Question

I've been searching for methods of RNA sequencing, and I always find that the step of rRNA removal is emphasized. However, in my research, I need to analyze both functional and taxonomic data from the RNA extracted from stool to study the gut microbiome.

Do I just to just synthesize cDNA and then use nextera xt for library preparation? or should I use another kit such as truseq stranded total rna / scriptseq v2?

Answer 1

For RNA analysis of the gut microbiome requiring both functional and taxonomic data, it's essential to choose the appropriate method of library preparation, with options like Nextera XT for cDNA synthesis and TruSeq or ScriptSeq kits for total RNA including rRNA.

Step-by-step explanation:

When studying the gut microbiome through RNA analysis, it is important to consider the goals of your research. Since you need to analyze both functional and taxonomic data, the removal of rRNA may not be necessary as it can provide valuable taxonomic information. For functional data analysis, cDNA synthesis followed by Nextera XT library preparation is a suitable method. However, if you need a complete overview of RNA including rRNA, the TruSeq Stranded Total RNA or ScriptSeq v2 kit might be a better choice. These kits are tailored towards preserving the totality of RNA, which might be crucial for your research on the gut microbiome.

In the context of metatranscriptomics, the extraction and analysis of RNA help in understanding the gene expression patterns of the microbial community. A thorough preparation of an RNA-Seq library, taking into account the presence of functions and taxonomic markers, such as rRNA, is imperative for accurate functional and taxonomic profiling, which constitutes an integral part of gut microbiome studies.