# Functional and Compositional Changes in Ileal Microbiota in Piglets During the Nursing Period Revealed by 16s rRNA Gene and Metagenomics

## TL;DR

This study shows how the gut microbes in piglets' ileum change and function during the nursing period, highlighting key developmental phases for gut health.

## Contribution

The study reveals specific functional and compositional shifts in ileal microbiota of piglets between day 21 and 28.

## Key findings

- Lactobacillus species like L. johnsonii and L. pontis dominate the ileal microbiota from day 7 onward.
- By day 21, ileal microbes are active in butanoate metabolism, with L. pontis playing a key role.
- By day 28, pathways for cysteine, methionine, and lysine metabolism become prominent, driven by specific Limosilactobacillus species.

## Abstract

This study explored how the gut microbes in the ileum (a part of the small intestine) of piglets develop and function during the nursing period. Using 16s rRNA gene sequencing methods, we found that the diversity of microbial species in the ileum remained relatively stable. Lactobacillus became dominant from day 7 onward, with specific species like Lactobacillus johnsonii and Limosilactobacillus pontis appearing at different stages. Functional analysis revealed that by day 21, using metagenomics analyses, the ileal microbes were especially active in butanoate metabolism. By day 28, pathways related to cysteine, methionine, and lysine metabolism became more prominent—processes vital for amino acid synthesis—primarily associated with Limosilactobacillus mucosae, Limosilactobacillus oris, and Limosilactobacillus pontis. These findings show that microbial community and functions change significantly between day 21 and 28, indicating a key developmental phase for gut health in piglets.

In piglets, the gut microbiota matures in a segment-specific manner during the nursing period, while fecal-based studies provide limited functional resolution across intestinal sites. We profiled the ileum using 16s rRNA gene sequencing and assessed segmental functions by shotgun metagenomics at selected ages. Ileal species richness and diversity were relatively stable across days. Lactobacillus were prominent from day 7, with stage-associated taxa including Lactobacillus johnsonii, Lactobacillus delbrueckii, Ligilactobacillus salivarius, and Limosilactobacillus pontis. Through metagenomic functional analysis, at 21 days, genes were enriched in butanoate metabolism, and Limosilactobacillus pontis as a potential probiotic played an important role in it. At day 28, metagenomic analysis indicated higher relative abundance in the ileum of pathways linked to cysteine and methionine metabolism and lysine biosynthesis, largely carried by Limosilactobacillus mucosae, Limosilactobacillus oris, and Limosilactobacillus pontis. These data describe the composition and function of the ileum in the intestines of piglets and indicate a differentiation period around day 21 to day 28.