Abstract
Ruminants fulfill their energy needs for growth primarily through microbial breakdown of plant biomass in the rumen. Several biotic and abiotic factors influence the efficiency of fiber degradation, which can ultimately impact animal productivity and health. To provide more insight into mechanisms involved in the modulation of fibrolytic activity, a functional DNA microarray targeting genes encoding key enzymes involved in cellulose and hemicellulose degradation by rumen microbiota was designed. Eight carbohydrate-active enzyme (CAZyme) families (GH5, GH9, GH10, GH11, GH43, GH48, CE1, and CE6) were selected which represented 392 genes from bacteria, protozoa, and fungi. The DNA microarray, designated as FibroChip, was validated using targets of increasing complexity and demonstrated sensitivity and specificity. In addition, FibroChip was evaluated for its explorative and semi-quantitative potential. Differential expression of CAZyme genes was evidenced in the rumen bacterium Fibrobacter succinogenes S85 grown on wheat straw or cellobiose. FibroChip was used to identify the expressed CAZyme genes from the targeted families in the rumen of a cow fed a mixed diet based on grass silage. Among expressed genes, those encoding GH43, GH5, and GH10 families were the most represented. Most of the F. succinogenes genes detected by the FibroChip were also detected following RNA-seq analysis of RNA transcripts obtained from the rumen fluid sample. Use of the FibroChip also indicated that transcripts of fiber degrading enzymes derived from eukaryotes (protozoa and anaerobic fungi) represented a significant proportion of the total microbial mRNA pool. FibroChip represents a reliable and high-throughput tool that enables researchers to monitor active members of fiber degradation in the rumen.
Highlights
Ruminants are among the most efficient herbivorous animals to convert plant biomass into edible products, principally due to a symbiotic relationship with microorganisms inhabiting the rumen
The FibroChip was designed with the objective to propose a high-throughput tool providing a rapid picture of the capacity of rumen microorganisms to degrade cellulose and hemicelluloses based on a targeted metatranscriptomic approach
We chose to focus on a few number of genes by targeting main ruminal fibrolytic microorganisms and selected carbohydrateactive enzyme (CAZyme) families that may have a pivotal role in cellulose and hemicellulose degradation
Summary
Ruminants are among the most efficient herbivorous animals to convert plant biomass into edible products, principally due to a symbiotic relationship with microorganisms inhabiting the rumen. The rumen microbiota is composed of a very diverse and complex population of bacteria, archaea, protozoa, and fungi. This microbial community has a remarkable ability to degrade and ferment. The efficiency of the plant biomass degradation depends on the activity of the microbial enzymes produced by the rumen microorganisms These enzymes include glycoside hydrolases (GH) active against the main plant structural polysaccharides (cellulose and hemicelluloses) and carbohydrate esterases (CE) which cleave polysaccharide substituents (Flint et al, 2012). Fibrolytic activity of rumen microorganisms can be affected by diverse biotic or abiotic factors, such as chemical composition and physical structure of the plant material, use of dietary additives, or microbiota dysbiosis leading to unfavorable ruminal conditions (Chaucheyras-Durand et al, 2012)
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