Neonatal diet impacts bioregional microbiota composition in piglets fed human breast milk or infant formula

Authors: BRINK, LAUREN - Arkansas Children'S Nutrition Research Center (ACNC); MATAZEL, KATELIN - Arkansas Children'S Nutrition Research Center (ACNC); PICCOLO, BRIAN - Arkansas Children'S Nutrition Research Center (ACNC); BOWLIN, ANNE - Arkansas Children'S Nutrition Research Center (ACNC); CHINTAPALLI, SREE - Arkansas Children'S Nutrition Research Center (ACNC); SHANKAR, KARTIK - Arkansas Children'S Nutrition Research Center (ACNC); YERUVA, LAXMI - Arkansas Children'S Nutrition Research Center (ACNC)

Submitted to: Journal of Nutrition
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/24/2019
Publication Date: 8/2/2019
Citation: Brink, L.R., Matazel, K., Piccolo, B.D., Bowlin, A.K., Chintapalli, S.V., Shankar, K., Yeruva, L. 2019. Neonatal diet impacts bioregional microbiota composition in piglets fed human breast milk or infant formula. Journal of Nutrition. https://doi.org/10.1093/jn/nxz170.
DOI: https://doi.org/10.1093/jn/nxz170

Interpretive Summary: Human milk (HM) has evolved to nourish the developing human infant. Aside from containing macro-and micronutrients, HM contains bioactive components, some of which are highly-conserved across species (such as lactoferrin, an iron-containing protein) while others are responsive to the environment (such as serum immunoglobulin A, which shows altered activities depending on pathogen exposure). Epidemiologic evidence demonstrates that babies fed HM have improved short- and long-term immune health outcomes compared to their formula-fed counterparts. This may come about through signals from the normal set of bacteria that live in the gastrointestinal (GI) tract (the "gut microbiome"). Bioactive components in HM appear to shape the gut microbiome of neonates, which may confer immunologic protection. HM and formula milk fed infants have been shown to have different microbiome profiles when measured in the stool. Currently, limited data exist on whether HM components influence the microbiome in region-specific ways in the GI tract. Considering the difficulty of obtaining multiple bioregional samples from human infants, one must turn to animal models to examine this question. The piglet is a good animal model for the study of GI tract development, as there are many similarities with humans in terms of the digestive and metabolic functions of the gut. Additionally, the establishment of microbiota in the pig is similar to human infants with respect to being influenced by early postnatal diet and weaning. We have previously established this model for the examination of HM feeding's effects on the humoral and cell-mediated immune response. The current study complements and extends our prior work by determining the bioregional microbiome in response to HM versus cow's milk formula (MF). Specifically, we determined if early postnatal diets differentially alter the microbiome short-term (postnatal day 21, PND21) and longer-term, post-weaned (postnatal day 51, PND51) stages of piglet growth. While some diet effects were seen in the small intestine, a more pronounced effect in the large intestine was observed: HM led to decreased bacterial diversity, along with shifts in beta diversity. Similar results were observed in stool samples from human infants fed with HM, further suggesting the piglet fed with HM is a good model to test questions that are relevant to human health. At PND21, Campylobacter was increased from the duodenum until the distal colon (DC) and Turicibacter was decreased in the HM group across the ileum, cecum, proximal colon (PC), DC and rectum. In addition, higher abundance of genera that belongs to the class Bacteroidia in the large intestine (cecum, PC and rectum) was observed in HM fed piglets in comparison to MF fed piglets. Differences due to diet were seen at the post-weaning PND51 time point; however, different taxa were generally altered. We conclude that the complex mixture of breastmilk components are key to shaping the gut microbiome, and future studies are needed to understand how normal bacterial colonization of the GI tract impacts immune programming and health outcomes later in life

Technical Abstract: Early infant diet influences postnatal gut microbial development, which in turn can modulate the developing immune system. However, it is not known how disparate diets such as human milk (HM) or formula differentially change microbiota patterns along multiple sections of the gastrointestinal (GI) tract. We aimed to characterize diet-specific bioregional microbiome differences in weaned and post-weaned piglet. Piglets were raised on a HM or dairy cow's milk based formula (MF) based diet from postnatal day (PND) 2 to PND21 and weaned to ad -libitum solid diet until PND51. Piglets were euthanized on either PND21 or PND51 and the contents within each section of the GI tract were obtained for 16s RNA sequencing. Data were analyzed using QIIME, diversity measurements and relative abundance testing methods to examine bioregional differences due to diet. While some diet effects were seen in the small intestine, a more pronounced effect in the large intestine was observed where HM led to decreased Shannon alpha diversity, along with shifts in beta diversity. At PND21, Campylobacter was increased from the duodenum until the distal colon (DC) and Turicibacter was decreased in the HM group across the ileum, cecum, proximal colon (PC), DC and rectum. In addition, higher abundance of genera that belongs to class Bacteroidia in the large intestine (cecum, PC and rectum) was observed in HM fed piglets in comparison to MF fed piglets. Differences due to diet were seen at the post-wean time point; however, different taxa were generally affected. This study highlights that HM feeding differentially effects microbiota in both a short-term and a sustained manner, and this difference is most pronounced in large intestinal regions. We find changes in the microbiota profile due to diet across GI regions and hypothesize that these differences could be influencing immune system development.