Browsing by Subject "16S rRNA sequencing"

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High-throughput sequencing techniques to analyze microbial communities in the gastrointestinal tract of broiler chickens
(2018) Borda Molina, Daniel Enrique; Camarinha-Silva, Amélia
Broiler chicken represents an excellent case-study to elucidate the inter-communication between the host and its microbial communities. The general aim of this thesis was to describe the changes in bacterial community structure that occurred in chickens, in response to different experimental diets. An update of the state of the art of the chicken gastrointestinal microbiota was done in chapter 2. The composition and functionality are described through the most recent technologies that provide taxonomic information at DNA level using 16S rRNA genes. Gene catalogs and their abundance are deciphered through shotgun metagenome sequencing, which is still at its infancy and only eight publications have been published so far. At the protein level, only two studies were found that contribute metaproteomic information. Thanks to these technologies many studies were able to focus on answering how feed supplementations altered the microbes in GIT sections. The second part presented in chapter 3 comprises an extensive investigation of the broiler chicken microbiota composition in digesta and mucosa of individual samples under varying supplementation of calcium, phosphorus, and phytase. The dietary impact on the distribution of the microbial communities was studied in the crop, ileum, and caecum through illumina sequencing of the 16S rRNA gene. One important outcome was the high variability in the microbial composition between individual samples. Significant differences were observed between the digesta and mucosa samples, supporting the hypothesis that being close to the host, mucosa-associated communities show a different composition. A calcium effect on the performance was observed, where values for body weight gain and feed conversion were lower in comparison to the other treatments. Microbial communities in the crop mucosa revealed a dietary effect, while in the digesta samples no significant changes were seen. Regarding the ileum mucosa, there was an effect of P addition on the microbial distribution. As expected, caeca-derived samples showed an increase in the diversity indexes when compared to the ileum and crop and butyrate producers were detected in higher abundance. A lower microbial diversity in the crop was linked to lower growth performance regarding the supplementation of Ca. Hence, each dietary treatment affected the microbial communities; nevertheless, none of the dietary treatments displayed a consistent effect across the studied gut sections. Additionally, the effects of supplementing different proteases and one phytase on the microbial community of the ileum of broiler chickens was assessed. Thus, the specific aim of chapter 4 was to determine how enzyme supplementation affects the microbiota composition in the ileum of broilers and whether these effects were related to differences in pre-caecal AA digestibility. Three different protease sources at a low and high level were included. The microbial taxonomy was assessed through 16S rRNA gene Illumina amplicon sequencing. Performance results revealed a significant increase in growth and feed efficiency in broilers fed with phytase only and the high dosage of protease C, in comparison to the control. Most of the AA showed a significant difference between the control diet and protease C at high dosage and phytase diets. Effects on microbiota composition were observed at the genus level for some protease and phytase supplementations. The genera Streptococcus, Lactobacillus, and uncultured Clostridiaceae were responsible for these differences. This study demonstrates that effects of enzyme supplementation were evident in the terminal small intestine microbiota composition, and, to a lesser extent, in pc AA digestibility. However, the changes in microbiota composition and pc AA digestibility could not be correlated which may indicate the absence of a causal relationship. Finally, an outlook with metagenome sequencing is presented in chapter 5, to further characterize the result of feeding strategies. Metabolism information, essential to microbial activities registered 50% of abundant genes in the supplemented diets while being reduced to 40% in the control samples Phosphatases pathways and butyrate production increased in the supplemented diets while calcium signaling pathway was higher in the control. In conclusion, within this project a method of standardization to study the microbiota along the gastrointestinal tract of broiler chickens was successfully established. The obtained results revealed a significant impact of both, enzyme and mineral supplementation in the individual sections of the GIT. Also, it was proved that even if the GIT works as an interconnected system, its compartmentalization creates different environmental conditions which influence the microbiota. This study provides insights into the responses of the bacteria and their functionality which were stimulated by the feed supplementations.