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.
When prebiotics and other fermentation substrates are delivered to animals as feed supplements, the typical goal is to improve weight gain and feed conversion. In this work, we examined pasture flock chicken cecal contents using next generation sequencing (NGS) to identify and understand the composition of the microbiome when prebiotics and fermentation substrates were supplemented. We generated 16S rRNA sequencing data for 120 separate cecal samples from groups of chickens receiving one of 3 prebiotics or fiber feed additives. The data indicated that respective feed additives enrich for specific bacterial community members and modulate the diversity of the microbiome. We applied synthetic learning in microbial ecology (SLiME) analysis to interpret 16S rRNA microbial community data and identify specific bacterial operational taxonomic units (OTU) that are predictive of the particular feed additives used in these experiments. The results suggest that feed can influence microbiome composition in a predictable way, and thus diet may have indirect effects on weight gain and feed conversion through the microbiome.
Biological supplements in poultry feed are of continued interest due to the improvements in growth performance, protection from pathogen invasion, and benefits in overall host health. The fermentation metabolites of Diamond V Original XPC™ (XPC) have previously been shown to improve commercial performance and reduce Salmonella in poultry. The current study sought to characterize the cecal microbiota using culture-independent analysis based on 16S rRNA gene in Coccivac-D sprayed broilers supplemented with XPC and/or Salinomycin (SAL). Ross 708 male broilers (n = 640) were assigned to one of 4 treatments: Cocci-vaccine (T1), Cocci-vaccine + XPC (T2), Cocci-vaccine + SAL (in the grower diet only) (T3), and Cocci-vaccine + SAL (in the grower diet only) + XPC (T4). Analysis with a PCR-based denaturing gradient gel electrophoresis (DGGE) indicated a shift in the microbial populations present at the various sampling ages - 16, 28, and 42 days. Phylogenetic analysis indicated further consistency in microbial communities directly related to bird age. Identification of microbial communities present and the assessment of their respective quantities using an Illumina MiSeq indicated treatment with XPC had no significant impact on microbial diversity (Chao1 index, observed operational taxonomic unit (OTU) and phylogenetic diversity (PD) whole tree). Sampling age revealed significantly greater diversity at 16 and 28 d (P < 0.05) as compared to the 42 d for the Shannon diversity index, while showing significantly decreased richness and diversity in the 42 d sampling age (Chao1 and observed OTU; P < 0.05). The results of the current study indicate that the chicken intestinal microbiota are impacted more by temporal changes rather than by the feed additive studied.
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