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

Abstract

Context. Gastrointestinal microorganisms play an important role in ruminant digestion and metabolism, immune regulation and disease prevention and control. Different parts of the digestive tract have different functions and microbial community structures.Aims. This study aims to explore the microbial diversity in the rumen and the small intestine of Xinong Saanen dairy goats.Methods. Rumen fluid and jejunum fluid from three Xinong Saanen dairy bucks with the average slaughter weight of 33.93 AE 0.68 kg were collected and analysed for microbial diversity, by using 16S rRNA gene high-throughput sequencing.Key results. In total, 1118 operational taxonomic units (OTUs) were identified, with 1020 OTUs and 649 OTUs being clustered to rumen and jejunum samples respectively. Alpha-diversity indices were significantly (P < 0.05) different between rumen and jejunum, as indicated by the fact that the rumen microbial community diversity, richness and uniformity/evenness were higher than those of jejunum. At the phylum level, the dominant phyla in the rumen were Bacteroidetes (66.7%) and Firmicutes (25.1%), accounting for 91.8% of the rumen microorganisms. The dominant phylum in the jejunum was Firmicutes, accounting for 73.0% of the jejunum microorganisms. At the genus level, the dominant bacteria in the rumen were Prevotella_1, norank_f_Bacteroidales_BS11_gut_group, Rikenellaceae_ RC9_gut_group, Christensenellaceae_R-7_group and Family_XIII_AD3011_group, whereas the dominant bacteria in the jejunum were Omboutsia, Aeriscardovia, Intestinibacter, unclassified_f_Peptostreptococcaceae and unclassified_f_Bifidobacteriaceae. Clusters of Orthologous Groups (COG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) results showed that the major functions of microorganisms in the rumen and jejunum were carbohydrate metabolism, amino acid metabolism, nucleotide metabolism, membrane transport and translation. Interestingly, fructose and mannose metabolism and peptidoglycan biosynthesis were abundant in the rumen, while homologous recombination and nucleotide excision repair were abundant in the jejunum.Conclusions. Our study clarified the differences in microbial diversity and community structure between the rumen and the jejunum in Xinong Saanen dairy goats. Prevotella was the most predominant genus in the rumen, compared with Romboutsia, Bifidobacterium as well as Peptostreptococcaceae genera, which were the predominant genera in the jejunum.Implications. In combination with the functional prediction of microorganisms and the metabolic characteristics of different parts of the digestive tract in ruminants, our findings provided information for further exploring the relationship among genes, species and functions of microorganisms and their hosts' nutritional and physiological functions.

The gastrointestinal microbiome of browsing goats (Capra hircus)

“…The most abundant genera in the stomachs were Prevotella , Rikenellaceae_RC9_gut_group and Christensenellaceae_R-7_group , which reached up to 44.5% in some of these GIT compartments. In previous studies on goats [ 32 , 44 ], members of Prevotella and families Rikenellaceae and Christensenellaceae were also found predominant in the rumen. In the present study, Prevotella alone reached up to 30.3% of the total abundance.…”

Spatial profiles of the bacterial microbiota throughout the gastrointestinal tract of dairy goats

“…First, a total of 1,023,714 clean reads with an average length of 1452 bp were sequenced from the microbial V1–V9 region, and 6669 distinct OTUs were ultimately identified, which were higher than previously sequenced on sheep (322–789 OTUs) (Wang et al 2017 ) and goats (1118 OTUs) (Li et al 2022 ), indicating that we were able to investigate the bacterial community with a higher resolution.…”

“…The Xinong Saanen dairy goat is a cultivated breed based on the Swiss Saanen dairy goat, which is known for high milk yield, outstanding reproductive performance, and stable genetic performance. Currently, more than half of China’s dairy goats have the lineage of Xinong Saanen dairy goats (Li et al 2022 ). However, research into their microbiome has tended to focus on the rumen or feces, without systematic research into the entire GITs.…”

Bacterial community and diversity in the rumen of 11 Mongolian cattle as revealed by 16S rRNA amplicon sequencing

“…All findings indicated that bacteria played an important role in nutrient digestion and absorption of ruminants. The fiber was digested through the bacteria in the rumen into volatile fatty acids, such as acetic acid, propionic acid, and butyric acid 57 , 58 . Meanwhile, the bacteria could convert the nitrogen-containing substances into amino acids and provided the nitrogen source for ruminants.…”