A clinicians’ review of the respiratory microbiome

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FIGURE 1
The respiratory microbiome. CMV: cytomegalovirus; EBV: Epstein–Barr virus.

TABLE 1

Summary of definitions

Microbiome	The combined genomes of all the microorganisms inhabiting a particular environment
Microbiota	Community of microorganisms in an environment
Metagenomics	The study of the whole genome of a community of microorganisms, allowing assessment of the functional potential of the microorganisms
RNA metatranscriptomics	The measurement of the total mRNA in a community, to allow representation of active gene expression at that time
Resistome	Collection of antibiotic resistance genes in a community
Metabolomics	Assessment of the metabolites of a given sample, allowing identification of metabolically active organisms
Proteomics	Assessment of proteins produced by the host and microbiota
Alpha diversity	The diversity of a sample, including the richness (number of species) or evenness (distribution of species)
Beta diversity	The measure of the similarity or dissimilarity of two communities

TABLE 2

Summary of the respiratory microbiome in health and disease

Respiratory microbiome	Micobiome	Virome	Mycobiome
In health	Bacteroidetes Proteobacteria Firmicutes Genus: Streptococcus, Prevotella, Veillonella	Anelloviridae Human herpes viruses Human papillomavirus	Ceriporia lacerate Saccharomyces cerevisiae Penicillium brevicompactum
Asthma	Proteobacteria Streptococcus Reduction in Prevotella and Veillonella	Cytomegalovirus Epstein–Barr virus	Psathyrella candolleana Termitomyces clypeatus Grifola sordulenta Malassezia pachydermatis
COPD	Proteobacteria Haemophilus Streptococcus	Picornaviruses Influenza Parainfluenza Respiratory syncytial viruses Adenoviruses	Alternaria Aspergillus Cladosporium Cryptococcus Mycosphaerella Penicillium Trametes Wickerhamomyces
Bronchiectasis	Pseudomonas Haemophilus Veillonella Prevotella	Siphoviridae Caudovirales Myoviridae Phycodnaviridae	Aspergillus Cryptococcus Clavispora
CF	Pseudomonas Staphylococcus Stenotrophomonas Burkholderia	Influenza Respiratory syncytial virus	Aspergillus Candida
IPF	Haemophilus Neisseria Streptococcus	Influenza A Human herpesvirus	Not yet established
Lung cancer	Veillonella Streptococcus Prevotella	Not yet established	Not yet established

Vol 18 Issue 1 Table of Contents

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