Center for Research on the Respiratory Microbiota of African Children (ReMAC): Abstract The microbiota (community of microorganisms) of the upper airways plays a key role in the development of lower respiratory tract infection (LRTI) in children. Most of the important bacterial LRTI pathogens also colonize the nasopharynx (NP), which often serves as the source of infection for LRTI in a child as well as the reservoir for transmission to other children. We have assembled an interdisciplinary collaboration between investigators at three leading African research institutions, in South Africa, The Gambia and Malawi, and a leading genomic center in the USA to address key questions on the determinants, composition and biological significance of the microbiota of the upper airways in African children. We will leverage several large existing cohorts and sample repositories to conduct three complementary but not co-dependent research projects, each done at multiple African sites. The first project will focus on comprehensive description of the NP microbiota (bacterial, fungal and viral components) in healthy African children over the first year of life, using longitudinal, frequently sampled cohorts. We will also study the role of the NP microbiota in resistance to colonization with the respiratory pathogen, Streptococcus pneumoniae, including modulation of vaccine-induced protection. The second project will investigate the role of the NP microbiota, including consideration of antimicrobial resistance, in the incidence, severity, and recurrence of LRTI in African children. The third project will examine the association between seasonality, inhaled environmental exposures (or pollutants), the household dust microbiota, and the microbiota of the NP and oropharynx in children from South Africa and The Gambia. We will use amplicon sequencing to define the bacterial and fungal components of the microbiota, targeted nucleic acid amplification testing for the viral component, and shotgun metagenomic sequencing to complement, validate and extend our findings. We will apply statistical modeling tools, including those derived from ecology, to understand the evolution of, interactions within, and determinants of, the microbiota. We will develop a Center for Research into the Respiratory Microbiota of African Children (ReMAC) which will build capacity for respiratory microbiota research in Africa, by establishing a sustainable, collaborative network of African and US investigators, with focus on specialized training, postgraduate study, technology transfer and career development. Successful completion of the proposed work will enhance our understanding of the ecology of the nasopharynx and of the pathogenesis of LRTI, promote the development of diagnostic or prognostic tools for children with LRTI, provide insight into whether therapeutic manipulation of the microbiota may be desirable and identify modifiable risk factors which negatively influence the composition of the microbiota. 1