Dietary modulation of intestinal integrity and functionality in weaned piglets using short-chain fructooligosaccharides, essential oils and sodium humate

Abstract

This dataset contains fecal microbiota sequencing data generated in the study “Dietary modulation of intestinal integrity and functionality in weaned piglets using short-chain fructooligosaccharides, essential oils and sodium humate.” Early weaning represents a critical challenge in intensive pig production, frequently associated with intestinal dysfunction, immune activation, and microbial instability. In the context of global restrictions on antibiotic growth promoters, nutritional strategies targeting gut health have gained increasing interest. This study evaluated the effects of short-chain fructooligosaccharides (scFOSs), essential oils of Lippia origanoides and Eugenia caryophyllata combined with sodium humate (EOs-SH), and their combination on intestinal functionality and microbial ecology in weaned piglets under commercial production conditions. The trial was conducted as a room-level feeding study with two independent temporal replicates. A total of 800 clinically healthy piglets, weaned at 21 ± 2 days of age, were allocated to four dietary treatments (100 piglets per treatment per replicate): a basal diet (control), basal diet supplemented with scFOSs, basal diet supplemented with EOs-SH, and a combined scFOSs–EOs treatment. Dietary treatments were applied for 15 days post-weaning. Fecal samples were collected at multiple time points during the post-weaning period and pooled at the room level to characterize treatment-associated microbial profiles. Microbiota composition was assessed by 16S rRNA gene sequencing, and the dataset includes taxonomic abundance tables and associated metadata. Microbiota analysis revealed distinct, treatment-specific patterns. Supplementation with EOs-SH reduced the relative abundance of several genera commonly associated with proinflammatory or dysbiotic states, including Clostridium sensu stricto 1, Terrisporobacter, Prevotella 115, and Subdoligranulum. In contrast, scFOSs supplementation markedly increased the abundance of Lactobacillus, consistent with its recognized prebiotic effect. The combined treatment did not induce relevant microbial shifts. This dataset provides a comprehensive resource for exploring diet-driven modulation of the gut microbiota during the early post-weaning period and supports the interpretation of intestinal functional and immunological outcomes reported in the associated manuscript. It may be useful for comparative microbiome analyses, meta-analyses, and the development of nutritional strategies aimed at improving gut health in antibiotic-free pig production systems.