Methods and Strategies to Examine the Human Breastmilk Microbiome

  • Lauren LeMay-Nedjelski
  • Julia Copeland
  • Pauline W. Wang
  • James Butcher
  • Sharon Unger
  • Alain Stintzi
  • Deborah L. O’ConnorEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1849)


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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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  • Lauren LeMay-Nedjelski
    • 1
    • 2
  • Julia Copeland
    • 3
  • Pauline W. Wang
    • 3
  • James Butcher
    • 4
    • 5
  • Sharon Unger
    • 2
    • 6
    • 7
  • Alain Stintzi
    • 4
    • 5
  • Deborah L. O’Connor
    • 1
    • 2
    • 7
    Email author
  1. 1.Faculty of Medicine, Department of Nutritional SciencesUniversity of TorontoTorontoCanada
  2. 2.Translational MedicineThe Hospital for Sick ChildrenTorontoCanada
  3. 3.Centre for the Analysis of Genome Evolution and FunctionUniversity of TorontoTorontoCanada
  4. 4.Ottawa Institute of Systems BiologyOttawaCanada
  5. 5.Department of Microbiology and ImmunologyUniversity of OttawaOttawaCanada
  6. 6.Faculty of Medicine, Department of PediatricsUniversity of TorontoTorontoCanada
  7. 7.Department of PediatricsMount Sinai HospitalTorontoCanada

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