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Background  The chicken gastrointestinal tract contains a diverse microbiota whose composition and structure play important roles in gut functionality. In this study, microbial shifts resulting from feed supplementation with  Bacillus subtilis  CSL2 were evaluated in broilers challenged and unchallenged with  Salmonella  Gallinarum. To analyse bacterial community composition and functionality, 454 GS-FLX pyrosequencing of 16S rRNA gene amplicons was performed.    Results  The Quantitative Insights into Microbial Ecology (QIIME) pipeline was used to analyse changes in the faecal microbiota over a 24-h period. A total of 718,204 sequences from broiler chickens were recorded and analysed. At the phylum level, Firmicutes, Bacteroidetes, and Proteobacteria were the predominant bacterial taxa. In  Salmonella -infected chickens (SC), Bacteroidetes were more highly abundant compared to control (NC) and  Bacillus -treated (BT) chickens. At the genus level, in the NC and BT groups,  Lactobacillus  was present at high abundance, and the abundance of  Turicibacter , unclassified  Enterobacteriaceae , and  Bacteroides  increased in SC broilers. Furthermore, taxon-independent analysis showed that the SC and BT groups were compositionally distinct at the end of the 24-h period. Further analysis of functional properties showed that  B. subtilis  CSL2 administration increased gut-associated energy supply mechanisms (i.e. carbohydrate transport and metabolism) to maintain a stable microbiota and protect gut integrity.    Conclusions  This study demonstrated that  S.  Gallinarum infection and  B. subtilis  CSL2 supplementation in the diet of broiler chickens influenced the diversity, composition, and functional diversity of the faecal microbiota. Moreover, the findings offer significant insights to understand potential mechanisms of  Salmonella  infection and the mode of action of probiotics in broiler chickens.    Electronic supplementary material  The online version of this article (doi:10.1186/s40104-016-0130-8) contains supplementary material, which is available to authorized users.

journal of animal science and biotechnology/journal of animal science and biotechnology

Effects of Bacillus subtilis CSL2 on the composition and functional diversity of the faecal microbiota of broiler chickens challenged with Salmonella Gallinarum