Strain identifier

BacDive ID: 132646

Type strain: Yes

Species: Herbinix luporum

Strain Designation: SD1D

Strain history: <- D. Köck, TU Munich, Freising-Weihenstephan, Germany; SD1D <- D. Köck {2014}

NCBI tax ID(s): 1679721 (species)

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General

@ref: 24435

BacDive-ID: 132646

DSM-Number: 100831

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

description: Herbinix luporum SD1D is an anaerobe, thermophilic, Gram-positive bacterium that forms circular colonies and was isolated from thermophilic biogas plant.

NCBI tax id

  • NCBI tax id: 1679721
  • Matching level: species

strain history

  • @ref: 24435
  • history: <- D. Köck, TU Munich, Freising-Weihenstephan, Germany; SD1D <- D. Köck {2014}

doi: 10.13145/bacdive132646.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Clostridia
  • order: Eubacteriales
  • family: Lachnospiraceae
  • genus: Herbinix
  • species: Herbinix luporum
  • full scientific name: Herbinix luporum Koeck et al. 2016

@ref: 24435

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Clostridiales

family: Lachnospiraceae

genus: Herbinix

species: Herbinix luporum

full scientific name: Herbinix luporum Koeck et al. 2016

strain designation: SD1D

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthmotilityconfidence
24929positive2.0-6.0 µm0.5 µmno
69480positive100

colony morphology

  • @ref: 24929
  • colony size: 2-5 mm
  • colony color: cream
  • colony shape: circular
  • medium used: solid GS2

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
24929solid GS2yes
24435CLOSTRIDIUM (GS) MEDIUM (DSMZ Medium 255)yeshttps://mediadive.dsmz.de/medium/255Name: CLOSTRIDIUM (GS) MEDIUM (DSMZ Medium 255) Composition: Morpholinopropane sulfonic acid 9.98004 g/l Yeast extract 5.98802 g/l Cellobiose 4.99002 g/l Urea 1.99601 g/l L-Cysteine HCl x H2O 0.998004 g/l K2HPO4 x 3 H2O 0.998004 g/l KH2PO4 0.499002 g/l MgCl2 x 6 H2O 0.499002 g/l CaCl2 x 2 H2O 0.0499002 g/l FeSO4 x 7 H2O 0.0012475 g/l Sodium resazurin 0.000499002 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
24929positivegrowth40-65thermophilic
24929positiveoptimum55thermophilic
24435positivegrowth55thermophilic

culture pH

@refabilitytypepHPH range
24929positivegrowth6.5-8.5alkaliphile
24929positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
24929anaerobe
69480anaerobe100

spore formation

@refspore formationconfidence
24929no
69480yes95.96

halophily

  • @ref: 24929
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-4 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2492916947citrate-degradation
2492928757fructose-carbon source
2492916813galactitol-fermentation
2492915443inulin-carbon source
2492917716lactose-carbon source
2492917716lactose-fermentation
2492917309pectin-carbon source
2492930911sorbitol-carbon source
2492917992sucrose-carbon source
2492916189sulfate-reduction
2492927897tryptophan-energy source
2492916199urea-degradation
2492937166xylan-carbon source
2492918222xylose-carbon source
2492922599arabinose+carbon source
2492917057cellobiose+carbon source
2492962968cellulose+carbon source
2492928260galactose+carbon source
2492917234glucose+carbon source
2492937684mannose+carbon source
2492928017starch+carbon source

metabolite production

  • @ref: 24929
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 24929
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
24929catalase-1.11.1.6
24929tryptophan deaminase-4.1.99.1

Isolation, sampling and environmental information

isolation

  • @ref: 24435
  • sample type: thermophilic biogas plant
  • geographic location: Viersen (Mackenstein 3)
  • country: Germany
  • origin.country: DEU
  • continent: Europe

isolation source categories

Cat1Cat2Cat3
#Engineered#Bioreactor
#Engineered#Industrial#Plant (Factory)
#Condition#Thermophilic (>45°C)

Safety information

risk assessment

  • @ref: 24435
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 24435
  • description: Herbinix sp. SD1D partial 16S rRNA gene, isolate SD1D
  • accession: LN626359
  • length: 1354
  • database: ena
  • NCBI tax ID: 1679721

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Herbinix luporum SD1DGCA_900070325completencbi1679721
66792Herbinix luporum SD1D2757320858completeimg1679721

GC content

@refGC-contentmethod
2492935.1genome sequence analysis
2443535.1sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes57no
flagellatedno77.517yes
gram-positiveyes88.378yes
anaerobicyes98.815no
aerobicno98.148yes
halophileno91.283no
spore-formingyes78.337yes
glucose-fermentyes71.079no
thermophileyes91.658yes
glucose-utilyes86.965no
motileyes69.608yes

External links

@ref: 24435

culture collection no.: DSM 100831, CECT 8959

straininfo link

  • @ref: 90959
  • straininfo: 402175

literature

  • topic: Phylogeny
  • Pubmed-ID: 27453473
  • title: Herbinix luporum sp. nov., a thermophilic cellulose-degrading bacterium isolated from a thermophilic biogas reactor.
  • authors: Koeck DE, Hahnke S, Zverlov VV
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.001324
  • year: 2016
  • mesh: Bacterial Typing Techniques, Base Composition, Biofuels/*microbiology, Cellobiose/metabolism, Cellulose/*metabolism, Clostridiales/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Fermentation, Germany, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA
  • topic2: Metabolism

Reference

@idauthorstitledoi/urlcataloguejournalpubmed
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
24435Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-100831Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 100831)
24929D. E. H. Koeck, Sarah,Zverlov, Vladimir V.Herbinix luporum sp. nov., a thermophilic cellulose-degrading bacterium isolated from a thermophilic biogas reactor10.1099/ijsem.0.001324IJSEM 66: 4132-4137 201627453473
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa1025Nucleic Acids Res. 49: D498-D508 202033211880
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
90959Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID402175.1