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A Method for Targeted 16S Sequencing of Human Milk Samples
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Published on: March 23, 2018

Human milk metagenome: a functional capacity analysis.

Tonya L Ward1, Sergey Hosid, Ilya Ioshikhes

  • 1Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1H 8M5, Canada.

BMC Microbiology
|May 28, 2013
PubMed
Summary

Human milk harbors a complex bacterial community, influencing infant gut colonization and immunity. This metagenomic study reveals its unique functional profile and immune-modulatory potential.

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Area of Science:

  • Microbiology
  • Human Health
  • Genomics

Background:

  • Human milk contains bacteria crucial for infant gut colonization.
  • Previous studies primarily used 16S rRNA analysis.
  • A comprehensive metagenomic approach is needed to understand milk's microbial functions.

Purpose of the Study:

  • To characterize the bacterial genera and open reading frames in human milk using metagenomics.
  • To compare the human milk metagenome with infant and maternal fecal metagenomes.
  • To identify immune-modulatory DNA motifs in human milk.

Main Methods:

  • Metagenomic sequencing of pooled human milk (10 donors) using Illumina.
  • Comparison of phylum-level and functional profiles with infant (n=5) and maternal (n=3) fecal metagenomes.
  • Analysis of bacterial open reading frames and immune-modulatory DNA motifs.

Main Results:

  • Human milk contained over 360 genera, dominated by Proteobacteria (65%) and Firmicutes (34%).
  • Key genera identified were Pseudomonas (61.1%), Staphylococcus (33.4%), and Streptococcus (0.5%).
  • Human milk metagenome showed lower diversity but enriched functions in nitrogen metabolism, membrane transport, and stress response compared to fecal samples.

Conclusions:

  • Human milk metagenome is complex, supporting infant gut microbial colonization and immunity.
  • Presence of immune-modulatory motifs suggests further functional analysis of human milk metagenome is essential.