The lung microbiome in health and disease

Abstract

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.

Microbiota Core in Central Lung Cancer with Streptococcal Enrichment as a Possible Diagnostic Marker

“…Our results reinforce the previously known particularities of the lung microbiota, which considerably differ from oral and stool microbial communities [29]. One important concern is the theoretical risk of contamination with the upper microbiota during the bronchoscopy, but our results allowed us to rule out significant contamination, as other authors had previously suggested [30][31][32]. Data analysis by various methodologies highlighted the particularities of the microbiota associated with cancer, but also defined the respiratory microbiota core in healthy conditions.…”

A Staphylococcus pro-apoptotic peptide induces acute exacerbation of pulmonary fibrosis

“…We found that, in addition to Staphylococcus nepalensis strain CNDG, sequences similar to corisin are highly conserved in several transglycosylases from other Staphylococcus species and some members of the microbial community that inhabit the normal or fibrotic lungs, including strains of Streptococcus pneumoniae and Mycobacterium abscessus 51,[58][59][60] . This observation suggests that a broad range of bacteria may be the source of corisin in pulmonary fibrosis.…”

Pulmonary Metagenomic Sequencing Suggests Missed Infections in Immunocompromised Children

“…To date, the majority of metagenomic sequencing assays have targeted amplicons within the 16S or 28S rRNA subunits, allowing detection of pulmonary bacteria or fungi, but not both, and not viruses [31]. Recently, unbiased mNGS assays have allowed detection of both bacterial and viral nucleic acid but have lacked ideal sensitivity for detecting filamentous mold [11,12].…”