Strain identifier

BacDive ID: 192

Type strain: Yes

Species: Actinomyces massiliensis

Strain Designation: 4401292

Strain history: CIP <- 2006, V. Roux, Timone Hosp., Marseille, France: strain 4401292

NCBI tax ID(s): 1167628 (strain), 461393 (species)

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General

@ref: 16669

BacDive-ID: 192

DSM-Number: 23047

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

description: Actinomyces massiliensis 4401292 is an anaerobe, mesophilic, Gram-positive bacterium that was isolated from human blood .

NCBI tax id

NCBI tax idMatching level
1167628strain
461393species

strain history

@refhistory
375282006, V. Roux, Timone Hosp., Marseille, France: strain 4401292
16669<- CCUG <- V. Roux, Timone Hospital, Marseille, France
67770CCUG 53522 <-- V. Roux 4401292.
67771<- DSM <- CCUG <- V Roux, Timone Hospital, Marseille, France
120847CIP <- 2006, V. Roux, Timone Hosp., Marseille, France: strain 4401292

doi: 10.13145/bacdive192.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Actinomycetales
  • family: Actinomycetaceae
  • genus: Actinomyces
  • species: Actinomyces massiliensis
  • full scientific name: Actinomyces massiliensis Renvoise et al. 2009

@ref: 16669

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Actinomycetaceae

genus: Actinomyces

species: Actinomyces massiliensis

full scientific name: Actinomyces massiliensis Renvoise et al. 2009 emend. Nouioui et al. 2018

strain designation: 4401292

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
28916positive0.5-1.7 µm0.35-0.74 µmrod-shaped
67771rod-shaped
67771positive
120847positiverod-shapedno

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
16669PYG MEDIUM (MODIFIED) (DSMZ Medium 104)yeshttps://mediadive.dsmz.de/medium/104Name: PYG MEDIUM (modified) (DSMZ Medium 104; with strain-specific modifications) Composition: Yeast extract 10.0 g/l Peptone 5.0 g/l Trypticase peptone 5.0 g/l Beef extract 5.0 g/l Glucose 4.0 g/l L-Cysteine HCl x H2O 0.5 g/l NaHCO3 0.4 g/l NaCl 0.08 g/l K2HPO4 0.04 g/l KH2PO4 0.04 g/l MgSO4 x 7 H2O 0.02 g/l CaCl2 x 2 H2O 0.01 g/l Hemin 0.005 g/l Ethanol 0.0038 g/l Resazurin 0.001 g/l Tween 80 Vitamin K1 NaOH Distilled water
37528MEDIUM 6 - Columbia agar with 10 % horse bloodyesDistilled water make up to (1000.000 ml);Columbia agar (39.000 g);Horseblood (100.000 ml)
120847CIP Medium 6yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=6

culture temp

@refgrowthtypetemperaturerange
16669positivegrowth37mesophilic
28916positivegrowth30-37mesophilic
28916positiveoptimum37mesophilic
37528positivegrowth30mesophilic
59924positivegrowth37mesophilic
67770positivegrowth37mesophilic
67771positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
16669anaerobe
28916anaerobe
59924microaerophile
67771anaerobe
120847facultative anaerobe

spore formation

@refspore formation
28916no
67771no

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2891628757fructose+carbon source
2891628260galactose+carbon source
2891617234glucose+carbon source
2891617716lactose+carbon source
2891617306maltose+carbon source
2891637684mannose+carbon source
2891633942ribose+carbon source
2891617992sucrose+carbon source
2891627082trehalose+carbon source
2891618222xylose+carbon source
2891617632nitrate+reduction
12084717632nitrate+reduction
12084716301nitrite+reduction
6838016199urea-hydrolysis
6838029016arginine-hydrolysis
6838029985L-glutamate-degradation
6838017632nitrate+reduction
6838027897tryptophan-energy source

metabolite production

@refChebi-IDmetaboliteproduction
12084735581indoleno
6838035581indoleno

metabolite tests

  • @ref: 68380
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

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
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase+3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
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-
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)-
68382esterase (C 4)+
68382alkaline phosphatase-3.1.3.1
68380serine arylamidase-
68380glutamyl-glutamate arylamidase-
68380histidine arylamidase-
68380glycin arylamidase-
68380alanine arylamidase-3.4.11.2
68380tyrosine arylamidase+
68380pyrrolidonyl arylamidase-3.4.19.3
68380leucine arylamidase+3.4.11.1
68380phenylalanine arylamidase+
68380leucyl glycin arylamidase-3.4.11.1
68380proline-arylamidase+3.4.11.5
68380L-arginine arylamidase-
68380alkaline phosphatase-3.1.3.1
68380tryptophan deaminase-4.1.99.1
68380alpha-fucosidase-3.2.1.51
68380glutamate decarboxylase-4.1.1.15
68380N-acetyl-beta-glucosaminidase-3.2.1.52
68380beta-glucuronidase-3.2.1.31
68380alpha-arabinosidase-3.2.1.55
68380beta-glucosidase-3.2.1.21
68380alpha-glucosidase+3.2.1.20
68380beta-Galactosidase 6-phosphate-
68380beta-galactosidase+3.2.1.23
68380alpha-galactosidase-3.2.1.22
68380arginine dihydrolase-3.5.3.6
68380urease-3.5.1.5
120847oxidase-
120847catalase-1.11.1.6
120847urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
120847--+--+----++-+-++---

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
16669---+-+----+/-+/---+---+-++-+-----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling dateisolation date
16669human blood (pleuropneumonia)MarseilleFranceFRAEurope
59924Human blood,39-yr-old man,pleuropneumoniaMarseille,Timone hospitalFranceFRAEurope2004-05-01
67770Human blood sample
67771From human blood (pleuropneumonia)MarseilleFranceFRAEurope
120847Human, BloodMarseilleFranceFRAEurope2004

isolation source categories

Cat1Cat2Cat3
#Infection#Inflammation
#Host#Human
#Host Body-Site#Oral cavity and airways#Lung
#Host Body Product#Fluids#Blood

taxonmaps

  • @ref: 69479
  • File name: preview.99_6038.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_124;96_2879;97_3538;98_4479;99_6038&stattab=map
  • Last taxonomy: Actinomyces massiliensis subclade
  • 16S sequence: AB545934
  • Sequence Identity:
  • Total samples: 48677
  • soil counts: 995
  • aquatic counts: 1557
  • animal counts: 45755
  • plant counts: 370

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
166692Risk group (German classification)
1208472Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
16669Actinomyces massiliensis strain 4401292 16S ribosomal RNA gene, partial sequenceEF5583671481ena1167628
67771Actinomyces massiliensis gene for 16S ribosomal RNA, partial sequenceAB5459341520ena1167628

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Actinomyces massiliensis 44012921167628.4wgspatric1167628
66792Actinomyces massiliensis 44012922548876973draftimg1167628
67771Actinomyces massiliensis 4401292GCA_000269805scaffoldncbi1167628

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno91.869no
gram-positiveyes95.341yes
anaerobicno77.928no
aerobicno91.702no
halophileno85.85no
spore-formingno90.584yes
flagellatedno96.803no
glucose-utilyes88.61yes
thermophileno96.083yes
glucose-fermentyes74.804no

External links

@ref: 16669

culture collection no.: DSM 23047, CCUG 53522, KCTC 15158, CSUR P18, JCM 16130, CIP 109360

straininfo link

@refstraininfo
69874395408
69875408795

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19244437Actinomyces massiliensis sp. nov., isolated from a patient blood culture.Renvoise A, Raoult D, Roux VInt J Syst Evol Microbiol10.1099/ijs.0.001503-02009Actinomyces/*classification/genetics/isolation & purification/physiology, Actinomycosis/*microbiology, Bacterial Typing Techniques, Blood/*microbiology, Culture Media, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, Humans, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species SpecificityCultivation
Genetics22933754Draft genome sequence of Actinomyces massiliensis strain 4401292T.Roux V, Robert C, Gimenez G, Gharbi R, Raoult DJ Bacteriol10.1128/JB.01039-122012Actinomyces/*genetics/isolation & purification/physiology, Actinomycosis/microbiology, Anaerobiosis, Bacteremia/microbiology, Bacterial Proteins/genetics, Blood/microbiology, DNA, Bacterial/*chemistry/*genetics, *Genome, Bacterial, Humans, Molecular Sequence Data, *Sequence Analysis, DNAPathogenicity

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
16669Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23047)https://www.dsmz.de/collection/catalogue/details/culture/DSM-23047
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
28916Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2535528776041
37528Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7093
59924Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 53522)https://www.ccug.se/strain?id=53522
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/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
68380Automatically annotated from API rID32A
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
69874Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID395408.1StrainInfo: A central database for resolving microbial strain identifiers
69875Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID408795.1StrainInfo: A central database for resolving microbial strain identifiers
120847Curators of the CIPCollection of Institut Pasteur (CIP 109360)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109360