The Human Microbiome Project began 10 years ago, leading
to a signifi cant growth in understanding of the role the human
microbiome plays in health and disease. In this article, we
explain with an emphasis on the lung, the origins of microbiome
research. We discuss how 16S rRNA gene sequencing
became the fi rst major molecular tool to examine the bacterial
communities present within the human body. We highlight
the pitfalls of molecular-based studies, such as false fi ndings
resulting from contamination, and the limitations of 16S rRNA
gene sequencing. Knowledge about the lung microbiome has
evolved from initial scepticism to the realisation that it might
have a signifi cant infl uence on many illnesses. We also discuss
the lung microbiome in the context of disease by giving
examples of important respiratory conditions. In addition, we
draw attention to the challenges for metagenomic studies of
respiratory samples and the importance of systematic bacterial
isolation to enable host–microbiome interactions to be
understood. We conclude by discussing how knowledge of the
lung microbiome impacts current clinical diagnostics.