Marcelo Freire, DDS, PhD, DMedSc

Associate Professor

Marcelo Freire is an associate professor in the Genomic Medicine and Infectious Disease Department at the J. Craig Venter Institute (JCVI). Prior to joining JCVI, Dr. Freire was an assistant faculty member at The Forsyth Institute and Harvard University (Division of Oral Medicine, Infection and Immunity). Early in his career, he worked on tissue biology of infectious diseases, biofilm-induced bone diseases and antibody engineering. As a dual-scientist and clinician, Dr. Freire’s initial training provided insights in human physiology and unmet clinical needs. As a current president of the Clinical and Translational Science Network (IADR), Dr. Freire is focused on applications of scientific innovations to health care. His research focuses on investigating biological deficiencies in chronic diseases.

Dr. Freire has extensive experience in host response, inflammation biology, transcriptomics and antibody engineering. Inflammation is a fundamental physiological process of normal and pathological conditions. He has led studies that developed novel therapeutics in control of chronic diseases. At JCVI, Dr. Freire is working on investigating links integrating microbiome, metabolism and immune response. In particular his lab is studying mechanisms controlling innate recognition, phagocytosis and activation signals of adaptive immune responses.

Dr. Freire received a DDS from College of Dentistry, Campos, Rio de Janeiro, a PhD in Craniofacial Molecular Biology from University of Southern California, and DMedSc in Oral Medicine and Infectious Diseases from Harvard University.  

Research Priorities

Inflammation Biology
  • Basic physiology of inflammatory response, with specific interest on neutrophils and granulocytes.
  • Chronic inflammation pathology including type 2 diabetes, cardiovascular diseases, cancer and periodontal diseases.
  • Activation of Phagocytosis
  • G-protein receptors regulation of inflammatory response.
  • Resolution of inflammation and tissue response.
  • Single cell heterogeneity.
Drug Discovery
  • Monoclonal antibody development.
  • Genomic and transcriptomic studies of novel biomarkers.
  • Engineering of agonist, antagonist and tethering therapeutics to host/microbial antigens.
  • Biomaterial and surface modification with biologics.
  • Phagocytosis of biomaterials.
Integration of Microbiome-Metabolism-Immune Systems
  • Host microbial interactions, including communications inducing metainflammation.
  • Evolution of immune sensing and responsiveness.
  • Transcriptional response regulation of cell plasticity.
  • Dietary perturbation of human/microbial biology.
  • Cell fate decisions in heterogeneous micro-environments.


Scientific data. 2022-11-16; 9.1: 702.
NETome: A model to Decode the Human Genome and Proteome of Neutrophil Extracellular Traps
Scieszka D, Lin YH, Li W, Choudhury S, Yu Y, Freire M
PMID: 36385149
Journal of dental research. 2022-10-01; 101.11: 1274-1288.
A Roadmap for the Human Oral and Craniofacial Cell Atlas
Caetano AJ, Human Cell Atlas Oral and Craniofacial Bionetwork, Sequeira I, Byrd KM
PMID: 36154725
Microbial ecology. 2021-11-01; 82.4: 1030-1046.
Oral Microbial Species and Virulence Factors Associated with Oral Squamous Cell Carcinoma
Torralba MG, Aleti G, Li W, Moncera KJ, Lin YH, Yu Y, Masternak MM, Golusinski W, Golusinski P, Lamperska K, Edlund A, Freire M, Nelson KE
PMID: 33155101
Microbial ecology. 2021-11-01; 82.4: 1047.
Correction to: Oral Microbial Species and Virulence Factors Associated with Oral Squamous Cell Carcinoma
Torralba MG, Aleti G, Li W, Moncera KJ, Lin YH, Yu Y, Masternak MM, Golusinski W, Golusinski P, Lamperska K, Edlund A, Freire M, Nelson KE
PMID: 33219400
Science advances. 2021-08-13; 7.33:
Coral microbiome manipulation elicits metabolic and genetic restructuring to mitigate heat stress and evade mortality
Santoro EP, Borges RM, Espinoza JL, Freire M, Messias CSMA, Villela HDM, Pereira LM, Vilela CLS, Rosado JG, Cardoso PM, Rosado PM, Assis JM, Duarte GAS, Perna G, Rosado AS, Macrae A, Dupont CL, Nelson KE, Sweet MJ, Voolstra CR, Peixoto RS
PMID: 34389536
BMC immunology. 2021-06-16; 22.1: 37.
Transcriptomics of type 2 diabetic and healthy human neutrophils
Kleinstein SE, McCorrison J, Ahmed A, Hasturk H, Van Dyke TE, Freire M
PMID: 34134627
NPJ vaccines. 2021-06-02; 6.1: 80.
Is the oral microbiome a source to enhance mucosal immunity against infectious diseases?
Zenobia C, Herpoldt KL, Freire M
PMID: 34078913
Trends in microbiology. 2021-06-01; 29.6: 551-561.
The Oral Host-Microbial Interactome: An Ecological Chronometer of Health?
Freire M, Nelson KE, Edlund A
PMID: 33279381
Journal of dental research. 2021-05-25; 220345211014432.
The Human Salivary Proteome Wiki: A Community-Driven Research Platform
Lau WW, Hardt M, Zhang YH, Freire M, Ruhl S
PMID: 34032471
Nature medicine. 2021-05-01; 27.5: 892-903.
SARS-CoV-2 infection of the oral cavity and saliva
Huang N, Pérez P, Kato T, Mikami Y, Okuda K, Gilmore RC, Conde CD, Gasmi B, Stein S, Beach M, Pelayo E, Maldonado JO, Lafont BA, Jang SI, Nasir N, Padilla RJ, Murrah VA, Maile R, Lovell W, Wallet SM, Bowman NM, Meinig SL, Wolfgang MC, Choudhury SN, Novotny M, Aevermann BD, Scheuermann RH, Cannon G, Anderson CW, Lee RE, Marchesan JT, Bush M, Freire M, Kimple AJ, Herr DL, Rabin J, Grazioli A, Das S, French BN, Pranzatelli T, Chiorini JA, Kleiner DE, Pittaluga S, Hewitt SM, Burbelo PD, Chertow D, NIH COVID-19 Autopsy Consortium, HCA Oral and Craniofacial Biological Network, Frank K, Lee J, Boucher RC, Teichmann SA, Warner BM, Byrd KM
PMID: 33767405
Frontiers in immunology. 2021-02-25; 12.619262.
The Impact of Oral-Gut Inflammation in Cerebral Palsy
Ferreira ACFM, Eveloff RJ, Freire M, Santos MTBR
PMID: 33717115
iScience. 2021-01-22; 24.1: 101941.
Impaired host response and the presence of Acinetobacter baumannii in the serum microbiome of type-II diabetic patients
Perera D, Kleinstein SE, Hanson B, Hasturk H, Eveloff R, Freire M, Ramsey M
PMID: 33426512
medRxiv : the preprint server for health sciences. 2020-10-27;
Integrated Single-Cell Atlases Reveal an Oral SARS-CoV-2 Infection and Transmission Axis
Huang N, Perez P, Kato T, Mikami Y, Okuda K, Gilmore RC, Domínguez Conde C, Gasmi B, Stein S, Beach M, Pelayo E, Maldonado J, LaFont B, Padilla R, Murrah V, Maile R, Lovell W, Wallet S, Bowman NM, Meinig SL, Wolfgang MC, Choudhury SN, Novotny M, Aevermann BD, Scheuermann R, Cannon G, Anderson C, Marchesan J, Bush M, Freire M, Kimple A, Herr DL, Rabin J, Grazioli A, French BN, Pranzatelli T, Chiorini JA, Kleiner DE, Pittaluga S, Hewitt S, Burbelo PD, Chertow D, Frank K, Lee J, Boucher RC, Teichmann SA, Warner BM, Byrd KM
PMID: 33140061
Journal of dental research. 2020-09-01; 99.10: 1131-1139.
Inflammatory Networks Linking Oral Microbiome with Systemic Health and Disease
Kleinstein SE, Nelson KE, Freire M
PMID: 32459164
Scientific reports. 2020-05-14; 10.1: 7954.
Longitudinal Study of Oral Microbiome Variation in Twins
Freire M, Moustafa A, Harkins DM, Torralba MG, Zhang Y, Leong P, Saffery R, Bockmann M, Kuelbs C, Hughes T, Craig JM, Nelson KE
PMID: 32409670
Frontiers in immunology. 2019-11-12; 10.2602.
Host-Microbial Interactions in Systemic Lupus Erythematosus and Periodontitis
Pessoa L, Aleti G, Choudhury S, Nguyen D, Yaskell T, Zhang Y, Li W, Nelson KE, Neto LLS, Sant'Ana ACP, Freire M
PMID: 31781106
Journal of proteome research. 2019-04-05; 18.4: 1907-1915.
Self-Assembled STrap for Global Proteomics and Salivary Biomarker Discovery
Lin YH, Eguez RV, Torralba MG, Singh H, Golusinski P, Goliusinski W, Golusinski W, Masternak M, Nelson KE, Freire M, Yu Y
PMID: 30848925
The International journal of periodontics & restorative dentistry. 2018-06-12; 38.5: 637–644.
A Histologic and Histomorphometric Retrospective Analysis of the Outcomes of Ridge Preservation Using Anorganic Bovine Bone Minerals and a Nonresorbable Membrane
Min S, Freire M, Bakshallian N, Bakhshalian N, Wu I, Zadeh HH
PMID: 29897354
Scientific reports. 2017-10-09; 7.1: 12848.
ERV1 Overexpression in Myeloid Cells Protects against High Fat Diet Induced Obesity and Glucose Intolerance
Sima C, Montero E, Nguyen D, Freire M, Norris P, Serhan CN, Van Dyke TE
PMID: 28993702
Molecular oral microbiology. 2017-02-01; 32.1: 74-88.
A bacterial-biofilm-induced oral osteolytic infection can be successfully treated by immuno-targeting an extracellular nucleoid-associated protein
Freire MO, Devaraj A, Young A, Navarro JB, Downey JS, Chen C, Bakaletz LO, Zadeh HH, Goodman SD
PMID: 26931773
Journal of immunology (Baltimore, Md. : 1950). 2017-01-15; 198.2: 718-728.
Neutrophil Resolvin E1 Receptor Expression and Function in Type 2 Diabetes
Freire MO, Dalli J, Serhan CN, Van Dyke TE
PMID: 27994073
Frontiers in microbiology. 2016-01-01; 7.1230.
Staphylococcus aureus Shifts toward Commensalism in Response to Corynebacterium Species
Ramsey MM, Freire MO, Gabrilska RA, Rumbaugh KP, Lemon KP
PMID: 27582729
Infection and immunity. 2015-02-01; 83.2: 792-801.
Impact of resolvin E1 on murine neutrophil phagocytosis in type 2 diabetes
Herrera BS, Hasturk H, Kantarci A, Freire MO, Nguyen O, Kansal S, Van Dyke TE
PMID: 25486994
Tissue engineering. Part A. 2011-12-01; 17.23-24: 2911-8.
Antibody-mediated osseous regeneration: a novel strategy for bioengineering bone by immobilized anti-bone morphogenetic protein-2 antibodies
Freire MO, You HK, Kook JK, Choi JH, Zadeh HH
PMID: 21870943
Journal of periodontology. 2011-05-01; 82.5: 778-89.
Development of an animal model for Aggregatibacter actinomycetemcomitans biofilm-mediated oral osteolytic infection: a preliminary study
Freire MO, Sedghizadeh PP, Schaudinn C, Gorur A, Downey JS, Choi JH, Chen W, Kook JK, Chen C, Goodman SD, Zadeh HH
PMID: 21222546

Inflammation: Friend or Foe?

JCVI Associate Professor, Marcelo Freire, DDS, PhD, DMSc, continues to lead the field as he investigates the critical role the human microbiome plays in inflammation as the pathway to chronic disease.


Coronavirus Research

Overview of various projects related to the novel coronavirus pandemic.


Saliva Proteome Database

The Human Salivary Proteome (HSP) Wiki as a public data portal for searching and retrieving custom-curated information about the proteome of human saliva.
Innovative Research Programs - Inflammation: Friend or Foe

Top scientists join forces to study leading theory behind long COVID

Several JCVI scientists will be contributing to the newly launched Long Covid Research Initiative — a collaboration of researchers, clinicians, and patients working to rapidly study and treat long Covid.

Collaborator Release

New wiki on salivary proteins may transform diagnostic testing and personalized medicine

Database curates info on inner workings of saliva, an attractive tool for noninvasive diagnostics and precision medicine

Collaborator Release

Study reveals mouth as primary source of COVID-19 infection, spread

UNC-Chapel Hill, NIH identify sites in the oral cavity where coronavirus can take hold

Workshop Alert

JCVI/AADR Fall Focused Symposium

Integrating Omic Datasets Towards Translation