Strain identifier

BacDive ID: 6356

Type strain: Yes

Species: Hespellia stercorisuis

Strain Designation: PC18

Strain history: CIP <- 2004, CCUG <- 2002, T.R. Whitehead, USDA, Peoria, USA: strain PC18

NCBI tax ID(s): 1121950 (strain), 180311 (species)

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General

@ref: 5950

BacDive-ID: 6356

DSM-Number: 15480

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

description: Hespellia stercorisuis PC18 is an anaerobe, mesophilic, Gram-positive bacterium that was isolated from stored swine manure.

NCBI tax id

NCBI tax idMatching level
1121950strain
180311species

strain history

@refhistory
5950<- T. R. Whitehead, National Center for Agricultural Utilization Research, USDA, Peoria, USA; PC18 <- T. R. Whitehead {1998}
123317CIP <- 2004, CCUG <- 2002, T.R. Whitehead, USDA, Peoria, USA: strain PC18

doi: 10.13145/bacdive6356.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Clostridia
  • order: Eubacteriales
  • family: Lachnospiraceae
  • genus: Hespellia
  • species: Hespellia stercorisuis
  • full scientific name: Hespellia stercorisuis Whitehead et al. 2004

@ref: 5950

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Clostridiales

family: Lachnospiraceae

genus: Hespellia

species: Hespellia stercorisuis

full scientific name: Hespellia stercorisuis Whitehead et al. 2004

strain designation: PC18

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
29938positive1.5-5.0 µm0.5-1.0 µmrod-shapedno
69480positive100
123317positiverod-shapedno

colony morphology

  • @ref: 57136
  • incubation period: 3 days

pigmentation

  • @ref: 29938
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5950WILKINS-CHALGREN ANAEROBE BROTH (N2/CO2) (DSMZ Medium 339a)yeshttps://mediadive.dsmz.de/medium/339aName: WILKINS-CHALGREN ANAEROBE BROTH (N2/CO2) (DSMZ Medium 339a) Composition: dehydrated Wilkins-Chalgren medium 33.0 g/l D-Glucose 5.0 g/l L-Cysteine HCl 0.3 g/l Sodium resazurin 0.0005 g/l Distilled water
5950CMC MEDIUM (N2/CO2) (DSMZ Medium 110a)yeshttps://mediadive.dsmz.de/medium/110aName: CMC MEDIUM (N2/CO2) (DSMZ Medium 110a) Composition: Ground beef 500.0 g/l Casitone 30.0 g/l Yeast extract 5.0 g/l K2HPO4 5.0 g/l D-Glucose 4.0 g/l Na2CO3 1.5 g/l Cellobiose 1.0 g/l Maltose 1.0 g/l Starch 1.0 g/l L-Cysteine HCl x H2O 0.5 g/l Sodium resazurin 0.0005 g/l NaOH Distilled water
36724MEDIUM 10 - Chocolate medium for Actinobacillus pleuropneumoniae, Capnocytophaga cynodegmi, Haemophilus and NeisseriayesDistilled water make up to (1000.000 ml);Columbia agar (39.000 g);Horseblood (100.000 ml);PolyVitex mischung (10.000 ml)
123317CIP Medium 45yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=45
123317CIP Medium 10yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=10

culture temp

@refgrowthtypetemperaturerange
5950positivegrowth37mesophilic
29938positiveoptimum37mesophilic
36724positivegrowth37mesophilic
57136positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
5950anaerobe
29938anaerobe
57136anaerobe
69480anaerobe99.542

spore formation

@refspore formationconfidence
29938no
69481no94
69480no98.806

observation

  • @ref: 29938
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2993817057cellobiose+carbon source
2993828757fructose+carbon source
2993817234glucose+carbon source
2993817306maltose+carbon source
2993837684mannose+carbon source
2993830911sorbitol+carbon source
2993817992sucrose+carbon source
2993827082trehalose+carbon source
2993818222xylose+carbon source
12331717632nitrate-reduction
12331716301nitrite-reduction

metabolite production

  • @ref: 123317
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

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
123317oxidase-
123317catalase-1.11.1.6
123317urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
123317--++-+-----+--------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling dateisolation date
5950stored swine manureIllinois, PeoriaUSAUSANorth America
57136Swine manure,storedIllinois,EurekaUSAUSANorth America1998-07-01
123317Swine manure, storedIllinoisUnited States of AmericaUSANorth America1998

isolation source categories

Cat1Cat2Cat3
#Host#Mammals#Suidae (Pig,Swine)
#Host Body Product#Gastrointestinal tract#Feces (Stool)

taxonmaps

  • @ref: 69479
  • File name: preview.99_3991.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_16;96_2028;97_2444;98_3023;99_3991&stattab=map
  • Last taxonomy: Hespellia stercorisuis subclade
  • 16S sequence: AF445264
  • Sequence Identity:
  • Total samples: 1712
  • soil counts: 18
  • aquatic counts: 219
  • animal counts: 1451
  • plant counts: 24

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
59501Risk group (German classification)
1233171Risk group (French classification)

Sequence information

16S sequences

  • @ref: 5950
  • description: Hespellia stercorisuis strain PPC18 16S ribosomal RNA gene, partial sequence
  • accession: AF445264
  • length: 1469
  • database: ena
  • NCBI tax ID: 180311

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Hespellia stercorisuis DSM 15480GCA_900142165scaffoldncbi1121950
66792Hespellia stercorisuis DSM 154801121950.3wgspatric1121950
66792Hespellia stercorisuis DSM 154802585428171draftimg1121950

GC content

  • @ref: 5950
  • GC-content: 43.7

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno94no
motileno89.319no
flagellatedno93.204yes
gram-positiveyes89.702yes
anaerobicyes99.507yes
aerobicno98.686no
halophileno74.32no
spore-formingno76.957yes
thermophileno99.496yes
glucose-utilyes92.168yes
glucose-fermentyes79.93no

External links

@ref: 5950

culture collection no.: DSM 15480, ATCC BAA 677, CCUG 46279, NRRL B-23456, CIP 108344

straininfo link

  • @ref: 75829
  • straininfo: 130840

literature

  • topic: Phylogeny
  • Pubmed-ID: 14742487
  • title: Hespellia stercorisuis gen. nov., sp. nov. and Hespellia porcina sp. nov., isolated from swine manure storage pits.
  • authors: Whitehead TR, Cotta MA, Collins MD, Lawson PA
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.02719-0
  • year: 2004
  • mesh: Animals, Clostridium/*classification/genetics/isolation & purification, DNA, Ribosomal/genetics, Genes, Bacterial/genetics, Manure/*microbiology, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Swine/*microbiology
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
5950Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15480)https://www.dsmz.de/collection/catalogue/details/culture/DSM-15480
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
29938Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2630928776041
36724Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5956
57136Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 46279)https://www.ccug.se/strain?id=46279
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 updates33211880Nucleic Acids Res. 49: D498-D508 2020
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
75829Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID130840.1StrainInfo: A central database for resolving microbial strain identifiers
123317Curators of the CIPCollection of Institut Pasteur (CIP 108344)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108344