Molecular Accounting and Profiling of Human Respiratory Microbial Communities: Toward Precision Medicine by Targeting the Respiratory Microbiome for Disease Diagnosis and Treatment

Abstract

The wide diversity of microbiota at the genera and species levels across sites and individuals is related to various causes and the observed differences between individuals. Efforts are underway to further understand and characterize the human-associated microbiota and its microbiome. Using 16S rDNA as a genetic marker for bacterial identification improved the detection and profiling of qualitative and quantitative changes within a bacterial population. In this light, this review provides a comprehensive overview of the basic concepts and clinical applications of the respiratory microbiome, alongside an in-depth explanation of the molecular targets and the potential relationship between the respiratory microbiome and respiratory disease pathogenesis. The paucity of robust evidence supporting the correlation between the respiratory microbiome and disease pathogenesis is currently the main challenge for not considering the microbiome as a novel druggable target for therapeutic intervention. Therefore, further studies are needed, especially prospective studies, to identify other drivers of microbiome diversity and to better understand the changes in the lung microbiome along with the potential association with disease and medications. Thus, finding a therapeutic target and unfolding its clinical significance would be crucial.

Alteration of the Respiratory Microbiome in Hospitalized Patients with Asthma–COPD Overlap during and after an Exacerbation

“…The salivary contents were separated from the sputum samples to minimize oral bacterial contamination. However, recent evidence indicated that salivary contamination of expectorated sputum had no effect on most sputum samples and that observations of high bacterial diversity likely properly reflect the taxa present in the lower airways [ 10 , 22 ]. The participants collected their sputum samples in sterile 30-mL conical tubes and were informed that the sputum is the viscous substance that comes from deep within lungs, not the watery fluid in the mouth.…”

“…It was suggested that healthy respiratory microbiota is distinct from that present in respiratory disorders [ 9 , 10 ]. Even when the patients are characterized by a clinically stable condition, they have lower airways displaying bacterial colonization [ 9 , 10 , 11 ].…”

“…It was suggested that healthy respiratory microbiota is distinct from that present in respiratory disorders [ 9 , 10 ]. Even when the patients are characterized by a clinically stable condition, they have lower airways displaying bacterial colonization [ 9 , 10 , 11 ]. Nevertheless, since the majority of research projects in this domain have been cross-sectional [ 10 ], it has not been possible to identify the nature of the relationship between the assessed outcomes and bacterial colonization.…”

“…Even when the patients are characterized by a clinically stable condition, they have lower airways displaying bacterial colonization [ 9 , 10 , 11 ]. Nevertheless, since the majority of research projects in this domain have been cross-sectional [ 10 ], it has not been possible to identify the nature of the relationship between the assessed outcomes and bacterial colonization. It is crucial to determine whether microorganisms are associated with exacerbations.…”

“…Some studies have looked into the changes in the microbiome of COPD and asthmatic patients. However, the microbiome among ACO patients is still unclear [ 10 , 15 , 16 ]. Profiling of bacterial populations in the airways of ACO patients will enhance the understanding of the relationship between the respiratory microbiome and the development and outcome of the illness.…”