The 2014 Beneficial Microbes Conference provides a forum for the exchange of the latest conceptual and technological research advances on resident microorganisms and their impact on the fitness of animals and plants. The meeting will bring together US and international researchers from multiple disciplines (microbiology, immunology, genomics, nutrition, ecology, systems biology, evolutionary biology and clinical science), and comprises five sessions: (1) Microbiota and the Gut-Brain Axis; (2) Evolutionary Dynamics of Host-Microbe Interactions; (3) Nutrition and Immune Function: Cross-Species Perspectives; (4) The Ecology of Host-Microbial Interactions; and (5) Beneficial Microbes in Human Health and Disease. Each session will include two invited talks, four talks selected from submitted abstracts and one further talk (invited or selected) with a quantitative flavor, to disseminate best practice in analysis of large datasets and facilitate discussion of outstanding barriers to computational analysis and mathematical modeling of host-microbial interactions. The conference will also include two poster sessions. Biologists are increasingly recognizing that animals and plants are multi-organismal, i.e. invariably associated with benign or beneficial microorganisms. The 2014 Beneficial Microbes Conference will provide the opportunity to exchange ideas and information on these interactions, and explore exciting new opportunities to promote the health and vigor of animals/plants of economic and conservation importance, including agricultural crops, pollinators, and pests. The conference includes advertised opportunities for break-out groups to discuss specific scientific topics and issues in professional development (e.g. careers). A Conference Discussion on Future Directions in Beneficial Microbes Research will be the foundation for a published commentary on research priorities to overcome current barriers to advancement of the field. The conference will be particularly useful to promote opportunities for early-career researchers, women and minorities, through invitation and travel assistance, ensuring that these participants are well-represented and their scientific career opportunities are fully supported.