection/catalogue/details/culture/DSM-348
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
20216Curators of the HKIhttp://www.leibniz-hki.de/de/Collection Description Leibniz-Institut für Naturstoff-Forschung und Infektionsbiologie e. V. Hans-Knöll-Institut (HKI)
36878Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/15767
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 updatesNucleic Acids Res. 49: D498-D508 202033211880
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.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)
77090Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID10565.1StrainInfo: A central database for resolving microbial strain identifiers
122203Curators of the CIPCollection of Institut Pasteur (CIP 53.45)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%2053.45