Silage production and utilization is an important source of forage in the USA (it represented ~44.2% of the total forage harvested in 2014). Understanding the microbial ecology of silages is critical to identify novel microorganisms for optimal silage making and to prevent the growth of pathogens that compromise the animal and food safety chain. We used next-generation sequencing (NGS) to characterize the silage ecology of oats and the use of silo-bags vs. buckets and the ecology of low-moisture corn silage. Inoculation improved whole-crop corn and oat silage quality because of a shift in the bacterial and fungal community composition during ensiling that favored aerobic stability. Both techniques of silo-types are comparable for characterizing the effect of inoculation on the most basic measurements of silage quality.