Strain identifier

BacDive ID: 7777

Type strain: Yes

Species: Rothia mucilaginosa

Strain Designation: 5762/67

Strain history: CIP <- 1971, CCM <- 1967, T. Bergan: strain 5762/67 Micrococcus mucilaginosus

NCBI tax ID(s): 553201 (strain), 43675 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 9055

BacDive-ID: 7777

DSM-Number: 20746

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

description: Rothia mucilaginosa 5762/67 is a microaerophile, mesophilic, Gram-positive bacterium that was isolated from throat.

NCBI tax id

NCBI tax idMatching level
553201strain
43675species

strain history

@refhistory
9055<- CCM <- T. Bergan, 5762/67
67770CCUG 20962 <-- CCM 2417 <-- T. Bergan 5762/67.
121156CIP <- 1971, CCM <- 1967, T. Bergan: strain 5762/67 Micrococcus mucilaginosus

doi: 10.13145/bacdive7777.20230509.8.1

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 mucilaginosa
  • full scientific name: Rothia mucilaginosa (Bergan and Kocur 1982 ex Migula 1900) Collins et al. 2000
  • synonyms

    • @ref: 20215
    • synonym: Stomatococcus mucilaginosus

@ref: 9055

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Micrococcaceae

genus: Rothia

species: Rothia mucilaginosa

full scientific name: Rothia mucilaginosa (Bergan and Kocur 1982) Collins et al. 2000 emend. Nouioui et al. 2018

strain designation: 5762/67

type strain: yes

Morphology

cell morphology

  • @ref: 121156
  • gram stain: positive
  • cell shape: coccus-shaped
  • motility: no

colony morphology

  • @ref: 121156

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
9055COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)yeshttps://mediadive.dsmz.de/medium/693Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base
9055TRYPTICASE 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
37615MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
121156CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
9055positivegrowth37mesophilic
9055positivegrowth30mesophilic
37615positivegrowth30mesophilic
47240positivegrowth37mesophilic
67770positivegrowth30mesophilic
121156positivegrowth30-41
121156nogrowth10psychrophilic
121156nogrowth22psychrophilic
121156nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
47240microaerophile
121156facultative anaerobe

murein

  • @ref: 9055
  • murein short key: A11.04
  • type: A3alpha L-Lys-L-Ala

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
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-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
121156hippurate+hydrolysis606565
121156nitrate+reduction17632
121156nitrite+reduction16301
68381arginine-hydrolysis29016
68381D-ribose-builds acid from16988
68381D-mannitol-builds acid from16899
68381sorbitol-builds acid from30911
68381lactose-builds acid from17716
68381trehalose+builds acid from27082
68381raffinose-builds acid from16634
68381sucrose+builds acid from17992
68381L-arabinose-builds acid from30849
68381D-arabitol-builds acid from18333
68381alpha-cyclodextrin-builds acid from40585
68381hippurate-hydrolysis606565
68381glycogen-builds acid from28087
68381pullulan-builds acid from27941
68381maltose+builds acid from17306
68381melibiose-builds acid from28053
68381melezitose+builds acid from6731
68381methyl beta-D-glucopyranoside+builds acid from320055
68381D-tagatose-builds acid from16443
68381urea-hydrolysis16199

metabolite production

@refChebi-IDmetaboliteproduction
12115635581indoleno
6838115688acetoinyes

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-test
6838115688acetoin+
12115615688acetoin-

enzymes

@refvalueactivityec
68381urease-3.5.1.5
68381beta-mannosidase-3.2.1.25
68381N-acetyl-beta-glucosaminidase-3.2.1.52
68381pyrrolidonyl arylamidase+3.4.19.3
68381beta-galactosidase-3.2.1.23
68381Alanyl-Phenylalanyl-Proline arylamidase+
68381alkaline phosphatase-3.1.3.1
68381alpha-galactosidase-3.2.1.22
68381beta-glucuronidase-3.2.1.31
68381arginine dihydrolase-3.5.3.6
121156oxidase-
121156beta-galactosidase-3.2.1.23
121156alcohol dehydrogenase-1.1.1.1
121156gelatinase-
121156amylase-
121156DNase-
121156caseinase-3.4.21.50
121156catalase-1.11.1.6
121156coagulase-
121156tween esterase-
121156gamma-glutamyltransferase-2.3.2.2
121156lecithinase-
121156lipase-
121156lysine decarboxylase-4.1.1.18
121156ornithine decarboxylase-4.1.1.17
121156phenylalanine ammonia-lyase-4.3.1.24
121156protease-
121156urease-3.5.1.5
68382alkaline phosphatase-3.1.3.1
68382esterase (C 4)-
68382esterase lipase (C 8)-
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase-
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382beta-glucosidase+3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
121156-----+----+----++---

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
121156----------+++-------+---+/---+--++-+-----+--------+/-

API rID32STR

@refADH Argbeta GLUbeta GARbeta GURalpha GALPALRIBMANSORLACTRERAFSACLARADARLCDEXAPPAbeta GALPyrAbeta NAGGTAHIPGLYGPULMALMELMLZMbeta DGTAGbeta MANUREVP
9055----------+-+---+-+-+---+-++---
9055-+--------+-+---+-+-----+-++---+

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
121156+------+-++------------------------+-------------------------------------------------------+-------

Isolation, sampling and environmental information

isolation

@refsample typesampling datecountryorigin.countrycontinentisolation date
9055throat
47240Human pharynx1967NorwayNOREurope
67770Human throatNorwayNOREurope
121156Human, ThroatNorwayNOREurope1967

isolation source categories

  • Cat1: #Host Body-Site
  • Cat2: #Oral cavity and airways
  • Cat3: #Throat

taxonmaps

  • @ref: 69479
  • File name: preview.99_16.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_13;97_13;98_15;99_16&stattab=map
  • Last taxonomy: Rothia mucilaginosa
  • 16S sequence: X87758
  • Sequence Identity:
  • Total samples: 218771
  • soil counts: 4381
  • aquatic counts: 6900
  • animal counts: 205395
  • plant counts: 2095

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
90552Risk group (German classification)
1211561Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218M.mucilaginosus 16S rRNA geneX877581467ena43675
20218S.mucilaginosus 16S rRNA geneX954831435ena43675

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Rothia mucilaginosa ATCC 25296553201.3wgspatric553201
66792Rothia mucilaginosa ATCC 25296645058800draftimg553201
67770Rothia mucilaginosa ATCC 25296GCA_000175615contigncbi553201

GC content

@refGC-contentmethod
905559.0
6777059thermal denaturation, midpoint method (Tm)
6777059.5genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
gram-positiveyes95.133no
anaerobicno97.158yes
halophileyes52.232no
spore-formingno95.222no
glucose-utilyes84.098no
thermophileno95.079yes
aerobicno84.002yes
motileno93.709no
flagellatedno96.527no
glucose-fermentyes72.824no

External links

@ref: 9055

culture collection no.: DSM 20746, ATCC 25296, CCM 2417, NCTC 10663, CCUG 20962, CIP 71.14, JCM 10910, GIFU 9911, GTC 311, IAM 14815, IFM 10890, IFO 15673, IMSNU 22101, NBRC 15673, NCDO 2360, NCIMB 702360, PCM 2415, CCUG 3707

straininfo link

  • @ref: 77220
  • straininfo: 389300

literature

topicPubmed-IDtitleauthorsjournalyearmeshtopic2DOI
Phylogeny16400987[Isolation and comparative analysis of glycolipid fractions in bifidobacteria].Novik GI, Astapovich NI, Grzegorzewicz A, Gamian AMikrobiologiia2005Bifidobacterium/*chemistry, Chromatography, Thin Layer, Glycolipids/*analysis/isolation & purificationEnzymology
Phylogeny23399044Identification of disulphide stress-responsive extracytoplasmic function sigma factors in Rothia mucilaginosa.Nambu T, Yamane K, Yamanaka T, Mashimo C, Maruyama H, Yoshida M, Hayashi H, Leung KP, Fukushima HArch Oral Biol2013Actinomycetaceae/genetics/*metabolism, Amino Acid Motifs/genetics, Bacterial Proteins/analysis/genetics/*isolation & purification, Diamide, Disulfides/*metabolism, Gene Expression Regulation, Bacterial/genetics, Genes, Regulator/genetics, Genome, Bacterial/genetics, Humans, Microarray Analysis, Oxidation-Reduction, Oxidative Stress/genetics/*physiology, Oxidoreductases/analysis/genetics, Phylogeny, Repressor Proteins/analysis/genetics, Reverse Transcriptase Polymerase Chain Reaction, Sequence Homology, Amino Acid, Sigma Factor/analysis/antagonists & inhibitors/genetics/*isolation & purification, Sulfhydryl Reagents, Thioredoxins/analysis/genetics, Transcription, Genetic/genetics, Up-Regulation/geneticsGenetics10.1016/j.archoralbio.2012.10.017
32345739Commensal Oral Rothia mucilaginosa Produces Enterobactin, a Metal-Chelating Siderophore.Uranga CC, Arroyo P Jr, Duggan BM, Gerwick WH, Edlund AmSystems202010.1128/mSystems.00161-20

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
9055Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20746)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20746
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
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
37615Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/10583
47240Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 20962)https://www.ccug.se/strain?id=20962
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68371Automatically annotated from API 50CH acid
68381Automatically annotated from API rID32STR
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
77220Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID389300.1StrainInfo: A central database for resolving microbial strain identifiers
121156Curators of the CIPCollection of Institut Pasteur (CIP 71.14)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%2071.14