Strain identifier

BacDive ID: 5377

Type strain: Yes

Species: Eggerthia catenaformis

Strain Designation: 1871

Strain history: CIP <- 1996, JCM <- ATCC <- L. Holdeman: strain VPI 2933 <- A. Prévot: strain 1871

NCBI tax ID(s): 999415 (strain), 31973 (species)

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General

@ref: 8909

BacDive-ID: 5377

DSM-Number: 20559

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

description: Eggerthia catenaformis 1871 is an anaerobe, spore-forming, mesophilic human pathogen that was isolated from pulmonary infection.

NCBI tax id

NCBI tax idMatching level
999415strain
31973species

strain history

@refhistory
8909<- ATCC <- L. Holdeman, VPI 2933 <- A. Prévot, 1871
67770ATCC 25536 <-- L. Holdeman VPI 2933 <-- A. Prévot 1871.
117214CIP <- 1996, JCM <- ATCC <- L. Holdeman: strain VPI 2933 <- A. Prévot: strain 1871

doi: 10.13145/bacdive5377.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Erysipelotrichia
  • order: Erysipelotrichales
  • family: Coprobacillaceae
  • genus: Eggerthia
  • species: Eggerthia catenaformis
  • full scientific name: Eggerthia catenaformis (Eggerth 1935) Salvetti et al. 2011

  • synonyms

    @refsynonym
    20215Bacteroides catenaformis
    20215Lactobacillus catenaformis
    20215Lactobacillus catenaforme
    20215Catenabacterium catenaforme

@ref: 8909

domain: Bacteria

phylum: Firmicutes

class: Erysipelotrichia

order: Erysipelotrichales

family: Coprobacillaceae

genus: Eggerthia

species: Eggerthia catenaformis

full scientific name: Eggerthia catenaformis (Eggerth 1935) Salvetti et al. 2011

strain designation: 1871

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no90.599
69480100positive
117214nopositiverod-shaped

colony morphology

  • @ref: 58018
  • incubation period: 2 days

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8909PYG 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
39108MEDIUM 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)
117214CIP Medium 20yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=20
117214CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
8909positivegrowth37mesophilic
39108positivegrowth37mesophilic
58018positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
8909anaerobe
58018anaerobe
69480anaerobe98.038

spore formation

@refspore formationconfidence
69481yes100
69480no99.999

murein

  • @ref: 8909
  • murein short key: A11.06
  • type: A3alpha L-Lys-L-Ala3

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
11721417632nitrate-reduction
11721416301nitrite-reduction

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
117214oxidase-
117214alcohol dehydrogenase-1.1.1.1
117214catalase-1.11.1.6
117214lysine decarboxylase-4.1.1.18
117214ornithine decarboxylase-4.1.1.17

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
117214----------++---+++--

Isolation, sampling and environmental information

isolation

@refsample type
8909pulmonary infection
58018Human pulmonary infection
67770Pulmonary infection
117214Human, Pulmonary infection

isolation source categories

Cat1Cat2Cat3
#Infection#Disease
#Host Body-Site#Oral cavity and airways#Airways

taxonmaps

  • @ref: 69479
  • File name: preview.99_3032.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_17083;96_1592;97_1900;98_2332;99_3032&stattab=map
  • Last taxonomy: Eggerthia catenaformis subclade
  • 16S sequence: LC145551
  • Sequence Identity:
  • Total samples: 19504
  • soil counts: 210
  • aquatic counts: 293
  • animal counts: 18916
  • plant counts: 85

Safety information

risk assessment

@refpathogenicity humanbiosafety levelbiosafety level comment
8909yes, in single cases1Risk group (German classification)
1172141Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Eggerthia catenaformis gene for 16S rRNA, partial sequence, strain: JCM 1121AB289059694ena999415
8909Lactobacillus catenaformis partial 16S rRNA gene, strain DSM 20559TAJ6215491506ena999415
67770Eggerthia catenaformis gene for 16S ribosomal RNA, partial sequence, strain: JCM 1121LC1455511411ena999415
67770L.catenaforme 16S ribosomal RNA small subunitM237291549ena31973

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Eggerthia catenaformis OT 569 = DSM 20559GCA_000340375scaffoldncbi999415
66792Eggerthia catenaformis OT 569 = DSM 20559999415.3wgspatric999415
66792Eggerthia catenaformis OT 569 = DSM 20559999415.14wgspatric999415
66792Eggerthia catenaformis OT 569, DSM 205592522572066draftimg999415
67770Eggerthia catenaformis OT 569 = DSM 20559GCA_000422605scaffoldncbi999415

GC content

  • @ref: 8909
  • GC-content: 31.7

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileno95.19no
flagellatedno97.241no
gram-positiveyes96.393no
anaerobicyes96.718yes
aerobicno98.793yes
halophileyes51.686no
spore-formingno87.182no
glucose-utilyes88.098no
thermophileno98.695yes
glucose-fermentyes76.148no

External links

@ref: 8909

culture collection no.: LMG 9915, CECT 4140, DSM 20559, ATCC 25536, CCUG 48174, CIP 104817, JCM 1121, VPI 2933, BCRC 14626, NRIC 1720

straininfo link

  • @ref: 74867
  • straininfo: 3265

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19060040Sharpea azabuensis gen. nov., sp. nov., a Gram-positive, strictly anaerobic bacterium isolated from the faeces of thoroughbred horses.Morita H, Shiratori C, Murakami M, Takami H, Toh H, Kato Y, Nakajima F, Takagi M, Akita H, Masaoka T, Hattori MInt J Syst Evol Microbiol10.1099/ijs.0.65543-02008Anaerobiosis, Animals, Feces/*microbiology, Horses/*microbiology, Lactobacillaceae/*classification/genetics/*physiology, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Species SpecificityGenetics
Phylogeny21112984Reclassification of Lactobacillus catenaformis (Eggerth 1935) Moore and Holdeman 1970 and Lactobacillus vitulinus Sharpe et al. 1973 as Eggerthia catenaformis gen. nov., comb. nov. and Kandleria vitulina gen. nov., comb. nov., respectively.Salvetti E, Felis GE, Dellaglio F, Castioni A, Torriani S, Lawson PAInt J Syst Evol Microbiol10.1099/ijs.0.029231-02010Bacterial Typing Techniques, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Genes, rRNA, Lactobacillus/*classification/genetics/physiology, Molecular Sequence Data, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic AcidGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8909Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20559)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20559
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
39108Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16768
58018Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 48174)https://www.ccug.se/strain?id=48174
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/
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
74867Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID3265.1StrainInfo: A central database for resolving microbial strain identifiers
117214Curators of the CIPCollection of Institut Pasteur (CIP 104817)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104817