Glossary¶
| Term | Definition |
|---|---|
| ADD Accumulated Degree Days | A cumulative measure of temperature exposure over time. Used in this workshop as a continuous proxy for time since sample collection. |
| Alpha Diversity | Diversity within a single sample. Common metrics include observed features (richness), Shannon entropy (richness + evenness), Pielou's evenness, and Faith's phylogenetic diversity. |
| ANCOM-BC Analysis of Compositions of Microbiomes with Bias Correction | A statistical method for identifying differentially abundant taxa between groups that accounts for the compositional nature of microbiome data. |
| ASV Amplicon Sequence Variant | An exact biological sequence inferred from amplicon sequencing after error correction. ASVs offer single-nucleotide resolution, unlike OTUs which cluster sequences at a similarity threshold. |
| Beta Diversity | Diversity between samples, how different two communities are from each other. Common metrics include Bray-Curtis dissimilarity, Jaccard distance, and UniFrac distance. |
| DADA2 Divisive Amplicon Denoising Algorithm 2 | A bioinformatics method that models sequencing errors to infer true biological sequences (ASVs) from amplicon data. |
| Faith's PD Faith's Phylogenetic Diversity | The total branch length of a phylogenetic tree spanned by the taxa in a sample. A phylogenetically informed alpha diversity metric. |
| Feature Table | A matrix where rows are samples, columns are features (ASVs or taxa), and values are counts (or frequencies). The central data structure in QIIME2. |
| GreenGenes2 GG2 | A comprehensive 16S rRNA reference database and taxonomy maintained by the Knight Lab. Used for taxonomic classification and phylogenetic placement in this workshop. |
| LME Linear Mixed Effects Model | A statistical model that accounts for both fixed effects (e.g., time, treatment) and random effects (e.g., individual subject). Used here to model longitudinal microbiome change while controlling for repeated measures within subjects. |
| Manifest File | A tab-separated file that maps sample IDs to the absolute paths of their FASTQ files, used by QIIME2 to import demultiplexed sequences. |
| OTU Operational Taxonomic Unit | A cluster of sequences grouped by similarity (typically 97% identity). Largely superseded by ASVs in modern microbiome analysis. |
| PCoA Principal Coordinates Analysis | An ordination technique that reduces a distance matrix to a set of axes that capture the largest sources of variation in community composition. Visualized as scatter plots in QIIME2. |
| PERMANOVA Permutational Multivariate Analysis of Variance | A non-parametric test for differences in community composition between groups, based on a distance matrix. |
| Pielou's Evenness | A measure of how evenly reads are distributed across ASVs in a sample, ranging from 0 (one taxon dominates) to 1 (all taxa equally abundant). |
| QZA / QZV | QIIME2 artifact (.qza) and visualization (.qzv) file formats. Both are ZIP archives containing data and provenance metadata. .qzv files can be viewed at view.qiime2.org. |
| Rarefaction | Randomly subsampling each sample to a fixed number of reads to normalize for unequal sequencing depth before diversity analysis. |
| SEPP SATe-enabled Phylogenetic Placement | A method for inserting query sequences (ASVs) into a reference phylogenetic tree rather than building a tree from scratch. |
| Shannon Entropy | An information-theoretic diversity metric that accounts for both richness (number of taxa) and evenness (their relative abundances). |
| UniFrac | A phylogenetically informed beta diversity metric that measures the fraction of branch length in a phylogenetic tree unique to one sample vs. another. Unweighted UniFrac uses presence/absence; weighted UniFrac incorporates relative abundances. |