Abstract
Early microbial colonization in the gut impacts animal performance and lifelong health. However, research on gut microbial colonization and development in young ruminants, especially after weaning, is currently limited. In this study, next-generation sequencing technology was performed to investigate the temporal dynamic changes of the microbial community in the jejunum and colon of goats at 1, 7, 14, 28, 42, 56, 70, and 84 days (d) of age. As age increased, significant increases in microbial diversity, including the number of Observed OTUs and the Shannon Index, were observed in both the jejunum and colon. Regarding beta diversity, significant shifts in community membership and structure from d1 to d84 were observed based on both Bray–Curtis and Jaccard distances. With increasing age, dominant genera in the jejunum shifted from Lactobacillus to unclassified Ruminococcaceae, unclassified Lachnospiraceae and unclassified Clostridiales through starter supplementation, whereas colonic dominant genera changed from Lactobacillus and Butyricicoccus, within d1–d28, to unclassified Ruminococcaceae, unclassified Clostridiales and Campylobacter after solid diet supplementation. The linear discriminant analysis (LDA) effect size (LEfSe) analysis revealed bacterial features that are stage-specific in the jejunum and colon, respectively. In the jejunum and colon, a significantly distinct structure and membership of the microbiota was observed across all ages. The growth stage-associated microbiota in each gut compartment was also identified as a marker for biogeography. Our data indicate the temporal and spatial differences of the gut microbiota in goats are important for their performance and health. Early microbial colonization can influence microbial composition in later life (e.g., post-weaning phase). This study provides insights that the temporal dynamics of gut microbiota development from newborn to post-weaning can aid in developing feeding strategies to improve goat health and production.
Highlights
With next-generation sequencing development, the gut microbiota, which plays important roles in nutrient digestion, health, and disease of animals, can be more deeply investigated
The diversity increased with age from d14 to d84, the Observed OTUs and Shannon Index were not statistically significant (p > 0.05), except for a low Shannon Index on d42 compared with d56
The lowest gut microbial diversity was observed on d1 (p < 0.05)
Summary
With next-generation sequencing development, the gut microbiota, which plays important roles in nutrient digestion, health, and disease of animals, can be more deeply investigated. The factors including anatomical developments, gut physiological environment, diet changes, weaning and administration of antibiotics can generate collateral effects that can influence gut microbiota development and may lead to microbial dysbiosis and subsequent diarrhea or other diseases [3,4,5,6]. When the rumen is not sufficiently developed and does not yet have ruminant function, digestion patterns of neonate kids are mostly dependent on the small and large intestines [8], and are more similar to those of monogastric animals. The intestine of ruminants plays important roles in early life, and its microbiota may differ from other mammals. Understanding the longitudinal changes of the intestinal microbiota allows us to better identify the roles of the microbiota in nutrient digestion and isolate probiotics
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