Strain identifier

BacDive ID: 17130

Type strain: Yes

Species: Megasphaera elsdenii

Strain Designation: LC1

Strain history: CIP <- 2000, JP Carlier, Institut Pasteur, Paris, France: strain AIP 10100 <- NCIB <- S.R. Elsden: strain LC1

NCBI tax ID(s): 1064535 (strain), 907 (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: 8831

BacDive-ID: 17130

DSM-Number: 20460

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-negative, human pathogen

description: Megasphaera elsdenii LC1 is an anaerobe, mesophilic, Gram-negative human pathogen that was isolated from rumen of sheep.

NCBI tax id

NCBI tax idMatching level
907species
1064535strain

strain history

@refhistory
8831<- ATCC <- NCIB <- S.R. Eldsden, LC1
67770DSM 20460 <-- ATCC 25940 <-- NCIB 8927 <-- S. R. Elsden LC1.
119020CIP <- 2000, JP Carlier, Institut Pasteur, Paris, France: strain AIP 10100 <- NCIB <- S.R. Elsden: strain LC1

doi: 10.13145/bacdive17130.20230509.8.1

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 elsdenii
  • full scientific name: Megasphaera elsdenii (Gutierrez et al. 1959) Rogosa 1971 (Approved Lists 1980)

  • synonyms

    • @ref: 20215
    • synonym: Peptostreptococcus elsdenii

@ref: 8831

domain: Bacteria

phylum: Firmicutes

class: Negativicutes

order: Selenomonadales

family: Veillonellaceae

genus: Megasphaera

species: Megasphaera elsdenii

full scientific name: Megasphaera elsdenii (Gutierrez et al. 1959) Rogosa 1971

strain designation: LC1

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480negative99.816
119020negativecoccus-shapedno

colony morphology

@refincubation period
88311-2 days
630981 day
119020

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8831PYG 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
34386MEDIUM 20 - for Anaerobic bacteriayesAgar (15.000 g);Glucose (5.000 g);Yeast extract (20.000 g);Tryptone (30.000 g);Cysteine hydrochloride (0.500 g);distilled water (1000.000 ml);Hemin solution -M00149 (25.000 ml)
119020CIP Medium 20yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=20

culture temp

@refgrowthtypetemperaturerange
8831positivegrowth37mesophilic
34386positivegrowth37mesophilic
63098positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
8831anaerobe
63098anaerobe
69480anaerobe100
119020anaerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.933

murein

  • @ref: 8831
  • murein short key: A31
  • type: A1gamma m-Dpm-direct

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
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
1190204853esculin-hydrolysis
11902017632nitrate-reduction
11902016301nitrite-reduction
11902017632nitrate+respiration
6838016199urea-hydrolysis
6838029016arginine-hydrolysis
6838016024D-mannose-fermentation
6838016634raffinose-fermentation
6838029985L-glutamate-degradation
6838017632nitrate-reduction
6838027897tryptophan-energy source

antibiotic resistance

  • @ref: 119020
  • ChEBI: 6909
  • metabolite: metronidazole
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

@refChebi-IDmetaboliteproduction
6836735581indoleno
11902035581indoleno
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
119020oxidase-
119020beta-galactosidase-3.2.1.23
119020gelatinase-
119020amylase-
119020DNase-
119020caseinase-3.4.21.50
119020catalase-1.11.1.6
119020tween esterase-
119020lecithinase-
119020lipase-
119020protease-
119020urease-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
119020--++-----++---------

API 20A

@refUREGLUMANLACSACMALSALXYLARAGELGLYCELMNEMLZRAFSORRHATREINDESC
8831-++--++/------------
8831-++--+--------------

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
8831-----------------------------

Isolation, sampling and environmental information

isolation

@refsample type
8831rumen of sheep
63098Rumen of sheep
67770Rumen of sheep
119020Animal, Sheep, rumen

isolation source categories

Cat1Cat2Cat3
#Host#Mammals#Caprinae (Sheep/Goat)
#Host Body-Site#Organ#Rumen

taxonmaps

  • @ref: 69479
  • File name: preview.99_1150.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_37;96_673;97_779;98_903;99_1150&stattab=map
  • Last taxonomy: Megasphaera elsdenii subclade
  • 16S sequence: LC036319
  • Sequence Identity:
  • Total samples: 29433
  • soil counts: 544
  • aquatic counts: 989
  • animal counts: 27646
  • plant counts: 254

Safety information

risk assessment

@refpathogenicity humanpathogenicity animalbiosafety levelbiosafety level comment
8831yes, in single casesyes, in single cases1Risk group (German classification)
1190201Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Megasphaera elsdenii gene for 16S rRNA, partial sequence, strain: DSM 20460, type AAB6097041174ena1064535
20218Megasphaera elsdenii gene for 16S rRNA, partial sequence, strain: DSM 20460, type BAB6097051174ena1064535
20218Megasphaera elsdenii ATCC 25940 16S ribosomal RNA gene, partial sequenceU950271426ena1064535
67770Megasphaera elsdenii gene for 16S ribosomal RNA, partial sequence, strain: JCM 1772LC0363191525ena907

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Megasphaera elsdenii DSM 20460 ATCC 25940GCA_003010495completencbi1064535
66792Megasphaera elsdenii DSM 20460GCA_000283495chromosomencbi1064535
66792Megasphaera elsdenii DSM 20460907.4completepatric1064535
66792Megasphaera elsdenii DSM 20460 strain ATCC 259401064535.9completepatric1064535
66792Megasphaera elsdenii DSM 204602511231071draftimg1064535
66792Megasphaera elsdenii ATCC 259402843666722completeimg1064535

GC content

  • @ref: 8831
  • GC-content: 52.7

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedno96.85no
gram-positiveno94.635no
anaerobicyes99.533yes
aerobicno97.673yes
halophileno88.306no
spore-formingno92.621no
glucose-utilyes70.258no
thermophileno97.71yes
motileno94.414no
glucose-fermentyes57.448no

External links

@ref: 8831

culture collection no.: DSM 20460, ATCC 25940, NCIB 8927, CCUG 64197, JCM 1772, CCUG 6199, CECT 390, CGMCC 1.2720, KCTC 5187, NCFB 2263, NCIMB 8927, VTT E-84221, CIP 106852, AIP 10100

straininfo link

  • @ref: 86129
  • straininfo: 38727

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Metabolism14519808Megasphaera elsdenii JCM1772T normalizes hyperlactate production in the large intestine of fructooligosaccharide-fed rats by stimulating butyrate production.Hashizume K, Tsukahara T, Yamada K, Koyama H, Ushida KJ Nutr10.1093/jn/133.10.31872003Animals, Butyrates/*metabolism, Cecum/anatomy & histology/metabolism/microbiology, Clostridium/*metabolism, Colony Count, Microbial, Dietary Carbohydrates/administration & dosage, Feces/chemistry, Intestinal Mucosa/anatomy & histology, Intestine, Large/metabolism/*microbiology, Lactic Acid/analysis/*biosynthesis, Male, Oligosaccharides/*administration & dosage, Probiotics, Rats, Rats, Sprague-Dawley, Specific Pathogen-Free OrganismsBiotechnology
Genetics21914887Genome sequence of the ruminal bacterium Megasphaera elsdenii.Marx H, Graf AB, Tatto NE, Thallinger GG, Mattanovich D, Sauer MJ Bacteriol10.1128/JB.05861-112011Animals, Fatty Acids, Volatile/*metabolism, Megasphaera/*genetics/metabolism, Molecular Sequence Data, Probiotics, Rumen/*microbiologyMetabolism
Metabolism22008515Intraruminal administration of Megasphaera elsdenii modulated rumen fermentation profile in mid-lactation dairy cows.Zebeli Q, Terrill SJ, Mazzolari A, Dunn SM, Yang WZ, Ametaj BNJ Dairy Res10.1017/S00220299110007072011Animal Feed/analysis, Animal Nutritional Physiological Phenomena, Animals, *Cattle, Cross-Over Studies, Diet/veterinary, Fatty Acids, Nonesterified/blood, Female, Fermentation, Hydrogen-Ion Concentration, Lactation/*physiology, Lactic Acid/metabolism, Megasphaera/*physiology, Probiotics/administration & dosage, Rumen/*microbiology
Metabolism24260205Comparative genome analysis of Megasphaera sp. reveals niche specialization and its potential role in the human gut.Shetty SA, Marathe NP, Lanjekar V, Ranade D, Shouche YSPLoS One10.1371/journal.pone.00793532013Amino Acids/metabolism, Fatty Acids, Volatile/metabolism, Gastrointestinal Tract/*microbiology, Genome, Bacterial/*genetics, Humans, Megasphaera/classification/*genetics/metabolism/physiology, Phylogeny, Vitamins/metabolismPhylogeny
Phylogeny24711592Megasphaera indica sp. nov., an obligate anaerobic bacteria isolated from human faeces.Lanjekar VB, Marathe NP, Ramana VV, Shouche YS, Ranade DRInt J Syst Evol Microbiol10.1099/ijs.0.059816-02014Adult, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Feces/*microbiology, Fermentation, Humans, India, Male, Megasphaera/*classification/genetics/isolation & purification, Middle Aged, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAPathogenicity
Phylogeny28742009Megasphaera hexanoica sp. nov., a medium-chain carboxylic acid-producing bacterium isolated from a cow rumen.Jeon BS, Kim S, Sang BIInt J Syst Evol Microbiol10.1099/ijsem.0.0018882017Animals, Bacterial Typing Techniques, Base Composition, Carboxylic Acids/*metabolism, Cattle/*microbiology, DNA, Bacterial/genetics, Fatty Acids/chemistry, Female, Megasphaera/*classification/genetics/isolation & purification, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rumen/*microbiology, Sequence Analysis, DNATranscriptome
Phylogeny28842275Preferential isolation of Megasphaera elsdenii from pig feces.Kajihara Y, Yoshikawa S, Cho Y, Ito T, Miyamoto H, Kodama HAnaerobe10.1016/j.anaerobe.2017.08.0132017Animals, Feces/*microbiology, Megasphaera elsdenii/classification/genetics/*isolation & purification/ultrastructure, Phylogeny, Polymerase Chain Reaction, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, SwineTranscriptome
Metabolism29331526Valerate production by Megasphaera elsdenii isolated from pig feces.Yoshikawa S, Araoka R, Kajihara Y, Ito T, Miyamoto H, Kodama HJ Biosci Bioeng10.1016/j.jbiosc.2017.12.0162018Animals, Butyrates/metabolism, Fatty Acids, Volatile/metabolism, Feces/*microbiology, Fermentation, Lactic Acid/metabolism, Megasphaera elsdenii/classification/genetics/*isolation & purification/*metabolism, Pentanoic Acids/*metabolism, Phylogeny, Propionates/metabolism, Rumen/metabolism/microbiology, Swine/*microbiology, Valerates/metabolismPhylogeny
Genetics30687829Complete Genome Sequences of Two Megasphaera elsdenii Strains, NCIMB 702410 and ATCC 25940.Hatmaker EA, Klingeman DM, O'Dell KB, Riley LA, Papanek B, Guss AMMicrobiol Resour Announc10.1128/MRA.01430-182019

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8831Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20460)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20460
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
34386Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/19028
63098Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 64197)https://www.ccug.se/strain?id=64197
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/
68367Automatically annotated from API 20A
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
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
86129Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID38727.1StrainInfo: A central database for resolving microbial strain identifiers
119020Curators of the CIPCollection of Institut Pasteur (CIP 106852)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106852