Comparison of microbial diversity in rumen and small intestine of Xinong Saanen dairy goats using 16S rRNA gene high-throughput sequencing

Context Gastrointestinal microorganisms play an important role in ruminant digestion and metabolism, immune regulation disease prevention control. Different parts of the digestive tract have different functions microbial community structures. Aims This study aims to explore diversity rumen small intestine Xinong Saanen dairy goats. Methods Rumen fluid jejunum from three bucks with average slaughter weight 33.93 ± 0.68 kg were collected analysed for diversity, by using 16S rRNA gene high-throughput sequencing. Key results In total, 1118 operational taxonomic units (OTUs) identified, 1020 OTUs 649 being clustered samples respectively. Alpha-diversity indices significantly (P < 0.05) between jejunum, as indicated fact that richness uniformity/evenness higher than those jejunum. At phylum level, dominant phyla Bacteroidetes (66.7%) Firmicutes (25.1%), accounting 91.8% microorganisms. The was Firmicutes, 73.0% genus bacteria Prevotella_1, norank_f_Bacteroidales_BS11_gut_group, Rikenellaceae_RC9_gut_group, Christensenellaceae_R-7_group Family_XIII_AD3011_group, whereas Omboutsia, Aeriscardovia, Intestinibacter, unclassified_f_Peptostreptococcaceae unclassified_f_Bifidobacteriaceae. Clusters Orthologous Groups (COG) Kyoto Encyclopedia Genes Genomes (KEGG) showed major carbohydrate amino acid nucleotide membrane transport translation. Interestingly, fructose mannose metabolism peptidoglycan biosynthesis abundant rumen, while homologous recombination excision repair Conclusions Our clarified differences structure Prevotella most predominant compared Romboutsia, Bifidobacterium well Peptostreptococcaceae genera, which genera Implications combination functional prediction metabolic characteristics ruminants, our findings provided information further exploring relationship among genes, species their hosts’ nutritional physiological functions.