However, not all colonising bacteria will cause disease Ð and so the ability to characterise the community of organisms in a patient, and to understand how this relates to the likelihood of disease offers many new opportunities for better patient/disease management.

Molecular approaches including Next generation sequencing (NGS) provide a potential method by which communities of organisms can be rapidly characterised without the need for bacterial culture. A number of studies have already demonstrated that by applying NGS-based approaches (such as 16S or deep sequencing metagenomics) it is possible to identify key organisms within a sample, however, while the potential of NGS-based approaches for characterising microbial populations has been demonstrated in the clinical setting, they are some way from being usable in a clinical setting.