Microbiota profiling of cows milk with and without traditional fermentation

Project title
Microbiota profiling of cows milk with and without traditional fermentation

People involved
Principal investigator : Prof Mike Levin
Support request made by: Pieter de Waal
Bioinformatics support team: Katie Lennard

Short description of project
Identification and description of the microbiome found in traditionally fermented milk products versus fresh, unpasteurized cow’s milk from rural South Africa. Three (3) milk samples will be collected from farms in rural Eastern Cape: unpasteurized cow’s milk, traditionally homemade fermented milk and commercially bought fermented milk. The three sample types will be compared.

Do the three sample types differ from each other?
How can this knowledge be translated into the Clinical Allergology?

Objectives
Perform preprocessing of Illumina MiSeq 16S reads (supplied by CPGR) using CBIO's dada2 pipeline and downstream exploratory analysis in R