There has been long-standing interest in the role of bacterial communities in the complex and heterogeneous disease of asthma. With the advent of 16s rRNA sequencing replacing traditional culture methods, a strong association between the presence of bacterial communities with asthma has emerged. These microbiota can be modulated by various environmental factors, including diet, antibiotics, and early-life microbial exposures. Microbiota in the gut and lungs can influence both the inception and progress of asthma. In babies and infants the presence of pathogenic bacteria in the lungs and gut has been associated with subsequent development of allergic sensitization and asthma. Lung microbiota are present in the airways of healthy subjects but are dysregulated in adults with asthma, with a reduced diversity and community composition that has been linked to severity and inflammatory phenotypes. Causality between certain gut microbiota and the development of allergic asthma has been shown in experiments conducted in neonatal mice. Manipulation of the airway microbiome, particularly in early life, might be a strategy to prevent or treat asthma, although the results of studies of probiotics used together with prebiotics have been overall negative. A better understanding of the regulation of both the lung and gut microbiota to derive appropriate targets for prevention or treatment of asthma is needed.