Metagenomics is a relatively new field of research based on high-throughput sequencing (or Next Generation Sequencing) and its popularity signifies a growing appreciation for the composition of microbial communities (microbiomes) and the genetic information their genomes carry. Metagenomics allows us to study the microbiome in its natural environment and learn about the cooperative and often symbiotic relationships between prokaryotes, eukaryotes, viruses, and archaea.

In this Omics Logic Metagenomics Specialization, we will explore how different types of analysis can be used to understand the microbial world. We will cover several bioinformatics approaches to the analysis of the microbiome. We will learn to compare microbial composition in different conditions, learn about the sequencing of viral samples and discuss how microbes evade the immune response of the host as well as evade treatment. We will do so in the context of several projects taken from high-impact publications.

Key Topics Covered:

Overview of Methods and Applications for Metagenomics Sequencing and Analysis

A program that embeds data-driven concepts into biological projects, spanning the student learning journey from observer to participant in research. Project-based learning for big data bioinformatics is to go beyond the theory with real datasets, projects, and expert mentors. Work with curated datasets from publicly available repositories with easy-to-follow tutorials.

Big Data Analysis Platform : Metagenomics Analysis on the T-Bioinfo Server

Many types of omics data require step-by-step preparation, exploration, annotation, & visualization to understand. The T-BioInfo platform was designed for big multi-omics data analysis hiding the complexities of data with a user-friendly & intuitive interface that eliminates the need for coding and advanced machine learning algorithms for data integration and mining.

Interpretation and Meaning: Statistical Analysis, Visualization & Interpretation using R

Online bioinformatics coding exercises to learn and explore R and Python scripting and understand how to analyze and visualize -omics data to extract meaningful insights from large biological datasets. Learn, practice, and achieve bioinformatics greatness with concise exercises and interesting challenges right in the comfort of your browser!

Future Directions: Full metagenomic sequencing, metatranscriptomics & functional analysis
Metagenomic sequencing data can be used to analyze microbiome composition & species diversity. In this program, you will learn about processing 16s rRNA data with DADA2, visualizing OTU abundance tables for diversity & using the Phyloseq R package that can help build phylogeny-aware species richness.

Program Syllabus : Metagenomics (Starting Jan 10, 2022)

SESSION TITLE	DESCRIPTION
	Introduction to Metagenomics: 16s metagenomics sequencing Session Topics: Introduction to NGS for Metagenomic Sequencing Whole Genome, 16s rRNA, and amplicon data types Overview of the entire course Overview of the tools and resources for this program ( learn.omicslogic.com courses, projects and datasets, and the T-BioInfo Analytics Platform), Expectations and schedule review for the training program, important deadlines Outcome: Learn about History & Significance of 16s rRNA in Metagenomics 16S Metagenomic Sequencing Library Preparation Sample collection and preparation DNA extraction 16S rRNA bacterial Amplification Library generation: amplicon PCR Overview of metagenomics sections in the platform and the OmicsLogic Learn site. Associated online course/resource: Introduction to Metagenomics Visualization of 16s metagenomics data Metagenomics 2 - L2: Studying Microbial Diversity using 16S Metagenomics
	Microbiome - functional bacterial community Session Topics: Mapping on databases (Silva, GreenGenes, NCBI) Hypervariable regions of ribosomal RNA and full genome databases Data Visualization Outcome: Learn about Understand 16S metagenomic analysis Pre-processing Data simulation Error correction Mapping to a reference database (Short overview) Generating the Abundance Table Post-processing and analysis short read OTUs for microbiome profiling Hypervariable regions (HVRs), Batch Effect Correction Non-significant reads Normalization Sequencing depth & classification. Associated online course/resource: The Microbiome and Human Health Metagenomics Data Visualization - Taxonomic Composition
	DADA2 Microbiome variability and composition Session Topics: Microbiome variability Composition based on amplicon sequencing (DADA2 pipeline) Outcome: Learn about Understand the Microbiome Diversity Learn to compare microbial composition in different conditions Learn about 16s amplicon sequencing and DADA2 analysis pipeline specifically designed for these kinds of studies. Associated online course/resource: PhyloSeq Analysis Dimensionality reduction: PCA & visualization Metagenomics 1 - L3: Practical 16s Metagenomics Analysis
	In-depth, Hands-on Project Example: American Gut and the Human Microbiome Variability Session Topics: In-depth, Hands-on Project Example 1: American Gut and the Human Microbiome Variability Outcome: Learn about Learn about the American Gut project: a citizen science project dedicated to metagenomics sequencing of world citizens that are contributing their microbiome samples to the study of microbiome variability Associated online course/resource: Metagenomics 1 - L1: Metagenomics Study and Importance Metagenomics 1 - L2 : Introduction to Metagenomics Analysis Algorithms
	In-depth, Hands-on Project Example: Microbiome, Diet and Anxiety - the Gut-brain Axis Session Topics: In-depth, Hands-on Project Example 2: Microbiome, Diet and Anxiety - the Gut-brain Axis Outcome: Learn about Brain-Gut Axis: how is the gut microbiome affected by diet and does it have an effect on anxiety apart from the diet itself? How can donor microbiomes help tackle this psychological and physiological condition? Associated online course/resource: Comparing DNA sequences using Phylogenetic Analysis Metagenomics 2 - L3: Sample Species Abundance, Alpha and Beta Diversity
	Developing your own project from NCBI publicly available data Session Topics: Online resources, file upload, download & analysis, Discussions, Troubleshooting, and Expert Feedback. Outcome: Learn about Data-driven Bioinformatics Research, How to prepare a Research proposal, Components of Big data Bioinformatics projects Associated online course/resource: Designing a Bioinformatics Research Project Metagenomics 2 - L1: Metagenomics Sequencing
	Metagenomics Project feedback & Review Session Topics: Discussions, Troubleshooting, suggestions, and Expert Feedback. Outcome: Expert feedback on your project