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Microbiome Analysis pp 63–86Cite as

Methods and Strategies to Examine the Human Breastmilk Microbiome

Part of the Methods in Molecular Biology book series (MIMB,volume 1849)

Abstract

It has recently been discovered that breastmilk is not sterile, but contains a vast array of microbes, known collectively as the breastmilk microbiome. The breastmilk microbiome field is in its infancy, but over the last decade, our understanding of the microbial communities that inhabit the human body has increased exponentially, due in large part to novel next-generation sequencing technologies. These culture-independent, high-throughput molecular technologies have allowed biologists to investigate the entirety of microbiota present in breastmilk, which was previously poorly known. These approaches are novel and the methodologies surrounding the exploration of the breastmilk microbiota remain in flux. The objectives of this chapter are to outline what is known thus far and detail the optimal methods and strategies to conducting a breastmilk microbiome study from subject recruitment and milk collection to DNA extraction, high-throughput sequencing and bioinformatics analyses.

Key words

  • Breastmilk
  • Breastfeeding
  • Microbiome
  • Lactation
  • Bacteria
  • Gastrointestinal tract
  • DNA extraction
  • 16S rRNA gene
  • Illumina MiSeq
  • Bioinformatics

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Authors and Affiliations

  1. Faculty of Medicine, Department of Nutritional Sciences, University of Toronto, Toronto, ON, Canada

    Lauren LeMay-Nedjelski & Deborah L. O’Connor

  2. Translational Medicine, The Hospital for Sick Children, Toronto, ON, Canada

    Lauren LeMay-Nedjelski, Sharon Unger & Deborah L. O’Connor

  3. Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, Canada

    Julia Copeland & Pauline W. Wang

  4. Ottawa Institute of Systems Biology, Ottawa, ON, Canada

    James Butcher & Alain Stintzi

  5. Department of Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada

    James Butcher & Alain Stintzi

  6. Faculty of Medicine, Department of Pediatrics, University of Toronto, Toronto, ON, Canada

    Sharon Unger

  7. Department of Pediatrics, Mount Sinai Hospital, Toronto, ON, Canada

    Sharon Unger & Deborah L. O’Connor

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  1. Lauren LeMay-Nedjelski
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  2. Julia Copeland
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  3. Pauline W. Wang
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  5. Sharon Unger
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  6. Alain Stintzi
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  7. Deborah L. O’Connor
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Correspondence to Deborah L. O’Connor .

Editor information

Editors and Affiliations

  1. Faculty of Computer Science, Dalhousie University, Halifax, NS, Canada

    Robert G. Beiko

  2. Department of Pathology & Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada

    Will Hsiao

  3. Program in Molecular Medicine, The Hospital for Sick Children, Toronto, ON, Canada

    Prof. Dr. John Parkinson

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LeMay-Nedjelski, L. et al. (2018). Methods and Strategies to Examine the Human Breastmilk Microbiome. In: Beiko, R., Hsiao, W., Parkinson, J. (eds) Microbiome Analysis. Methods in Molecular Biology, vol 1849. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-8728-3_5

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  • DOI: https://doi.org/10.1007/978-1-4939-8728-3_5

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