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Matthew Kelly

Associate Professor of Pediatrics
Pediatrics, Infectious Diseases

Research Interests


As a pediatrician with specialty training in infectious diseases and global health, my career goal is to develop strategies that use targeted manipulation of the microbiome for the prevention and treatment of infections in children. My current research focuses on elucidating the complex relationships that exist between sociodemographic factors, the upper respiratory microbiome, and colonization by pneumonia pathogens among infants in Botswana. Ultimately, we aim to develop microbiome therapeutics that effectively prevent pneumonia and other respiratory infections in children. 

Selected Grants


The impact of the oral microbiome on pulmonary function among people with HIV in Botswana

ResearchCo-Mentor · Awarded by National Institutes of Health · 2024 - 2029

Clinical and host microbiome features in the development of acute otitis media

ResearchCo-Mentor · Awarded by National Institutes of Health · 2023 - 2028

Duke Center for Advancement of Child Health (CAtCH).

Inst. Training Prgm or CMEMentor · Awarded by National Institutes of Health · 2021 - 2026

Host-microbe interactions and SARS-CoV-2 susceptibility and symptoms in a novel human challenge model

ResearchPrincipal Investigator · Awarded by National Institutes of Health · 2023 - 2025

Host-microbe interactions in a novel SARS-CoV-2 human challenge model

ResearchPrincipal Investigator · Awarded by American Lung Association · 2023 - 2025

The impact of the oral microbiome on pulmonary function among people with HIV in Botswana

ResearchCo-Mentor · Awarded by National Institutes of Health · 2024 - 2029

Clinical and host microbiome features in the development of acute otitis media

ResearchCo-Mentor · Awarded by National Institutes of Health · 2023 - 2028

Duke Center for Advancement of Child Health (CAtCH).

Inst. Training Prgm or CMEMentor · Awarded by National Institutes of Health · 2021 - 2026

Host-microbe interactions and SARS-CoV-2 susceptibility and symptoms in a novel human challenge model

ResearchPrincipal Investigator · Awarded by National Institutes of Health · 2023 - 2025

Host-microbe interactions in a novel SARS-CoV-2 human challenge model

ResearchPrincipal Investigator · Awarded by American Lung Association · 2023 - 2025

Early life B cell responses and inflammation following SARS-CoV-2 infection

ResearchPrincipal Investigator · Awarded by Weill Cornell Medicine · 2022 - 2024

Unified Program for Therapeutics in Children

Inst. Training Prgm or CMEPreceptor · Awarded by National Institutes of Health · 2019 - 2024

Rational identification of Corynebacterium strains for use as probiotics

ResearchPrincipal Investigator · Awarded by Ann & Robert H. Lurie Children's Hospital of Chicago · 2022 - 2024

Gene expression profiling of children with SARS-CoV-2 infection or exposure

ResearchPrincipal Investigator · Awarded by Merck & Co., Inc. · 2021 - 2023

PTN 2.0 Task Order 7 HIV Lactation

Clinical TrialCo Investigator · Awarded by Eunice Kennedy Shriver National Institute of Child Health and Human Development · 2020 - 2023

Clinical and gut microbial risk factors for Gram-negative bacterial late-onset sepsis among premature infants in Singapore

ResearchPrincipal Investigator · Awarded by KK Women's and Children's Hospital · 2020 - 2023

Postdoctoral Training in Genomic Medicine Research

Inst. Training Prgm or CMEMentor · Awarded by National Institutes of Health · 2017 - 2023

Nasopharyngeal Microbiome and Risk of Bacterial Pathogen Colonization in Infants

ResearchPrincipal Investigator · Awarded by National Institutes of Health · 2018 - 2023

The effect of household air pollution on the health outcomes of infants in Botswana

ResearchMentor · Awarded by Thrasher Research Fund · 2018 - 2022

Early life B cell responses and inflammation following SARS-CoV-2 infection

ResearchCo-Principal Investigator · Awarded by National Institutes of Health · 2021 - 2022

LOC-IMPAACT Leadership Group-IMPAACT 2018 Protocol Co-Vice Chair

ResearchPrincipal Investigator · Awarded by Johns Hopkins University · 2017 - 2021

The impact of HIV infection or exposure on the upper respiratory microbiome of children in Botswana

FellowshipMentor · Awarded by Vanderbilt University Medical Center · 2019 - 2021

VTEU Task C Option 2 Protocol 14-0079.B1C1.0028

ResearchInvestigator · Awarded by National Institutes of Health · 2017 - 2021

Fungal biomarkers for diagnosis and response to therapy for pediatric candidemia

ResearchPrincipal Investigator · Awarded by Duke University · 2016 - 2020

LOC-IMPAACT Leadership Group-IMPAACT 2018 Protocol Vice Chair support

ResearchPrincipal Investigator · Awarded by Johns Hopkins University · 2017 - 2018

RFTP 2016 CISA 03 - Option 1 - Fever after Simultaneous Vaccination (Lead)

ResearchInvestigator · Awarded by Centers for Disease Control and Prevention · 2017 - 2018

American Society of Tropical Medicine and Hygiene

FellowshipPrincipal Investigator · Awarded by Burroughs Wellcome Fund · 2016 - 2018

Multi-center studies to improve diagnosis and treatment of pediatric candidiasis

ResearchPrincipal Investigator · Awarded by Duke University · 2016 - 2018

VTEU Task C Option 1 Protocol 14-0079.B1C1.0028

ResearchFellow · Awarded by National Institutes of Health · 2016 - 2018

RFTP 2016 CISA 03 - Base - Fever after simultaneous vaccination (Lead)

ResearchInvestigator · Awarded by Centers for Disease Control and Prevention · 2016 - 2017

VTEU Task B Base Protocol 14-0079.B1C1.0028

ResearchFellow · Awarded by National Institutes of Health · 2015 - 2016

The Effect of In Utero Exposure to HIV and Antiretroviral Therapy on the Microbiology and Outcomes of Severe Pneumonia

ResearchPrincipal Investigator · Awarded by International AIDS Society · 2013 - 2016

External Relationships


  • Invivyd
  • Merck Sharpe & Dohme (Merck & Co, USA)

This faculty member (or a member of their immediate family) has reported outside activities with the companies, institutions, or organizations listed above. This information is available to institutional leadership and, when appropriate, management plans are in place to address potential conflicts of interest.