Feed efficiency phenotypes in lambs involve changes in ruminal, colonic, and small-intestine-located microbiota

Area of Science:

• Animal Science
• Microbiology
• Genetics

Background:

• Rumen microbiota differences are known between efficient and inefficient animals.
• Hindgut and small intestine microbiota variations related to feed efficiency are understudied.
• Understanding the full gastrointestinal tract (GIT) microbial landscape is crucial for feed efficiency.

Purpose of the Study:

• To investigate microbiota variations across the entire GIT in lambs with extreme feed efficiency phenotypes.
• To identify specific microbial taxa associated with feed efficiency in different GIT regions.
• To determine if feed efficiency is influenced by microbial communities beyond the rumen.

Main Methods:

• Sampling of rumen, duodenum, jejunum, ileum, colon, and feces from 12 lambs at feed efficiency extremes.
• 16S rRNA gene sequencing (V3-V4 region) for microbial profiling.
• Analysis of beta-diversity and relative abundances of operational taxonomic units (OTUs) using ANOSIM and Bonferroni correction.

Main Results:

• Distinct microbial communities were identified in most GIT locations, with significant differences between rumen, duodenum, and colon.
• Beta-diversity analysis showed greater microbial dissimilarity between anatomically distant GIT regions.
• Thirteen OTUs, including fibrolytic (Fibrobacteres, Ruminococcaceae) and health-associated (Bifidobacteriaceae, Christensenellaceae) taxa, differed significantly between efficient and inefficient lambs.
• Reduced Proteobacteria were observed in the small intestine and distal GIT of efficient animals.

Conclusions:

• Feed efficiency is associated with microbial community structures throughout the entire GIT, not just the rumen.
• Efficient lambs exhibited increased fibrolytic taxa in the rumen and colon, and higher bifidobacterial levels in the small intestine.
• Reduced abundance of Proteobacteria in the small intestine and distal GIT of efficient lambs suggests a link to gut health and improved feed utilization.