Rochester, Minnesota




Joseph H. Skalski, M.D., studies how the microbiota (particularly fungal organisms) influence lung diseases such as asthma and chronic obstructive pulmonary disease (COPD). Imbalances of the microbiota are increasingly recognized to play a role in the development and progression of disease. Dr. Skalski uses nonculture-based DNA sequencing techniques to study the microbiota, which generates a more complete profile of microorganisms and their relative distribution compared with traditional culture techniques.

Focus areas

  • Lung mycobiota. Because the lung environment is not sterile, Dr. Skalski studies how the presence, abundance and diversity of fungal and bacterial microorganisms in the lung may alter the course of respiratory illness.
  • Gut-lung axis. The main reservoir of commensal microbes is in the gastrointestinal tract. Interactions between gut microbes, the immune system and metabolites produced by these organisms may have a distant effect on lung function. Dr. Skalski studies how imbalances of the microorganisms in the gastrointestinal tract may affect the onset and severity of lung disease.
  • Pulmonary fungal infections. Lung infections with fungal organisms such as aspergillus and pneumocystis are a common and life-threatening problem in patients with decreased immune function. Dr. Skalski studies how the immune system recognizes and responds to fungal pathogens.

Significance to patient care

Researchers are just beginning to understand how alterations of the microbiota can influence the onset and severity of respiratory diseases. Dr. Skalski hopes that the development of better tools to profile the microbiome, combined with an enhanced understanding of harmful and beneficial microbial patterns, will lead to more personalized and individualized therapies for patients with lung disease.


See my publications


Administrative Appointment

  1. Mayo Clinic Scholar, Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine

Academic Rank

  1. Assistant Professor of Medicine


  1. Chief Fellow Pulmonary and Critical Care Fellowship Program, Programs in Rochester, Mayo School of Graduate Medical Education, Mayo Clinic College of Medicine
  2. Chief Resident Internal Medicine Residency Program
  3. Resident Internal Medicine Residency Program
  4. MD University of Wisconsin School of Medicine
  5. BA - Integrated Science Program, Mathematics, European History Northwestern University

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