Springer Science+Business Media, LLC 2012. All rights reserved. Modem molecular methods are currently growing exponentially, enhancing our ability to evaluate the microbiome of animals and the interaction of the complex consortium of organisms with the host. Current limitations include a lack of ability to propagate many types of bacteria that might prove to be valuable direct-fed microbial resources. Also lacking are genomic tools for animal origin probiotics. During the past few years, however, an incredible revolution in the area of evaluating the microbiome of animals has been initiated with the advent of molecular methods such as the pyrosequencing-based bTEFAP. Metagenomic molecular and bioinformatics tools and resources are likely to continue to revolutionize our understanding of how probiotics interact and enhance gut health in animals, particularly those of economic importance. Future directions in whole-community transplants (e.g., fecal bacterial transplant therapy) seem a logical step from single bacterial direct-fed microbials especially as modern methods for ensuring and monitoring safety and efficacy are now becoming available.
