Microbiota profiling of cows milk with and without traditional fermentation

See attached publication

I met with Pieter and Mike they are happy with the results, just needed some guidance on interpretation. With regards to the the uniformity seen across urban samples they were apparently all collected from the same sight and the negative control run by CPGR was negative so shouldn't be a problem. I will write the methods section for bioinformatic work done for their manuscript.

There were several ~80 taxa (merged at lowest available taxonomic annotation) that were differentially abundant or differentially absent/present (|FC| >= 1.5 %; presence >= 60% in at least one group; FDR . <= 0.05) when comparing fermented (N=5) vs. unfermented (N=4) milk. Lactococcus and Leuconostoc species were present at higher levels in the the fermented products as expected. The majority of hits were however actually ones that were (strangely?) uniformly present in the unfermented milk (3 of urban and 1 of rural origin). It could be that the urban samples were all collected from the same site which may explain the otherwise odd level of similarity (the elution buffer negative control did not however have any detectable amplicons based on the CPGR's report). One urban sample was clearly infected with Salmonella enterica which was the dominant organism in this sample.

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.

Mainly they are looking for improved species-level resolution with a few specific species they are hoping to see. I will run the data through our dada2 pipeline and take it from there.
The data was copied to ilifu /ceph/cbio/users/katie/Levin/raw/