Metagenomics

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

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:

Microbiome

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
Microbiome Variability and 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:

American gut and the human microbiome variability

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:

Microbiome diet and anxiety

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:

Project on NCBI data

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:

Metagenomics project

Metagenomics Project feedback & Review

Session Topics:

  • Discussions, Troubleshooting, suggestions, and Expert Feedback.

Outcome:

  • Expert feedback on your project

 

OMICSLOGIC METAGENOMICS LIVE SESSIONS

  • Overview of Methods and Applications for Metagenomics Sequencing and Analysis
  • Big Data Analysis Platform : Metagenomics  Analysis on the T-Bioinfo Server
  • Interpretation and Meaning: Statistical Analysis, Visualization & Interpretation using R 
  • Future Directions: Full metagenomic sequencing, metatranscriptomics and functional analysis

GUEST SPEAKERS 

image_2021_12_30T16_48_31_051Z Chris Taylor (1)

 

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