The first VSOB will be devoted to a Bioinformatics School (SBIS2022) at theoretical and practical levels with the topic: “Microbiome analysis in agricultural work and research”.
Plant roots and animal guts host a large and diverse microbial community including bacteria, fungi, viruses. These microbes play a critical role in nutrient uptake, improving host tolerance and agricultural productivity, and reducing the use of fertilizer and pesticides. The culture-free, high-throughput technology enables the investigation of complex microbial communities in agricultural systems since the majority of these bacteria are strict anaerobes and cannot be cultivated under standard laboratory conditions.
The purpose of the workshop is to enhance the knowledge, appreciation, and application of amplicon sequencing and shotgun metagenomics related to the breadth of microbial diversity in a wide variety of organisms and habitats. Students will use bioinformatics tools, practice analysis, and interpret metagenomic datasets to analyze different agricultural microbiomes.
2. Brief background
What is the microbiome? The gathering of microorganisms that inhabit a particular environment is observed referred to as the microbiome. The microbiome includes all microorganism life: bacteria, archaea, fungi, and viruses. Microbiomes exist on and inside plants, animals, insects, amphibians, birds, and etc. They conjointly exist in niches to themselves during a large choice of terrestrial, marine, and aquatic environments. Several of those environments are extreme together with hot springs, deep ocean thermal vents, and undersea rock formations.
Moreover, microbes in soil, root system and in animal gut are essential for agriculture. Next generation DNA sequencing-based methods allow us to profile the diverse community of microbes in these ecosystems. The methods allow us to detect and quantify both good and bad fungi and bacteria, down to strain level specificity and with high sensitivity, and to understand what they do in different settings and over time. This all sounds great, but how does it work in practice?
3. Course objectives
Students can explain how “microbial-omics” data are used to understand the soil microbiome and its role in agricultural study.
Students can understand how to perform study design, power calculations and logistical challenges in conducting agricultural microbiome studies in both wet-lab and dry-lab aspects.
For wet-lab, students will be able to explore storage protocols and laboratory procedures such as DNA extraction, library preparation, NGS sequencing in soil samples; including the need for appropriate and stringent quality control.
For dry-lab, students are familiar with and can use and apply modern bioinformatics technologies used in microbiome research. Processing of sequencing data, including QC, annotation, generation of microbiota profiles from bacteria or fungi and first data analyses, which will include a comprehensive overview of steps to obtain insight into the data by supervised and unsupervised analyses, including understanding of alpha- and beta- diversity, biomarker identification and multivariate modeling.