von Felde, A. | Search bioRxiv

bioRxiv2025

Composition and short chain fatty acid formation of pig fecal microbiota during growth on predigested wheat and rye in vitro

BackgroundWhile wheat is the most commonly used cereal in pig feeding, rye has gained renewed interest as a component in pig diets due to its positive effects on gut health. The effects of distinct cereal sources on the composition and functionality of gut microbiota are, however, poorly investigated so far. In vitro studies offer a valuable approach to gain detailed insights on this matter, however, require a substrate that closely mimics the conditions found in the large intestine. In this study, we performed predigestion of cereal substrates using ileo-cecally fistulated minipigs simulating the upper gastrointestinal digestion. The composition of microbiota, total cell counts, and short chain fatty acid concentrations after a 24-hour incubation were analysed. Results were compared to cultures containing native substrates. ResultsBoth acetate and propionate concentration were significantly higher in predigested rye compared to predigested wheat (8.17 {+/-} 2.71 vs. 6.55 {+/-} 2.16 mmol/l and 3.40 {+/-} 0.436 vs. 2.64 {+/-} 0.337 mmol/l, respectively), whereas butyrate concentrations were not different. Substantial differences were observed between native and predigested substrates with a higher butyrate production on the former. Bacterial cell counts were higher in predigested substrates and elevated in rye cultures compared to respective wheat incubations. Bacterial communities differed markedly between the two predigested cereals as well as between native and predigested substrates. Several known butyrate and propionate producers - for example Agathobacter, Blautia, Coprococcus, Mediterraneibacter and Roseburia - grew significantly more on predigested rye than on predigested wheat. Bifidobacterium, Clostridium sensu stricto, and Succinivibrio were significantly more abundant on native substrates compared to their predigested forms. ConclusionRye promoted higher production of acetate and propionate compared with wheat along with a distinct bacterial community composition. Predigestion of substrates was crucial in in vitro experiments for gaining adequate insights into growth and substrate degradation by colonic microbiota.

microbiology↗

bioRxiv2025

Uncovering differences in rye and wheat degradation by human gut microbiota applying a quantitative multi-metaOmics in vitro approach

While wheat is the most common grain used in bread-making worldwide, rye is popular in many European countries too. Rye is associated with several health benefits, which is attributed to its comparatively higher fiber content (primarily fructans and arabinoxylans) that promote production of short chain fatty acids (SCFA) by gut microbiota, in particular butyrate. Intervention studies revealed bacterial alterations upon rye administration, however, the detailed mechanisms involved in its degradation are not understood. We grew fecal communities (n=20) on pre-digested rye and wheat, respectively, demonstrating that rye was yielding higher cell and SCFA concentrations in almost all samples along with distinct abundances of many taxa. A multi metaOmics (metagenomics/metatranscriptomics) approach (n=5 donors) showed higher bacterial growth rates for most taxa on rye compared to wheat. The higher growth rate of rye was accompanied by increased expression of genes involved in growth and energy generation suggesting higher carbon substrate accessibility. The carbohydrate active enzyme repertoire was greatly distinct between communities growing on the two substrates with several specific glycoside hydrolases increasingly expressed in rye containing cultures. Agathobacter faecis was revealed as the key butyrogenic species for rye degradation and its expression pattern based on metagenome assembled genomes showed adaptation to growth on rye via expression of genes involved in arabinoxylan degradation and fructose (major monomer of fructans) uptake. Our study verifies higher SCFA production from rye over wheat and gives detailed insights into molecular mechanisms involved. It supports that the observed health benefits of rye are mediated by gut microbiota.

microbiology↗