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Research Project: MICROBIAL INTERACTIONS AND MANAGEMENT APPROACHES TO REDUCE PATHOGENIC BACTERIA IN POULTRY

Location: Food and Feed Safety Research

Title: Metagenomics of prebiotic and probiotic supplemented broilers gastrointestinal tract microbiome

Author
item Sohail, Muhammed Umar - Government College University
item Hume, Michael
item Anwar, Haseeb - Government College University
item Hussain, Ghulam - Government College University
item Shabbir, Muhammad Zubair - University Of Veterinary And Animal Sciences
item Nisbet, David - Dave
item Ahmad, Shakeel - Pakistan University Of Agriculture
item Kamran, Zahid - Pakistan University Of Agriculture

Submitted to: Indo American Journal of Pharmaceutical Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/15/2014
Publication Date: 9/30/2014
Publication URL: http://handle.nal.usda.gov/10113/61626
Citation: Sohail, M., Hume, M.E., Anwar, H., Hussain, G., Shabbir, M., Nisbet, D.J., Ahmad, S., Kamran, Z. 2014. Metagenomics of prebiotic and probiotic supplemented broilers gastrointestinal tract microbiome. Indo American Journal of Pharmaceutical Research. 4:3780-3784.

Interpretive Summary: A statistical technique was used to examine bacterial composition and function in broiler chickens subjected to heat stress. The broilers were treated with a long sugar molecule or a mixture of beneficial bacteria to determine if the treatment would decrease the debilitating effects of heat stress. Intestinal contents were collected for DNA extraction. Specific marker genes, whose identities are unique for each bacterium, were sequenced using a molecular technique. The marker gene sequences were used to identify bacteria and to associate these bacteria with specific sets of bacterial metabolic functions within the total population of intestinal bacteria. The main bacterial genes assessed were associated predominantly with metabolism and environmental information processing. Among different treatment groups, genetic information processing genes were higher in broilers treated with the mixture of beneficial bacteria compared to the other groups. However, no differences were observed for other metabolic and cellular process genes detected. In conclusion, the study revealed that broiler chicken intestinal bacteria significantly contribute to the broiler metabolism and nutrient absorption, and heat stress and supplements did not significantly change these functions. These results are of interest to researchers and producers seeking maximize broiler intestinal bacteria population heath to reduce the effects of heat stress and improve broiler chicken production.

Technical Abstract: Phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) is a recently developed computational approach for prediction of functional composition of a microbiome comparing marker gene data with a reference genome database. The procedure established significant link between the phylogeny and function in human subject studies and have been thoroughly reviewed. In the current study, we used PICRUSt for predicting metagenomics in broilers subjected to heat stress (HS), and supplemented with prebiotic and probiotic. Cecal digesta were taken for DNA extraction. The sample DNA was sequenced using 16S rRNA high throughput pyrosequencing. The 16S rRNA genome sequences were denoised, chimera checked, and analyzed using Qiime and PICRUSt to predict the functional capacities of the bacteria. Functional genes content inference was consigned according to Kyoto Encyclopedia of Genes and Genomics Orthology (KO) Hierarchy and compared using Linear Discriminant Analysis and the Kruskal–Wallis test. The core gene contents of broilers gut microbiome were predominantly associated with metabolism (52.3%) and environmental information processing (27.4%). Among metabolic processes, carbohydrates metabolism (20.0%) was highest, followed by xenobiotics (11.0%), amino acids (7.9%), and lipids metabolism (3.3%). The information processing gene contents included membrane transportation (21.0%), signal transduction (3.1%), and signaling molecules interaction (3.2%). Other significant functional pathways identified in the broilers gut microbiome are genetic information (7.6%), cellular (0.86%), and organismal (0.21%) processes. About 12.3% gene contents observed in this study were unclassified. Among different treatment groups, genetic information processing was higher (P < 0.05) in the probiotic supplemented group compared to all the other groups. However, no significantly different (P > 0.05) were observed for other metabolic and cellular processes. In conclusion, the present study reveals that gut microbiome of broilers significantly contributes to the host metabolism and nutrients absorption, and the stress and supplements have no significant effect to change these functions.