Strain identifier

BacDive ID: 7780

Type strain: Yes

Species: Rothia aeria

Strain Designation: A 1-17B, A1-17B

Strain history: CIP <- 2004, JCM <- 2001, T. Ezaki: strain A1-17B

NCBI tax ID(s): 172042 (species)

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General

@ref: 5297

BacDive-ID: 7780

DSM-Number: 14556

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-positive, coccus-shaped, human pathogen

description: Rothia aeria A 1-17B is an aerobe, mesophilic, Gram-positive human pathogen that was isolated from air in the Russian space lab. Mir.

NCBI tax id

  • NCBI tax id: 172042
  • Matching level: species

strain history

@refhistory
5297<- T. Ezaki, GTC, Gifu University, Japan; A 1-17B
67770T. Ezaki A1-17B.
116057CIP <- 2004, JCM <- 2001, T. Ezaki: strain A1-17B

doi: 10.13145/bacdive7780.20230509.8.1

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 aeria
  • full scientific name: Rothia aeria Li et al. 2004

@ref: 5297

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Micrococcaceae

genus: Rothia

species: Rothia aeria

full scientific name: Rothia aeria Li et al. 2004

strain designation: A 1-17B, A1-17B

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotility
30012positivecoccus-shaped
116057positiverod-shapedno

colony morphology

@refcolony colorincubation periodmedium used
18516Beige (1001)10-14 daysISP 2
18516Beige (1001)10-14 daysISP 3
18516Beige (1001)10-14 daysISP 4
1851610-14 daysISP 5
18516Beige (1001)10-14 daysISP 6
1851610-14 daysISP 7
116057

multicellular morphology

@refforms multicellular complexmedium name
18516noISP 2
18516noISP 3
18516noISP 4
18516noISP 5
18516noISP 6
18516noISP 7

pigmentation

  • @ref: 30012
  • production: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5297TRYPTICASE 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
18516ISP 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
18516ISP 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:
18516ISP 4yesName: ISP 4; DSM 547 Solution I: Difco soluble starch, 10.0 g. Make a paste of the starch with a small amount of cold distilled water and bring to a volume of 500 ml. Solution II: CaCO3 2.0 g K2HPO4 (anhydrous) 1.0 g MgSO4 x 7 H2O 1.0 g NaCl 1.0 g (NH4)2SO4 2.0 g Distilled water 500.0 ml Trace salt solution (see below) 1.0 ml The pH should be between 7.0 and 7.4. Do not adjust if it is within this range. Mix solutions I and II together. Add 20.0 g agar. Liquify agar by steaming at 100°C for 10 to 20 min. Trace element solution: FeSO4 x 7 H2O 0.1 g MnCl2 x 4 H2O 0.1 g ZnSO4 x 7 H2O 0.1 g Distilled water 100.0 ml
18516ISP 5yesName: ISP 5 (5323) Composition L-Asparagine 1.0 g/l Glycerol 10.0 g/l K2HPO4 1.0 g/l Salt solution (see preparation) 1.0 ml/l Agar 20.0 g/l Preparation: Salt solution 1.0 g FeSO4 x 7 H2O 1.0 g MnCl2 x 4 H2O 1.0 g ZNSO4 x 7 H2O in 100 ml water Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.2 Usage: Maintenance and taxonomy Organisms: All Actinomycetes
18516ISP 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
18516ISP 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
40001MEDIUM 29- Brain heart agaryesDistilled water make up to (1000.000 ml);Brain heart infusion agar (52.000 g)
116057CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72
116057CIP Medium 29yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=29

culture temp

@refgrowthtypetemperaturerange
18516positiveoptimum28mesophilic
5297positivegrowth28mesophilic
30012positiveoptimum30mesophilic
40001positivegrowth30mesophilic
59370positivegrowth37mesophilic
67770positivegrowth28mesophilic
116057positivegrowth25-41
116057nogrowth10psychrophilic
116057nogrowth15psychrophilic
116057nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
30012aerobe
59370microaerophile
116057obligate aerobe

halophily

@refsaltgrowthtested relationconcentration
116057NaClpositivegrowth0-4 %
116057NaClnogrowth6 %
116057NaClnogrowth8 %
116057NaClnogrowth10 %

observation

  • @ref: 67770
  • observation: quinones: MK-7

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1851662968cellulose+
1851616634raffinose-
1851626546rhamnose-
1851628757fructose+
1851629864mannitol-
1851617268myo-inositol-
1851618222xylose-
1851617992sucrose-
1851622599arabinose-
1851617234glucose+
3001223652dextrin+carbon source
3001228757fructose+carbon source
3001217234glucose+carbon source
3001224996lactate+carbon source
3001217306maltose+carbon source
3001237684mannose+carbon source
3001237657methyl D-glucoside+carbon source
3001217814salicin+carbon source
3001217992sucrose+carbon source
3001227082trehalose+carbon source
300124853esculin+hydrolysis
3001217632nitrate+reduction
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837132528turanose+builds acid from
6837128066gentiobiose-builds acid from
6837117151xylitol-builds acid from
6837128087glycogen-builds acid from
6837128017starch-builds acid from
6837116634raffinose-builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837127082trehalose+builds acid from
6837117992sucrose+builds acid from
6837128053melibiose-builds acid from
6837117716lactose-builds acid from
6837117306maltose+builds acid from
6837117057cellobiose-builds acid from
683714853esculin-builds acid from
6837127613amygdalin-builds acid from
6837159640N-acetylglucosamine-builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol-builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose-builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose+builds acid from
6837115824D-fructose+builds acid from
6837117634D-glucose+builds acid from
6837112936D-galactose-builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose-builds acid from
6837116988D-ribose-builds acid from
6837130849L-arabinose-builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol-builds acid from
11605716947citrate-carbon source
1160574853esculin+hydrolysis
116057606565hippurate+hydrolysis
11605717632nitrate+reduction
11605716301nitrite-reduction
11605717632nitrate-respiration
683794853esculin+hydrolysis
6837916199urea-hydrolysis
683795291gelatin-hydrolysis
6837917992sucrose+fermentation

antibiotic resistance

  • @ref: 116057
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 116057
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11605715688acetoin+
11605717234glucose+

enzymes

@refvalueactivityec
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
116057oxidase-
116057beta-galactosidase-3.2.1.23
116057alcohol dehydrogenase-1.1.1.1
116057gelatinase-
116057amylase-
116057DNase-
116057caseinase-3.4.21.50
116057catalase+1.11.1.6
116057tween esterase-
116057gamma-glutamyltransferase-2.3.2.2
116057lecithinase-
116057lipase-
116057lysine decarboxylase-4.1.1.18
116057ornithine decarboxylase-4.1.1.17
116057phenylalanine ammonia-lyase-4.3.1.24
116057tryptophan deaminase-
116057urease-3.5.1.5
68382esterase lipase (C 8)-
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
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

API coryne

@refPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELSAC
18516+/-++--+-+--+

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
18516++--++++-+----++--+
116057----++-+-+----++----

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
116057----------+++----------+/--+/--+--++-------+---------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
116057+--++--+-++------+-------------+---+-------------+----++------------+---+--+-+-++----------+-------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountry
5297air in the Russian space lab. MirSpace
59370Air sample from the Russian space station MirSpace
67770Air in the Russian space station Mir
116057Environment, Air in the Russian Station Mir

isolation source categories

Cat1Cat2Cat3
#Engineered#Laboratory
#Environmental#Air#Indoor Air

taxonmaps

  • @ref: 69479
  • File name: preview.99_6180.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_13;97_13;98_4581;99_6180&stattab=map
  • Last taxonomy: Rothia aeria subclade
  • 16S sequence: AB071952
  • Sequence Identity:
  • Total samples: 26353
  • soil counts: 408
  • aquatic counts: 571
  • animal counts: 25218
  • plant counts: 156

Safety information

risk assessment

@refpathogenicity humanbiosafety levelbiosafety level comment
5297yes, in single cases1Risk group (German classification)
185162Hazard group
1160571Risk group (French classification)

Sequence information

16S sequences

  • @ref: 5297
  • description: Rothia aeria gene for 16S rRNA, partial sequence
  • accession: AB071952
  • length: 1338
  • database: ena
  • NCBI tax ID: 172042

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Rothia aeria JCM 11412GCA_002355935completencbi172042
66792Rothia aeria strain FDAARGOS_1137172042.130completepatric172042
66792Rothia aeria strain JCM 11412172042.4completepatric172042
66792Rothia aeria JCM 114122806310706completeimg172042

GC content

@refGC-contentmethod
529757.8
6777057.8high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedno96.734no
gram-positiveyes95.554yes
anaerobicno98.285yes
aerobicno71.182no
halophileyes58.49no
spore-formingno92.122no
glucose-utilyes81.689yes
thermophileno98.573no
motileno93.46no
glucose-fermentno50no

External links

@ref: 5297

culture collection no.: CCUG 51932, JCM 11412, DSM 14556, GTC 867, CIP 108437, IFM 10514, NCIMB 14248

straininfo link

  • @ref: 77223
  • straininfo: 131532

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15143031Rothia aeria sp. nov., Rhodococcus baikonurensis sp. nov. and Arthrobacter russicus sp. nov., isolated from air in the Russian space laboratory Mir.Li Y, Kawamura Y, Fujiwara N, Naka T, Liu H, Huang X, Kobayashi K, Ezaki TInt J Syst Evol Microbiol10.1099/ijs.0.02828-02004Air Microbiology, Arthrobacter/*classification/genetics/*isolation & purification/metabolism, Base Composition, Carbon/metabolism, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/genetics, Fatty Acids/analysis, Humans, Micrococcaceae/*classification/genetics/*isolation & purification/metabolism, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Rhodococcus/*classification/genetics/*isolation & purification/metabolism, Russia, Space Flight, *SpacecraftMetabolism
Genetics28034856Complete Genome Sequence of Rothia aeria Type Strain JCM 11412, Isolated from Air in the Russian Space Laboratory Mir.Nambu T, Tsuzukibashi O, Uchibori S, Yamane K, Yamanaka T, Maruyama H, Wang PL, Mugita N, Morioka H, Takahashi K, Komasa Y, Mashimo CGenome Announc10.1128/genomeA.01444-162016Phylogeny

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
5297Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 14556)https://www.dsmz.de/collection/catalogue/details/culture/DSM-14556
18516Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM14556.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
30012Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2637628776041
40001Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6059
59370Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 51932)https://www.ccug.se/strain?id=51932
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
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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
77223Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID131532.1StrainInfo: A central database for resolving microbial strain identifiers
116057Curators of the CIPCollection of Institut Pasteur (CIP 108437)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108437