Strain identifier

BacDive ID: 132967

Type strain: Yes

Species: Megasphaera massiliensis

Strain Designation: NP3

Strain history: <- J.-C. Lagier, Timone Hospital, Marseille, France; NP3

NCBI tax ID(s): 1232428 (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 8.1 (current version)

General

@ref: 24755

BacDive-ID: 132967

DSM-Number: 26228

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

description: Megasphaera massiliensis NP3 is a mesophilic bacterium that was isolated from feces of a 32-year-old HIV-infected human patient.

NCBI tax id

  • NCBI tax id: 1232428
  • Matching level: species

strain history

  • @ref: 24755
  • history: <- J.-C. Lagier, Timone Hospital, Marseille, France; NP3

doi: 10.13145/bacdive132967.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Negativicutes
  • order: Veillonellales
  • family: Veillonellaceae
  • genus: Megasphaera
  • species: Megasphaera massiliensis
  • full scientific name: Megasphaera massiliensis Padmanabhan et al. 2016

@ref: 24755

domain: Bacteria

phylum: Firmicutes

class: Negativicutes

order: Selenomonadales

family: Veillonellaceae

genus: Megasphaera

species: Megasphaera massiliensis

full scientific name: Megasphaera massiliensis Padmanabhan et al. 2016

strain designation: NP3

type strain: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
24755PYG MEDIUM (MODIFIED) (DSMZ Medium 104)yeshttps://mediadive.dsmz.de/medium/104Name: PYG MEDIUM (modified) (DSMZ Medium 104) 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 5.0 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
24755COLUMBIA 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

culture temp

  • @ref: 24755
  • growth: positive
  • type: growth
  • temperature: 37
  • range: mesophilic

Physiology and metabolism

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836727082trehalose-builds acid from
6836762345L-rhamnose+builds acid from
6836730911sorbitol-builds acid from
6836716634raffinose-builds acid from
683676731melezitose-builds acid from
6836716024D-mannose-builds acid from
6836717057cellobiose-builds acid from
6836717754glycerol-builds acid from
683674853esculin+hydrolysis
683675291gelatin-hydrolysis
6836730849L-arabinose-builds acid from
6836765327D-xylose+builds acid from
6836717814salicin-builds acid from
6836717306maltose+builds acid from
6836717992sucrose-builds acid from
6836717716lactose-builds acid from
6836716899D-mannitol+builds acid from
6836717634D-glucose+builds acid from
6836716199urea-hydrolysis
6836727897tryptophan-energy source
6838016199urea-hydrolysis
6838029016arginine-hydrolysis
6838016024D-mannose-fermentation
6838016634raffinose-fermentation
6838029985L-glutamate-degradation
6838017632nitrate-reduction
6838027897tryptophan-energy source

metabolite production

@refChebi-IDmetaboliteproduction
6836735581indoleno
6838035581indoleno

metabolite tests

@refChebi-IDmetaboliteindole test
6838035581indole-
6836735581indole-

enzymes

@refvalueactivityec
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
68367beta-glucosidase+3.2.1.21
68367gelatinase-
68367urease-3.5.1.5

API 20A

@refINDUREGLUMANLACSACMALSALXYLARAGELESCGLYCELMNEMLZRAFSORRHATRE
24755--++--+-+--+------+-

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
24755-----------------------------

Isolation, sampling and environmental information

isolation

  • @ref: 24755
  • sample type: feces of a 32-year-old HIV-infected human patient
  • geographic location: Marseille (patient residence)
  • country: France
  • origin.country: FRA
  • continent: Europe

isolation source categories

Cat1Cat2Cat3
#Infection#Disease
#Infection#Patient
#Host#Human
#Host Body Product#Gastrointestinal tract#Feces (Stool)

taxonmaps

  • @ref: 69479
  • File name: preview.99_23321.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_37;96_1630;97_1951;98_2400;99_23321&stattab=map
  • Last taxonomy: Megasphaera massiliensis subclade
  • 16S sequence: JX424772
  • Sequence Identity:
  • Total samples: 13353
  • soil counts: 125
  • aquatic counts: 623
  • animal counts: 12545
  • plant counts: 60

Safety information

risk assessment

  • @ref: 24755
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 24755
  • description: Megasphaera massiliensis strain NP3 16S ribosomal RNA gene, partial sequence
  • accession: JX424772
  • length: 1519
  • database: ena
  • NCBI tax ID: 1232428

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Megasphaera massiliensis NP3GCA_000455225scaffoldncbi1232428
66792Megasphaera massiliensis NP32547132182draftimg1232428

GC content

  • @ref: 24755
  • GC-content: 50.2
  • method: sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno91.787no
flagellatedno95.174no
gram-positiveno95.583no
anaerobicyes99.314no
aerobicno96.677no
halophileno81.317no
spore-formingno92.614no
thermophileno98.388yes
glucose-utilyes72.285no
glucose-fermentyes56.999no

External links

@ref: 24755

culture collection no.: DSM 26228, CSUR P245

straininfo link

  • @ref: 91244
  • straininfo: 403381

Reference

@idauthorstitledoi/urlcatalogue
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
24755Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-26228Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 26228)
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
68367Automatically annotated from API 20A
68380Automatically annotated from API rID32A
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
91244Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID403381.1