Faculty Bibliography

Oral flora are frequently found in normal individuals' lungs without known harm. We hypothesize that a lung microbiome enriched by oral taxa would be associated with a higher degree of inflammation. We studied 29 asymptomatic subjects (9 nonsmokers and 20 smokers) with preserved lung function. Nasal bronchoscopy was performed with two separate bronchoscopes to retrieve supraglotic and lower airway samples. Bronchoalveolar lavage (BAL) cell count, BAL cytokines (Luminex), and exhaled nitric oxide defined pulmonary inflammation. Quantitative PCR measured 16S rRNA gene concentration and 454 sequences defined the microbiome. Supraglotic samples had the highest 16S rRNA concentration, BAL was intermediate, and saline used for the BAL had the lowest concentration. Nonsmokers and smokers were similar in BAL cell differential and lung microbiome. BAL samples segregated into two distinct groups that we called pneumotypes. Pneumotype background predominant taxa (pneumotypeBPT) was similar to the saline background in rDNA concentration or microbial community. Pneumotype supraglotic-characteristic taxa (pneumotypeSCT) has higher rDNA concentration and high relative abundance of SCT, such as Prevotella and Veillonella. PneumotypeSCT was associated with multiple measures of lung inflammation, including higher BAL neutrophils, IL-8, and levels of exhaled nitric oxide. PneumotypeSCT also had higher BAL lymphocytes and fractalkine, a chemokine that correlates with T helper type 17:T regulatory cell ratio in the BAL. These data suggest that a pneumotype with high relative abundance of supraglotic bacteria, such as Prevotella and Veillonella, is associated with increased innate and cellular inflammation.

The development of culture-independent techniques has revolutionized our understanding of how our human cells interact with the even greater number of microbial inhabitants of our bodies. As part of this revolution, data are increasingly challenging the old dogma that in health, the lung mucosa is sterile. To understand how the lung microbiome may play a role in human health, we identified five major questions for lung microbiome research: (1) Is the lung sterile? (2) Is there a unique core microbiome in the lung? (3) How dynamic are the microbial populations? (4) How do pulmonary immune responses affect microbiome composition? and (5) Are the lungs influenced by the intestinal immune responses to the gut microbiome? From birth, we are exposed to continuous microbial challenges that shape our microbiome. In our changing environment, perturbation of the gut microbiome affects both human health and disease. With widespread antibiotic use, the ancient microbes that formerly resided within us are being lost, for example, Helicobacter pylori in the stomach. Animal models show that antibiotic exposure in early life has developmental consequences. Considering the potential effects of this altered microbiome on pulmonary responses will be critical for future investigations.

Microbes are readily cultured from epithelial surfaces of the skin, mouth, and colon. In the last 10 years, culture-independent DNA-based techniques demonstrated that much more complex microbial communities reside on most epithelial surfaces; this includes the lower airways, where bacterial culture had failed to reliably demonstrate resident bacteria. Exposure to a diverse bacterial environment is important for adequate immunological development. The most common microbes found in the lower airways are also found in the upper airways. Increasing abundance of oral characteristic taxa is associated with increased inflammatory cells and exhaled nitric oxide, suggesting that the airway microbiome induces an immunological response in the lung. Furthermore, rhinovirus infection leads to outgrowth of Haemophilus in patients with chronic obstructive pulmonary disease, and human immunodeficiency virus-infected subjects have more Tropheryma whipplei in the lower airway, suggesting a bidirectional interaction in which the host immune defenses also influence the microbial niche. Quantitative and/or qualitative changes in the lung microbiome may be relevant for disease progression and exacerbations in a number of pulmonary diseases. Future investigations with longitudinal follow-up to understand the dynamics of the lung microbiome may lead to the development of new therapeutic targets.

INTRODUCTION: Abnormality in distal lung function may occur in obesity due to reduction in resting lung volume; however, airway inflammation, vascular congestion and/or concomitant intrinsic airway disease may also be present. The goal of this study is to 1) describe the phenotype of lung function in obese subjects utilizing spirometry, plethysmography and oscillometry; and 2) evaluate residual abnormality when the effect of mass loading is removed by voluntary elevation of end expiratory lung volume (EELV) to predicted FRC. METHODS: 100 non-smoking obese subjects without cardio-pulmonary disease and with normal airflow on spirometry underwent impulse oscillometry (IOS) at baseline and at the elevated EELV. RESULTS: FRC and ERV were reduced (44+/-22, 62+/-14% predicted) with normal RV/TLC (29+/-9%). IOS demonstrated elevated resistance at 20 Hz (R20, 4.65+/-1.07 cmH2O/L/s); however, specific conductance was normal (0.14+/-0.04). Resistance at 5-20 Hz (R5-20, 1.86+/-1.11 cmH2O/L/s) and reactance at 5 Hz (X5, -2.70+/-1.44 cmH2O/L/s) were abnormal. During elevation of EELV, IOS abnormalities reversed to or towards normal. Residual abnormality in R5-20 was observed in some subjects despite elevation of EELV (1.16+/-0.8 cmH2O/L/s). R5-20 responded to bronchodilator at baseline but not during elevation of EELV. CONCLUSIONS: This study describes the phenotype of lung dysfunction in obesity as reduction in FRC with airway narrowing, distal respiratory dysfunction and bronchodilator responsiveness. When R5-20 normalized during voluntary inflation, mass loading was considered the predominant mechanism. In contrast, when residual abnormality in R5-20 was demonstrable despite return of EELV to predicted FRC, mechanisms for airway dysfunction in addition to mass loading could be invoked.

Rationale: Early COPD is characterized by inflammation leading to lung destruction. Recent data supports that enrichment of the lung microbiome with supraglottic characteristic taxa (SCT) is associated with inflammation. We hypothesize that in subjects with early COPD, areas at higher risk for microaspiration (right) or with greater degree of parenchymal abnormalities will be enriched with SCT or potential pathogenic taxa (PPT) compared to their contralateral lung segment. Methods: Subjects with early emphysema were enrolled for research bronchoscopy from the NYU/EDRN cohort. An independent radiologist semiquantitatively assessed all Chest CT scans: six-point score based on the presence of parenchymal damage in three zones (upper, middle, and lower). Broncho-alveolar lavages (BAL) were obtained from the right middle lobe and lingula segments. Sequencing 16S rDNA performed with 454 pyrosequence. Results: A total of 15 subjects with early COPD were studied. CT scans demonstrated n=7 with normal lower zones and n=8 with symmetrical or asymmetrical emphysema in the lower zones (p=ns). We used Wilcoxon paired comparisons to analyze the microbiome in areas of greater degree of parenchymal abnormalities (if asymmetric) or right compared to the contralateral lung segment. Data showed that the areas of greater abnormalities or right were associated with increased relative abundance (RA) of Haemophilus (RA 0.00170+/-0.002 vs. 0.00084+/-0.001, p=0.04), Neisseria (RA 0.0048+/-0.005 vs. 0.0023+/-0.003, p=0.028), Parvimonas (RA 0.017+/-0.003 vs. 0.0002+/-0.0008, p=0.05), and Serratia (RA 0.0122+/-0.02 vs. 0.0033+/-0.003, p=0.03) compared with the contralateral segment. Streptococcus appeared not to have a predilection for at-risk segments at the genus level. However, at the OTU level, Streptococcus mitis and Streptococcus pneumoniae species were higher in lung segments with more emphysema or right lung segments. Conclusions: Our data shows that areas of greater parenchymal damage or at higher risk for microaspiration (right) are enriched with potentially pathogenic taxa, such as Parvimonas, Neisseria, Haemophilus, Serratia, and Streptococcus. These taxa are known to be in high relative abundance in the oral and supraglottic region. Some of these taxa have been found to be at higher RA after viral infections, suggesting that enrichment of these low relative abundance taxa may play a critical role in disease. However, other supraglottic characteristic taxa such as Prevotella and Veillonella were not increased in these regions. These observations suggest a distinct selection pressure between the upper and lower airway microbiome