When it comes to microbial identification and stratification, ribosomal RNA (rRNA) sequencing produces the greatest accuracy. Between highly conserved nuclear ribosomal DNA (rDNA) genes positions the Internally Transcribed Spacer (ITS) (18S, 5.8S, 28S). The ITS is an acceptable marker for identifying species because it is hypervariable and distinctive among species but mildly unchanged among individuals from the same species. It can reflect the disparities between fungal genera, species, and even strains. Furthermore, ITS sequence fragments are short (ITS1 and ITS2 are 350 bp and 400 bp, respectively) and involve interspecific polymorphisms. These short fragments can be easily amplified, sequenced, and analyzed. ITS sequencing is ideal for identifying and quantifying known fungi, as well as discovering new ones.
Microbial identification can be more quickly and accurately done when using microSEQ compared to using other routine phenotypic techniques. Analyzing the sequence of the 16S rRNA gene and the LSU-D2 area can identify strains that are poorly described, rarely isolated, or have phenotypic variants, and is routinely employed for the identification of mycobacteria. This method can be used to find new pathogens and bacteria that haven't been cultured before. The MicroSEQ platform has been used by a variety of organizations for microbial identification duties such as routine QC microbiology.
But what are the differences between the MicroSEQ-based LSU sequencing and ITS sequencing, and how do researchers choose the method for fungal profiling? This article will give you a basic clue. Some of the differences between the two are shown below:
- The use of the D1/D2 hypervariable area of the LSU ribosomal RNA gene and the ITS domain of the rRNA gene for mold and yeast identification is well established, but research into the commercially accessible MicroSeq fungal sequencing kit, which enhances only the D2 region of the D1/D2 complex for classifying medically important fungi, has been limited.
- Moreover, many research projects of the D2 area of the LSU rRNA gene, ITS1, or ITS2 sequencing center on yeasts and commonly encountered fungi.
- Phenotypic methods can easily misidentify unusual fungi. But additional genes, other than the D2 area of the LSU rRNA gene, can help. And the ITS area needs to be examined for classifying unusual fungi to the genus or species level.
- At a genus level, the D2 area of the LSU rRNA gene is conducted similarly to ITS; however, when species identification is required, although the sequence outcomes for the D2 area of the LSU rRNA gene using MycoBank rather than GenBank are enhanced, the D2 area of the LSU rRNA gene can be underperformed compared to ITS.
- By simplifying the establishment and set-up process for sequence-based identification, the MicroSeq D2 LSU rDNA Fungal Identification Kit can effectively facilitate the adoption of molecular techniques.
- The MicroSeq D2 LSU rDNA Fungal Identification Kit accurately recognizes fungi to the genus level, with some capability to spot a fungal species using GenBank or MycoBank to obtain the most information.
About CD Genomics
CD Genomics provides the research community with high-quality next-generation sequencing, third-generation sequencing, genotyping, microarray, and population genetics services. CD Genomics has become an influential service provider for the industry and continues to innovate, keeping up with the forefront of scientific research and leading the latest and most comprehensive genomics technical support.
CD Genomics provides microbial sequencing solutions of various routes and offers comprehensive bioinformatics analysis. CD Genomics has launched various services for fungal identification, including fungal ITS sequencing, MicroSeq, and fungal whole-genome sequencing. Meanwhile, CD Genomics is flexible to customers’ needs and dedicated to providing satisfying services.
