Points lying on or near the dotted line have equal or similar abundance in both metagenomes. Points closer to the x-axis are more abundant in the feces metagenome, whereas points closer to the y-axis are more PI3K inhibitor abundant in the human milk metagenome. Red dots signify those with significantly different proportions between the two metagenomes (Student’s t-test, P < 0.05). Breast-fed and formula-fed infants’ feces values are an average of five individuals, and mothers’ feces values are an average of three individuals. All subjects are unrelated. Immune-modulatory DNA motifs in human milk and feces When contigs were searched for the
presence of immune suppressive motifs, TCAAGCTTGA was found in 0.02% of the human-milk assembled contigs (11 sites, Table 2) with an occurrence 1.5 times that of the human genome alone (once per 844,000 bp compared to once per 1,276,500 bp in the human genome, Z-score −1.6). The contigs positive for TCAAGCTTGA aligned to the genomes of Pseudomonas (45%), Nocardia (9%), Staphylococcus (9%) and contigs of unknown origin (36%, Table 3). When the contigs from BF-infants’ feces, FF-infants’ feces and mothers’ feces were scanned for TCAAGCTTGA, it was found at a relative occurrence
of 1.19, 1.64, and 1.64 times that in the human genome, respectively (Table 2). Another immune suppressive site, TTAGGG was observed 1,684 times in the human milk metagenome CHIR-99021 molecular weight (3.2% of contigs), and at a relative occurrence 0.48 times that of the human genome (once per 5,600 bp
compared to once per 2,670 bp, Z-score 22.54, Table 2). Contigs containing TTAGGG corresponded to genomes of Staphylococcus (59%), Pseudomonas (10%), Lactobacillus (0.5%), 21 other known prokaryotic genomes (2.7%), and contigs from unknown genomes (27%, HSP90 Table 3). When the contigs from BF-infants’ feces, FF-infants’ feces and mothers’ feces were scanned for TTAGGG, this sequence was observed at a relative occurrence of 0.33, 0.18 and 0.26 times that in the human genome, respectively (Table 2). Assembled contigs were also searched for the presence of synthetically-assembled immune suppressive or immune stimulatory DNA motifs (7 and 5 motifs, respectively), such as those used in vaccine production (Additional file 6[23–27]). No synthetically-assembled sequences were observed in the human-milk contigs, whereas three motifs were found in less than 5 × 10-4% of contigs from the fecal metagenomes (maximum of 4 hits per 834,774 contigs, Additional file 6). Table 2 Occurrence of immune suppressive motifs in various metagenomes Sequence Number of hits Base pairs per hit Relative occurrence (Z-score) TCAAGCTTGA 11 844,000 (Human Milk) 1.51 (−1.6) 344 1,077,000 (BF Infant) 1.19 (−0.74) 124 779,000 (FF Infant) 1.64 (−1.84) 268 777,000 (Mother) 1.64 (−1.85) 2,245 1,276,500 (Human Genome) TTAGGG 1,684 5,600 (Human Milk) 0.48 (22.54) 18,118 8,200 (BF Infant) 0.33 (42.