Strain identifier

BacDive ID: 5373

Type strain: Yes

Species: Holdemania filiformis

Strain history: <- ATCC <- L.V. Moore, VPI J1-31B-1 <- W.E.C. Moore (Eubacterium sp.)

NCBI tax ID(s): 545696 (strain), 61171 (species)

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General

@ref: 4586

BacDive-ID: 5373

DSM-Number: 12042

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

description: Holdemania filiformis DSM 12042 is an anaerobe, spore-forming, mesophilic bacterium that was isolated from human feces.

NCBI tax id

NCBI tax idMatching level
545696strain
61171species

strain history

  • @ref: 4586
  • history: <- ATCC <- L.V. Moore, VPI J1-31B-1 <- W.E.C. Moore (Eubacterium sp.)

doi: 10.13145/bacdive5373.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Erysipelotrichia
  • order: Erysipelotrichales
  • family: Erysipelotrichaceae
  • genus: Holdemania
  • species: Holdemania filiformis
  • full scientific name: Holdemania filiformis Willems et al. 1997

@ref: 4586

domain: Bacteria

phylum: Firmicutes

class: Erysipelotrichia

order: Erysipelotrichales

family: Erysipelotrichaceae

genus: Holdemania

species: Holdemania filiformis

full scientific name: Holdemania filiformis Willems et al. 1997

type strain: yes

Morphology

cell morphology

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

Culture and growth conditions

culture medium

  • @ref: 4586
  • name: PYG MEDIUM (MODIFIED) (DSMZ Medium 104)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/104
  • composition: Name: 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

culture temp

  • @ref: 4586
  • growth: positive
  • type: growth
  • temperature: 37
  • range: mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
4586anaerobe
69480anaerobe96.969

spore formation

@refspore formationconfidence
69481yes92
69480no97.573

murein

  • @ref: 4586
  • murein short key: B13
  • type: B1delta {L-Ser} [L-Ala] D-Glu-L-Asp-L-Lys

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6838016199urea-hydrolysis
6838029016arginine-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
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
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

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
4586---+-+/--------+--------++---+-

Isolation, sampling and environmental information

isolation

  • @ref: 4586
  • sample type: human feces

isolation source categories

Cat1Cat2Cat3
#Host#Human
#Host Body Product#Gastrointestinal tract#Feces (Stool)

taxonmaps

  • @ref: 69479
  • File name: preview.99_7121.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_507;96_3340;97_4097;98_5239;99_7121&stattab=map
  • Last taxonomy: Holdemania filiformis
  • 16S sequence: Y11466
  • Sequence Identity:
  • Total samples: 34919
  • soil counts: 49
  • aquatic counts: 486
  • animal counts: 34370
  • plant counts: 14

Safety information

risk assessment

  • @ref: 4586
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 4586
  • description: H.filiformis 16S rRNA gene
  • accession: Y11466
  • length: 1391
  • database: ena
  • NCBI tax ID: 61171

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Holdemania filiformis DSM 12042GCA_000157995scaffoldncbi545696
66792Holdemania filiformis DSM 12042545696.5wgspatric545696
66792Holdemania filiformis VPI J1-31B-1, DSM 12042643886103draftimg545696

GC content

  • @ref: 4586
  • GC-content: 38

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes92no
motileno93.577no
flagellatedno97.126no
gram-positiveyes95.651no
anaerobicyes97.689yes
aerobicno97.398yes
halophileno78.275no
spore-formingno76.247no
thermophileno99.036yes
glucose-utilyes90.556no
glucose-fermentyes64.417no

External links

@ref: 4586

culture collection no.: DSM 12042, ATCC 51649, CCUG 39501, VPI J1-31B-1

straininfo link

  • @ref: 74863
  • straininfo: 45309

literature

  • topic: Phylogeny
  • Pubmed-ID: 9336928
  • title: Phenotypic and phylogenetic characterization of some Eubacterium-like isolates containing a novel type B wall murein from human feces: description of Holdemania filiformis gen. nov., sp. nov.
  • authors: Willems A, Moore WE, Weiss N, Collins MD
  • journal: Int J Syst Bacteriol
  • DOI: 10.1099/00207713-47-4-1201
  • year: 1997
  • mesh: Cell Wall/chemistry, Clostridium/chemistry/*classification/genetics/metabolism, DNA, Bacterial/analysis, Eubacterium/chemistry/*classification/genetics/metabolism, Fatty Acids/analysis, Feces/*microbiology, Humans, Molecular Sequence Data, Peptidoglycan/*analysis, Phylogeny, RNA, Ribosomal, 16S/analysis
  • topic2: Metabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
4586Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 12042)https://www.dsmz.de/collection/catalogue/details/culture/DSM-12042
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
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
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
74863Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID45309.1StrainInfo: A central database for resolving microbial strain identifiers