MICROBIAL DIVERSITY AND METABOLOMICS OF RUMINAL FLUID IN SHEEP AND GOATS FED WITH CASSAVA PEELS, CONCENTRATE RATION AND Panicum maximum.

Abstract

ABSTRACT Efficient feed utilization is crucial to enhancing productivity and overall health of ruminal animals. However, the precise mechanisms of microbial communities, enzymatic profile and metabolisms remain unclear. Hence, a comprehensive and quantitative metabolomics analysis of five different dietary treatments in sheep and goats were investigated. Forty sheep (twenty adults and twenty growers) and forty goats (twenty adults and twenty growers) were divided into five groups of dietary treatments: Dried Cassava peels (CP) 100%, Dried Cassava peels and Panicum maximum grass (CPG) 50:50, Panicum maximum grass and animal feed concentrate (GAF) 50:50, Dried Cassava peels and Animal feed concentrates in combination (CPAF) 50:50, and dried cassava peels with animal feed concentrate and Panicum maximum grass (CPGAF) 40:20:40. During the feeding experiment, health status of animals was closely monitored using haematological and serum biochemical parameters. At the end of 10 weeks, ruminal fluid samples were collected. Gas chromatography-mass spectrometry (GC-MS) was employed to determine short-chain fatty acids (SCFAs). Microbial enzymatic profile of the ruminal fluids which include: Amylolytic, Proteolytic and Cellulolytic population were determined using cultural approach. Metagenomic analysis of full length 16S rRNA bacterial genes in ruminal fluid samples were sequenced using PacBio and taxonomic information was determined based on QIMME2 for the five diets in sheep and goat. Untargeted metabolome was characterized using gas chromatography of a time-of-flight mass spectrometer. Data obtained was subjected to Analysis of Variance (ANOVA) and means were separated by Turkey’s test using SAS software. Statistical significance was taken with p value ≤ 0.05. Reduced level of packed cell volume was observed in CP, while other diets did not alter the haematology of the animals. Results demonstrated distinct variations in the metabolites and microbial enzymatic profiles among the different dietary treatments. SCFA production in sheep was highest (9.20 mg/L) in those fed with CPGAF while CPAF fed goat had a peak value of 4.59 mg/L. Higher abundance of amylolytic, proteolytic and cellulolytic population of 2.7x106 and 2.6x105 and 1.6x106 CFU/ml was observed in sheep fed with CPGAF, CPGAF and GAF respectively. These groups displayed higher levels of SCFAs, and microbial enzyme potentials. CPGAF produced highest sequence reads of 10202 and 8616 in Sheep and Goat respectively. Bacteroidetes, Firmicutes, and Proteobacteria were top three most abundant phyla representing ~90% of all samples. Microbiological diversity was found in the community, with CPAF having the most evenness. There were a lot of similarities between CPAF and CPG groups in terms of genetic diversity. Bacterial microbiome of CPAF was more diverse, with a higher concentration of motility proteins, two-component systems, bacterial secretion systems, and the formation and breakdown of secondary metabolites. Lower richness of microbiome gene content and taxa was tightly linked to lower feed efficiency. Major families present are Bifidobacteriaceae, Prevotellaceae, Lachnospiraceae, Christensenellaceae, Bacillaceae, Rikenellaceae, Atopobiaceae, Muribaculaceae, and Ruminococcaceae. In conclusion, this study revealed CPGAF had the most improved productivity effect on sheep while GAF supported goat more.