A Metagenomic Insight Into the Hindgut Microbiota and Their Metabolites for Dairy Goats Fed Different Rumen Degradable Starch

Abstract

High starch diets have been proven to increase the risk of hindgut acidosis in high-yielding dairy animals. As an effective measurement of dietary carbohydrate for ruminants, studies on rumen degradable starch (RDS) and the effects on the gut microbiota diversity of carbohydrate-active enzymes (CAZymes), and Kyoto Encyclopedia of Genes and Genomes (KEGG) Orthology functional categories are helpful to understand the mechanisms between gut microbiota and carbohydrate metabolism in dairy goats. A total of 18 lactating goats (45.8 ± 1.54 kg) were randomly divided equally into three dietary treatments with low dietary RDS concentrations of 20.52% (LRDS), medium RDS of 22.15% (MRDS), and high RDS of 24.88% (HRDS) on a DM basis for 5 weeks. Compared with the LRDS and MRDS groups, HRDS increased acetate molar proportion in the cecum. For the HRDS group, the abundance of family Ruminococcaceae and genus Ruminococcaceae UCG-010 were significantly increased in the cecum. For the LRDS group, the butyrate molar proportion and the abundance of butyrate producer family Bacteroidale_S24-7, family Lachnospiraceae, and genus Bacteroidale_S24-7_group were significantly increased in the cecum. Based on the BugBase phenotypic prediction, the microbial oxidative stress tolerant and decreased potentially pathogenic in the LRDS group were increased in the cecum compared with the HRDS group. A metagenomic study on cecal bacteria revealed that dietary RDS level could affect carbohydrate metabolism by increasing the glycoside hydrolase 95 (GH95) family and cellulase enzyme (EC 3.2.1.4) in the HRDS group; increasing the GH13_20 family and isoamylase enzyme (EC 3.2.1.68) in the LRDS group. PROBIO probiotics database showed the relative gene abundance of cecal probiotics significantly decreased in the HRDS group. Furthermore, goats fed the HRDS diet had a lower protein expression of Muc2, and greater expression RNA of interleukin-1β and secretory immunoglobulin A in cecal mucosa than did goats fed the LRDS diet. Combined with the information from previous results from rumen, dietary RDS level altered the degradation position of carbohydrates in the gastrointestinal (GI) tract and increased the relative abundance of gene encoded enzymes degrading cellulose in the HRDS group in the cecum of dairy goats. This study revealed that the HRDS diet could bring disturbances to the microbial communities network containing taxa of the Lachnospiraceae and Ruminococcaceae and damage the mucus layer and inflammation in the cecum of dairy goats.

Dietary Amylose/Amylopectin Ratio Modulates Cecal Microbiota and Metabolites in Weaned Goats

“…The results clearly showed that cecal bacterial composition was affected by feeding different ratios of dietary amylose/amylopectin. The predominant identified mucosa-and digesta-associated phyla were Firmicutes and Bacteroidetes, followed by the phyla Spirochaetes and Verrucomicrobia, which is in line with earlier reports on dairy goats fed different levels of rumen degradable starch ( 4 ). The presence of Spirochaetaes in the colon mucosa of lamb fed a non-pelleted and pelleted high-grain diet has been documented ( 40 ).…”

“…Feeding a high rumen degradable starch increased the risk of intestinal inflammation in the hindgut of dairy goats, as evidenced by an increase in the expression of interleukin-1β and secretory immunoglobulin A (SIgA), and accumulate short-chain fatty acids (SCFAs), and disturbance of microbial function ( 4 ). Developing efficient feeding approaches for ruminant animals needs the maintenance of optimal rumen and hindgut fermentation in the modern feeding system.…”

Mucosal Microbiota and Metabolome in the Ileum of Hu Sheep Offered a Low-Grain, Pelleted or Non-pelleted High-Grain Diet

“…For instance, metabolic and microbial changes in the intestinal mucosa of humans with some diseases (such as inflammatory bowel disease) exhibit interdependent and co-directional relationships (McHardy et al, 2013;Ahmed et al, 2016); probiotics such as bifidobacteria and lactobacillus can inhibit the proliferation of pathogenic bacteria and regulate the intestinal immunity by directly adhering to the intestinal mucosa and their metabolites (He et al, 2001;Hammes and Hertel, 2006). For animals, various factors, especially diets, have important effects on the intestinal microbiota and its metabolites (Wang et al, 2019;Yao et al, 2021). Hence, understanding the different dietary effects on intestinal mucosal microbiota and metabolites would provide favorable information for the subsequent development of dietary probiotics in ruminants.…”

Metagenomic Analysis of in Vitro Ruminal Fermentation Reveals the Role of the Copresent Microbiome in Plant Biomass Degradation

“…The remaining 1 species-level MAG (M10_35: family Lachnospiraceae , genus UBA629 , species 900317915) was simultaneously associated with propionic acid and butyric acid production in RUSITEC. The higher-level taxa to which these MAGs belong have been shown in previous studies to be associated with the production of SCFAs. , However, members of rumen Lachnospiriaceae were also found to belong to heritable rumen species . With the addition of rumen in the in vitro fermentation conditions in the current study, some members of the Lachnospiraceae family were still the copresent rumen microbiome.…”