Strain identifier

BacDive ID: 3054

Type strain: Yes

Species: Eggerthella lenta

Strain Designation: 1899 B

Strain history: STAFF 1026 <-- ATCC 25559 <-- W. E. C. Moore VPI 0255 <-- A. Prévot 1899B.

NCBI tax ID(s): 479437 (strain), 84112 (species)

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General

@ref: 1003

BacDive-ID: 3054

DSM-Number: 2243

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

description: Eggerthella lenta 1899 B is an anaerobe, mesophilic human pathogen that was isolated from rectal tumor.

NCBI tax id

NCBI tax idMatching level
84112species
479437strain

strain history

@refhistory
1003<- J. R. Andreesen; <- ATCC; ATCC 25559 <- W. E. C. Moore; VPI 0255 <- A. R. Prevot; 1899 B
67770STAFF 1026 <-- ATCC 25559 <-- W. E. C. Moore VPI 0255 <-- A. Prévot 1899B.

doi: 10.13145/bacdive3054.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Coriobacteriia
  • order: Eggerthellales
  • family: Eggerthellaceae
  • genus: Eggerthella
  • species: Eggerthella lenta
  • full scientific name: Eggerthella lenta (Eggerth 1935) Wade et al. 1999

  • synonyms

    @refsynonym
    20215Eubacterium lentum
    20215Eggerthella lenta
    20215Bacteroides lentus

@ref: 1003

domain: Bacteria

phylum: Actinobacteria

class: Coriobacteriia

order: Coriobacteriales

family: Eggerthellaceae

genus: Eggerthella

species: Eggerthella lenta

full scientific name: Eggerthella lenta (Eggerth 1935) Wade et al. 1999 emend. Maruo et al. 2008 emend. Nouioui et al. 2018

strain designation: 1899 B

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480no95.079
69480100positive

multimedia

  • @ref: 66793
  • multimedia content: EM_DSM_2243_1.jpg
  • caption: electron microscopic image
  • intellectual property rights: © HZI/Manfred Rohde

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
1003COLUMBIA 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
1003CHOPPED MEAT MEDIUM (DSMZ Medium 78)yeshttps://mediadive.dsmz.de/medium/78Name: CHOPPED MEAT MEDIUM (DSMZ Medium 78) Composition: Ground beef 500.0 g/l Casitone 30.0 g/l Agar 15.0 g/l Ethanol 9.5 g/l (optional) K2HPO4 5.0 g/l Yeast extract 5.0 g/l L-Cysteine HCl 0.5 g/l Haemin 0.005 g/l (optional) Resazurin 0.001 g/l Vitamin K3 0.0005 g/l (optional) Vitamin K1 (optional) NaOH (optional) Distilled water
1003WILKINS-CHALGREN ANAEROBE BROTH (DSMZ Medium 339)yeshttps://mediadive.dsmz.de/medium/339Name: WILKINS-CHALGREN ANAEROBE BROTH (DSMZ Medium 339) Composition: dehydrated Wilkins-Chalgren medium 33.0 g/l L-Cysteine HCl 0.3 g/l Sodium resazurin 0.0005 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
1003positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
1003anaerobe
69480anaerobe99.999

spore formation

@refspore formationconfidence
69481no97
69480no99.983

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6838016199urea-hydrolysis
6838016024D-mannose-fermentation
6838016634raffinose-fermentation
6838029985L-glutamate-degradation
6838017632nitrate-reduction
6838027897tryptophan-energy source

metabolite production

  • @ref: 68380
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

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

enzymes

@refvalueactivityec
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
68380alkaline phosphatase-3.1.3.1
68380tryptophan deaminase-4.1.99.1
68380alpha-fucosidase-3.2.1.51
68380glutamate decarboxylase-4.1.1.15
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
68380urease-3.5.1.5

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
1003-----------------------------
1003-+---------------------------
1003-+---------------------------
46592-+-------+-------++---------+
1003-+---------------------------

Isolation, sampling and environmental information

isolation

@refsample type
1003rectal tumor
46592Human rectal tumor
67770Rectal tumor

isolation source categories

  • Cat1: #Host Body-Site
  • Cat2: #Gastrointestinal tract
  • Cat3: #Rectum

taxonmaps

  • @ref: 69479
  • File name: preview.99_161.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15800;96_120;97_127;98_142;99_161&stattab=map
  • Last taxonomy: Eggerthella lenta subclade
  • 16S sequence: AB558167
  • Sequence Identity:
  • Total samples: 42736
  • soil counts: 49
  • aquatic counts: 1212
  • animal counts: 41431
  • plant counts: 44

Safety information

risk assessment

  • @ref: 1003
  • pathogenicity human: yes
  • pathogenicity animal: yes
  • biosafety level: 2
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Eggerthella lenta 16S ribosomal RNA gene, partial sequenceAF2923751500ena479437
1003Eubacterium lentum gene for 16S rRNA, partial sequenceAB0118171472ena479437
67770Eggerthella lenta gene for 16S ribosomal RNA, partial sequence, strain: JCM 9979AB5581671470ena84112

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Eggerthella lenta DSM 2243GCA_000024265completencbi479437
66792Eggerthella lenta DSM 2243479437.5completepatric479437
66792Eggerthella lenta strain ATCC 2555984112.19wgspatric84112
66792Eggerthella lenta strain DSM 224384112.13wgspatric84112
66792Eggerthella lenta strain UCSF224384112.12wgspatric84112
66792Eggerthella lenta VPI 0255, DSM 2243644736358completeimg479437
67770Eggerthella lenta DSM 2243GCA_003339975scaffoldncbi84112
67770Eggerthella lenta ATCC 25559GCA_003340105scaffoldncbi84112

GC content

  • @ref: 1003
  • GC-content: 65.0
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno97no
motileno93.303no
flagellatedno98.068no
gram-positiveyes82.284no
anaerobicyes98.217yes
aerobicno95.053no
halophileno91.126no
spore-formingno88.239no
thermophileno99.635yes
glucose-utilyes69.492no
glucose-fermentno58.593no

External links

@ref: 1003

culture collection no.: CCUG 17323 A, DSM 2243, ATCC 25559, VPI 0255, JCM 9979, CCUG 17323, CIP 106637, KCTC 3265, NCTC 11813, VTT E-001735

straininfo link

  • @ref: 72574
  • straininfo: 44722

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Metabolism39496Bile salt 3 alpha- and 12 alpha-hydroxysteroid dehydrogenases from Eubacterium lentum and related organisms.MacDonald IA, Jellett JF, Mahony DE, Holdeman LVAppl Environ Microbiol10.1128/aem.37.5.992-1000.197919793-Hydroxysteroid Dehydrogenases/*biosynthesis/metabolism, Arginine/metabolism, Bile Acids and Salts/metabolism, Cell-Free System, Eubacterium/*enzymology/metabolism, Hydrogen-Ion Concentration, Hydroxysteroid Dehydrogenases/*biosynthesis/metabolism, Substrate SpecificityEnzymology
Pathogenicity384308Immuno-electron microscopic localization of a choriogonadotropin-like antigen in cancer-associated bacteria.Slifkin M, Pardo M, Pouchet-Melvin GR, Acevedo HFOncology10.1159/0002253431979*Antigens, Bacterial, Bacterial Infections/immunology, Cell Wall/immunology, Chorionic Gonadotropin/*immunology, Colonic Neoplasms/*microbiology, Escherichia coli/*immunology, Eubacterium/*immunology, Humans, Immunoenzyme Techniques, Microscopy, Electron, Rectal Neoplasms/*microbiology
Metabolism3729400Reduction of digoxin to 20R-dihydrodigoxin by cultures of Eubacterium lentum.Robertson LW, Chandrasekaran A, Reuning RH, Hui J, Rawal BDAppl Environ Microbiol10.1128/aem.51.6.1300-1303.19861986Chromatography, High Pressure Liquid, Digoxin/*analogs & derivatives/*metabolism, Eubacterium/*metabolism, Feces/microbiology, HumansPathogenicity
Metabolism9693583Experimental root canal infections in conventional and germ-free mice.Sobrinho AP, Barros MH, Nicoli JR, Carvalho MA, Farias LM, Bambirra EA, Bahia MG, Vieira ECJ Endod10.1016/S0099-2399(98)80021-61998Animals, Antibiosis, Bacteria, Anaerobic/*growth & development/metabolism, Bacteriocins/metabolism, Dental Pulp Cavity/*microbiology, *Disease Models, Animal, Ecosystem, Enterococcus faecalis/growth & development/metabolism, Escherichia coli/growth & development/metabolism, Eubacterium/growth & development/metabolism, Fusobacterium nucleatum/growth & development/metabolism, Germ-Free Life, Mice, Peptostreptococcus/growth & development/metabolism, Porphyromonas/growth & development/metabolism
Phylogeny10555354Phylogenetic evidence for the transfer of Eubacterium lentum to the genus Eggerthella as Eggerthella lenta gen. nov., comb. nov.Kageyama A, Benno Y, Nakase TInt J Syst Bacteriol10.1099/00207713-49-4-17251999Bacterial Typing Techniques, DNA Primers, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Eubacterium/*classification/genetics, Feces/microbiology, Genes, rRNA, Humans, Molecular Sequence Data, Phylogeny, Polymerase Chain Reaction, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species SpecificityPathogenicity
Phylogeny17046543Production of equol from daidzein by gram-positive rod-shaped bacterium isolated from rat intestine.Minamida K, Tanaka M, Abe A, Sone T, Tomita F, Hara H, Asano KJ Biosci Bioeng10.1263/jbb.102.2472006Actinobacteria/genetics/*growth & development/isolation & purification, Animals, Base Sequence, Equol, Humans, Intestines/microbiology, Isoflavones/*biosynthesis/*metabolism/pharmacology, Molecular Sequence Data, Phytoestrogens/*metabolism/pharmacology, RNA, Ribosomal, 16S/genetics, RatsPathogenicity
Cultivation17584471Production of antagonistic substance by Eikenella corrodens isolated from the oral cavity of human beings with and without periodontal disease.Apolonio AC, Carvalho MA, Ribas RN, Sousa-Gaia LG, Santos KV, Lana MA, Nicoli JR, Farias LMJ Appl Microbiol10.1111/j.1365-2672.2006.03211.x2007Acute Disease, *Antibiosis, Bacteriocins/*biosynthesis, Bacteriological Techniques, Chronic Disease, Culture Media, Eikenella corrodens/*metabolism/physiology, Gingiva/microbiology, Humans, Microbial Sensitivity Tests/methods, Mouth/*microbiology, Periodontitis/*microbiologyPathogenicity
Genetics21304654Complete genome sequence of Eggerthella lenta type strain (IPP VPI 0255).Saunders E, Pukall R, Abt B, Lapidus A, Glavina Del Rio T, Copeland A, Tice H, Cheng JF, Lucas S, Chen F, Nolan M, Bruce D, Goodwin L, Pitluck S, Ivanova N, Mavromatis K, Ovchinnikova G, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Chain P, Meincke L, Sims D, Brettin T, Detter JC, Goker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Han CStand Genomic Sci10.4056/sigs.335922009
Phylogeny23869769Isolation and characterization of novel S-equol-producing bacteria from brines of stinky tofu, a traditional fermented soy food in Taiwan.Abiru Y, Ueno T, Uchiyama SInt J Food Sci Nutr10.3109/09637486.2013.8169362013Actinobacteria/genetics/*metabolism, *DNA, Bacterial, Diet, Equol/*metabolism, Fermentation, *Food Microbiology, Humans, Isoflavones/metabolism, Phylogeny, RNA, Ribosomal, 16S, Salts, Soy Foods/*microbiology, Soybeans/*metabolism/microbiology, TaiwanMetabolism
Phylogeny24947740Isolation and characterization of rat intestinal bacteria involved in biotransformation of (-)-epigallocatechin.Takagaki A, Kato Y, Nanjo FArch Microbiol10.1007/s00203-014-1006-y2014Actinobacteria/classification/genetics/*isolation & purification/metabolism, Animals, Bacteria/classification/genetics/*isolation & purification/metabolism, Biotransformation, Catechin/*analogs & derivatives/metabolism, Feces/*microbiology, Lactones/metabolism, Metabolic Networks and Pathways, Pentanoic Acids/metabolism, RatsMetabolism
Metabolism25947926Bioconversion of (-)-epicatechin, (+)-epicatechin, (-)-catechin, and (+)-catechin by (-)-epigallocatechin-metabolizing bacteria.Takagaki A, Nanjo FBiol Pharm Bull10.1248/bpb.b14-008132015Actinobacteria/metabolism, Bacteria/*metabolism, *Bioreactors, Biotransformation, Catechin/analogs & derivatives/*metabolism, Clostridium/metabolism, Hydroxylation
Phylogeny28326685Hugonella massiliensis gen. nov., sp. nov., genome sequence, and description of a new strictly anaerobic bacterium isolated from the human gut.Elsawi Z, Togo AH, Beye M, Dubourg G, Andrieu C, Armsrtong N, Richez M, di Pinto F, Bittar F, Labas N, Fournier PE, Raoult D, Khelaifia SMicrobiologyopen10.1002/mbo3.4582017Actinobacteria/chemistry/*classification/genetics/*isolation & purification, Anaerobiosis, Base Composition, Cluster Analysis, DNA, Ribosomal/chemistry/genetics, Feces/microbiology, Female, France, Gastrointestinal Tract/*microbiology, Humans, Middle Aged, Molecular Sequence Annotation, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization, *Whole Genome SequencingGenetics
Metabolism29274283Mechanistic and structural insight into promiscuity based metabolism of cardiac drug digoxin by gut microbial enzyme.Kumar K, Jaiswal SK, Dhoke GV, Srivastava GN, Sharma AK, Sharma VKJ Cell Biochem10.1002/jcb.266382018Actinobacteria/*enzymology/isolation & purification, Amino Acid Sequence, Bacterial Proteins/*chemistry/*metabolism, Cardiotonic Agents/*metabolism, Digoxin/*metabolism, *Gastrointestinal Microbiome, Gastrointestinal Tract/enzymology/*microbiology, Humans, Molecular Dynamics Simulation, Protein Conformation, Sequence HomologyEnzymology
Metabolism29617190Bile acid oxidation by Eggerthella lenta strains C592 and DSM 2243(T).Harris SC, Devendran S, Mendez-Garcia C, Mythen SM, Wright CL, Fields CJ, Hernandez AG, Cann I, Hylemon PB, Ridlon JMGut Microbes10.1080/19490976.2018.14581802018Actinobacteria/classification/enzymology/genetics/*metabolism, Bile Acids and Salts/*metabolism, Clostridium/metabolism, Feces/microbiology, Genome, Bacterial/genetics, Humans, Hydrogen, Hydroxysteroid Dehydrogenases/chemistry/genetics/isolation & purification/*metabolism, Metabolic Networks and Pathways/genetics, Nitrogen/metabolism, Oxidation-Reduction, Recombinant Proteins/isolation & purification/metabolism, Substrate SpecificityEnzymology
Phylogeny29900700Eggerthella timonensis sp. nov, a new species isolated from the stool sample of a pygmy female.Bilen M, Fonkou MDM, Tomei E, Armstrong N, Bittar F, Lagier JC, Daoud Z, Fournier PE, Raoult D, Cadoret FMicrobiologyopen10.1002/mbo3.5752018Actinobacteria/*classification/genetics/*isolation & purification, Anaerobiosis, Bacterial Typing Techniques, Base Composition, Catalase/analysis, Child, Cluster Analysis, Congo, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Feces/*microbiology, Female, Genotype, Humans, Locomotion, Mass Spectrometry, Microscopy, Electron, Transmission, Oxidoreductases/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Temperature, Whole Genome SequencingGenetics
Stress36296301Eggerthella lenta DSM 2243 Alleviates Bile Acid Stress Response in Clostridium ramosum and Anaerostipes caccae by Transformation of Bile Acids.Pedersen KJ, Haange SB, Zizalova K, Viehof A, Clavel T, Lenicek M, Engelmann B, Wick LY, Schaap FG, Jehmlich N, Rolle-Kampczyk U, von Bergen MMicroorganisms10.3390/microorganisms101020252022

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
1003Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 2243)https://www.dsmz.de/collection/catalogue/details/culture/DSM-2243
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
46592Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 17323 A)https://www.ccug.se/strain?id=17323
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)
66793Mukherjee et al.10.1038/nbt.3886GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life 35: 676-683 201728604660
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/
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.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
72574Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID44722.1StrainInfo: A central database for resolving microbial strain identifiers