Early postnatal diets affect the bioregional small intestine microbiome and ileal metabolome in neonatal piglets

Authors: PICCOLO, BRIAN - Arkansas Children'S Nutrition Research Center (ACNC); MERCER, KELLY - Arkansas Children'S Nutrition Research Center (ACNC); BHATTACHARYA, SUDEEPA - Arkansas Children'S Nutrition Research Center (ACNC); BOWLIN, A - Arkansas Children'S Nutrition Research Center (ACNC); SARAF, MANISH - Arkansas Children'S Nutrition Research Center (ACNC); PACK, LINDSAY - Arkansas Children'S Nutrition Research Center (ACNC); CHINTAPALLI, S - Arkansas Children'S Nutrition Research Center (ACNC); SHANKAR, K - Arkansas Children'S Nutrition Research Center (ACNC); Ferruzzi, Mario; Badger, Thomas; YERUVA, L - Arkansas Children'S Nutrition Research Center (ACNC)

Submitted to: Journal of Nutrition
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/5/2017
Publication Date: 6/28/2017
Citation: Piccolo, B.D., Mercer, K.E., Bhattacharya, S., Bowlin, A.K., Saraf, M.K., Pack, L., Chintapalli, S.V., Shankar, K., Adams, S.H., Badger, T.M., Yeruva, L. 2017. Early postnatal diets affect the bioregional small intestine microbiome and ileal metabolome in neonatal piglets. Journal of Nutrition. doi:10.3945/jn.117.252767.

Interpretive Summary: Breastfeeding is known to provide superior nutrition and be protective of certain diseases in newborns and infants. Breastfeeding may also help with gut and immune system development. These positive effects may be due in part to the interaction between breast milk and naturally-occurring bacteria residing throughout the entire gut, but the majority of research has focused on bacteria residing in the lower gut (colon). Very little or no research has looked at the effect of early diet on the bacteria in the small intestine where the immune system is active. Since it is very difficult to obtain samples from the small intestine in infants and children, a 21 day old piglet model was used to determine bacteria profiles of small intestine contents in response to differing postnatal diets: some piglets were fed by their mothers, and others were fed with either a dairy- or soy-based infant formula. In addition we measured metabolites from the small intestine tissue to see if there were any relationships between the bacteria and how the small intestine cells are functioning. In the early region of the small intestine (duodenum), we found that piglets fed by their mothers had more types of bacteria when compared to piglets fed to both formula groups. All diet groups had very distinct diet-specific bacteria profiles in this region. In total, there were 77 bacterial groups altered due to dietary differences in the early region of the small intestine. In the middle region of the small intestine (jejunum) the piglets fed by their mothers had a bacteria profile that were still distinct from the formula fed groups, but the two formula groups now had very similar bacteria profiles. In total, 48 bacterial groups were different due to diet. In the lower region of the small intestine (ileum), the bacteria profiles mirrored the middle region and only 19 bacterial groups were changed by diet. Many of diet-associated metabolites shared a close relationship changes in bacterial groups in the ileum of the small intestine. This study provides new insight into how diet can change the profile of bacteria in the very inner part of our gut. It appears that diet has very distinct effects on the early region of the small intestine and then has weaker effects in the middle and end regions. This may be very important for how natural bacteria influence the developing gut in infants, when the gut and immune system are growing and learning how to deal with the outside environment. Specific components of breast milk and formulas that lead to changes in the infant’s gut bacteria and their intestinal metabolism are under study. This helps build the scientific evidence base relating to breastfeeding recommendations, and the information could lead to better strategies for making specific formulas that promote optimal gut function in newborns.

Technical Abstract: Exclusive breastfeeding is known to be protective against gastrointestinal disorders and may modify gut development. Although the gut microbiome has been implicated, little is known about how early diet impacts the small intestinal microbiome, and how microbial shifts impact gut metabolic physiology. We hypothesize that exclusive infant formula feeding will promote a unique small intestine microbial profile compared to exclusive breastfeeding in neonatal piglets. To address these knowledge gaps, small intestinal contents from 21-day old neonatal piglets that were either provided ad-libitum access to sow-feeding, or dairy- or soy-based infant formulas were subjected to 16S rRNA sequencing. Ileum tissue metabolomics analyses were assessed by LC-MS. Greater a-diversity was observed in the duodenum of sow-fed piglets compared to formula groups (P < 0.05). No differences were observed in the ileum. Firmicutes represented the most abundant phylum across all diets in the duodenum (78.8%, 80.1% and 53.4% relative abundance in sow, dairy, and soy groups), followed by Proteobacteria in sow (12.2%) and dairy (12.4%) groups and Cyanobacteria in soy (36.2%) fed animals. In contrast to the duodenum, Proteobacteria was the dominant phylum in the ileum with > 60% relative abundance in all groups. In the duodenum, 77 genera were altered by diet, followed by 48 in the jejunum and 19 in the ileum. Metabolomics analyses revealed associations among ileum tissue metabolites (e.g., acylcarnitines and 3-aminoisobutyric acid) and diet-responsive microbial genera. These results indicate that neonatal diet has regional effects on the small intestine microbiome, with the most pronounced effects in the duodenum. These regional effects may be important factors when considering gut tissue metabolism and development in the postnatal period.