Human milk metagenome: a functional capacity analysis

Abstract

BackgroundHuman 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.ResultsThe 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.ConclusionsOur 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.

Microbiota of Human Breast Tissue

“…It has also been documented that wild-type mice fed a high-fat diet have a gut microbiota enriched in Firmicutes (37). Of interest, Proteobacteria is also the principal phylum in human milk (38), with many of the same bacteria that we detected in tissue, raising the possibility that the tissue microbiota could be a source of bacterial inocula for babies. Some of the organisms detected in breast tissue have been found at other body sites, such as Lactobacillus iners and Prevotella (vagina), Enterobacteriaceae (gastrointestinal tract), Fusobacterium and Streptococcus (oral cavity), Propionibacterium and Micrococcus (skin), and Pseudomonas (respiratory tract).…”

Necrotizing Enterocolitis: The Mystery Goes On

“…In addition to numerous other bioactive components that are conducive to human premature gastrointestinal tract development [40], it has been found recently that microbes present in human milk may act as commensal gastrointestinal microorganisms [41,42] and potentially have beneficial effects for the developing gastrointestinal tract. The taxa from individual mother's samples over time remains similar, but each mother's samples differ from other mothers' milk microbiota [41], suggesting a specific microbial ecology for each mother-infant dyad.…”

Crying in infants

“…34 These sex-biased differences in quality of milk may in turn affect bacterial colonization of the intestines. With respect to bacteria, human breast milk contains over 360 prokaryotic genera, 35 and may be an important direct source of lactobacilli and bifidobacteria, 36 as well as of other bacteria for the infant. [37][38][39] These findings are relatively new, and many questions about the role of maternal milk remain.…”