Rabbit Microbiota Changes Throughout the Intestinal Tract
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Author
Velasco-Galilea, María
Rafel, Oriol
González-Rodríguez, Olga
Sánchez, Juan P.
Publication date
2018-09-13ISSN
1664-302X
Abstract
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.
Document Type
Article
Document version
Published version
Language
English
Subject (CDU)
636 - Animal husbandry and breeding in general. Livestock rearing. Breeding of domestic animals
Pages
14
Publisher
Frontiers Media
Is part of
Frontiers in Microbiology
Citation
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.
Grant agreement number
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
Program
Genètica i Millora Animal
Sostenibilitat en Biosistemes
This item appears in the following Collection(s)
- ARTICLES CIENTÍFICS [2831]
Except where otherwise noted, this item's license is described as http://creativecommons.org/licenses/by/4.0/