Succession and determinants of the early life nasopharyngeal microbiota in a South African birth cohort

Microbiome

Research

Kilaza S. Mwaikono¹  Lesley Workman²  Heather J. Zar³  Sugnet Gardner-Lubbe⁴  Shantelle Claassen-Weitz⁵  Mark P. Nicol⁶  Stephanie Harris Mounaud⁷  William C. Nierman⁷  Yao Xia⁸ 

[1] Computational Biology Group and H3ABioNet, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa;Department of Science and Laboratory Technology, Dar Es Salaam Institute of Technology, Dar Es Salaam, Tanzania;Department of Paediatrics and Child Health, Red Cross War Memorial Children’s Hospital, Cape Town, South Africa;SAMRC Unit on Child & Adolescent Health, University of Cape Town, Cape Town, South Africa;Department of Paediatrics and Child Health, Red Cross War Memorial Children’s Hospital, Cape Town, South Africa;SAMRC Unit on Child & Adolescent Health, University of Cape Town, Cape Town, South Africa;Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa;Department of Statistics and Actuarial Science, Faculty of Economic and Management Sciences, Stellenbosch University, Stellenbosch, South Africa;Division of Medical Microbiology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa;Division of Medical Microbiology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa;Marshall Centre, Division of Infection and Immunity, School of Biomedical Sciences, University of Western Australia, Perth, Australia;J. Craig Venter Institute, Rockville, MD, USA;Marshall Centre, Division of Infection and Immunity, School of Biomedical Sciences, University of Western Australia, Perth, Australia;Center for Artificial Intelligence and Machine Learning, School of Science, Edith Cowan University, Joondalup, Australia;

关键词: 16S rRNA gene;    Birth cohort;    Microbiome;    High-throughput sequencing;    Infant;    Longitudinal;    Low- and middle-income country;    Microbiota;    Nasopharyngeal;    Upper respiratory tract;   

DOI  :  10.1186/s40168-023-01563-5

 received in 2022-06-21, accepted in 2023-04-30,  发布年份 2023

来源: Springer

【 摘 要 】

BackgroundBacteria 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.MethodsWe 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.ResultsCorynebacterium 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.ConclusionsIn 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.9NqP-bpPho7pt36-yeLZTtVideo Abstract

【 授权许可】

CC BY   
© The Author(s) 2023

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