Bovine rumen and faecal microbiome adaptation to seaweeds and exotic forages

Abstract

Seaweeds are an underdeveloped but valuable agriculture resource. Valorizing their value as CO2 sinks, sustainable biomasses, and their promise as inhibitors of enteric methane emissions within ruminant livestock remains an important line of research. However, the dietary fate of seaweeds and other marine feedstocks within the ruminant digestive system is unknown. In this thesis, I explore the adaptation of ruminant microbiomes to three distinct seaweeds. The first study explores the adaptation of artificial ruminant systems to the brown seaweed Saccharina latissima; the second study explores the faecal and rumen microbiota of cattle supplemented red seaweed Mazzaella japonica; in the final study, I investigated the faecal microbiota of a rewilded herd of cattle on Meares Island to identify the adaptation towards unique shoreline foraging and the consumption of green seaweed. In all three studies, shotgun metagenomic datasets and functional prediction of seaweed saccharification pathways revealed the adaptation of the cattle microbiota to their respective seaweed supplementation. Further, biochemical characterization of carbohydrate-active enzymes from metagenomic sequences and isolated microorganisms confirmed that all bovine microbiomes had the capabilities to saccharify their respective seaweed cell wall polysaccharides. Local and international collaborations further corroborated these studies using metaproteomic, glycomic, and enzyme crystallographic analysis. Together, these studies represent the first fine-scale analysis of the adaptation of the ruminant gastrointestinal tract microbiome to seaweed polysaccharides. The adaptability of the ruminant gastrointestinal tract microbiota to distinct seaweed polysaccharides suggests that agriculture solutions can be tailored to locally grown seaweed supplementation.