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Breastmilk, Stool, and Meconium: Bacterial Communities in South Africa

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Abstract

Human milk optimizes gut microbial richness and diversity, and is critical for proper immune development. Research has shown differing microbial composition based on geographic location, providing evidence that diverse biospecimen data is needed when studying human bacterial communities. Yet, limited research describes human milk and infant gut microbial communities in Africa. Our study uses breastmilk, stool, and meconium samples from a South African birth cohort to describe the microbial diversity, identify distinct taxonomic units, and determine correlations between bacterial abundance in breastmilk and stool samples. Mother-infant dyads (N = 20) were identified from a longitudinal birth cohort in the Vhembe district of Limpopo Province, South Africa. Breastmilk, meconium, and stool samples were analyzed using 16S ribosomal RNA sequencing of the V4–V5 gene region using the MiSeq platform for identification and relative quantification of bacterial taxa. A non-metric multidimensional scaling using Bray–Curtis distances of sample Z-scores showed that meconium, stool, and breastmilk microbial communities are distinct with varying genus. Breastmilk was mostly comprised of Streptococcus, Staphylococcus, Veillonella, and Corynebacterium. Stool samples showed the highest levels of Bifidobacterium, Faecalibacterium, Bacteroides, and Streptococcus. Alpha diversity measures found that stool samples have the highest Shannon index score compared to breastmilk and meconium. The abundance of Bifidobacterium (r = 0.57), Blautia (r = 0.59), and Haemophilus (r = 0.69) was correlated (p < 0.1) between breastmilk and stool samples. Despite the importance of breastmilk in seeding the infant gut microbiome, we found evidence of distinct bacterial communities between breastmilk and stool samples from South African mother-infant dyads.

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Funding

This study was funded by the National Institute of Environmental Health Sciences (grant number 1R01ES020360-01, PI Eskenazi). J. Chevrier is supported by a Canada Research Chairs in Global Environmental Health and Epidemiology.

Author information

Authors and Affiliations

  1. Maternal and Child Health Program, School of Public Health, University of California Berkeley, 1995 University Ave, Suite 265, Berkeley, CA, 94704, USA

    Jordyn T. Wallenborn

  2. Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, University of Basel, Basel, Switzerland

    Jordyn T. Wallenborn

  3. Center for Environmental Research and Children’s Health, University of California Berkeley, Berkeley, CA, USA

    Robert B. Gunier & Brenda Eskenazi

  4. California Institute for Quantitative Biosciences, Genomics Sequencing Laboratory, University of California Berkeley, Berkeley, CA, USA

    Derek J. Pappas

  5. Department of Epidemiology, Biostatistics and Occupational Health, Faculty of Medicine, McGill University, Montreal, Quebec, Canada

    Jonathan Chevrier

Authors
  1. Jordyn T. Wallenborn
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  2. Robert B. Gunier
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  3. Derek J. Pappas
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  4. Jonathan Chevrier
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  5. Brenda Eskenazi
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Contributions

Dr. Jordyn Wallenborn conceptualized and designed the study. Drs. Wallenborn, Pappas, and Gunier completed all analyses. Drs. Eskenazi and Chevrier conceptualized and designed the study, designed data collection instruments, and coordinated and supervised data collection. The first draft of the manuscript was written by Dr. Wallenborn and all authors commented on previous versions of the manuscript. All authors read and approved the final manuscript.

Corresponding author

Correspondence to Jordyn T. Wallenborn.

Ethics declarations

Ethics Approval

All procedures performed in studies involving human participants were in accordance with the ethical standards of the institutional and/or national research committee and with the 1964 Helsinki Declaration and its later amendments or comparable ethical standards. The Institutional Review Boards at the University of California, Berkeley; McGill University; the University of Pretoria; the Limpopo Department of Health and Social Development; and the Ethics Committee of Tshilidzini Hospital approved the study.

Consent to Participate

Informed consent was obtained from all individual participants included in the study.

Consent for Publication

The authors affirm that human research participants provided informed consent for publication.

Conflict of Interest

The authors declare no competing interests.

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Wallenborn, J.T., Gunier, R.B., Pappas, D.J. et al. Breastmilk, Stool, and Meconium: Bacterial Communities in South Africa. Microb Ecol 83, 246–251 (2022). https://doi.org/10.1007/s00248-021-01758-z

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  • DOI: https://doi.org/10.1007/s00248-021-01758-z

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