Sugarcane bagasse is the residual material left after the stems have been crushed for sugar and is one of the most abundant agricultural wastes around the world. In Australia, it is usually incinerated to generate electricity at the mill or for the grid. However, it also has potential to be used as low cost feed for livestock and/or as a substrate in solid state fermentation to generate whole cell animal feed supplements. When bagasse is stored in piles in the open for long periods it develops into a unique ecological niche and is colonised by microbes originating from the sugarcane, the soil nearby or spores in the environment. Due to the microbial activity and the structure of the pile, it also develops into a variable environment with oxygen, temperature and pH gradients from the surface to the deeper layers. The gradient means that microorganisms will have location-specific features that allow growth in different environments. Such features may include a tolerance to low pH, high temperature, or low oxygen levels. The microbial community in bagasse piles is thus a potential resource for the discovery of useful and novel microbes and industrial enzymes. We have used traditional culturing and metabarcoding to understand the diversity of microorganisms found in a bagasse pile and develop a pipeline for the discovery of new enzymes. We now have a collection of 150 microorganisms displaying cellulase, xylanase, mannanase, lipase, phytase and protease activities. Apart from hosting biomass degraders, the bagasse is a suitable environment for the growth and maintenance of oleaginous yeasts and microbes with probiotic potential, that could be especially suited to inclusion in low cost fibrous animal feeds. We have sequenced the genomes of some of these strains and carried out preliminary poultry feed trials to test their effects in vivo compared to some commercial livestock feed supplements and link their genomic variation with probiotic function.