Integrative clustering by colonic volatile fatty acids reveals microbiota and host physiological variation in weaned piglets

TL;DR

This study identifies two distinct volatile fatty acid (VFA) profiles in weaned piglets, linking gut microbiota and metabolism to intestinal health and growth performance.

Contribution

The study introduces a novel integrative clustering approach to classify VFA phenotypes and connects them to gut microbiota and host physiology in weaned piglets.

Findings

The HSCFA group showed higher VFA concentrations, lower ammonia, and better intestinal health indicators like increased villus height.

The HBCFA group had elevated branched-chain fatty acids and ammonia, along with less beneficial microbes like Escherichia-Shigella.

An XGBoost model identified key genera like Lactobacillus and Escherichia-Shigella that distinguish the two VFA phenotypes.

Abstract

Volatile fatty acids (VFAs) reflect microbial fermentation linking gut microbiota, metabolism and host physiology. However, endogenous VFA profiles and their physiological relevance remain insufficiently characterized. This study aimed to identify distinct VFA phenotypes in weaned piglets and reveal how microbial fermentation patterns connect gut metabolism with animal health and performance.

In this study, we integrated six independent trials comprising 164 weaned piglets. Here, k-means clustering of six VFAs in colonic digesta to identified two metabolite phenotypes: high level of short-chain fatty acids (HSCFA) and high level of branched-chain fatty acids (HBCFA). Generally, The HSCFA group exhibited significantly higher concentrations of VFA (P < 0.001), and lower levels of ammonia and serum urea (P < 0.001), consistent with enhanced carbohydrate fermentation and reduced nitrogen output. Additionally, the HSCFA group had significantly greater villus height in the distal small intestine (P < 0.01), lower mid-colonic pH (P < 0.001) and thrombocyte counts (P < 0.01). In contrast, the HBCFA group showed elevated levels of branched-chain fatty acids and ammonia (P < 0.001), as well as enrichment of Escherichia-Shigella, Rikenellaceae dgA-11 gut group and Prevotella (adjusted P < 0.05). The HSCFA group was enriched in Lactobacillus, Mitsuokella and Dialister (adjusted P < 0.05), and exhibited higher final body weight and average daily gain (P < 0.05), indicating better growth performance. To explore associations between gut microbiota and VFA phenotypes, an XGBoost classification model was trained, based on genus-level composition, to predict the metabolic phenotype. It achieved a moderate accuracy and identified Unclassified Eubacterium coprostanoligenes group, Lactobacillus and Escherichia-Shigella as important genera contributing to group separation.

Clustering based on colonic VFA profiles identified distinct microbial and physiological patterns that may influence gut function and growth performance in weaned piglets. The enrichment of beneficial microbes and fermentation products in the HSCFA group suggests a more favorable intestinal environment, while protein fermentation in the colon seems associated with reduced animal performance and less beneficial intestinal environment.

The online version contains supplementary material available at 10.1186/s40104-026-01353-7.

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