Marcelo Freire

Marcelo Freire, DDS, PhD, DMedSc

Associate Professor

Bio

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.  

Publications

Publications

Journal of breath research. 2026-02-10; 20.1:

Psychosocial burden of halitosis: association between volatile sulfur compounds and quality of life in adults

Carneiro MC, de Menezes MLR, Caminha RDG, Freire M, Santos PSDS
PMID: 41610441

Advances in experimental medicine and biology. 2026-01-01; 1492.747-773.

Salivary Proteome Role in Infection and Immunity

Carneiro MC, da Silva NDG, Ventura TMO, da Silva Santos PS, Buzalaf MAR, Freire M
PMID: 41225125

Proceedings of the National Academy of Sciences of the United States of America. 2025-11-04; 122.44: e2507092122.

Inflammasome targeting for periodontitis prevention is sex dependent

Alves T, Swanson KV, Girnary MS, Freire M, Moss K, Divaris K, Beck J, Santos PCP, Brickey WJ, Wrobel JA, Min HY, Syed M, Morelli T, Seaman WT, Preisser JS, Hu D, Preisser H, Makhanova N, Susin C, Vias NP, Styner M, Zhang S, Pirih FQ, Chang J, Gill HS, Lietzan AD, Webster-Cyriaque J, Ting JPY, Marchesan JT
PMID: 41144672

The Lancet. Infectious diseases. 2025-05-01; 25.5: e294-e306.

Targeting the SARS-CoV-2 reservoir in long COVID

Proal AD, Aleman S, Bomsel M, Brodin P, Buggert M, Cherry S, Chertow DS, Davies HE, Dupont CL, Deeks SG, Ely EW, Fasano A, Freire M, Geng LN, Griffin DE, Henrich TJ, Hewitt SM, Iwasaki A, Krumholz HM, Locci M, Marconi VC, Mehandru S, Muller-Trutwin M, Painter MM, Pretorius E, Price DA, Putrino D, Qian Y, Roan NR, Salmon D, Tan GS, VanElzakker MB, Wherry EJ, Van Weyenbergh J, Yonker LM, Peluso MJ
PMID: 39947217

BMC immunology. 2025-04-18; 26.1: 34.

Natural and induced immune responses in oral cavity and saliva

Matsuoka M, Soria SA, Pires JR, Sant'Ana ACP, Freire M
PMID: 40251519

Scientific reports. 2024-11-12; 14.1: 27637.

Major alteration of lung microbiome and the host responses in critically ill COVID-19 patients with high viral load

Bustos IG, Wiscovitch-Russo R, Singh H, Sievers BL, Matsuoka M, Freire M, Tan GS, Cala MP, Guerrero JL, Martin-Loeches I, Gonzalez-Juarbe N, Reyes LF
PMID: 39532981

PloS one. 2024-07-25; 19.7: e0300408.

Sputum production and salivary microbiome in COVID-19 patients reveals oral-lung axis

Lu KY, Alqaderi H, Bin Hasan S, Alhazmi H, Alghounaim M, Devarajan S, Freire M, Altabtbaei K
PMID: 39052548

ACS synthetic biology. 2024-04-19; 13.4: 1128-1141.

Minimal Bacterial Cell JCVI-syn3B as a Chassis to Investigate Interactions between Bacteria and Mammalian Cells

Bittencourt DMC, Brown DM, Assad-Garcia N, Romero MR, Sun L, Palhares de Melo LAM, Freire M, Glass JI
PMID: 38507598

PNAS nexus. 2024-04-01; 3.4: pgae126.

Host-microbiome associations in saliva predict COVID-19 severity

Alqedari H, Altabtbaei K, Espinoza JL, Bin-Hasan S, Alghounaim M, Alawady A, Altabtabae A, AlJamaan S, Devarajan S, AlShammari T, Ben Eid M, Matsuoka M, Jang H, Dupont CL, Freire M
PMID: 38617584

Frontiers in public health. 2024-02-21; 12.1348441.

Association between risk of obstructive sleep apnea severity and risk of severe COVID-19 symptoms: insights from salivary and serum cytokines

Dinh Y, Alawady A, Alhazmi H, Altabtbaei K, Freire M, Alghounaim M, Devarajan S, Al Mulla F, Bin-Hassan S, Alqaderi H
PMID: 38476500

Frontiers in immunology. 2023-10-19; 14.1220610.

Oral mucosa immunity: ultimate strategy to stop spreading of pandemic viruses

Jang H, Matsuoka M, Freire M
PMID: 37928529

Nature immunology. 2023-10-01; 24.10: 1778.

Author Correction: SARS-CoV-2 reservoir in post-acute sequelae of COVID-19 (PASC)

Proal AD, VanElzakker MB, Aleman S, Bach K, Boribong BP, Buggert M, Cherry S, Chertow DS, Davies HE, Dupont CL, Deeks SG, Eimer W, Ely EW, Fasano A, Freire M, Geng LN, Griffin DE, Henrich TJ, Iwasaki A, Izquierdo-Garcia D, Locci M, Mehandru S, Painter MM, Peluso MJ, Pretorius E, Price DA, Putrino D, Scheuermann RH, Tan GS, Tanzi RE, VanBrocklin HF, Yonker LM, Wherry EJ
PMID: 37723351

Nature immunology. 2023-10-01; 24.10: 1616-1627.

SARS-CoV-2 reservoir in post-acute sequelae of COVID-19 (PASC)

Proal AD, VanElzakker MB, Aleman S, Bach K, Boribong BP, Buggert M, Cherry S, Chertow DS, Davies HE, Dupont CL, Deeks SG, Eimer W, Ely EW, Fasano A, Freire M, Geng LN, Griffin DE, Henrich TJ, Iwasaki A, Izquierdo-Garcia D, Locci M, Mehandru S, Painter MM, Peluso MJ, Pretorius E, Price DA, Putrino D, Scheuermann RH, Tan GS, Tanzi RE, VanBrocklin HF, Yonker LM, Wherry EJ
PMID: 37667052

Plants (Basel, Switzerland). 2023-07-20; 12.14:

Exploring the Proteomic Profile of Soybean Bran: Unlocking the Potential for Improving Protein Quality and Quantity

Molinari MDC, Fuganti-Pagliarini R, Yu Y, Florentino LH, Mertz-Henning LM, Lima RN, Bittencourt DMC, Freire MO, Rech E
PMID: 37514318

Heliyon. 2023-07-04; 9.7: e17958.

Persistent immune and clotting dysfunction detected in saliva and blood plasma after COVID-19

Jang H, Choudhury S, Yu Y, Sievers BL, Gelbart T, Singh H, Rawlings SA, Proal A, Tan GS, Qian Y, Smith D, Freire M
PMID: 37483779

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

Frontiers in immunology. 2018-06-12; 9.1300.

Resolvin E1 Promotes Bone Preservation Under Inflammatory Conditions

El Kholy K, Freire M, Chen T, Van Dyke TE
PMID: 29946319

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

Projects

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.

Video

Coronavirus Research

Overview of various projects related to the novel coronavirus pandemic.

Video

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.

Team

Wan Hin Choi

Software Engineer

Salim Abraham Soria

Research Associate I

Michele Matsuoka

Research Associate II

Shuvrajyoti Deb Roy, MS

Intern

I-Lin "Link" Wu

Software Engineer II

Video

Innovative Research Programs - Inflammation: Friend or Foe

News

18-Sep-2024
Collaborator Release

Prebys Introduces 2024 Grant Funding to Enhance Career Opportunities for Youth Across San Diego County

Organizations Receiving Part of the $5.89 Million Foster a Thriving San Diego Workforce

Prebys funds 24 grantees as part of a commitment to ensuring San Diego County youth are thriving and actively engaged in their communities

18-Apr-2024
Press Release

Groundbreaking study reveals oral microbiome’s role in immune response and COVID-19 severity

Newly developed AI model shows that saliva is a better predictor of COVID-19 severity than existing blood tests

22-Feb-2024
Collaborator Release

New LongCOVID research launched by PolyBio’s global consortium of scientists

Funding will deepen research on the persistence of the SARS-CoV-2 virus in LongCOVID patients and launch new clinical trials

08-Sep-2022
Reuters

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.

25-May-2021
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

27-Oct-2020
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

22-Aug-2019
Workshop Alert

JCVI/AADR Fall Focused Symposium

Integrating Omic Datasets Towards Translation