The role of breast-feeding in infant immune system: a systems perspective on the intestinal microbiome

Abstract

BackgroundThe human intestinal microbiota changes from being sparsely populated and variable to possessing a mature, adult-like stable microbiome during the first 2 years of life. This assembly process of the microbiota can lead to either negative or positive effects on health, depending on the colonization sequence and diet. An integrative study on the diet, the microbiota, and genomic activity at the transcriptomic level may give an insight into the role of diet in shaping the human/microbiome relationship. This study aims at better understanding the effects of microbial community and feeding mode (breast-fed and formula-fed) on the immune system, by comparing intestinal metagenomic and transcriptomic data from breast-fed and formula-fed babies.ResultsWe re-analyzed a published metagenomics and host gene expression dataset from a systems biology perspective. Our results show that breast-fed samples co-express genes associated with immunological, metabolic, and biosynthetic activities. The diversity of the microbiota is higher in formula-fed than breast-fed infants, potentially reflecting the weaker dependence of infants on maternal microbiome. We mapped the microbial composition and the expression patterns for host systems and studied their relationship from a systems biology perspective, focusing on the differences.ConclusionsOur findings revealed that there is co-expression of more genes in breast-fed samples but lower microbial diversity compared to formula-fed. Applying network-based systems biology approach via enrichment of microbial species with host genes revealed the novel key relationships of the microbiota with immune and metabolic activity. This was supported statistically by data and literature.Electronic supplementary materialThe online version of this article (doi:10.1186/s40168-015-0104-7) contains supplementary material, which is available to authorized users.

Connection between gut microbiome and brain development in preterm infants

“…while formula‐fed infants have a higher diversity and increased levels of Escherichia coli , Clostridium difficile , Bacteroides fragilis , and Lactobacilli (Backhed et al, ; Bezirtzoglou, Tsiotsias, & Welling, ; Favier, Vaughan, De Vos, & Akkermans, ; Penders et al, ). Even though the intestinal microbiota diversity is significantly lower (Backhed et al, ; Thompson, Monteagudo‐Mera, Cadenas, Lampl, & Azcarate‐Peril, ), in breastfed infants, their microbial communities interact significantly more with host genes compared with formula‐fed infants, and their transcriptomic activities are more associated with immune response and metabolic activities (Praveen, Jordan, Priami, & Morine, ; Schwartz et al, ). For example, there is enrichment for anti‐inflammatory genes and genes required for the utilization of human milk oligosaccharides (HMOs) from breastmilk in breastfed infant host epithelial cells (Schwartz et al, ).Utilization of different HMOs, for example, fucosylated oligosaccharides, can promote the growth of Bifidobacterium longum and several species of Bacteroides leading to a transition from proinflammatory bacteria such as E. coli and Clostridium perfringens (Marcobal et al, ; Yu et al, ).…”

The microbiota in inflammatory bowel disease: current and therapeutic insights

“…Additionally, formula-fed infants demonstrate more “adult”-like patterns of intestinal microbiota. Interestingly, intestinal microbiota of breast milk-fed infants are significantly less diverse than formula-fed infants, but their microbial genes demonstrated more robust interactions with host immune system, metabolism and biosynthesis 42. There is a reduced risk of development of IBD among infants who were breastfed 43.…”

Oral Microbiota in Infants Fed a Formula Supplemented with Bovine Milk Fat Globule Membranes - A Randomized Controlled Trial

“…Thus, protection against infections from milk could be mediated by direct effects on pathogens, or by factors influencing the ecology of the gastrointestinal (GI) tract. The latter is supported by the fact that the complex microbiomes of the GI tract (mouth and gut) differ distinctly between breast-fed and formula-fed infants [6, 7]. …”