Three distinct pneumotypes characterize the microbiome of the lung in BALB/cJ mice

Abstract

Bacteria can rarely be isolated from normal healthy lungs using conventional culture techniques, supporting the traditional belief that the lungs are sterile. Yet recent studies using next generation sequencing report that bacterial DNA commonly found in the upper respiratory tract (URT) is present at lower levels in the lungs. Interpretation of that finding is complicated by the technical limitations and potential for contamination introduced when dealing with low biomass samples. The current work sought to overcome those limitations to clarify the number, type and source of bacteria present in the lungs of normal mice. Results showed that the oral microbiome is diverse and highly conserved whereas murine lung samples fall into three distinct patterns. 33% of the samples were sterile, as they lacked culturable bacteria and their bacterial DNA content did not differ from background. 9% of samples contained comparatively higher amounts of bacterial DNA whose composition mimicked that detected in the URT. A final group (58%) contained smaller amounts of microbial DNA whose composition was correlating to that of rodent chow and cage bedding, likely acquired by inspiration of food and bedding fragments. By analyzing each sample independently rather than working with group averages, this work eliminated the bias introduced by aspiration-contaminated samples to establish that three distinct microbiome pneumotypes are present in normal murine lungs.

The Influence of Lung Microbiota on Lung Carcinogenesis, Immunity, and Immunotherapy

“…Willis et al also found that up to 50% of the bacterial DNA from sinus tissue was derived from nonviable sources [20]. The traditional view that viable bacteria are rarely present in normal healthy lungs is consistent with the lungs being actively surveilled by immune cells and the observation that 30% of tissue samples were sterile in the Scheiermann and Klinman study [16]. In line with these findings, Segal et al reported that the bacterial DNA content in some human lung samples could not be distinguished from that of background/negative control samples [18].…”

“…Currently, it has been estimated that a ratio of bacteria to human cells in the body is close to 1:1 [75]. [13,[15][16][17][18]. It should be noted that different studies suggest that most bacterial DNA detected in the lungs might come from nonviable bacteria.…”

“…It should be noted that different studies suggest that most bacterial DNA detected in the lungs might come from nonviable bacteria. Indeed it has been found that more than 90% of microbial DNA was DNase I sensitive, indicating that this DNA originated from nonviable microorganisms [16,19]. Willis et al also found that up to 50% of the bacterial DNA from sinus tissue was derived from nonviable sources [20].…”

The Lung Microbiota of Healthy Mice Are Highly Variable, Cluster by Environment, and Reflect Variation in Baseline Lung Innate Immunity

“…Given the ubiquitous use of mice in the study of inflammatory lung disease, it is crucial to determine the immunologic and biologic significance of variation in murine lung bacteria. One research group reported their difficulty in detecting lung bacteria in one-third of the healthy adult mice studied (49). Despite technical limitations to their approach (e.g., omitting quantification of total bacterial DNA burden, studying a single shipment of mice, using small sections of excised lung tissue rather than whole lungs, not using the touchdown PCR protocol preferred for low-biomass amplification [50]), the authors interpreted this lack of signal as evidence of lung sterility.…”

The Complex Role of the Microbiome in Non-Small Cell Lung Cancer Development and Progression

“…Traditionally, healthy lungs were believed to be sterile-except for infections-since conventional culture techniques rarely isolated bacteria from them. However, with the advent of next-generation sequencing (NGS) technologies, a wide variety of bacterial DNA has been commonly detected in the lower respiratory tract of healthy individuals [8][9][10]. The lung microbiome is relatively low in biomass, with 10 3 to 10 5 bacteria per gram of tissue in healthy lungs [11].…”