Wiki¶

Sample processing details from Pieter de Waal¶

'The Illumina® 16S metagenomics workflow will be used to analyze the three differently sourced milk types. Each sample will be analyzed in duplicate, producing a total number of six extracted libraries. A positive control will also be included in the analyses. The hypervariable V3 and V4 regions of the 16S ribosomal RNA gene (16S rRNA) will be amplified, using an Illumina® pre-designed primer pair. Barcoding for multiplexing of the samples will entail the use of the Nextera XT®-Index Kit.'

Data expected¶

'Data collection will take place from 01/03/2019 to 03/03/2019. The samples will be transported to CPGR on Monday, 04/03/2019. Results of the data analysis will be available within two weeks from then.'

Bioinformatic analyses to be done¶

• Preprocessing of raw fastq files using the dada2 pipeline
• 'Alpha and beta diversity (Shannon diversity (H′) and Bray-Curtis dissimilarity index). Calculation of the relative abundance of each OTU per specimen. Fisher’s exact test for two-way tables. Construction of Log ratio biplots, dendograms and other illustrative (graphical) representation of data analysis.'

Raw data¶

Raw (.fastq) copied from CPGR flashdisk to ilifu 26/6/2019
/ceph/cbio/users/katie/Levin/raw/