Applications of high-throughput sequencing

Although different instruments for massively parallel sequencing exist, each with their own chemistry, resolution, error types, error frequencies, throughput and costs; the principle behind them is similar: to deduce an original sequence of bases by sampling many templates. The wide array of applications derives from the biological sources and methods used to manufacture the sequencing libraries and the analytic routines employed. By using DNA as source material, a whole genome can be sequenced or, through amplification methods, a more detailed reconstruction of a specific locus can be obtained. Transcriptomes can also be studied by capturing and sequencing different types of RNA. Other capture methods such as cross-linking followed by immunoprecipitation can be used to study DNA-protein interactions. We will explore these applications and others in the following sections and explain the different analysis strategies that are used to analyze each data type

The Gut Microbiome in Inflammatory Bowel Disease

International audienc

“We are what we eat”: How diet impacts the gut microbiota in adulthood

The important role of the microbes residing in our gut, collectively called the microbiota, in human health is widely acknowledged. There are numerous factors that have an impact on the microbiota in the gut of which diet is considered a crucial one. In this chapter we highlight our current knowledge on the ecology of the microbiota in adults and how it is affected by diet. We summarize observations from different cross-sectional and intervention studies that focused on the impact of diet on microbiota composition and activity. Special attention is paid to which microbial metabolites can be produced in the gut; how these are affected by different dietary components such as carbohydrates, fat, and proteins; and how these are associated to human health. Finally, we provide recommendations for future intervention studies in order to improve our understanding of the complex interplay between microbes, diet, and ourselves