Abstract
Bacterial communities in gastrointestinal tracts (GIT) play an important role in animal health and performance. Despite its importance, little information is available on the establishment of microbial populations in the goat GIT or on changes occurring during early development. Therefore, this study investigated the bacterial community dynamics of the rumen, duodenum, jejunum, ileum, cecum, and colon in 15 goats at five developmental stages (0, 14, 28, 42, and 56 days old) by using 16S rDNA sequencing and quantitative real-time PCR technology. 940 genera were found to belong to 44 phyla distributed along the GIT. As a whole, the microbial richness and diversity showed a clear increasing trend as the kids aged and alpha diversity differed significantly among GIT compartments mainly occurring at middle day ages (14 and 28 days). Principal coordinate analysis indicated that the bacterial community displayed distinct temporal and spatial specificity along the GIT in preweaning goats. As kids aged, the phylum Firmicutes was replaced by Bacteroidetes in rumen, whereas Proteobacteria in the large intestine was displaced by Firmicutes. The phylum Proteobacteria was mainly present in the small intestine in older animals. In the rumen, taxa, such as Bacillus and Lactococcus decreased and Prevotella, Treponema, Ruminococcus, and unclassified Prevotellaceae increased with the age of kids. Furthermore, a lower proportion of taxa, such as Lactobacillus and Bacteroides was observed with higher abundances of both Christensenellaceae_R_7 and Ruminococcus in duodenum and jejunum in older animals. In the large intestine, the microbiota displayed taxonomic dynamics with increases of Ruminococcaceae UCG 005, unclassified Lachnospiraceae, Barnesiella, and Blautia as kids aged. Predicted pathway analysis suggested that genes involved in amino acid metabolism, and translation were abundant in both rumen and duodenum, while genes involved in membrane transport and carbohydrate metabolism were enriched in the large intestine. These results indicate that both the microbial colonization process and potential function exert a temporal-spatial specificity throughout the GIT of goats. This study provides new insight into the temporal dynamics of GIT microbiota development during preweaning and will aid to develop strategies for improving animal health and downstream production.
Highlights
The microbiomes of the gastrointestinal tract (GIT) of mammalian animals have been increasingly identified as a critical factor in animal health, development, and productivity (Holmes et al, 2012; Yeoman and White, 2014)
Individual-based rarefaction curves were generated for each sample to assess whether the operational taxonomic unit (OTU) coverage was sufficient to accurately describe the bacterial composition of each region (Figure S1)
This study investigated the bacterial community dynamics along the GIT during the preweaning development of goats
Summary
The microbiomes of the gastrointestinal tract (GIT) of mammalian animals have been increasingly identified as a critical factor in animal health, development, and productivity (Holmes et al, 2012; Yeoman and White, 2014). A typical example of these relationships in the rumen is the fibro lytic activity, which facilitates the conversion of plant fibers to soluble small compounds (acetate, propionate, and butyrate). These compounds are absorbed and metabolized for the energy requirements of the animal and for other physiological purposes (Mackie, 2002; Jami et al, 2013; Mao et al, 2015). The GIT is of great significance due to the ability of its microbiomes to transform the heat energy stored in plant structural carbohydrates into animal products, such as meat, wool, and milk (Jami et al, 2013)
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