Provided herein are agents, compositions, and methods for agricultural use, e.g., for altering the level, activity, or metabolism of one or more microorganisms resident in a host nematode or arthropod (e.g., honeybee or silkworm), the alteration resulting in an increase in the fitness of the host. The invention features a composition that includes an agent (e.g., phage, peptide, small molecule, antibiotic, or combinations thereof) that can alter the host's microbiota in a manner that is beneficial to the host. By promoting favorable microbial levels, microbial activity, microbial metabolism, and/or microbial diversity, the agents described herein may be used to increase the fitness of a variety of beneficial nematodes or arthropods, such as bees and silkworms, utilized in agriculture and commerce.