Transcriptome analysis reveals persistent effects of neonatal diet on small intestine gene expression profile in a porcine model
Authors: Saraf Manish Kumar , Bowlin Anne Kidd , Chen Celine , Dawson Harry , Badger Thomas M , Yeruva Venkat Laxmi 
Published: June 2021

Breastfeeding is associated with several benefits affecting gut development and immune function. Compared to breast feeding, infant formula feeding is linked to a greater risk for gut dysfunction, ear and respiratory tract infections, and allergies. The beneficial effects appear to last at least through puberty, but the mechanism(s) underlying these long lasting effects have not been investigated. We hypothesized that relative to formula feeding, neonatal breast milk‐feeding favors the development of the gastrointestinal tract and immune system even after post‐weaning from the neonatal diet. This hypothesis was tested using a piglet model, where piglets (n=12 males/group) were fed either human breast‐milk (HBM), dairy‐based formula (FM) or sow milk (SM) from postnatal day 2 to 21, followed by a common ad libitum diet weaning solid diet until day 51. A significant reduction was found in small intestine length in HBM‐fed relative to SM‐fed groups (910±13 vs 984±19, 930±24 cm) and in small intestine weigh (362±9.7 vs 420±17 g, p<0.05) of HBM‐fed relative to SM‐ and FM‐fed. Transcriptome data were analyzed with reference to Dawson laboratory's in‐house gene reference database. Gene expression data revealed a differential expression of 99 genes in HBM‐fed in comparison to SM‐fed piglets p<0.05). Furthermore, FM‐fed piglets showed a differential expression of 583 genes (p<0.05) in comparison to those SM‐fed. In addition, the HBM group demonstrated a 2 to 58 fold up‐regulation of 101 genes and 2 to 8 fold down regulation of 39 genes relative to FM‐fed piglets. Panther analyses of the gene list suggested the most impacted biological system was cellular process (37 genes) followed by metabolism (31 genes), development (19 genes), response to stimuli such as stress, external, internal, biotic, and toxic (16 genes), and immune system (13 genes i.e. 2‐to‐19 fold increase in ABCC12, BRAF, CALCRL, CD46, CXCL8, CXCL11, C8a, DMBT1 and a 2 fold decrease in CD79B, and ASGR1, p<0.05) in HBM‐fed relative to FM‐fed piglets. In HBM‐fed piglets the major immune system pathways being regulated in the small intestine were those relayed to cytokine receptor signaling, gonadotropin release hormone receptor, chemokine/cytokine, interleukin, PDGF, TGF‐β, Wnt signaling, B‐Cell activation, cadherin, and integrin signaling. In summary, transcriptome analyses indicate that in the small intestine of piglets HBM‐feeding altered immune and other pathways, and gene targets compared to the formula‐fed group, even 30 days after being weaned onto a common diet. Studies are underway to confirm the expression data by real‐time PCR. The role of the microbiota is also being evaluated to understand the association between microbiota and host biological processes and immune system development. These findings will inform the understanding of mechanism(s) underlying benefits of human breast milk for intestinal growth, function, and development.Support or Funding InformationThis work was funded by USDA‐ARS Project 6026‐5100‐010‐05S and 1235‐51000‐055‐00D.