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Metagenomics of prebiotic and probiotic supplemented broilers gastrointestinal tract microbiome

Muhammad Umar Sohail, Michael E. Hume, Haseeb Anwar, Ghulam Hussain, Muhammad Zubair Shabbir, David James Nisbet, Shakeel Ahmad, Zahid Kamran
Indo American journal of pharmaceutical research 2014 v.4 no.7 pp. 3780-3784
DNA, absorption, amino acids, broiler chickens, broiler feeding, carbohydrates, cecum, databases, digesta, discriminant analysis, genes, genetic markers, heat stress, intestinal absorption, lipid metabolism, metagenomics, microbiome, nutrients, phylogeny, prebiotics, prediction, probiotics, ribosomal RNA, sequence analysis, signal transduction, xenobiotics
Phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) is a recently developed computational approach for prediction of metagenomics , comparing marker gene data with a reference genome database. In the current study, we used PICRUSt for predicting metagenomics in broilers subjected to heat stress, and supplemented with prebiotic and probiotic. Cecal digesta were taken for DNA extraction. DNA was sequenced using 16S rRNA pyrosequencing. Sequences were analyzed using Qiime and PICRUSt to predict metagenomics. Functional genes content inference was consigned according to Kyoto Encyclopedia of Genes and Genomics Orthology 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 included; membrane transportation (21.0%), signal transduction (3.1%), and signaling molecules interaction (3.2%). Other significant pathways identified in the broilers gut microbiome are genetic information (7.6%), cellular (0.86%), and organismal (0.21%) processes. About 12.3% genome in this study was 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 significant differences (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 effects to change these functions.