Next week’s journal club papers on the lung microbiome

Does immunodeficiency associated with HIV infection associate with an altered microbiota in the lungs? In a recent issue of the American Journal of Respiratory and Critical Care Medicine Lozupone et, al. show that it does, by reporting that 13% of HIV-positive subjects have lung communities dominated by Tropheryma whipplei, which decreased in relative abundance after antiretroviral therapy. This bacterium is known as the cause of Whipple’s disease, a rare disease with widespread infection and symptoms that is eventually fatal if untreated. Further work will be needed to determine if T. whipplei colonization of the lungs leads to adverse clinical outcomes but colonization by this nasty opportunistic pathogen was unexpected and needs to be monitored.

Within the same issue, Morris et, al. propose a comprehensive evaluation of the normal human lung microbiome by not only designing a multicenter study with standardized collection and processing protocols but also by considering it in the context of the upper respiratory tract. They also evaluate the impact of smoking on the microbiota of both the mouth and the lungs. What they found is that not all organisms in the lungs originate from the mouth suggesting that there is selection for a lung-specific microbial community and that smoking alters communities in the mouth but not in the lungs. 

Join us next Friday (June 28th) at 2 p.m. at the Phoenix for a lively discussion of our favourite human-associated microbial community – the lung microbiome!

General talking points we could cover:

  • What is the impact of T. whipplei in the airways?
  • Why doesn’t smoking alter the lung microbiome?
  • What are the challenges of sampling the lower airways?
  • Are the lower airways effectively sterile or is there a viable lung microbiome in healthy individuals?
  • DNA signatures vs viable organisms – where do we draw the line and how can we better address this?

Again free beer may be in attendance.

Lozupone, C., Cota-Gomez, A., Palmer, B. E., Linderman, D. J., Charlson, E. S., Sodergren, E., Mitreva, M., et al. (2013). Widespread Colonization of the Lung by Tropheryma whipplei in HIV Infection. American journal of respiratory and critical care medicine187(10), 1110-7. Retrieved from

Morris, A., Beck, J. M., Schloss, P. D., Campbell, T. B., Crothers, K., Curtis, J. L., Flores, S. C., et al. (2013). Comparison of the respiratory microbiome in healthy nonsmokers and smokers. American journal of respiratory and critical care medicine187(10), 1067-75. Retrieved from


About Jennifer Stearns

Farncombe Family Chair in Microbial Ecology and Bioinformatics and Assistant Professor at McMaster University
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