Recently, immune suppressive motifs (TTAGGG and TCAAGCTTGA) that are able to counter the effects of CpGs have been discovered in Lactobacillus[11]. If immune-modulatory motifs occur in human milk derived DNA, they could contribute

to proper immune development find more by decreasing exaggerated inflammatory responses to colonizing bacteria, which are seen in infants with necrotizing enterocolitis [12]. Human milk bacteria have previously been analyzed by culture-dependent and -independent mechanisms, confirming the presence of a magnitude of bacterial phylotypes [13–20]. In one study, Staphylococcus and Streptococcus dominated the milk microbiome of most mothers, whereas commercially well known bovine milk-associated genera, Lactobacillus and Bifidobacterium, contributed as minor

milk microbiota members (2–3% of genera) [17]. Another study showed that the human milk microbiome changes over time, and may be dependent on the mother’s weight and the baby’s mode of delivery [20]. Most recent methods for determining the milk microbiome have included amplification of 16S ribosomal RNA genes (rRNA) followed by pyrosequencing [17, 20]. Although this technique is widely accepted as a means to determine microbial diversity, it does present limitations such as a lack of information on the functional capacity of the microbes within the milk matrix and also prevents data accumulation on the selleck kinase inhibitor types of DNA motifs to which an infant is exposed. In this study we performed

a metagenomic analysis of the bacteria in human milk using Illumina sequencing and the MG-RAST pipeline [21]. The aims were to determine the genera of bacteria in human milk, search for immune-modulatory DNA motifs, and determine the types of bacterial open reading Atorvastatin frames (ORFs) in human milk that may influence bacterial presence and stability in this complex yet foundational food matrix. Results Phyla and genera within human milk Metagenome sequencing of a pooled human milk sample resulted in 261,532,204 sequenced reads of 51 bp, which were binned into those aligning to the human genome (186,010,988, 72.01 ± 3.06%), known prokaryotic genomes (1,331,996, 0.53 ± 0.16%) or those not aligning to either category (74,189,220, 27.46 ± 3.72%, Additional file 1). Using a best hit analysis of the 1,331,996 51-bp sequences, 75% aligned to Staphylococcus, 15% to Pseudomonas, 2% to Edwardsiella, and 1% to Pantoea, Treponema, Streptococcus and Campylobacter, respectively (Figure  1). The remaining 3% of the known prokaryotic sequences mapped to 361 bacterial genera, demonstrating the diversity of the human milk metagenome while confirming the presence of key genera like Akkermansia (Additional file 2). Figure 1 Best hit analysis of 51 bp DNA sequences from human milk. DNA from human milk was sequenced using Illumina sequencing followed by alignment to known prokaryotic genomes.