Overview

This section examines the community structure - i.e. the proportion, variance and abundance of taxonomic groups found in each sample and treatment group.

Amplicon sequence variants

Taxonomic groups in this study are based on Amplicon sequence variants (ASV), inferred using the DADA2 software package by matching the sample sequences to the Silva ribosomal RNA sequence database.

DADA2 infers sample sequences exactly and resolves differences of as little as 1 nucleotide.

SILVA provides comprehensive, quality checked and regularly updated datasets of aligned small (16S/18S, SSU) and large subunit (23S/28S, LSU) ribosomal RNA (rRNA) sequences for all three domains of life (Bacteria, Archaea and Eukarya).

6a. Results summary

You can see a summary of

asv_table

Summary of sequence reads

Run the below code cell to output some basic read stats:

cat("Number of samples = ", nrow(samples_table), "\n")
cat("Total number of 16S reads = ", sum(apply(asvtable[2:ncol(asvtable)], 2, sum)), "\n")
cat("Minimum number of reads (per sample) = ", min(apply(asvtable[2:ncol(asvtable)], 2, sum)), "\n")
cat("Maximum number of reads (per sample) = ", max(apply(asvtable[2:ncol(asvtable)], 2, sum)), "\n")
cat("Mean number of reads (per sample) = ", round(mean((apply(asvtable[2:ncol(asvtable)], 2, sum)))), "\n")

Summary of ASVs assigned to taxa