The Composition and Predictive Function of the Fecal Microbiota Differ Between Young and Adult Donkeys

Abstract

The community of microorganisms inhabiting the gastrointestinal tract of monogastric herbivores played critical roles in the absorption of nutrients and keeping the host healthy. However, its establishment at different age groups has not been quantitatively and functionally examined. The knowledge of microbial colonization and its function in the intestinal tract of different-age donkeys is still limited. By applying the V3–V4 region of the bacterial 16S rRNA gene and functional prediction on fecal samples from different-age donkeys, we characterized the gut microbiota during the different age groups. In contrast to the adult donkeys, the gut microbiota diversity and richness of the young donkeys showed significantly less resemblance. The microbial data showed that diversity and richness increased with age, but a highly individual variation of microbial composition was observed at month 1. Principal coordinate analysis (PCoA) revealed a significant difference across five time points in the feces. The abundance of Bacteroides, Lactobacillus, and Odoribacter tended to decrease, while the proportion of Streptococcus was significantly increased with age. For functional prediction, the relative abundance of pathways had a significant difference in the feces across different age groups, for example, Terpenoids and Polyketides and Folding, Sorting, and Degradation (P < 0.05 or P < 0.01). The analysis of beta diversity (PCoA and LEfSe) and microbial functions predicted with PICRUSt (NSTIs) clearly divided the donkeys into foals (≤3 months old) and adults (≥7 months old). Microbial community composition and structure had distinctive features at each age group, in accordance with functional stability of the microbiota. Our findings established a framework for understanding the composition and function of the fecal microbiota to differ between young and adult donkeys.

Non‐invasive monitoring of multiple wildlife health factors by fecal microbiome analysis

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Integrated multi-omics reveals novel microbe-host lipid metabolism and immune interactions in the donkey hindgut

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The diversity analysis and gene function prediction of intestinal bacteria in three equine species

“…Study of the intestinal microbiota of equine genera by traditional culture method has certain limitations ( Milinovich et al, 2006 ), as approximately 70% of the microbiota cannot be cultured in the laboratory, making it difficult to determine the entire microbial composition and largely limiting its application in taxonomy ( Julliand and Grimm, 2016 ; Park et al, 2021 ). The 16S ribosomal RNA (16S rRNA) gene high-throughput sequencing technology, as a novel technical tool for microbial diversity research, is now widely used in animal intestinal flora research, such as Illumina Hiseq-based technology to study different species ( Liu et al, 2020 ), age ( Xing et al, 2020 ), site ( Su et al, 2020 ), and other The structure and diversity of the intestinal microflora under the influence of different factors. In addition, the prediction of intestinal microbial gene function by PICRUSt2 analysis method to further explore the relationship between intestinal flora and host has become a hot research topic.…”