18S ITS Mycobiome profiling

  • Selective profiling of the fungal population of the Mycobiome
  • Sequencing the complete 2.5Kb 18S-ITS1-5.8S-ITS2 region
  • 90% of unique 18S-ITS1/2 molecules assigned at the species or genus level
  • Accurate UMI based quantification
  • 40X lower error rates than classical Illumina workflows

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While High-Throughput sequencing methods have been revolutionizing Biology, studies of fungal communities have not kept up with this pace.
The big challenge here is to find genomic regions that are short enough for standard NGS approaches, but variable enough to distinguish one species from another. Often, researchers do have to choose between sequencing portions of the 18S ribosomal RNA gene, the internal transcribed spacer 1 (ITS1) or ITS2. However, each of these regions possesses unique taxonomic biases, and none of them are sufficient, on their own, for accurate identification at the species level and, in some cases, at the genus level.

With the LoopSeq technology, it is possible to cover the entire 18S ribosomal RNA gene and both ITS1 and ITS2. This enables accurate classification and quantification, compared to the classical Illumina workflows.

The LoopSeq Mycobiome kit enables assembly of the vast majority of reads into the full length 18S-ITS1/2 sequence. The figure on the left shows the reads of a synthetic community, composed of 2 species, being assembled into 2 main peaks. One peak for the full length 18S-ITS1/2 region of Saccharomyces cerevisiae and the other for the full length 18S-ITS1/2 region of Cryptococcus neoformans.
When applied to a soil sample containing a complex and unknown number of diverse fungal species (figure on the right), the distribution of the read lengths reflects the complexity of the sample with a mean peak around 2,4Kb, a minor peak around 2,8Kb and a number of reads of different lengths suggesting sequence from a range of organisms.


LoopSeq’s longer read-length directly translates into more accurate taxonomic assignment.
Using a defined mock community consisting of an equal number of 4 fungal species, only 48% of the unassembled short reads could correctly identify organisms at the genus level (left side) and 26% at the species level (right side). In contrast, when these same short reads were assembled into the full length synthetic long-reads, more organisms were correctly identified at a higher taxonomic resolution, with 93% of contigs larger than 1Kb able to provide correct identification at genus level and 66% at the species level.

Mycobiome 18S-ITS1/2 sequencing & analysis service

  • Service includes library prep, sequencing and Data analysis
  • Results delivered as easy to understand reports and raw data files
  • Contigs queried against EnsemblFungi, UniteCommunity and Silva databases
  • Scalable pricing, depending on number of samples (minimal 8 samples)
  • Highly attractive volume pricing

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