Strain identifier

BacDive ID: 1603

Type strain: Yes

Species: Hungatella xylanolytica

Strain Designation: X5-1

Strain history: <- A.J.B. Zehnder, X5-1

NCBI tax ID(s): 384636 (species)

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General

@ref: 1474

BacDive-ID: 1603

DSM-Number: 3808

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

description: Hungatella xylanolytica X5-1 is an anaerobe, spore-forming, mesophilic bacterium that was isolated from methane producing cattle manure.

NCBI tax id

  • NCBI tax id: 384636
  • Matching level: species

strain history

  • @ref: 1474
  • history: <- A.J.B. Zehnder, X5-1

doi: 10.13145/bacdive1603.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Clostridia
  • order: Eubacteriales
  • family: Clostridiaceae
  • genus: Hungatella
  • species: Hungatella xylanolytica
  • full scientific name: Hungatella xylanolytica (Scholten-Koerselman et al. 1988) García-López et al. 2020

  • synonyms

    @refsynonym
    20215Lacrimispora xylanolytica
    20215Bacteroides xylanolyticus

@ref: 1474

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Bacteroidales

family: Clostridiaceae

genus: Hungatella

species: Hungatella xylanolytica

full scientific name: Hungatella xylanolytica (Scholten-Koerselman et al. 1988) García-López et al. 2020

strain designation: X5-1

type strain: yes

Morphology

cell morphology

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

colony morphology

  • @ref: 1474
  • incubation period: 1-2 days

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
1474COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)yeshttps://mediadive.dsmz.de/medium/693Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base
1474PYG MEDIUM WITH VOLATILE FATTY ACIDS (DSMZ Medium 328)yeshttps://mediadive.dsmz.de/medium/328Name: PYG MEDIUM WITH VOLATILE FATTY ACIDS (DSMZ Medium 328) Composition: Yeast extract 10.0 g/l Glucose 5.0 g/l Beef extract 5.0 g/l Trypticase 5.0 g/l L-Cysteine HCl x H2O 0.5 g/l (NH4)2SO4 0.5 g/l NaHCO3 0.4 g/l NaCl 0.08 g/l KH2PO4 0.04 g/l K2HPO4 0.04 g/l MgSO4 x 7 H2O 0.0192 g/l CaCl2 x 2 H2O 0.012 g/l Haemin 0.005 g/l Vitamin K1 0.001 g/l Resazurin 0.001 g/l iso-Valeric acid DL-2-Methylbutyric acid n-Valeric acid n-Butyric acid Propionic acid Acetic acid iso-Butyric acid Distilled water

culture temp

@refgrowthtypetemperaturerange
1474positivegrowth37mesophilic
58067positivegrowth30-37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
1474anaerobe
58067anaerobe
69480anaerobe97.801

spore formation

@refspore formationconfidence
69481yes99
69480yes99.447

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836727082trehalose-builds acid from
6836762345L-rhamnose-builds acid from
6836730911sorbitol-builds acid from
6836716634raffinose-builds acid from
683676731melezitose-builds acid from
6836716024D-mannose-builds acid from
6836717057cellobiose-builds acid from
6836717754glycerol-builds acid from
683674853esculin+hydrolysis
683675291gelatin-hydrolysis
6836730849L-arabinose-builds acid from
6836765327D-xylose-builds acid from
6836717814salicin-builds acid from
6836717306maltose-builds acid from
6836717992sucrose-builds acid from
6836717716lactose-builds acid from
6836716899D-mannitol-builds acid from
6836717634D-glucose-builds acid from
6836716199urea-hydrolysis
6836727897tryptophan-energy source
6838016199urea-hydrolysis
6838016024D-mannose+fermentation
6838016634raffinose+fermentation
6838029985L-glutamate-degradation
6838017632nitrate-reduction
6838027897tryptophan-energy source

metabolite production

@refChebi-IDmetaboliteproduction
6836735581indoleno
6838035581indoleno

metabolite tests

@refChebi-IDmetaboliteindole test
6838035581indole-
6836735581indole-

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
68380alpha-glucosidase+3.2.1.20
68380beta-Galactosidase 6-phosphate-
68380beta-galactosidase+3.2.1.23
68380alpha-galactosidase+3.2.1.22
68380urease-3.5.1.5
68367beta-glucosidase+3.2.1.21
68367gelatinase-
68367urease-3.5.1.5

API 20A

@refINDUREGLUMANLACSACMALSALXYLARAGELESCGLYCELMNEMLZRAFSORRHATRE
1474-----------+--------

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
1474-+/-++-+++--++-----------------
1474-+++-+++--++-----------------

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
1474methane producing cattle manureNetherlandsNLDEurope
58067Methane producing cattle manure

isolation source categories

Cat1Cat2Cat3
#Host#Mammals#Bovinae (Cow, Cattle)
#Host Body Product#Gastrointestinal tract#Feces (Stool)

taxonmaps

  • @ref: 69479
  • File name: preview.99_12655.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_16;96_286;97_316;98_351;99_12655&stattab=map
  • Last taxonomy: Lacrimispora
  • 16S sequence: DQ497992
  • Sequence Identity:
  • Total samples: 396
  • soil counts: 62
  • aquatic counts: 37
  • animal counts: 247
  • plant counts: 50

Safety information

risk assessment

  • @ref: 1474
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 1474
  • description: Bacteroides xylanolyticus 16S ribosomal RNA gene, partial sequence
  • accession: DQ497992
  • length: 1378
  • database: ena
  • NCBI tax ID: 384636

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Hungatella xylanolytica DSM 3808GCA_002934545contigncbi384636
66792Bacteroides xylanolyticus strain DSM 3808384636.4wgspatric384636
66792Bacteroides xylanolyticus DSM 38082739367553draftimg384636

GC content

  • @ref: 1474
  • GC-content: 34.8

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes99no
gram-positiveyes52.593no
anaerobicyes98.164yes
halophileno94.14no
spore-formingyes82.515no
glucose-utilyes88.865no
aerobicno98.188yes
flagellatedyes53.222no
thermophileno99.603no
motileyes81.406no
glucose-fermentyes70.806no

External links

@ref: 1474

culture collection no.: DSM 3808, CCUG 48289

straininfo link

  • @ref: 71248
  • straininfo: 47762

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Metabolism3813526Bacteroides xylanolyticus sp. nov., a xylanolytic bacterium from methane producing cattle manure.Scholten-Koerselman I, Houwaard F, Janssen P, Zehnder AJAntonie Van Leeuwenhoek10.1007/BF004234151986Animals, Bacteroides/classification/*isolation & purification/metabolism/ultrastructure, Carbohydrate Metabolism, Cattle, *Cellulase, Culture Media, Fermentation, Glycoside Hydrolases/metabolism, Hydrogen-Ion Concentration, *Manure, Methane/biosynthesis, Microscopy, Electron, Microscopy, Electron, Scanning, Polysaccharides/*metabolism, Temperature, Xylan Endo-1,3-beta-Xylosidase, Xylans/*metabolismPhylogeny
Metabolism8048843D-xylose catabolism in Bacteroides xylanolyticus X5-1.Biesterveld S, Kok MD, Dijkema C, Zehnder AJ, Stams AJArch Microbiol10.1007/BF003077741994Bacteroides/*enzymology/growth & development, Biological Transport, Energy Metabolism/physiology, Fermentation, Pentose Phosphate Pathway/physiology, Pyruvates/metabolism, Pyruvic Acid, Xylose/antagonists & inhibitors/*metabolismEnzymology
16349187Xylose and Glucose Utilization by Bacteroides xylanolyticus X5-1 Cells Grown in Batch and Continuous Culture.Biesterveld S, Oude Elferink SJ, Zehnder AJ, Stams AJAppl Environ Microbiol10.1128/aem.60.2.576-580.19941994
16349240Regulation of Product Formation in Bacteroides xylanolyticus X5-1 by Interspecies Electron Transfer.Biesterveld S, Zehnder AJ, Stams AJAppl Environ Microbiol10.1128/aem.60.4.1347-1352.19941994
16887561Polysaccharide inducible outer membrane proteins of Bacteroides xylanolyticus X5-1.Fields MW, Ryals PE, Anderson KLAnaerobe10.1006/anae.1996.00641997
Phylogeny36352237Lacrimispora defluvii PI-S10-B5A(T) sp. nov., an Obligate Anaerobe, Isolated from an Industrial Waste and Reclassification of Hungatella xylanolytica as Lacrimispora xylanolytica and Clostridium indicum as Lacrimispora indica Comb. nov.Urvashi, Gundawar K, Sharma S, Choksket S, Sharma M, Grover V, Patil PB, Korpole SCurr Microbiol10.1007/s00284-022-03096-w2022RNA, Ribosomal, 16S/genetics, Phylogeny, *Industrial Waste, DNA, Bacterial/genetics, Bacterial Typing Techniques, Sequence Analysis, DNA, *Clostridium, Bacteria, Anaerobic/genetics, Phospholipids/analysis, Fatty Acids/analysisTranscriptome

Reference

@idauthorscataloguedoi/urltitle
1474Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 3808)https://www.dsmz.de/collection/catalogue/details/culture/DSM-3808
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
58067Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 48289)https://www.ccug.se/strain?id=48289
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)
68367Automatically annotated from API 20A
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
71248Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID47762.1StrainInfo: A central database for resolving microbial strain identifiers