Microbiome and Bioinformatics

Explore the meaning of the microbiome and opportunities in microbiome research and bioinformatics using free, no-programming software.

Examine the central dogma from dna to rna to protein, genome differences between prokaryotes and eukaryotes, and how 16s rna and ITS regions identify microbes via conserved and variable regions.

Explore amplicon and shotgun sequencing, decide target organisms and genes (such as the 16 rrna gene), and understand barcoding enables multiplexing and de-multiplexing for sample-specific reads.

Compare reads to reference databases to assign taxonomic identifications, creating a tab delimited abundance table of samples by entities, then normalize to reveal differential abundance between groups.

Explore microbial diversity by comparing alpha metrics like richness and evenness with Shannon or Simpson indices, and assess beta diversity using Jaccard, Bray-Curtis, and UniFrac with ordination plots.

Conduct a hands-on sixteens ribosomal DNA analysis with the esmap browser, covering quality control, taxonomy, microbial composition, alpha and beta diversities, differential abundances, and functional prediction.

Run quality control and filtering for Illumina amplicon microbiome data. View results, explore the feature table, and understand sampling depth and rarefaction.

Perform taxonomic analysis and phylogenetic tree generation using the V4 classifier with green genes IDs, compare reference databases, and interpret interactive stacked bar plots and heat maps of microbial composition.

Explore alpha diversity analysis using rarefaction with the Chime tool, interpreting observed otus, phylogenetic diversity, and evenness across samples and group comparisons.

Use the LFC tool with LDA effect size to identify taxa discriminative between male and female groups, graphs and a cladogram, then predict microbial functions with Picrust and KEGG.