Strain identifier

BacDive ID: 5415

Type strain: Yes

Species: Peptoclostridium acidaminophilum

Strain Designation: al-2

Strain history: <- U. Zindel <- H. Lebertz <- F. Widdel, al-2

NCBI tax ID(s): 1286171 (strain), 1731 (species)

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General

@ref: 1530

BacDive-ID: 5415

DSM-Number: 3953

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-positive, motile, curved-shaped

description: Peptoclostridium acidaminophilum al-2 is an anaerobe, mesophilic, Gram-positive bacterium that was isolated from waste water ditch.

NCBI tax id

NCBI tax idMatching level
1286171strain
1731species

strain history

  • @ref: 1530
  • history: <- U. Zindel <- H. Lebertz <- F. Widdel, al-2

doi: 10.13145/bacdive5415.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Clostridia
  • order: Eubacteriales
  • family: Peptostreptococcaceae
  • genus: Peptoclostridium
  • species: Peptoclostridium acidaminophilum
  • full scientific name: Peptoclostridium acidaminophilum (Zindel et al. 1989) Galperin et al. 2016
  • synonyms

    • @ref: 20215
    • synonym: Eubacterium acidaminophilum

@ref: 1530

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Clostridiales

family: Peptostreptococcaceae

genus: Peptoclostridium

species: Peptoclostridium acidaminophilum

full scientific name: Peptoclostridium acidaminophilum (Zindel et al. 1989) Galperin et al. 2016

strain designation: al-2

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
25060positive2.0-8.0 µm0.5-1.5 µmcurved-shapedyes
69480positive100

Culture and growth conditions

culture medium

  • @ref: 1530
  • name: EBA MEDIUM (DSMZ Medium 454)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/454
  • composition: Name: EBA MEDIUM (DSMZ Medium 454) Composition: Glycine 2.09205 g/l NaCl 1.04603 g/l KCl 0.523013 g/l MgSO4 x 7 H2O 0.523013 g/l NH4Cl 0.261506 g/l KH2PO4 0.209205 g/l CaCl2 x 2 H2O 0.156904 g/l Na2SeO3 x 5 H2O 0.00263014 g/l HCl 0.00261506 g/l FeCl2 x 4 H2O 0.00156904 g/l Resazurin 0.00104603 g/l CoCl2 x 6 H2O 0.000198745 g/l MnCl2 x 4 H2O 0.000104603 g/l ZnCl2 7.32218e-05 g/l Na2MoO4 x 2 H2O 3.76569e-05 g/l NiCl2 x 6 H2O 2.51046e-05 g/l H3BO3 6.27615e-06 g/l CuCl2 x 2 H2O 2.09205e-06 g/l Biotin NaHCO3 Na2S Distilled water

culture temp

@refgrowthtypetemperaturerange
1530positivegrowth34mesophilic
25060positivegrowth15.0-40.0
25060nogrowth42thermophilic

culture pH

@refabilitytypepH
25060positivegrowth6.5-8.4
25060positiveoptimum7.1-7.4

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
1530anaerobe
25060obligate anaerobe
69480anaerobe99.438

spore formation

  • @ref: 25060
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
25060NaClnogrowth6 %
25060NaClminimum0.001-0.002 M

murein

  • @ref: 1530
  • murein short key: A31
  • type: A1gamma m-Dpm-direct

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2506017632nitrate-reduction
2506016189sulfate-reduction
2506016094thiosulfate-reduction
2506016856glutathione+assimilation
2506017201glycylglycine+assimilation
2506063961glycylglycylglycine+assimilation
2506027612hydantoin+assimilation

enzymes

@refvalueactivityec
25060catalase-1.11.1.6
25060cytochrome oxidase-1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
1530waste water ditchnear KonstanzGermanyDEUEurope
25060anaerobic black mud from a waste water ditchnear Konstanz

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Mud (Sludge)
#Condition#Anoxic (anaerobic)
#Engineered#Waste#Wastewater

taxonmaps

  • @ref: 69479
  • File name: preview.99_4467.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_16294;96_2232;97_2703;98_3356;99_4467&stattab=map
  • Last taxonomy: Peptoclostridium acidaminophilum subclade
  • 16S sequence: AF071416
  • Sequence Identity:
  • Total samples: 2680
  • soil counts: 102
  • aquatic counts: 636
  • animal counts: 1891
  • plant counts: 51

Safety information

risk assessment

  • @ref: 1530
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 1530
  • description: Clostridium acidaminophilum 16S ribosomal RNA gene, partial sequence
  • accession: AF071416
  • length: 1508
  • database: ena
  • NCBI tax ID: 1286171

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Peptoclostridium acidaminophilum DSM 3953 al-2GCA_000597865completencbi1286171
66792Eubacterium acidaminophilum DSM 39531286171.3completepatric1286171
66792Peptoclostridium acidaminophilum DSM 3953 strain al-21286171.8plasmidpatric1286171
66792Peptoclostridium acidaminophilum al-22562617038completeimg1286171

GC content

@refGC-content
153044.0
2506044

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno88no
motileyes75.022no
flagellatedno70.464no
gram-positiveyes62.143no
anaerobicyes99.637no
halophileno92.301no
spore-formingyes79.019no
glucose-utilyes78.528no
aerobicno98.627yes
thermophileno75.586no
glucose-fermentyes54.03no

External links

@ref: 1530

culture collection no.: DSM 3953, ATCC 49065

straininfo link

  • @ref: 74904
  • straininfo: 42275

literature

  • topic: Genetics
  • Pubmed-ID: 24926057
  • title: Complete Genome Sequence of Amino Acid-Utilizing Eubacterium acidaminophilum al-2 (DSM 3953).
  • authors: Poehlein A, Andreesen JR, Daniel R
  • journal: Genome Announc
  • DOI: 10.1128/genomeA.00573-14
  • year: 2014

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
1530Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 3953)https://www.dsmz.de/collection/catalogue/details/culture/DSM-3953
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
25060M. Y. B. Galperin, V.,Tolstoy, I.,Yutin, N.10.1099/ijsem.0.001548Phylogenomic analysis of the family Peptostreptococcaceae (Clostridium cluster XI) and proposal for reclassification of Clostridium litorale (Fendrich et al. 1991) and Eubacterium acidaminophilum (Zindel et al. 1989) as Peptoclostridium litorale gen. nov. comb. nov. and Peptoclostridium acidaminophilum comb. novIJSEM 66: 5506-5513 201627902180
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
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)
74904Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID42275.1StrainInfo: A central database for resolving microbial strain identifiers