The human microbiota comprises of the ecological community of commensal and pathogenic microorganisms that colonise the human body along with the complex interactions of these microbes with the host. The advent of culture-independent methodologies has revealed the complex and dynamic community of microbes harboured by the human body. Whilst numerous studies conducted on the gut have shown the link between microbiota and a number of human diseases and conditions, very little is documented about the respiratory tract due to the difficulty in collecting GM samples. In addition, not much is known about the effect of chemical exposure on lung microbiota dysbiosis and subsequent linkage to respiratory tract infections. This study critically analyses the known and unknown facts about chemically induced lung microbiota (LM) dysbiosis and disease. The lungs are a non-sterile environment harbouring a microbiota configuration that is distinct from that which inhabits the gastrointestinal tract and other parts of the human body. It is now being recognized that LM can directly impact immunity in manner that can result in disease. Significant differences in community composition have been shown between the LM of diseased lungs with those of healthy subjects. Studies have linked LM dysbiosis with human diseases such Idiopathic Pulmonary Fibrosis, lung inflammation, chronic obstructive pulmonary disease (COPD), asthma, and lung cancer. However, it is not known whether LM dysbiosis initiates/promotes disease pathogenesis or is merely a biomarker of disease. Furthermore, what metabolites can be linked to individual disease conditions? Do metabolites play significant roles in LM dysbiosis and disease as they do in GM dysbiosis? Most importantly, is LM amenable to therapeutic manipulation in a manner that can change disease progression? Finally, in order to fully understand the role of LM on human diseases, there is need to investigate other lung microorganisms other than bacteria and viruses.