Metagenomics of microbial communities on human skin

The microbiota of the skin forms a vital component of the body's ecosystem, particularly in preventing colonisation by pathogenic bacteria (microflora protection). The microbial community has also been implicated in non infective skin conditions such as eczema and Acne (Cogen et al. Br J Dermatol.158:442-55; Segre J Clin Invest. 116:1150-8.). Cutaneous bacteria are responsible for individual body odour characteristics (Austin & Ellis J Steroid Biochem Mol Biol. 87:105-10.), which are largely defined by the metabolic end products they produce. The composition of the skin surface microbial community must be understood to enable the development of new generations of personal care products. Previous attempts to study the skin microbial communities have had limited success primarily due to technological hurdles -the sampling inadequacy of culture-based techniques and the limited penetration obtained by conventional analysis of clone libraries. Here, traditional community profiling techniques will be followed by deep 16S ribosomal RNA gene sequencing and metagenomic shotgun DNA sequencing. The student will carry out all steps from sampling through to molecular biology and bioinformatic analysis and they will receive training in this at the School of Biological Sciences while drawing on the expertise of the industrial partner, located nearby, in sampling the skin microflora and determining its biochemistry and general microbiology. The experimental programme has three components: 1. Profiling microbial communities using trRFLP; 2. In depth elucidation of the composition of selected microbial communities by pyrosequencing of16S ribosomal RNA 3. Metabolic reconstruction via metagenomic shotgun sequencing. The student will first establish a baseline by investigating the stability of skin microbial community structure from a number of individuals within a volunteer population. The CASE partner has experience of this type of study and will ensure ethical compliance. The student will use TRFLP (Liu et al. Appl. Environ. Microbiol. 63: 4516-4522) to profile samples at multiple time-points to examine how populations change over time and between individuals. This will comprise the first year of the project at which point we we will have a much improved understanding of the stability of skin microbial communities and the extent of variation between individuals. This information will be vital for designing the subsequent experiments in which large databases of sequence information will be assembled and analysed.. 16S sequences will be interrogated directly using 454 pyrosequencing and species identified using alignment with public databases. The student will identify and differentiate those taxa that are cosmopolitan, specific to groups or individuals and those likely to change in abundance over time. Hypotheses will be generated on the relationships/correlations between microbial species identity and abundance, the age and sex of individuals and disease status for example. Simple qPCR- experiments will be designed to test hypotheses. To understand the metabolic processes present in microbial communities, the student will prepare whole genomic DNA and total RNA, and perform metagenomic shotgun sequencing on these samples using 454 pyrosequencing. Assembly and annotation of these data will be performed in order to reconstruct the metabolic potential of the microbial communities (using data from the DNA sample) as well as information about which pathways are active (using data from the RNA sample). Phylogenetic analysis of the genic sequences will be used to identify which bacterial taxa appear to be responsible for certain processes. Intensive bioinformatics training will be provided to the student for this part of the project, and will have the support of several postdoctoral bioinformatics scientists.