Whole Genome Metagenomic Comparison of Microbial Communities and Activities in Solid and Liquid Rumen Microenvironments in Beef Steers

Abstract

Previous research has established distinctions between microbial communities that associate with either the solid or liquid rumen microenvironments utilizing 16S rRNA sequencing. Whole genome metagenomic sequencing (WGS) facilitates comprehensive analysis of a microorganism’s entire genome, producing strain level data and providing insights into microbial functionality. The objective of our study was to utilize WGS to characterize microbial species and enzyme profiles associated with the liquid versus solid rumen microenvironments in beef steers consuming forage. Four steers consuming forage were utilized in a 4 × 4 Latin Square experiment; on d 14 of each period, rumen contents were separated into solid and liquid samples and DNA was extracted then sequenced using WGS. Alpha and beta diversity measures revealed differences between solid and liquid microenvironments. There were also differences in enzyme profiles: carbohydrate-active enzyme classes were different across microenvironments, except glycosyl transferase. Further, the solid microenvironment was enriched in enzymes related to energy production/conversion and nutrient transport and metabolism, while the liquid microenvironment was enriched in coenzyme transport and metabolism enzymes. Species associated with cellulolytic activities were generally more abundant in the solid microenvironment while those associated with amylolytic activity were more abundant in the liquid. Genes related to methanogenesis were also different across microenvironments. Our findings offer valuable insights into the stratification of microorganisms across rumen microenvironments, expanding on existing literature with findings from next-generation sequencing and application to forage-based beef systems.