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

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. <i>Lactobacillus</i> were prominent from day 7, with stage-associated taxa including <i>Lactobacillus johnsonii</i>, <i>Lactobacillus delbrueckii</i>, <i>Ligilactobacillus salivarius</i>, and <i>Limosilactobacillus pontis</i>. Through metagenomic functional analysis, at 21 days, genes were enriched in butanoate metabolism, and <i>Limosilactobacillus pontis</i> 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 <i>Limosilactobacillus mucosae</i>, <i>Limosilactobacillus oris</i>, and <i>Limosilactobacillus pontis</i>. 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.