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Rabbit Microbiota Changes Throughout the Intestinal Tract Velasco-Galilea, María Piles, Miriam Viñas, Marc Rafel, Oriol González-Rodríguez, Olga Guivernau, Miriam Sánchez, Juan P. Producció Animal Genètica i Millora Animal Sostenibilitat en Biosistemes 636 To gain insight into the importance of carefully selecting the sampling area for intestinal microbiota studies, cecal and fecal microbial communities of Caldes meat rabbit were characterized. The animals involved in the study were divided in two groups according to the feed intake level they received during the fattening period; ad libitum (n = 10) or restricted to 75% of ad libitum intake (n = 11). Cecum and internal hard feces were sampled from sacrificed animals. Assessment of bacterial and archaeal populations was performed by means of Illumina sequencing of 16S rRNA gene amplicons in a MiSeq platform. A total of 596 operational taxonomic units (OTUs) were detected using QIIME software. Taxonomic assignment revealed that microbial diversity was dominated by phyla Firmicutes (76.42%), Tenericutes (7.83%), and Bacteroidetes (7.42%); kingdom Archaea was presented at low percentage (0.61%). No significant differences were detected between sampling origins in microbial diversity or richness assessed using two alpha-diversity indexes: Shannon and the observed number of OTUs. However, the analysis of variance at genus level revealed a higher presence of genera Clostridium, Anaerofustis, Blautia, Akkermansia, rc4-4, and Bacteroides in cecal samples. By contrast, genera Oscillospira and Coprococcus were found to be overrepresented in feces, suggesting that bacterial species of these genera would act as fermenters at the end of feed digestion process. At the lowest taxonomic level, 83 and 97 OTUs in feces and cecum, respectively, were differentially represented. Multivariate statistical assessment revealed that sparse partial least squares discriminant analysis (sPLSDA) was the best approach for this purpose. Interestingly, the majority of the most discriminative OTUs selected by sPLS-DA were found to be differentially represented between sampling origins in univariate analysis. Our study provides evidence that the choice of intestinal sampling area is relevant due to important differences in some taxa’s relative abundance that have been revealed between rabbits’ cecal and fecal microbiota. An appropriate sampling intestinal area should be chosen in each microbiota assessment. info:eu-repo/semantics/publishedVersion 2018-09-13 info:eu-repo/semantics/article Velasco-Galilea, María, Miriam Piles, Marc Viñas, Oriol Rafel, Olga González-Rodríguez, Miriam Guivernau, and Juan P. Sánchez. 2018. "Rabbit Microbiota Changes Throughout The Intestinal Tract". Frontiers In Microbiology 9. Frontiers Media SA. doi:10.3389/fmicb.2018.02144. 1664-302X http://hdl.handle.net/20.500.12327/182 https://doi.org/10.3389/fmicb.2018.02144 eng Frontiers in Microbiology INIA/Programa Nacional de Proyectos de Investigación Fundamental/RTA2011-00064-00-00/ES/Mejora genética de la eficacia alimentaria en especies prolíficas/ EC/H2020/633531/EU/Adapting the feed, the animal and the feeding techniques to improve the efficiency and sustainability of monogastric livestock production systems/Feed-a-Gene Attribution 4.0 International http://creativecommons.org/licenses/by/4.0/ info:eu-repo/semantics/openAccess 14 Frontiers Media