Strain identifier

BacDive ID: 7637

Type strain: Yes

Species: Rothia kristinae

Strain Designation: PM 129

Strain history: CIP <- 1981, CCM <- W.E. Kloos: strain PM 129

NCBI tax ID(s): 1349768 (strain), 37923 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 8440

BacDive-ID: 7637

DSM-Number: 20032

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, mesophilic, Gram-positive, coccus-shaped

description: Rothia kristinae PM 129 is a facultative anaerobe, mesophilic, Gram-positive bacterium that was isolated from human skin.

NCBI tax id

NCBI tax idMatching level
1349768strain
37923species

strain history

@refhistory
8440<- W.E. Kloos, PM 129
67770GIFU 9131 <-- ATCC 27570 <-- W. E. Kloos PM 129.
120502CIP <- 1981, CCM <- W.E. Kloos: strain PM 129

doi: 10.13145/bacdive7637.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Micrococcaceae
  • genus: Rothia
  • species: Rothia kristinae
  • full scientific name: Rothia kristinae (Kloos et al. 1974) Nouioui et al. 2018

  • synonyms

    @refsynonym
    20215Micrococcus kristinae
    20215Kocuria kristinae

@ref: 8440

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Micrococcaceae

genus: Rothia

species: Rothia kristinae

full scientific name: Rothia kristinae (Kloos et al. 1974) Nouioui et al. 2018

strain designation: PM 129

type strain: yes

Morphology

cell morphology

  • @ref: 120502
  • gram stain: positive
  • cell shape: coccus-shaped
  • motility: no

colony morphology

@refcolony colorincubation periodmedium used
18416Cream (9001)10-14 days5006
18416Cream (9001)10-14 days5425
18416Cream (9001)10-14 days5428
18416Cream (9001)10-14 days5530
18416Cream (9001)10-14 daysISP 2
120502

multicellular morphology

@refforms multicellular complexmedium name
18416noISP 2
18416no5006
18416no5425
18416no5428
18416no5530

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8440CORYNEBACTERIUM AGAR (DSMZ Medium 53)yeshttps://mediadive.dsmz.de/medium/53Name: CORYNEBACTERIUM AGAR (DSMZ Medium 53) Composition: Agar 15.0 g/l Casein peptone 10.0 g/l NaCl 5.0 g/l Glucose 5.0 g/l Yeast extract 5.0 g/l Distilled water
18416ISP 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
184165006yesMedium: 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
184165425yesName: 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
184165428yes
184165530yes
40056MEDIUM 29- Brain heart agaryesDistilled water make up to (1000.000 ml);Brain heart infusion agar (52.000 g)
120502CIP Medium 29yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=29

culture temp

@refgrowthtypetemperaturerange
18416positiveoptimum28mesophilic
8440positivegrowth37mesophilic
40056positivegrowth30mesophilic
67770positivegrowth28mesophilic
120502positivegrowth22-41
120502nogrowth10psychrophilic
120502nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 120502
  • oxygen tolerance: facultative anaerobe

compound production

  • @ref: 20216
  • compound: Aldolase

murein

  • @ref: 8440
  • murein short key: A11.07
  • type: A3alpha L-Lys-L-Ala4

observation

  • @ref: 67770
  • observation: quinones: MK-7(H2)

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
68371arbutin+builds acid from18305
68371amygdalin-builds acid from27613
68371N-acetylglucosamine-builds acid from59640
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
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
120502hippurate-hydrolysis606565
120502nitrate-reduction17632
120502nitrite-reduction16301
68379nitrate+reduction17632
68379esculin-hydrolysis4853
68379urea-hydrolysis16199
68379gelatin-hydrolysis5291
68379D-glucose+fermentation17634
68379D-ribose-fermentation16988
68379D-xylose-fermentation65327
68379D-mannitol-fermentation16899
68379maltose+fermentation17306
68379lactose-fermentation17716
68379sucrose-fermentation17992
68379glycogen-fermentation28087

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinyes
6836835581indoleno
6836816136hydrogen sulfideno
12050235581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
6836815688acetoin+
6836835581indole-
12050215688acetoin+

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
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-
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
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
120502oxidase-
120502beta-galactosidase-3.2.1.23
120502alcohol dehydrogenase-1.1.1.1
120502gelatinase+/-
120502amylase-
120502DNase-
120502caseinase-3.4.21.50
120502catalase+1.11.1.6
120502coagulase-
120502tween esterase-
120502gamma-glutamyltransferase-2.3.2.2
120502lecithinase-
120502lipase-
120502lysine decarboxylase-4.1.1.18
120502ornithine decarboxylase-4.1.1.17
120502phenylalanine ammonia-lyase+4.3.1.24
120502protease-
120502urease-3.5.1.5

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
18416+-+---+----+---+---

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
18416+--------+----+----
120502+---+----++---++----

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
18416---------+-

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
120502+---+/------+++-----+-+/---++/-+-+--++-+-----+---------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
120502++-++--+-++------+----+--+-----+--+++------------+-------+--------------++-+---++---------+------+-

Isolation, sampling and environmental information

isolation

@refsample type
8440human skin
51329Human skin
67770Human skin
120502Human, Skin

isolation source categories

Cat1Cat2Cat3
#Host#Human
#Host Body-Site#Organ#Skin, Nail, Hair

taxonmaps

  • @ref: 69479
  • File name: preview.99_4251.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_875;97_2582;98_3203;99_4251&stattab=map
  • Last taxonomy: Rothia kristinae subclade
  • 16S sequence: X80749
  • Sequence Identity:
  • Total samples: 20724
  • soil counts: 2017
  • aquatic counts: 2439
  • animal counts: 15476
  • plant counts: 792

Safety information

risk assessment

@refbiosafety levelpathogenicity humanbiosafety level comment
184161
84401yes, in single casesRisk group (German classification)
1205021Risk group (French classification)

Sequence information

16S sequences

  • @ref: 20218
  • description: M.kristinae 16S rDNA
  • accession: X80749
  • length: 1475
  • database: ena
  • NCBI tax ID: 37923

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Kocuria kristinae NBRC 153541349768.3wgspatric1349768
66792Kocuria kristinae strain NCTC1103837923.19wgspatric37923
66792Rothia kristinae strain ATCC 2757037923.24wgspatric37923
66792Rothia kristinae strain FDAARGOS_86437923.27completepatric37923
66792Rothia kristinae NBRC 153542731957608draftimg1349768
67770Rothia kristinae NBRC 15354GCA_001570865contigncbi1349768
67770Rothia kristinae ATCC 27570GCA_004136565contigncbi37923
67770Rothia kristinae NCTC11038GCA_900452535contigncbi37923

GC content

@refGC-contentmethod
844066.8
6777066.8thermal denaturation, midpoint method (Tm)
6777071.9genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
gram-positiveyes96.071no
anaerobicno99.222no
halophileyes73.655no
spore-formingno94.375no
glucose-utilyes83.647no
aerobicyes77.124no
flagellatedno96.938no
motileno95.012no
thermophileno97.004no
glucose-fermentyes61.115yes

External links

@ref: 8440

culture collection no.: DSM 20032, ATCC 27570, CCM 2690, CCUG 33026, JCM 7237, CIP 81.69, GIFU 9131, IAM 13590, IFO 15354, LMG 14215, NBRC 15354, NCIMB 14427, NCTC 11038, NRRL B-14835, VKM Ac-2190, VKM B-1811

straininfo link

  • @ref: 77081
  • straininfo: 14405

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny12656171Kocuria polaris sp. nov., an orange-pigmented psychrophilic bacterium isolated from an Antarctic cyanobacterial mat sample.Reddy GSN, Prakash JSS, Prabahar V, Matsumoto GI, Stackebrandt E, Shivaji SInt J Syst Evol Microbiol10.1099/ijs.0.02336-02003Antarctic Regions, Cyanobacteria/isolation & purification, Ecosystem, Micrococcaceae/*classification/genetics/*isolation & purification/metabolism, Molecular Sequence Data, Phenotype, Phylogeny, Pigmentation, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Water MicrobiologyEnzymology
Phylogeny19502308Kocuria halotolerans sp. nov., an actinobacterium isolated from a saline soil in China.Tang SK, Wang Y, Lou K, Mao PH, Xu LH, Jiang CL, Kim CJ, Li WJInt J Syst Evol Microbiol10.1099/ijs.0.006627-02009Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genotype, Micrococcaceae/*classification/genetics/isolation & purification/physiology, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Sodium Chloride, Soil/analysis, *Soil Microbiology, Species SpecificityGenetics
Phylogeny19648328Kocuria koreensis sp. nov., isolated from fermented seafood.Park EJ, Roh SW, Kim MS, Jung MJ, Shin KS, Bae JWInt J Syst Evol Microbiol10.1099/ijs.0.012310-02009Base Composition, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, *Fermentation, Micrococcaceae/*classification/genetics/*isolation & purification/metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Seafood/*microbiologyGenetics
Phylogeny36085195Rothia santali sp. nov., endophytic bacteria isolated from sandalwood (Santalum album L.) seedling.Tuikhar N, Kirdat K, Nair G, Padma S, Thorat V, Swetha P, Sathe S, Sundararaj R, Yadav AArch Microbiol10.1007/s00203-022-03237-62022Bacteria, India, Micrococcaceae, *Oils, Volatile, RNA, Ribosomal, 16S/genetics, *Santalum/genetics, Seedlings, *Sesquiterpenes

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8440Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20032)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20032
18416Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM20032.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
20216Curators of the HKIhttp://www.leibniz-hki.de/de/Collection Description Leibniz-Institut für Naturstoff-Forschung und Infektionsbiologie e. V. Hans-Knöll-Institut (HKI)
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
40056Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/11233
51329Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 33026)https://www.ccug.se/strain?id=33026
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/
68368Automatically annotated from API 20E
68371Automatically annotated from API 50CH acid
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
77081Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID14405.1StrainInfo: A central database for resolving microbial strain identifiers
120502Curators of the CIPCollection of Institut Pasteur (CIP 81.69)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%2081.69