Characterization of microbial communities from rumen and large intestine of lactating creole goats grazing in arid plant communities

Abstract

Arid plant communities provide variable diets that can affect digestive microbial communities of free-foraging ruminants. Thus, we used next-generation sequencing of 16S and 18S rDNA to characterize microbial communities in the rumen (regurgitated digesta) and large intestine (faeces) and diet composition of lactating creole goats from five flocks grazing in native plant communities in the Sonoran Desert in the rainy season. The bacterial communities in the rumen and large intestine of the five flocks had similar alpha diversity (Chao1, Shannon, and Simpson indices). However, bacterial community compositions were different: a bacterial community dominated by Proteobacteria in the rumen transitioned to a community dominated by Firmicutes in the large intestine. Bacterial communities of rumen were similar across flocks; similarly occurred with large-intestine communities. Archaea had a minimum presence in the goat digestive tract. We detected phylum Basidiomycota, Ascomycota, and Apicomplexa as the main fungi and protozoa. Analyses suggested different diet compositions; forbs and grasses composed the bulk of plants in the rumen and forbs and shrubs in faeces. Therefore, lactating goats consuming different diets in the Sonoran Desert in the rainy season share a similar core bacterial community in the rumen and another in the large intestine and present low archaeal communities.

Deciphering the Impact of Nutrient Composition and Tissue Structure on Rumen Microbiome Dynamics in Roughage Degradation

“…The presence of pyruvate oxidation genes in Prevotella equips these species to flourish in nutrient-scarce environments, leading to their abundance during the early feed fermentation stages [56,57,62]. Concurrently, Chytridiomycota, Ascomycota, and Mucoromycota were identified as the primary anaerobic fungi phyla in the rumen for different roughages, consistent with findings for cows and goats [63]. Anaerobic fungi are instrumental in rumen fiber degradation, primarily leveraging rhizomorph systems and a spectrum of cellulolytic enzymes [64].…”

Impact of Nutrient Composition on Rumen Microbiome Dynamics and Roughage Degradation

“…The presence of pyruvate oxidation genes in Prevotella enables these species to ourish in nutrient-scarce environments, leading to their abundance during the early feed fermentation stages [30,31,36]. Concurrently, Chytridiomycota, Ascomycota, and Mucoromycota were identi ed as the primary anaerobic fungi phyla in the rumen for different roughages, consistent with ndings in cows and goats [37]. Anaerobic fungi are instrumental in rumen ber degradation, primarily utilizing rhizomorph systems and a spectrum of cellulolytic enzymes [38].…”