microbiome 2



The human microbiome is the community of microorganisms living on and in the human body, the majority of which inhabit the intestines.  These microorganisms are important collaborators in human physiology, and are essential for the proper functioning of our immune and digestive systems.  Increasingly, evidence is emerging to suggest that the disruption of this community, particularly in early life, may underpin the development of non-communicable diseases (including asthma, allergies, obesity, and autoimmune diseases).  In early life we acquire our microbes largely from our mothers, through direct contact and breastfeeding.  Human milk is a major source of beneficial microbes and is the primary driver of the infant gut microbiome.  The group seeks to understand factors that affect the human milk microbiome, including maternal diet and health.  We also aim to optimise and standardise analysis of the human milk microbiome to better understand its composition.  We currently have two PhD students and a postdoc working in this field.  We have a number of student projects available for honours and masters students (see below).  Prospective PhD students are welcome to discuss potential projects with us.


Distribution of bacteria in different human milk fractions

Human milk contains a diverse range of bacteria which play an important role in seeding the infant microbiome and programming metabolic and immune function. Research interest in the human milk microbiome is growing; however, there are a number of methodological challenges in this field. For instance, the fat fraction of milk is routinely discarded in microbiome experiments. For this project we will fractionate milk and separately examine the bacteria in the fat and skim fractions. We will use qPCR, spike-in assays, and next generation sequencing to assess whether or not we are losing valuable information by discarding the fat in such studies. The results of this study are likely to be highly impactful in this field. This project is suitable for an honours or masters student.

Effects of cold storage on the breast milk microbiome

Many mothers express breast milk for their infants.  There are recommendations for the length of time at which breast milk should be stored in the fridge or freezer, largely based around the time at which milk goes “off”.  The effect of cold storage on the milk microbiome is unknown.  To date, studies have attempted to answer this question using culture-dependant techniques, and have arrived at conflicting results.  For this project we will use state of the art bacterial gene sequencing techniques to assess the stability of the breast milk microbiome during cold storage.  There is also the option to include an additional study to examine the “real world” practice of cold storage of breast milk, using surveys or home visits.  This will help us to understand the ways in which mothers store and thaw their milk, to better inform the test conditions that we use. This project is suitable for an honours or masters student.