Succession and determinants of the early life nasopharyngeal microbiota in a South African birth cohort
Year: 2023
Type: article
Study design: Observational Study
Abstract: BACKGROUND: Bacteria colonizing the nasopharynx play a key role as gatekeepers of respiratory health. Yet, dynamics of early life nasopharyngeal (NP) bacterial profiles remain understudied in low- and middle-income countries (LMICs), where children have a high prevalence of risk factors for lower respiratory tract infection. We investigated longitudinal changes in NP bacterial profiles, and associated exposures, among healthy infants from low-income households in South Africa. METHODS: We used short fragment (V4 region) 16S rRNA gene amplicon sequencing to characterize NP bacterial profiles from 103 infants in a South African birth cohort, at monthly intervals from birth through the first 12 months of life and six monthly thereafter until 30 months. RESULTS: Corynebacterium and Staphylococcus were dominant colonizers at 1 month of life; however, these were rapidly replaced by Moraxella- or Haemophilus-dominated profiles by 4 months. This succession was almost universal and largely independent of a broad range of exposures. Warm weather (summer), lower gestational age, maternal smoking, no day-care attendance, antibiotic exposure, or low height-for-age z score at 12 months were associated with higher alpha and beta diversity. Summer was also associated with higher relative abundances of Staphylococcus, Streptococcus, Neisseria, or anaerobic gram-negative bacteria, whilst spring and winter were associated with higher relative abundances of Haemophilus or Corynebacterium, respectively. Maternal smoking was associated with higher relative abundances of Porphyromonas. Antibiotic therapy (or isoniazid prophylaxis for tuberculosis) was associated with higher relative abundance of anerobic taxa (Porphyromonas, Fusobacterium, and Prevotella) and with lower relative abundances of health associated-taxa Corynebacterium and Dolosigranulum. HIV-exposure was associated with higher relative abundances of Klebsiella or Veillonella and lower relative abundances of an unclassified genus within the family Lachnospiraceae. CONCLUSIONS: In this intensively sampled cohort, there was rapid and predictable replacement of early profiles dominated by health-associated Corynebacterium and Dolosigranulum with those dominated by Moraxella and Haemophilus, independent of exposures. Season and antibiotic exposure were key determinants of NP bacterial profiles. Understudied but highly prevalent exposures prevalent in LMICs, including maternal smoking and HIV-exposure, were associated with NP bacterial profiles. Video Abstract.
Source: Microbiome
Institutions: University of Cape Town, Stellenbosch University, Edith Cowan University, The University of Western Australia, Dar es Salaam Institute of Technology, J. Craig Venter Institute, South African Medical Research Council, Red Cross War Memorial Children's Hospital, Institute of Infectious Disease and Molecular Medicine
Language: English
Topic: Gut microbiota and health
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: gold
Estimated APC paid: $4,590
Funders: Bill and Melinda Gates Foundation, L'Oreal USA, National Research Foundation, South African Medical Research Council, University of Cape Town, National Institutes of Health, Medical Research Council, National Health and Medical Research Council, National Human Genome Research Institute, National Institute of Allergy and Infectious Diseases
Awards: The nasopharyngeal microbiome and respiratory disease in African children, G2464639231, The microbial ecology of the upper airways in children, J. Craig Venter Institute - to use new molecular technologies to elucidate the nasopharyngeal microbiome in GEMS & PERCH sites where factors such as ethnicity, environment, an..., G3685900323, Center for Research on the Respiratory Microbiota of African Children (ReMAC)
OpenAlex ID: W4379364369