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

Abstract

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.

Spatial heterogeneity and stability of bacterial community in the gastrointestinal tracts of broiler chickens

“…These approaches offer an opportunity to comprehensively analyze uncultured and rare microbial communities from various environmental samples and can be also applied to improve poultry production and enhance food safety (Diaz-Sanchez et al, 2013;Park et al, 2013). To date, in the field of poultry science, only a few studies have been performed to investigate microbial communities by using high-throughput sequencing (Callaway et al, 2009;Singh et al, 2012;Yin et al, 2013).…”

Application of Molecular Approaches for Understanding Foodborne Salmonella Establishment in Poultry Production

“…Continued advances in a variety of genetic functional screening techniques coupled with high throughput sequencing approaches have now made it possible to contemplate a much more comprehensive resolution to understanding the complex nature of biological systems such as Salmonella-host relationships [272,[275][276][277][278]. These approaches should help uncover some of the more subtle nuances in pathogenesis mechanisms and in turn achieve a better understanding of how Salmonella interacts with its poultry host [278,279]. The following sections will discuss these developments in general terms and how they might be used for understanding foodborne Salmonella functionality and subsequent application in vaccine development.…”

Patterns of community assembly in the developing chicken microbiome reveal rapid primary succession

“…Broiler chicken meat comprises the majority of the poultry meat industry, and ensuring the health and productivity of broilers has become a key aspect of this industry (Ballou et al., ). Recent studies using high throughput sequencing, have shown the role of the gastrointestinal tract (GIT) microbiome in gastrointestinal development, nutrient absorption, and pathogen invasion resistance (Crhanova et al., ; Pan & Yu, ; Park et al., ; Pedroso & Lee, ; Yeoman et al., ). Concurrently, initiatives to control antibiotic use in production animals, especially the restriction in use of growth promoters worldwide to prevent the emergence of antibiotic resistance has made the manipulation of intestinal microbiomes in poultry an attractive alternative to support innate immunity and improve health (Kogut & Arsenault, ; Pedroso & Lee, ), as well as productivity (Singh et al., ).…”