This lecture series will provide an introduction to the sequencing and analysis of microbial communities. We will introduce various sequencing approaches to studying the microbiota in humans, model organisms, and environmental samples with an emphasis on 16S rDNA sequencing. We will cover common sequencing file formats and approaches to performing primary and secondary analysis on them with a focus on the Illumina MiSeq platform. A research data set will be used to provide hands on exercises applying the techniques covered in lectures. We will also discuss approaches to broader assessments of the metagenomics of microbial communities.
This first lecture will provide an introduction to the goals of this lecture series, what to expect, and the logistics of participating in the lectures. We will then review a brief history of sequencing technologies and applications in preparation for launching into the topic of microbial community sequencing and analysis.
The second lecture will cover common sequencing file formats and interpretation. We will then introduce the microbiome in general and discuss some potential targets of sequencing microbiota.
The third lecture will cover the human vaginal microbiome and the disease bacterial vaginosis. We will discuss and review a paired sexual partner study that was conducted in New Orleans and show results of a method for further assessing nucleotide variation in the 16S rRNA gene.
This lecture has been cancelled due to severe weather in Southeast Louisiana that has caused several tornado warnings and severe thunderstorms. Lectures will resume next week.
The fourth lecture will cover the mouse gut microbiome and the concept of the gut-brain axis. We will discuss and review a study involving fecal microbiota transplant in mice investigating behavioral changes induced by gut microbiota that were shaped by a high fat diet.
The fifth lecture will introduce the concepts of primary and secondary data analysis for microbial community sequencing. We will cover the UPARSE method of primary data analysis and formation of Operational Taxonomic Units (OTUs).
Mardi Gras Day: No Lecture this week!
The sixth lecture will introduce the approach for primary data analysis used by DADA2. This is a new approach to primary analysis that replaces the concept of Operational Taxonomic Units (OTUs) with more sensitive analysis methods. We will walk through the steps of the analysis in detail over the course of several lectures.
The seventh lecture will continue covering the DADA2 approach to primary data analysis. We will finish walking through the steps of the analysis in detail ending with the production of an intermediate data structure to facilitate secondary data analysis.
The eighth lecture will introduce the concept of secondary data analysis using QIIME (Quantitative Insights Into Microbial Ecology). This is a widely used microbiome data analysis software system. We will walk through the steps of secondary data analysis in detail over the course of several lectures.
Spring Break: No Lecture this week!
The ninth lecture will continue covering the QIIME system for secondary data analysis. We will cover analysis and visualization of taxonomic summaries in detail.
The tenth lecture will finish covering the QIIME system for secondary data analysis. We will cover analysis and visualization of the diversity within and between samples.
The eleventh lecture will introduce an alternative approach for secondary data analysis using Phyloseq. This is a more recently developed microbiome data analysis package. We will walk through the steps of secondary data analysis in detail.
The last lecture will finish the discussion of secondary data analysis using Phyloseq. We will wrap up the lecture with a brief overview of other metagenomic approaches that are available.
You can join the Google Groups Forum to post any questions or comments you may have about the lecture series.