85 Can feces be used to represent the cecal microbiota in horses?

Abstract

The fecal microbiota has been accepted as representative of the microbiota of horses' large intestine, but it is important to know which compartment the fecal microbiota most resembles, since the composition of the microbiota changes in each compartment. The study's aim was to compare fecal and cecal microbiota in to determine if the former provides a reasonable approximation of the latter. The Ethics Committee on Animal Research (2057/21-FCAV/UNESP) approved this study. In a 3-way Crossover Design, 5 healthy mixed-breed horses (BW: 384 ± 9.5 kg) were fed 3 different diets: hay, fiber and oil (FO), and sugar and starch (SS). Diets with added concentrate (FO and SS) kept the proportion of dry matter from hay at 1.5%/BW and concentrate at 0.5%/BW. Rectal sampling was used to collect feces, and cecal fluid samples were obtained from a cecal cannula. The microbiota was identified using Illumina MiSeq sequencing of the V4 region of the 16S rRNA gene. DADA2 was used to analyze the data (version 1.24.0). We used the Shannon index and the Chao1 index for α diversity, and Jaccard and Bray-Curtis for β diversity (abundance). DADA2 was used to assess the statistical significance of diversity metrics. Regardless of diet, the microbiota in the cecum and feces showed differences in diversity and abundance (P < 0.01). The Jaccard and Bray distances between the cecum and the feces were 57.4% and 48.4%, respectively, indicating a difference between the 2 sites studied.There was no phylum difference between diets (P > 0.01). The most abundant phyla in the cecum were Proteobacteria, Verrucomicrobiota, and Desulfobacterota, which differed from the literature (Bacteroidota and Firmicutes). Proteobacteria is commonly found in the ilium, and it is possible that the phylum gained access to the cecum through extravasation of this compartment. Furthermore, the positioning of the cannula, closer to the ilium opening in the cecum, may have contributed to the finding of a greater abundance of this phylum. The Verrucomicrobiota is commonly found in the cecum, and little is known about the Desulfobacterota. In the feces, the most abundant phyla were similar to those previously reported, including Bacteroidota, Firmicutes, and Fibrobacterota. The large difference between the microbiota of the cecum and the feces can be attributed to the greater distance between the collection sites, as it is known that the microbiota composition changes in each compartment. The fecal microbiota is an overview of what happens in the large intestine but may not effectively represent other intestinal compartments. Finally, the fecal microbiota does not represent the cecal microbiota.