Illumina Miseq platform analysis caecum bacterial communities of rex rabbits fed with different antibiotics

Zou, Fuqin; Zeng, Dong; Wen, Bin; Sun, Hao; Zhou, Yi; Yang, Mingyue; Peng, Zhirong; Xu, Shengyu; Wang, Hesong; Fu, Xiangchao; Du, Debin; Zeng, Yan; Zhu, Hongxiang; Pan, Kangcheng; Jing, Bo; Wang, Ping

doi:10.1186/s13568-016-0273-1

Cited by 28 publications

(30 citation statements)

References 61 publications

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“…Similar to the cecal microbial characterization at class level of rex rabbits performed by Zou et al (2016) our results revealed that the predominant class was Clostridia . But in contrast, they found Bacteroidia as the second predominant class while it was the third, followed by Mollicutes , according to our results.…”

Section: Discussionsupporting

confidence: 81%

Rabbit Microbiota Changes Throughout the Intestinal Tract

et al. 2018

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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 (sPLS-DA) 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.

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Section: Discussionsupporting

confidence: 81%

Rabbit Microbiota Changes Throughout the Intestinal Tract

et al. 2018

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“…Despite not having observed significant differences between the presence or not of antibiotic in the feed, nor between feeding regimes, it is noteworthy to mention that samples collected from animals fed AL in both farms had a greater, although not significant, richness than those fed R. This fact is consistent with previous studies in mice that observed a lower alpha diversity in animals with a restricted level of feeding[14-O'Neil et al, 2017; 15-Chen et al, 2016; 16- Zarrinpar et al, 2014]. Surprisingly, but in agreement with our results, studies performed in pigs[17-Soler et al, 2017], chicken[18-Kumar et al, 2018] and Rex rabbits[5] also did not show clear significant differences on alpha diversity indexes between animals fed on diets with antibiotics with respect to those on diets free of antibiotics. Nevertheless, these studies were able to detect differences in the relative abundances of some specific species between…”

supporting

confidence: 94%

Housing Conditions, Level of Feeding and Presence of Antibiotics in The Feed Shape Rabbit Cecal Microbiota

Velasco-Galilea¹,

Guivernau²,

Piles³

et al. 2020

Preprint

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Background: the effect of the production environment and different management practices in rabbit cecal microbiota remains poorly understood. While previous studies have proved the impact of the age or the feed composition, research in the housing conditions and other animal management aspects, such as the presence of antibiotics in the feed or the level of feeding, is still needed. Characterization of microbial diversity and composition of growing rabbits raised under different conditions could help better understand the role these practices play in cecal microbial communities and how it may result in different animal performance. Results: four hundred twenty-five meat rabbits raised in two different facilities, fed under two feeding regimes ( ad libitum or restricted) with feed supplemented or free of antibiotics, were selected for this study. A 16S rDNA-based assessment through the MiSeq Illumina sequencing platform was performed on cecal samples collected from these individuals at slaughter. Different univariate and multivariate approaches were conducted to unravel the influence of the different factors on microbial alpha diversity and composition at phylum, genus and OTU taxonomic levels. The animals raised in the facility harboring the most stable environmental conditions had greater, and less variable, microbial richness and diversity. Bootstrap univariate analyses of variance and sparse partial least squares-discriminant analyses endorsed that the farm exerted the largest influence on rabbit microbiota since the relative abundances of many taxa were found differentially represented between both facilities at all taxonomic levels characterized. Furthermore, only five OTUs were needed to achieve a perfect classification of samples according to the facility where animals were raised. The level of feeding and the presence of antibiotics did not modify the global alpha diversity but had an impact on some bacteria relative abundances, albeit in a small number of taxa compared with the farm, which is consistent with the lower sample classification power according to these factors achieved using microbial information. Conclusions: this study reveals different degrees of influence attributable to environment and animal management. It highlights the importance of offering a controlled breeding environment that reduces differences in microbial cecal composition that could be causative of different animal performance.

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“…However, there are discrepancies between studies in establishing which other phyla are also prevalent in this ecosystem. Whereas we found phyla Tenericutes and Bacteroidetes representing 7.22% and 5.93% of the cecal microbial composition, respectively, Chen et al 2019[7] and Zou et al 2016[5] reported Bacteroidetes as the second predominant phylum representing 18% and 20% of New Zealand White and Rex rabbit cecal microbial composition, respectively. Conversely, other studies that have previously characterized meat rabbit fecal microbiota identi ed higher relative abundances of phyla Proteobacteria and Verrucomicrobia al., 2018; 10-Eshar and Weese, 2014].…”

contrasting

confidence: 71%

Housing conditions, level of feeding and presence of antibiotics in the feed shape rabbit cecal microbiota

Velasco-Galilea¹,

Guivernau²,

Piles³

et al. 2020

Preprint

View full text Add to dashboard Cite

Background: the effect of the production environment and different management practices in rabbit cecal microbiota remains poorly understood. While previous studies have proved the impact of the age or the feed composition, research in the housing conditions and other animal management aspects, such as the presence of antibiotics in the feed or the level of feeding, is still needed. Characterization of microbial diversity and composition of growing rabbits raised under different conditions could help better understand the role these practices play in cecal microbial communities and how it may result in different animal performance.Results: four hundred twenty-five meat rabbits raised in two different facilities, fed under two feeding regimes (ad libitum or restricted) with feed supplemented or free of antibiotics, were selected for this study. A 16S rRNA gene-based assessment through the MiSeq Illumina sequencing platform was performed on cecal samples collected from these individuals at slaughter. Different univariate and multivariate approaches were conducted to unravel the influence of the different factors on microbial alpha diversity and composition at phylum, genus and OTU taxonomic levels. The animals raised in the facility harboring the most stable environmental conditions had greater, and less variable, microbial richness and diversity. Bootstrap univariate analyses of variance and sparse partial least squares-discriminant analyses endorsed that farm exerted the largest influence on rabbit microbiota since the relative abundances of many taxa were found differentially represented between both facilities at all taxonomic levels characterized. Furthermore, only five OTUs were needed to achieve a perfect classification of samples according to the facility where animals were raised. The level of feeding and the presence of antibiotics did not modify the global alpha diversity but had an impact on some bacteria relative abundances, albeit in a small number of taxa compared with farm, which is consistent with the lower sample classification power according to these factors achieved using microbial information.Conclusions: this study reveals different degrees of influence attributable to environment and animal management. It highlights the importance of offering a controlled breeding environment that reduces differences in microbial cecal composition that could be causative of different animal performance.

show abstract

Illumina Miseq platform analysis caecum bacterial communities of rex rabbits fed with different antibiotics

Cited by 28 publications

References 61 publications

Rabbit Microbiota Changes Throughout the Intestinal Tract

Rabbit Microbiota Changes Throughout the Intestinal Tract

Housing Conditions, Level of Feeding and Presence of Antibiotics in The Feed Shape Rabbit Cecal Microbiota

Housing conditions, level of feeding and presence of antibiotics in the feed shape rabbit cecal microbiota

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