Strain identifier

BacDive ID: 1579

Type strain: Yes

Species: Acetomicrobium faecale

Strain Designation: St. T

Strain history: M.-L. Fardeau; IRD-MIO, Aix-Marseille Univ., France <-- DSM 20678 <-- J. Winter; Univ. Regensburg, Germany; St. T.

NCBI tax ID(s): 937334 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 9000

BacDive-ID: 1579

DSM-Number: 20678

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, spore-forming, thermophilic, Gram-positive

description: Acetomicrobium faecale St. T is an anaerobe, spore-forming, thermophilic bacterium that was isolated from sewage sludge.

NCBI tax id

  • NCBI tax id: 937334
  • Matching level: species

strain history

@refhistory
9000<- J. Winter, St. T
67770M.-L. Fardeau; IRD-MIO, Aix-Marseille Univ., France <-- DSM 20678 <-- J. Winter; Univ. Regensburg, Germany; St. T.

doi: 10.13145/bacdive1579.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/synergistota
  • domain: Bacteria
  • phylum: Synergistota
  • class: Synergistia
  • order: Synergistales
  • family: Synergistaceae
  • genus: Acetomicrobium
  • species: Acetomicrobium faecale
  • full scientific name: Acetomicrobium faecale corrig. Winter et al. 1988
  • synonyms

    @refsynonym
    20215Acetomicrobium faecalis
    20215Caldicoprobacter faecalis

@ref: 9000

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Bacteroidales

family: Caldicoprobacteraceae

genus: Caldicoprobacter

species: Caldicoprobacter faecalis

full scientific name: Caldicoprobacter faecalis (Winter et al. 1988) Bouanane-Darenfed et al. 2015

strain designation: St. T

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: positive
  • confidence: 100

Culture and growth conditions

culture medium

  • @ref: 9000
  • name: ACETOMICROBIUM FAECALIS MEDIUM (DSMZ Medium 412)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/412
  • composition: Name: ACETOMICROBIUM FAECALIS MEDIUM (DSMZ Medium 412) Composition: NaHCO3 6.0 g/l Na-acetate 5.0 g/l Glucose 4.0 g/l Yeast extract 2.0 g/l Trypticase peptone 2.0 g/l L-Cysteine HCl x H2O 0.5 g/l KH2PO4 0.255 g/l (NH4)2SO4 0.255 g/l K2HPO4 0.225 g/l MgSO4 x 7 H2O 0.03 g/l Nitrilotriacetic acid 0.015 g/l NaCl 0.01 g/l MnSO4 x H2O 0.005 g/l CoSO4 x 7 H2O 0.0018 g/l ZnSO4 x 7 H2O 0.0018 g/l FeSO4 x 7 H2O 0.001 g/l Resazurin 0.001 g/l CaCl2 x 2 H2O 0.001 g/l NiCl2 x 6 H2O 0.0003 g/l AlK(SO4)2 x 12 H2O 0.0002 g/l Na2MoO4 x 2 H2O 0.0001 g/l H3BO3 0.0001 g/l Pyridoxine hydrochloride 0.0001 g/l CuSO4 x 5 H2O 0.0001 g/l Nicotinic acid 5e-05 g/l (DL)-alpha-Lipoic acid 5e-05 g/l Thiamine HCl 5e-05 g/l Riboflavin 5e-05 g/l p-Aminobenzoic acid 5e-05 g/l Calcium D-(+)-pantothenate 5e-05 g/l Biotin 2e-05 g/l Folic acid 2e-05 g/l Na2WO4 x 2 H2O 4e-06 g/l Na2SeO3 x 5 H2O 3e-06 g/l Vitamin B12 1e-06 g/l Distilled water

culture temp

@refgrowthtypetemperaturerangeconfidence
9000positivegrowth70thermophilic
67770positivegrowth70thermophilic
69480thermophilic100

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
9000anaerobe
69480anaerobe99.686

spore formation

  • @ref: 69481
  • spore formation: yes
  • confidence: 100

murein

  • @ref: 9000
  • murein short key: A31
  • type: A1gamma m-Dpm-direct

Isolation, sampling and environmental information

isolation

@refsample type
9000sewage sludge
67770Sewage sludge

isolation source categories

  • Cat1: #Engineered
  • Cat2: #Waste
  • Cat3: #Sewage sludge

taxonmaps

  • @ref: 69479
  • File name: preview.99_28926.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3079;96_14245;97_17365;98_21577;99_28926&stattab=map
  • Last taxonomy: Caldicoprobacter
  • 16S sequence: FR749983
  • Sequence Identity:
  • Total samples: 1261
  • soil counts: 174
  • aquatic counts: 123
  • animal counts: 903
  • plant counts: 61

Safety information

risk assessment

  • @ref: 9000
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Acetomicrobium faecale partial 16S rRNA gene, type strain DSM 20678T, clone 1FR7499801543ena937334
20218Acetomicrobium faecale partial 16S rRNA gene, type strain DSM 20678T, clone 3FR7499821541ena937334
20218Acetomicrobium faecale partial 16S rRNA gene, type strain DSM 20678T, clone 4FR7499831537ena937334
9000Acetomicrobium faecale partial 16S rRNA gene, type strain DSM 20678T, clone 2FR7499811542ena937334

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Caldicoprobacter faecalis strain DSM 20678937334.3wgspatric937334
66792Caldicoprobacter faecalis DSM 206782693429901draftimg937334
67770Caldicoprobacter faecalis DSM 20678GCA_900115765scaffoldncbi937334

GC content

@refGC-contentmethod
900045.0
6777045thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileno52.381no
flagellatedno93.819no
gram-positiveyes87.101no
anaerobicyes98.456yes
halophileno94.83no
spore-formingyes80.858no
glucose-utilyes92.547no
aerobicno97.94no
thermophileyes100yes
glucose-fermentyes57.678no

External links

@ref: 9000

culture collection no.: DSM 20678, JCM 30420

straininfo link

  • @ref: 71224
  • straininfo: 49667

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny23041645Caldicoprobacter guelmensis sp. nov., a thermophilic, anaerobic, xylanolytic bacterium isolated from a hot spring.Bouanane-Darenfed A, Ben Hania W, Hacene H, Cayol JL, Ollivier B, Fardeau MLInt J Syst Evol Microbiol10.1099/ijs.0.043497-02012Algeria, Bacteria, Anaerobic/classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Fermentation, Gram-Positive Bacteria/*classification/genetics/isolation & purification, Hot Springs/*microbiology, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Xylans/metabolismEnzymology
Phylogeny26297233Reclassification of Acetomicrobium faecale as Caldicoprobacter faecalis comb. nov.Bouanane-Darenfed A, Ben Hania W, Cayol JL, Ollivier B, Fardeau MLInt J Syst Evol Microbiol10.1099/ijsem.0.0004092015Bacterial Typing Techniques, Base Composition, Clostridiales/*classification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Gram-Positive Bacteria/genetics, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
9000Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20678)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20678
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
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/
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
71224Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID49667.1StrainInfo: A central database for resolving microbial strain identifiers