RNA sequencing is a valuable tool brought about by advances in next generation sequencing (NGS) technology. Initially used for transcriptome mapping, it has grown to become one of the ‘gold standards’ for studying molecular changes that occur in niche environments or within and across infections. It employs high-throughput sequencing with many advantages over previous methods. In this chapter, we review the experimental approaches of RNA sequencing from isolating samples all the way to data analysis methods. We focus on a number of NGS platforms that offer RNA sequencing with each having their own strengths and drawbacks. The focus will also be on how RNA sequencing has led to developments in the field of host-pathogen interactions using the dual RNA sequencing technique. Besides dual RNA sequencing, this review also explores the application of other RNA sequencing techniques such as single cell RNA sequencing as well as the potential use of newer techniques like ‘spatialomics’ and ribosome-profiling in host-pathogen interaction studies. Finally, we examine the common challenges faced when using RNA sequencing and possible ways to overcome these challenges.
Part of the book: Applications of RNA-Seq in Biology and Medicine
The human gastrointestinal tract harbors an extremely complex and dynamic microbial community, including archaea, bacteria, viruses and eukaryota. This gut microbiota usually works with the host to promote health but can sometimes initiate or promote disease. Dysbiosis relationship in gut health indicating the role gut microbiota in promoting the development and progression of brain health. The human gut microbiota is a complex and dynamics microbial community that plays an important role in protecting the host against pathogenic microbes, modulating immunity and regulating metabolic processes. The insights can be elucidated with help of latest omics technology and animal model studies.
Part of the book: Effect of Microbiota on Health and Disease