345 Insights into gut microbiome changes from birth to peri weaning period in pastured goat kids.

Abstract The gut microbiome is involved in a wide range of metabolic, immunologic and physiological processes that work to ensure the health, performance and overall wellbeing of animals. Understanding the changes that occur in microbiome structure during growth in healthy animal hosts may give us a foundation onto which to build disease intervention and growth performance enhancing strategies that utilize gut microbial manipulations among other insights. In this study, we used shotgun metagenomics sequencing of fecal DNA to evaluate the diversity, prevalence and changes in abundance of gut microbial populations in a cohort of twelve goats followed from birth until one week after weaning. Sampling points included were 48hrs after birth, 7days, 28days, 42days, weaning day, 2days and 7days after weaning. We report significant differences in alpha and beta microbial diversity as goat kids transition through the different growth phases. Overall the microbial richness and diversity increases significantly from two days of birth to one week after weaning with highest diversity detected at 28days of age and 2 days after weaning and lowest at 42 days of age. Significant differences in the prevalence and abundance of key bacterial taxa was also detected. The top eight phyla detected in this cohort of goats were Proteobacteria, Bacteroidetes, Firmicutes, Actinobacteria, Verrucomicrobia, Fibrobacteres, Euryarchaeota and Candidatus Saccharibacteria in descending order although individual phyla abundance varied among age groups. The phylum Bacteroidetes was most abundant in goats up to 42days of age while Actinobacteria were predominantly detected in peri weaned goats. Among the genera, Bacteroides, Escherichia, Clostridium, Phocaeicola, and Alistipes, were top five most abundant and prevalent in goat kids during the pre-weaning period. On the other hand, Athrobacter, Acinetobacter, Psychrobacter and Psychrobacillus were the most abundant genera around the peri-weaning period. At species and strain level, there were also key differences in the prevalence and abundance of beneficial microbial species belonging to Lactobacillus, Bifidobacterium, Enterococcus, Pediococcus genera and pathogenic species like E. coli, Campylobacter spp and Salmonella spp before and around weaning. This study offers new insight into previously unknown age-based differences in gut microbial communities in pastured goats. The information could also help in understanding age specific risk of microbial diseases and potential beneficial microbial species that could be targeted for use as direct fed microbial for each age group.