Microbiota profiling of cows milk with and without traditional fermentation

Both read trim strategies and taxonomic DB used will be considered to try and improve species-level resolution compared to the data supplied by CPGR. CPGR used GreenGenes 13.5 and Illumina's commercial pipeline (for which the process is unknown).
Primary inspection of default parameters with our dada2 pipeline showed only 64/595 ASVs identified down to species level (The 595 is the filtered table after removing very low abundance ASVs from the original ~2900). See Wiki tab for more.