Gut microbiota sequencing: From single studies to large-scale analysis

Thomas Clavel 1,Ilias Lagkouvardos2
1University Hospital RWTH Aachen, Germany; 
2ZIEL Institute, TU Munich, Freising, Germany

Since the discovery of Polymerase Chain Reaction and pio- neering work on 16S ribosomal RNA genes in the 1980s, the use of molecular techniques to study microbial ecosystems and pathogenic microorganisms has been increasing exponentially. Because microbial communities inhabiting various body sites such as the skin or the intestine can influence our physiology, there has been a massive interest in studying their diversity, func- tions, and role in the development of acute and chronic diseases. In my presentation, I will talk about sequencing approaches to study microbial communities, especially human body microbiota, and give opinions on their potential and limitations. Moreover, I will present a new bioinformatic tool, the Integrated Microbial Next Generation Sequencing (IMNGS) platform, for user-friendly, large-scale studies of 16S rRNA gene amplicon datasets. IMNGS uniformly and systematically screens for, retrieves, processes, and analyses all prokaryotic 16S rRNA amplicon data available in the Sequence Read Archive (SRA) and uses them to build sample- specific sequence databases. Using a web interface, this massively integrated sequence resource can be queried and used to address a broad range of questions of relevance in microbial ecology and applied microbiology. The platform also offers a complete work- flow for de novo analysis of users’ own raw 16S rRNA amplicon data. This new resource can be accessed at [1–3]. References
[1] Clavel, Lagkouvardos, Hiergeist, Microbiome sequencing: challenges and opportunities for molecular medicine, Expert Rev. Mol. Diagn. 16 (2016) 795.
[2] Lagkouvardos, Joseph, Kapfhammer, Giritli, Horn, Haller, Clavel, IMNGS: a massive open resource of processed 16S rRNA microbial profiles for ecology and diversity studies, Sci. Rep. 6 (2016) 33721.
[3] Lagkouvardos, Kumar, Fischer, Clavel, Rhea: a transparent and modular R pipeline for microbial profiling based on 16S rRNA gene amplicons, PeerJ 5 (2017) e2836.

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