Most of the ruminants are herbivorous animals that use rumen fermentation to break down feed, which includes dairy cows. Plant fiber is a staple diet for ruminants, who do not have the digestive system to break it down. Because of this, ruminants and microbes that can produce enzymes to break plant polymers have a symbiotic relationship. To achieve full digestion, different microflora species such as bacteria, protozoa, fungi, archaea, and bacteriophage are hosted at different concentrations. At a specific stratum, the feed is broken down after ingestion. Cellulolytic bacteria break down the polysaccharide plant fibrils, and other bacteria act on the resulting substrate. This series of degradation processes serves as the foundation for both full digestion and the extraction of energy from the consumed food. The microbiota’s composition adapts easily to the dairy cow’s shifting feeding preferences. The integrity of the local community’s flora determines both digestion and total energy production. The gastrointestinal (GI) tract and several other organs are severely impacted by disturbances in the homogeneity of the gastrointestinal microbiome. Numerous metabolic illnesses are also brought on by this discord in social relationships. Bloating can occasionally result from the dominance of methanogens, and ruminal acidosis is the result of a high-sugar diet. Likewise, reticuloperitonitis, ulcers, diarrhea, etc., are also sparked by a disrupting microflora constitution. This chapter discusses the role of symbiotic microflora in the development of several major metabolic diseases. Future multiomics research will offer a platform to ascertain how we can physiologically and phenotypically enhance dairy cows for better growth and milk production.