Early Diet Has Differential Effects on the Small Intestine Microbiome by Region in Neonatal Piglets
Authors: Piccolo Brian , Bowlin Anne , Saraf Manish , Mercer Kelly , Bhattacharya Sudeepa , Chintapalli Sree , Adams Sean , Shankar Kartik , Badger Thomas , Yeruva Laxmi 
Published: June 2021

Exclusive breast milk feeding is known to be protective against gastrointestinal disorders in newborn infants and may reduce the risk of allergies and upper respiratory tract infections well into childhood. Although the exact mechanism of these beneficial effects has not been identified, the gut microbiome is thought to play a major role. Due to the invasiveness of collecting small intestinal contents in infants, the effect of breast milk feeding on the microbiome in the small intestine remains to be explored. To address this gap, we collected duodenal, jejunal, and ileal contents from 21‐day old neo‐natal piglets that were either provided ad‐libitum access to sow‐feeding, or provided dairy milk‐ or soy‐based infant formula diets. Intestinal contents from the duodenum, jejunum, and ileum were collected and assessed for 16S rRNA by Illumina sequencing. Data shown in text are median relative abundances. In the duodenum, Firmicutes represented the most abundant phyla across all diets (78.4%, 86.%, and 53.6% in sow, milk, and soy groups, respectively) followed by Proteobacteria in sow‐ and milk‐fed animals (12.2% and 12.4%, respectively) and Cyanobacteria in soy‐fed animals (37.1%). A total of 15 distinct phyla were detected only in the duodenum of sow‐fed piglets, whereas only 5 and 2 unique phyla were detected in milk‐ and soy‐fed piglets, respectively. This was confirmed with higher α‐diversity measurements (Observed OTUs and Chao1; p < 0.05) in the sow‐fed group compared to formula‐fed groups. The Firmicutes to Proteobacteria ratio in sow‐fed piglets remained similar in the jejunum, but was reversed in milk‐fed piglets; whereas this ratio in the jejunum of soy‐fed piglets became similar to those observed in the jejunum of milk‐fed piglets (i.e., higher Proteobacteria relative to Firmicutes). The large bloom of Cyanobacteria seen in the duodenum of soy‐fed piglets was no longer apparent in the jejunum. In the ileum, the Firmicutes to Proteobactera ratio of sow‐fed animals was reversed and became similar to those observed in the jejenum of formula groups; this ratio was unchanged from the jejunum to the ileum in formula‐fed animals. A total of 86 genera were significantly altered by diet across each intestinal region, with 36 unique to the duodenum, 5 unique genera to the jejunum, and 2 in the ileum. At least 56 genera were significantly altered in both formula groups relative to sow‐fed piglets in the duodenum, followed by 28 in the jejunum, and 8 in the ileum. These results suggest that early infant diet has a pronounced effect in the duodenum, with greater microbial diversity and abundance in breast fed animals. However, the impact of diet on diversity and microbial abundance is reduced in the middle and distal regions of the small intestine. Current studies are leveraging metabolomics to understand the potential factors that link the small intestinal microbiome and tissue metabolism, and the results are also to be presented.Support or Funding InformationThis study was supported by USDA‐ARS Project 6026‐51000‐010‐05S.