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Rabbit Microbiota Changes Throughout the Intestinal Tract
- Source :
- IRTA Pubpro. Open Digital Archive, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Frontiers in Microbiology, Vol 9 (2018), Frontiers in Microbiology
- Publication Year :
- 2018
- Publisher :
- Frontiers Media, 2018.
-
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. info:eu-repo/semantics/publishedVersion
- Subjects :
- 0301 basic medicine
Microbiology (medical)
paired analysis
636 - Explotació i cria d'animals. Cria del bestiar i d'animals domèstics
food.ingredient
Firmicutes
lcsh:QR1-502
Zoology
Gut flora
Microbiology
Coprococcus
feed restriction
lcsh:Microbiology
03 medical and health sciences
food
cecal microbiota
Feces
Illumina dye sequencing
2. Zero hunger
Tenericutes
fecal microbiota
biology
gut microbiota
Bacteroidetes
biology.organism_classification
030104 developmental biology
Bacteroides
meat rabbit
Subjects
Details
- Database :
- OpenAIRE
- Journal :
- IRTA Pubpro. Open Digital Archive, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Frontiers in Microbiology, Vol 9 (2018), Frontiers in Microbiology
- Accession number :
- edsair.doi.dedup.....9ee09ac19ac82cd26021bd9486e21c24