Abstract
The examination of the pulmonary microbiome in patients with non-chronic disease states has not been extensively examined. Traditional culture based screening methods are often unable to identify bacteria from bronchoalveolar lavage samples. The advancement of next-generation sequencing technologies allows for a culture-independent molecular based analysis to determine the microbial composition in the lung of this patient population. For this study, the Ion Torrent PGM system was used to assess the microbial complexity of culture negative bronchoalveolar lavage samples. A group of samples were identified that all displayed high diversity and similar relative abundance of bacteria. This group consisted of Hydrogenophaga, unclassified Bacteroidetes, Pedobacter, Thauera, and Acinetobacter. These bacteria may be representative of a common non-pathogenic pulmonary microbiome associated within this population of patients.
Highlights
While numerous studies have examined the gut microbiome in relation to disease, the lung microbiome by comparison has not been extensively examined
Fourteen did not grow bacteria by standard plating techniques at Parkland Hospital and results of the other sample was reported as normal “respiratory tract flora” (BAL133) (Table 1)
Culture negative bronchoalveolar lavage (BAL) samples were dominated by three phyla: Proteobacteria (46.98%), Firmicutes (19.14%), and Bacteroidetes (18.51%), In addition, Actinobacteria comprised a majority of BAL133 and smaller proportions of BALs 189, and 201(Fig 1A)
Summary
While numerous studies have examined the gut microbiome in relation to disease, the lung microbiome by comparison has not been extensively examined. Culture-independent molecular methods enabled by so-called next-generation or massively parallel sequencing (MPS) technologies have allowed for the advancement of studies of the lung and its resident microbial populations. Bacteria found in the lungs can be classified into two categories: potentially pathogenic microorganisms (PMMs) and non-potentially pathogenic microorganisms (nonPMMs) which are sometimes referred to as “normal respiratory tract flora” and are not typically associated with infections in non-immunocompromised individuals. Well-known pulmonary PMMs include Pseudomonas aeruginosa, Haemophilus spp., Staphylococcus aureus, Streptococcus pneumonia, Moraxella catarrhalis, and members of the Enterobacteriaceae. A few examples of non-PMMs include: Streptococcus viridans group, Candida spp., Corynebacterium spp., and Neisseria spp. Previous pulmonary microbiome research centered largely on chronic disease states such as cystic fibrosis, chronic obstructive pulmonary disorder (COPD), asthma, and smoking
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