18 (94.85)   20,612 10,200 (Mother) 0.26 (57.92)   1,082,623 2,670 (Human

Genome)   DNA motifs TTAGGG and TCAAGCTTGA were searched for in contigs derived from human milk, breast-fed infants’ feces (BF infant), formula-fed infants’ feces (FF infant) and mothers’ feces. Relative occurrence is in comparison to the human genome. Table 3 Occurrence of immune suppressive motifs TTAGGG and TCAAGCTTGA in contigs from human milk Sequence Genus Number of hits TCAAGCTTGA Pseudomonas 5   Nocardia 1   Staphylococcus 1   Unknown 4 TTAGGG Staphylococcus 1000   Pseudomonas 169   Lactobacillus 8   Bacillus 6   Streptococcus 6   Streptomyces 4   Tetragenococcus this website 4   Other 25   Unknown 461 Discussion Genera within human milk Determining the human milk metagenome, a bodily fluid notably absent from the human microbiome project [28], is crucial for enabling better insight on the process of infant GI colonization and immune development. By pooling DNA from ten human milk samples and subjecting it to Illumina sequencing we have demonstrated the large diversity of the human milk metagenome

with over 56,000 contigs aligning to 177 bacterial genera (Figure  2). Previous studies investigating the microbiome of human milk have used both culture-dependent and -independent approaches. Using 16S rRNA sequencing, Hunt et al. have reported several predominant species in human milk including a core of genera found in 15 human milk samples across time: Streptococcus, Staphylococcus, Serratia, Pseudomonas, Corynebacteria, Ralstonia, Propionibacteria, Sphingomonas, and Bradyrhizobiaceae[17]. Other studies showed colostrum was populated TNF-alpha inhibitor mostly by Weisella and Leuconostoc, followed by Staphylococcus, Streptococcus, and Lactococcus, and that Akkermansia were more prevalent in overweight mothers [20, 29]. Using a best hit MGCD0103 order analysis of the 51 bp Illumina reads, alignments for Akkermansia,

Propionibacteria, Sphingomonas and Weisella were observed (Additional file 2), but because of the Molecular motor small number of base pairs used for the alignment (51 bp) and the lack of assembled contigs associated with these microbes, their presence in our milk samples is a tentative identification. Using PCR-denaturing gradient gel electrophoresis and quantitative PCR, two studies from Martin et al. reported the presence of Bifidobacterium breve, B. adolescentis, B. bifidum and B. dentium in human milk, which differs from our findings (Figure  2, [15, 16]). This is likely due to the method of DNA extraction used in our study, as we did not incorporate bead-beating as a means to extract DNA from the hard to rupture Bifidobacterium[30]. The differences between the previously reported microbial communities and our analysis may also be due, in part, to the geographic location of the mothers, which has been shown to greatly impact the microbiome of individuals [31].