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Human milk metagenome: a functional capacity analysis

Tonya L Ward1, Sergey Hosid12, Ilya Ioshikhes12* and Illimar Altosaar12*

Author Affiliations

1 Department of Biochemistry, Microbiology and Immunology; and Ottawa Institute of Computational Biology and Bioinformatics, University of Ottawa, Ottawa, ON, K1H 8M5, Canada

2 Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON, K1H 8M5, Canada

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BMC Microbiology 2013, 13:116  doi:10.1186/1471-2180-13-116

Published: 25 May 2013



Human milk contains a diverse population of bacteria that likely influences colonization of the infant gastrointestinal tract. Recent studies, however, have been limited to characterization of this microbial community by 16S rRNA analysis. In the present study, a metagenomic approach using Illumina sequencing of a pooled milk sample (ten donors) was employed to determine the genera of bacteria and the types of bacterial open reading frames in human milk that may influence bacterial establishment and stability in this primal food matrix. The human milk metagenome was also compared to that of breast-fed and formula-fed infants’ feces (n = 5, each) and mothers’ feces (n = 3) at the phylum level and at a functional level using open reading frame abundance. Additionally, immune-modulatory bacterial-DNA motifs were also searched for within human milk.


The bacterial community in human milk contained over 360 prokaryotic genera, with sequences aligning predominantly to the phyla of Proteobacteria (65%) and Firmicutes (34%), and the genera of Pseudomonas (61.1%), Staphylococcus (33.4%) and Streptococcus (0.5%). From assembled human milk-derived contigs, 30,128 open reading frames were annotated and assigned to functional categories. When compared to the metagenome of infants’ and mothers’ feces, the human milk metagenome was less diverse at the phylum level, and contained more open reading frames associated with nitrogen metabolism, membrane transport and stress response (P < 0.05). The human milk metagenome also contained a similar occurrence of immune-modulatory DNA motifs to that of infants’ and mothers’ fecal metagenomes.


Our results further expand the complexity of the human milk metagenome and enforce the benefits of human milk ingestion on the microbial colonization of the infant gut and immunity. Discovery of immune-modulatory motifs in the metagenome of human milk indicates more exhaustive analyses of the functionality of the human milk metagenome are warranted.

Human milk; Microbiome; Metagenome; Bacteria; Illumina; DNA; Open reading frames; Immune-modulatory motifs; Infant feces