Dr. Lemon and her laboratory use a multi-disciplinary approach that includes bacterial genetics, molecular biology, small molecule discovery, microbial ecology and the newer -omics to gain an in-depth understanding of the role and dynamics of the human microbiome in health and disease, with a focus on the nose and throat.

Bacteria live on us, “in” us, and on surfaces all around us. Among the common constituents of healthy upper respiratory tract microbiota are some of the most significant bacterial pathogens, e.g., Staphylococcus aureus and Streptococcus pneumoniae. The carriage rate and disease burden of these pathogens is particularly high in children. The emergence and spread of antibiotic resistant clones, such as community acquired-methicillin resistant S. aureus (CA-MRSA), accentuates the urgent need for new therapies to both treat and prevent these infections. Interestingly, some people do not carry either S. aureus or S. pneumoniae and are, therefore, at low risk for infection. This leads to the hypothesis that, among the constituents of nostril and throat microbiota, there are beneficial microbes that interfere with pathogen carriage. Such beneficial bacteria could be the basis for novel prophylactics/therapeutics. The long-term research goal of the Lemon Lab is to develop new, and sustainable, approaches to manage the composition of upper respiratory tract microbiota in order to prevent infections.

Lemon Lab Forsyth Page


Dr. Lemon is an Assistant Professor of Pediatrics in the Division of Infectious Diseases, Boston Children’s Hospital and Harvard Medical School. She is also an Associateistant Member of Staff at the Forsyth Institute, which is affiliated with the Harvard School of Dental Medicine, where her laboratory is located. Dr. Lemon received her Ph.D. in biology from the Massachusetts Institute of Technology and her M.D. from Harvard Medical School. She completed her pediatric residency and a fellowship in Pediatric Infectious Diseases at Boston Children's Hospital. She completed mentored research with Dr. Roberto Kolter at Harvard Medical School prior to starting her own laboratory at the Forsyth.

Selected Publications

  1. Wollenberg MS, Claesen J, Escapa IF, Aldridge KL, Fischbach MA, Lemon KP Propionibacterium-Produced Coproporphyrin III Induces Staphylococcus aureus Aggregation and Biofilm Formation. mBio. 2014;5(4):e01286-14.
  2. Lemon KP, Armitage GC, Relman DA, Fischbach MA. Microbiota-Targeted Therapies: An Ecological Perspective. Review. Science Translational Medicine. 2012; 4(137):137rv5.
  3. The Human Microbiome Project Consortium. Structure, Function and Diversity of the Healthy Human Microbiome. Nature. 2012; 486 (7402):215-21.
  4. Segata N, Kinder Haake S§, Mannon P§, Lemon KP§, Waldron L, Gevers D, Huttenhower C, Izard J. Composition of the Adult Digestive Tract Bacterial Microbiome Based on Seven Mouth Surfaces, Tonsils, Throat and Stool Samples. Genome Biology. 2012; 13(6):R42. (§contributed equally)
  5. Lemon KP, Klepac-Ceraj V, Schiffer HK, Brodie EL, Lynch SV, and Kolter R. Comparative analyses of the bacterial microbiota of the human nostril and oropharynx. mBio. 2010; 1(3): pii: e00129-10.
  6. Klepac-Ceraj V, Lemon KP, Martin TR, Allgaier M, Kembel SW, Knapp AA, Lory S, Brodie EL, Lynch SV, Bohannan BJM, Green JL, Maurer BA and Kolter R. Relationship Between Cystic Fibrosis Respiratory Tract Bacterial Communities and Age, Genotype, Antibiotics and Pseudomonas aeruginosa. Environmental Microbiology. 2010; 12(5):1293-1303.

Researcher Services

Researcher Areas

  • Human Upper Respiratory Tract Microbiome
  • Bacterial interspecies interactions

Research Departments

Research Divisions


Publications powered by Harvard Catalyst Profiles

  1. Johnston CD, Cotton SL, Rittling SR, Starr JR, Borisy GG, Dewhirst FE, Lemon KP. Systematic evasion of the restriction-modification barrier in bacteria. Proc Natl Acad Sci U S A. 2019 Jun 04; 116(23):11454-11459. View abstract
  2. Escapa IF, Chen T, Huang Y, Gajare P, Dewhirst FE, Lemon KP. New Insights into Human Nostril Microbiome from the Expanded Human Oral Microbiome Database (eHOMD): a Resource for the Microbiome of the Human Aerodigestive Tract. mSystems. 2018 Nov-Dec; 3(6). View abstract
  3. Markey L, Shaban L, Green ER, Lemon KP, Mecsas J, Kumamoto CA. Pre-colonization with the commensal fungus Candida albicans reduces murine susceptibility to Clostridium difficile infection. Gut Microbes. 2018 11 02; 9(6):497-509. View abstract
  4. Bomar L, Brugger SD, Lemon KP. Bacterial microbiota of the nasal passages across the span of human life. Curr Opin Microbiol. 2018 02; 41:8-14. View abstract
  5. Klein BA, Lemon KP, Gajare P, Jospin G, Eisen JA, Coil DA. Draft Genome Sequences of Dermacoccus nishinomiyaensis Strains UCD-KPL2534 and UCD-KPL2528 Isolated from an Indoor Track Facility. Genome Announc. 2017 Feb 23; 5(8). View abstract
  6. Klein BA, Lemon KP, Faller LL, Jospin G, Eisen JA, Coil DA. Draft Genome Sequence of Curtobacterium sp. Strain UCD-KPL2560 (Phylum Actinobacteria). Genome Announc. 2016 Oct 06; 4(5). View abstract
  7. Ramsey MM, Freire MO, Gabrilska RA, Rumbaugh KP, Lemon KP. Staphylococcus aureus Shifts toward Commensalism in Response to Corynebacterium Species. Front Microbiol. 2016; 7:1230. View abstract
  8. Brugger SD, Bomar L, Lemon KP. Commensal-Pathogen Interactions along the Human Nasal Passages. PLoS Pathog. 2016 07; 12(7):e1005633. View abstract
  9. Bomar L, Brugger SD, Yost BH, Davies SS, Lemon KP. Corynebacterium accolens Releases Antipneumococcal Free Fatty Acids from Human Nostril and Skin Surface Triacylglycerols. MBio. 2016 Jan 05; 7(1):e01725-15. View abstract
  10. Franzosa EA, Huang K, Meadow JF, Gevers D, Lemon KP, Bohannan BJ, Huttenhower C. Identifying personal microbiomes using metagenomic codes. Proc Natl Acad Sci U S A. 2015 Jun 02; 112(22):E2930-8. View abstract
  11. Wollenberg MS, Claesen J, Escapa IF, Aldridge KL, Fischbach MA, Lemon KP. Propionibacterium-produced coproporphyrin III induces Staphylococcus aureus aggregation and biofilm formation. MBio. 2014 Jul 22; 5(4):e01286-14. View abstract
  12. Segata N, Haake SK, Mannon P, Lemon KP, Waldron L, Gevers D, Huttenhower C, Izard J. Composition of the adult digestive tract bacterial microbiome based on seven mouth surfaces, tonsils, throat and stool samples. Genome Biol. 2012 Jun 14; 13(6):R42. View abstract
  13. Lemon KP, Armitage GC, Relman DA, Fischbach MA. Microbiota-targeted therapies: an ecological perspective. Sci Transl Med. 2012 Jun 06; 4(137):137rv5. View abstract
  14. Nyame TT, Lemon KP, Kolter R, Liao EC. High-throughput assay for bacterial adhesion on acellular dermal matrices and synthetic surgical materials. Plast Reconstr Surg. 2011 Nov; 128(5):1061-8. View abstract
  15. Lemon KP, Klepac-Ceraj V, Schiffer HK, Brodie EL, Lynch SV, Kolter R. Comparative analyses of the bacterial microbiota of the human nostril and oropharynx. MBio. 2010 Jun 22; 1(3). View abstract
  16. Lemon KP, Freitag NE, Kolter R. The virulence regulator PrfA promotes biofilm formation by Listeria monocytogenes. J Bacteriol. 2010 Aug; 192(15):3969-76. View abstract
  17. Klepac-Ceraj V, Lemon KP, Martin TR, Allgaier M, Kembel SW, Knapp AA, Lory S, Brodie EL, Lynch SV, Bohannan BJ, Green JL, Maurer BA, Kolter R. Relationship between cystic fibrosis respiratory tract bacterial communities and age, genotype, antibiotics and Pseudomonas aeruginosa. Environ Microbiol. 2010 May; 12(5):1293-303. View abstract
  18. Lemon KP, Earl AM, Vlamakis HC, Aguilar C, Kolter R. Biofilm development with an emphasis on Bacillus subtilis. Curr Top Microbiol Immunol. 2008; 322:1-16. View abstract
  19. Lemon KP, Higgins DE, Kolter R. Flagellar motility is critical for Listeria monocytogenes biofilm formation. J Bacteriol. 2007 Jun; 189(12):4418-24. View abstract
  20. Lemon KP, Moriya S, Ogasawara N, Grossman AD. Chromosome replication and segregation. Bacillus subtilis and its closest relatives: From genes to cells. Sonenshein AL, Hoch JA, Losick R, editors. 2002; 73-86. View abstract
  21. Lemon KP, Grossman AD. The extrusion-capture model for chromosome partitioning in bacteria. Genes Dev. 2001 Aug 15; 15(16):2031-41. View abstract
  22. Lemon KP, Kurtser I, Grossman AD. Effects of replication termination mutants on chromosome partitioning in Bacillus subtilis. Proc Natl Acad Sci U S A. 2001 Jan 02; 98(1):212-7. View abstract
  23. Lemon KP, Grossman AD. Movement of replicating DNA through a stationary replisome. Mol Cell. 2000 Dec; 6(6):1321-30. View abstract
  24. Katherine Paige Lemon. DNA replication and chromosome partitioning in Bacillus subtilis. 2000. View abstract
  25. Lemon KP, Kurtser I, Wu J, Grossman AD. Control of initiation of sporulation by replication initiation genes in Bacillus subtilis. J Bacteriol. 2000 May; 182(10):2989-91. View abstract
  26. Lemon KP, Grossman AD. Localization of bacterial DNA polymerase: evidence for a factory model of replication. Science. 1998 Nov 20; 282(5393):1516-9. View abstract
  27. Monfar M, Lemon KP, Grammer TC, Cheatham L, Chung J, Vlahos CJ, Blenis J. Activation of pp70/85 S6 kinases in interleukin-2-responsive lymphoid cells is mediated by phosphatidylinositol 3-kinase and inhibited by cyclic AMP. Mol Cell Biol. 1995 Jan; 15(1):326-37. View abstract
  28. Chung J, Grammer TC, Lemon KP, Kazlauskas A, Blenis J. PDGF- and insulin-dependent pp70S6k activation mediated by phosphatidylinositol-3-OH kinase. Nature. 1994 Jul 07; 370(6484):71-5. View abstract
  29. Dumont FJ, Altmeyer A, Kastner C, Fischer PA, Lemon KP, Chung J, Blenis J, Staruch MJ. Relationship between multiple biologic effects of rapamycin and the inhibition of pp70S6 protein kinase activity. Analysis in mutant clones of a T cell lymphoma. J Immunol. 1994 Feb 01; 152(3):992-1003. View abstract