Modifying the gastrointestinal ecology in alternatively raised poultry and the potential for molecular and metabolomic assessment

Consumer demand for nonconventional poultry products continues to increase in the United States. In pasture flock and organic poultry production, probiotics and prebiotic feed additives have potential advantages because they are thought to promote intestinal health and may offer a replacement for current intervention strategies that are not considered acceptable for these production systems. Prebiotics have been demonstrated to produce effects on the gastrointestinal tract including modulation of microflora by promoting selective increases in beneficial bacteria concomitant with decreases in undesirable bacteria. In-depth assessment of microbial community changes during host growth and development as well as the establishment of beneficial microbial species by adding biologicals such as probiotics and prebiotics is important to achieve predictable and consistent improvements in chicken health and productivity. To analyze microflora shifts and metabolites produced by bacteria in the gut as well as host responses to biological additives, sophisticated molecular techniques are now available and are becoming more widely used. Polymerase chain reaction assays, denaturing gradient gel electrophoresis, and temperature gradient gel electrophoresis offer approaches for detecting microbial shifts in the gut. Likewise, the employment of microarrays and molecular analysis of gut tissues can reveal insight into gut physiological and responses to dietary and other changes. Recent application of 16S rDNA sequencing and analysis utilizing basic local alignment search tool (BLAST) and FASTA databases on poultry gut samples have the potential to provide a much more in-depth assessment of the gut microbiome. Utilizing ultra pressure liquid chromatography-mass spectroscopy profiling, metabolomic assessment of gut contents will also allow for parallel comparisons of changes in the gut contents with microbiome and physiological responses. Combining all these technologies will provide a plenary understanding of poultry gut health in alternative production systems.