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

Abstract

The gastrointestinal tract (GIT) is stationed by a dynamic and complex microbial community with functions in digestion, metabolism, immunomodulation, and reproduction. However, there is relatively little research on the composition and function of microorganisms in different GIT segments in dairy goats. Herein, 80 chyme samples were taken from ten GIT sites of eight Xinong Saanen dairy goats and then analyzed and identified the microbial composition via 16S rRNA V1-V9 amplicon sequencing. A total of 6669 different operational taxonomic units (OTUs) were clustered, and 187 OTUs were shared by ten GIT segments. We observed 264 species belonging to 23 different phyla scattered across ten GITs, with Firmicutes (52.42%) and Bacteroidetes (22.88%) predominating. The results revealed obvious location differences in the composition, diversity, and function of the GIT microbiota. In LEfSe analysis, unidentified_Lachnospiraceae and unidentified_Succinniclassicum were significantly enriched in the four chambers of stomach, with functions in carbohydrate fermentation to compose short-chain fatty acids. Aeriscardovia, Candidatus_Saccharimonas, and Romboutsia were significantly higher in the foregut, playing an important role in synthesizing enzymes, amino acids, and vitamins and immunomodulation. Akkermansia, Bacteroides, and Alistipes were significantly abundant in the hindgut to degrade polysaccharides and oligosaccharides, etc. From rumen to rectum, α-diversity decreased first and then increased, while β-diversity showed the opposite trend. Metabolism was the major function of the GIT microbiome predicted by PICRUSt2, but with variation in target substrates along the regions. In summary, GIT segments play a decisive role in the composition and functions of microorganisms. KEY POINTS: • The jejunum and ileum were harsh for microorganisms to colonize due to the presence of bile acids, enzymes, faster chyme circulation, etc., exhibiting the lowest α-diversity and the highest β-diversity. • Variability in microbial profiles between the three foregut segments was greater than four chambers of stomach and hindgut, with a higher abundance of Firmicutes dominating than others. • Dairy goats dominated a higher abundance of Kiritimatiellaeota than cows, which was reported to be associated with fatty acid synthesis.

Keywords: 16S rRNA; Dairy goats; Diversity; GIT; Microbial profiles.

Fig. 1

Valid sequences and diversity indexes of ten GIT microbial populations. a The number of clean reads sequenced from ten GIT chyme samples. b The average length of clean reads sequenced from ten GIT chyme samples. c The number of OTUs annotated to ten GIT chyme samples. d The goods coverage index of ten GIT chyme samples. e The Shannon index of ten GIT chyme samples. f The Simpson index of ten GIT chyme samples. g The Chao1 index of ten GIT chyme samples. h The ACE index of ten GIT chyme samples. i The unweighted UniFrac index of ten GIT chyme samples

Fig. 2

The shared OTUs of ten GIT segments. a The OTUs shared by ten GIT segments. b The OTUs shared by four chambers of stomach. c The OTUs shared by six intestinal segments

Fig. 3

β-diversity analysis of ten GIT segments. a The non-metric multidimensional scaling (NMDS) plot based on Bray–Curtis distance. b Principal coordinate analysis (PCOA) based on Bray–Curtis distance. c The principal component analysis plot (PCA) based on Bray–Curtis distance. d The hierarchical tree shows the UPGMA clustering result

Fig. 4

Microbial composition of the ten GIT segments. aThe phylum-level microbial composition of each GIT segment. b The genus-level microbial composition of each GIT segment. c The Firmicutes composition of each GIT segment. d The Bacteroidetes composition of each GIT segment. e The Kiritimatiellaeota composition of each GIT segment. f The unidentified_Lachnospiraceae composition of each GIT segment. g The Succiniclasticum composition of each GIT segment. h The unidentified_Ruminococcaceae composition of each GIT segment

Fig. 5

LEfSe cladogram showing the taxonomic differences of ten GIT segments. a LEfSe analysis of the ten GIT segment. b LEfSe analysis of three GIT clusters: stomach (rumen, reticulum, omasum, abomasum); foregut (duodenum, jejunum, ileum), and hindgut (cecum, colon, rectum). The node size corresponds to the average relative abundance of the taxa. Coloring principle: Taxa with no significant differences are colored in yellow, while differentiated biomarkers follow the group color

Fig. 6

GIT microbial co-occurrence network analysis. a The co-occurrence of microbiota in the four chambers of stomach. b The co-occurrence of microbiota in the foregut. c The co-occurrence of microbiota in the hindgut. Red line: Spearman’s rank correlation coefficient > 0.40. Blue line: Spearman’s rank correlation coefficient <  − 0.40. The size of nodes was proportional to the relative abundance of genera; the color of nodes was the level of closeness centrality (red, high; grey, medium; green, low)

Fig. 7

Distribution of the predicted functional pathway a Biological functions enriched based on KEGG level 1 of ten GITs. b Biological functions enriched based on KEGG level 1 in different GITs. c The differential metabolic pathways between stomach and foregut based on the KEGG level 2. d The differential metabolic pathways between stomach and hindgut based on the KEGG level 2. e The differential metabolic pathways between foregut and hindgut based on the KEGG level 2. Stomach (rumen, reticulum, omasum, abomasum); foregut (duodenum, jejunum, ileum), hindgut (cecum, colon, rectum)