The human microbiota has become more diverse than what scientists believed when the Human Microbiome Project started over a year ago. Initially, the lung and stomach, two unique mucosal surfaces, were not even initially included in the sample collections. As culture-independent methods of studying the microbiome has expanded, it revealed that there are diverse and unique communities that exist within these organs, but there is little knowledge about what influences these communities. A new paper out of Gary Huffnagle’s group at the University of Michigan decided to look at just that.
In their analysis, Bassis et al. began to look at potential sources of microbes, including the mouth and nasal passages. The mouth is exposed to and produces more biomass daily, with saliva production and access to nutrients via food being chief among them. The nose is known to harbour important bacteria and potential pathogens. Based on the findings of their work, it appears that the mouth microbes have greater influence in what reaches the stomach and lungs, but that the lungs can control which bacteria take hold, as they looked at the elimination of Prevotella from the mouth microbial communities into the lung.
In our journal club at 3:30pm on Friday, March 27th at West End pub, I look forward to discussing:
(1) Their methodology for sample collection and sequencing
(2) Their microbial diversity analysis, especially their use of θyc distances
(3) Their model utilizing Prevotella for species elimination
Abstract: No studies have examined the relationships between bacterial communities along sites of the upper aerodigestive tract of an individual subject. Our objective was to perform an intrasubject and intersite analysis to determine the contributions of two upper mucosal sites (mouth and nose) as source communities for the bacterial microbiome of lower sites (lungs and stomach). Oral wash, bronchoalveolar lavage (BAL) fluid, nasal swab, and gastric aspirate samples were collected from 28 healthy subjects. Extensive analysis of controls and serial intrasubject BAL fluid samples demonstrated that sampling of the lungs by bronchoscopy was not confounded by oral microbiome contamination. By quantitative PCR, the oral cavity and stomach contained the highest bacterial signal levels and the nasal cavity and lungs contained much lower levels. Pyrosequencing of 16S rRNA gene amplicon libraries generated from these samples showed that the oral and gastric compartments had the greatest species richness, which was significantly greater in both than the richness measured in the lungs and nasal cavity. The bacterial communities of the lungs were significantly different from those of the mouth, nose, and stomach, while the greatest similarity was between the oral and gastric communities. However, the bacterial communities of healthy lungs shared significant membership with the mouth, but not the nose, and marked subject-subject variation was noted. In summary, microbial immigration from the oral cavity appears to be the significant source of the lung microbiome during health, but unlike the stomach, the lungs exhibit evidence of selective elimination ofPrevotella bacteria derived from the upper airways.