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

2020 ◽  
Author(s):  
María Velasco-Galilea ◽  
Miriam Guivernau ◽  
Miriam Piles ◽  
Marc Viñas ◽  
Oriol Rafel ◽  
...  
Keyword(s):  
Management Practices ◽  
Alpha Diversity ◽  
Housing Conditions ◽  
Animal Performance ◽  
Production Environment ◽  
Feed Composition ◽  
Animal Management ◽  
Cecal Microbiota ◽  
Relative Abundances ◽  
The Impact

Abstract 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.

scholarly journals Housing Conditions, Level of Feeding and Presence of Antibiotics in the Feed Shape Rabbit Cecal Microbiota

2020 ◽  
Author(s):  
María Velasco-Galilea ◽  
Miriam Guivernau ◽  
Miriam Piles ◽  
Marc Viñas ◽  
Oriol Rafel ◽  
...  
Keyword(s):  
Management Practices ◽  
Alpha Diversity ◽  
Housing Conditions ◽  
Animal Performance ◽  
Production Environment ◽  
Feed Composition ◽  
Animal Management ◽  
Cecal Microbiota ◽  
Relative Abundances ◽  
The Impact

Abstract 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.

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

2020 ◽  
Author(s):  
María Velasco-Galilea ◽  
Miriam Guivernau ◽  
Miriam Piles ◽  
Marc Viñas ◽  
Oriol Rafel ◽  
...  
Keyword(s):  
Alpha Diversity ◽  
Rrna Gene ◽  
Housing Conditions ◽  
Animal Performance ◽  
Production Environment ◽  
Feed Composition ◽  
Animal Management ◽  
Cecal Microbiota ◽  
Relative Abundances ◽  
The Impact

Abstract 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.

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

2020 ◽  
Author(s):  
María Velasco-Galilea ◽  
Miriam Guivernau ◽  
Miriam Piles ◽  
Marc Viñas ◽  
Oriol Rafel ◽  
...  
Keyword(s):  
Alpha Diversity ◽  
Rrna Gene ◽  
Housing Conditions ◽  
Animal Performance ◽  
Production Environment ◽  
Feed Composition ◽  
Animal Management ◽  
Cecal Microbiota ◽  
Relative Abundances ◽  
The Impact

Abstract 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 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.

scholarly journals Breeding farm, level of feeding and presence of antibiotics in the feed influence rabbit cecal microbiota

2020 ◽  
Vol 2 (1) ◽  
Author(s):  
María Velasco-Galilea ◽  
Miriam Guivernau ◽  
Miriam Piles ◽  
Marc Viñas ◽  
Oriol Rafel ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Management Practices ◽  
Alpha Diversity ◽  
Rrna Gene ◽  
Animal Performance ◽  
Production Environment ◽  
Feed Composition ◽  
Cecal Microbiota ◽  
Relative Abundances ◽  
The Impact

Abstract 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 breeding farm 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 conditions exerted an important 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 that factors associated with the farm effect and other management factors, such as the presence of antibiotics in the diet or the feeding level, modify cecal microbial communities. It highlights the importance of offering a controlled breeding environment that reduces differences in microbial cecal composition that could be responsible for different animal performance.

scholarly journals Breeding farm, level of feeding and presence of antibiotics in the feed influence rabbit cecal microbiota

2020 ◽  
Author(s):  
María Velasco-Galilea ◽  
Miriam Guivernau ◽  
Miriam Piles ◽  
Marc Viñas ◽  
Oriol Rafel ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Management Practices ◽  
Alpha Diversity ◽  
Rrna Gene ◽  
Animal Performance ◽  
Production Environment ◽  
Feed Composition ◽  
Cecal Microbiota ◽  
Relative Abundances ◽  
The Impact

Abstract 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 breeding farm 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 conditions exerted an important 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 that factors associated with the farm effect and other management factors, such as the presence of antibiotics in the diet or the feeding level, modify cecal microbial communities. It highlights the importance of offering a controlled breeding environment that reduces differences in microbial cecal composition that could be responsible for different animal performance.

scholarly journals Assessing the impact of storage time on the stability of stool microbiota richness, diversity, and composition

Gut Pathogens ◽  
2021 ◽  
Vol 13 (1) ◽  
Author(s):  
Elizabeth A. Holzhausen ◽  
Maria Nikodemova ◽  
Courtney L. Deblois ◽  
Jodi H. Barnet ◽  
Paul E. Peppard ◽  
...  
Keyword(s):  
Community Composition ◽  
Storage Time ◽  
New Technologies ◽  
Alpha Diversity ◽  
Population Based ◽  
Individual Variability ◽  
Storage Duration ◽  
Relative Abundances ◽  
The Impact ◽  
Baseline Sample

Abstract Background New technologies like next-generation sequencing have led to a proliferation of studies investigating the role of the gut microbiome in human health, particularly population-based studies that rely upon participant self-collection of samples. However, the impact of methodological differences in sample shipping, storage, and processing are not well-characterized for these types of studies, especially when transit times may exceed 24 h. The aim of this study was to experimentally assess microbiota stability in stool samples stored at 4 °C for durations of 6, 24, 48, 72, and 96 h with no additives to better understand effects of variable shipping times in population-based studies. These data were compared to a baseline sample that was immediately stored at − 80 °C after stool production. Results Compared to the baseline sample, we found that the alpha-diversity metrics Shannon’s and Inverse Simpson’s had excellent intra-class correlations (ICC) for all storage durations. Chao1 richness had good to excellent ICC. We found that the relative abundances of bacteria in the phyla Verrucomicrobia, Actinobacteria, and Proteobacteria had excellent ICC with baseline for all storage durations, while Firmicutes and Bacteroidetes ranged from moderate to good. We interpreted the ICCs as follows: poor: ICC < 0.50, moderate: 0.50 < ICC < 0.75, good: 0.75 < ICC < 0.90, and excellent: ICC > 0.90. Using the Bray–Curtis dissimilarity index, we found that the greatest change in community composition occurred between 0 and 24 h of storage, while community composition remained relatively stable for subsequent storage durations. Samples showed strong clustering by individual, indicating that inter-individual variability was greater than the variability associated with storage time. Conclusions The results of this analysis suggest that several measures of alpha diversity, relative abundance, and overall community composition are robust to storage at 4 °C for up to 96 h. We found that the overall community richness was influenced by storage duration in addition to the relative abundances of sequences within the Firmicutes and Bacteroidetes phyla. Finally, we demonstrate that inter-individual variability in microbiota composition was greater than the variability due to changing storage durations.

scholarly journals Impacts of Seasonal Housing and Teat Preparation on Raw Milk Microbiota: a High-Throughput Sequencing Study

2016 ◽  
Vol 83 (2) ◽  
Author(s):  
Conor J. Doyle ◽  
David Gleeson ◽  
Paul W. O'Toole ◽  
Paul D. Cotter
Keyword(s):  
High Throughput ◽  
Management Practices ◽  
High Throughput Sequencing ◽  
Raw Milk ◽  
Downstream Processing ◽  
Outdoor Environment ◽  
Production Environment ◽  
Production Chain ◽  
Network Analyses ◽  
The Impact

ABSTRACT In pasture-based systems, changes in dairy herd habitat due to seasonality results in the exposure of animals to different environmental niches. These niches contain distinct microbial communities that may be transferred to raw milk, with potentially important food quality and safety implications for milk producers. It is postulated that the extent to which these microorganisms are transferred could be limited by the inclusion of a teat preparation step prior to milking. High-throughput sequencing on a variety of microbial niches on farms was used to study the patterns of microbial movement through the dairy production chain and, in the process, to investigate the impact of seasonal housing and the inclusion/exclusion of a teat preparation regime on the raw milk microbiota from the same herd over two sampling periods, i.e., indoor and outdoor. Beta diversity and network analyses showed that environmental and milk microbiotas separated depending on whether they were sourced from an indoor or outdoor environment. Within these respective habitats, similarities between the milk microbiota and that of teat swab samples and, to a lesser extent, fecal samples were apparent. Indeed, SourceTracker identified the teat surface as the most significant source of contamination, with herd feces being the next most prevalent source of contamination. In milk from cows grazing outdoors, teat prep significantly increased the numbers of total bacteria present. In summary, sequence-based microbiota analysis identified possible sources of raw milk contamination and highlighted the influence of environment and farm management practices on the raw milk microbiota. IMPORTANCE The composition of the raw milk microbiota is an important consideration from both a spoilage perspective and a food safety perspective and has implications for milk targeted for direct consumption and for downstream processing. Factors that influence contamination have been examined previously, primarily through the use of culture-based techniques. We describe here the extensive application of high-throughput DNA sequencing technologies to study the relationship between the milk production environment and the raw milk microbiota. The results show that the environment in which the herd was kept was the primary driver of the composition of the milk microbiota composition.

scholarly journals Effects of Italian Ryegrass (IRG) Supplementation on Animal Performance, Gut Microbial Compositions and Odor Emission from Manure in Growing Pigs

Agronomy ◽  
2020 ◽  
Vol 10 (5) ◽  
pp. 647
Author(s):  
Sungkwon Park ◽  
Sungback Cho ◽  
Okhwa Hwang
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Bacterial Community Structure ◽  
Growing Pigs ◽  
Italian Ryegrass ◽  
Animal Performance ◽  
Odor Emission ◽  
Relative Abundances ◽  
Odorous Compounds ◽  
The Impact

Fermentable carbohydrate (FC) is a promising material to reduce odor emission from pig manure. This study was conducted to investigate the impact of diets containing Italian ryegrass (IRG), as a FC, on animal performance, odorous chemical and bacterial composition of manure. Pigs were weighed and fed diets containing various levels of IRG powder (0%, 0.5%, 1.0% and 1.5%) for 28 days. At the end of the trial, manure was collected to analyze the chemical composition, odorous compounds and bacterial community structure. As dietary IRG levels increased, concentrations of phenols and indoles were decreased by 12% and 37% compared with control, respectively, without changes in growth performance. IRG treatment increased the relative abundances of genera belong to the family Lachnospiraceae, Ruminococcaceae, Veillonellaceae, Peptostreptococcaceae and Lactobacillaceae, in order Clostridiales of phylum Firmicutes, but decreased the relative abundances of genus Sphaerochaeta in phylum Spirochaetes and genus AB243818_g of family Porphyromonadaceae in phylum Bacteroidetes when compared with control. Results from the current study demonstrate that IRG supplemented diets had a beneficial effect of reducing the odorous compounds in manure, possibly by altering the bacterial community structure towards predominantly carbohydrate utilizing microorganisms in the large intestine.

The Impact of Shariah Governance and Corporate Governance on the Risk Management Practices: Evidence from Local and Foreign Islamic Banks in Malaysia

2018 ◽  
Vol 15 (2) ◽  
pp. 1-20
Author(s):  
Sabri Embi ◽  
Zurina Shafii
Keyword(s):  
Risk Management ◽  
Corporate Governance ◽  
Management Practices ◽  
Principal Component ◽  
T Test ◽  
The Body ◽  
Primary Data ◽  
Islamic Banks ◽  
Shariah Governance ◽  
The Impact

The purpose of this study is to examine the impact of Shariah governance and corporate governance (CG) on the risk management practices (RMPs) of local Islamic banks and foreign Islamic banks operating in Malaysia. The Shariah governance comprises the Shariah review (SR) and Shariah audit (SA) variables. The study also evaluates the level of RMPs, CG, SR, and SA between these two type of banks. With the aid of SPSS version 20, the items for RMPs, CG, SR, and SA were subjected to principal component analysis (PCA). From the PCA, one component or factor was extracted each for the CG, SR, and RMPs while another two factors were extracted for the SA. Primary data was collected using a self-administered survey questionnaire. The questionnaire covers four aspects ; CG, SR, SA, and RMPs. The data received from the 300 usable questionnaires were subjected to correlation and regression analyses as well as an independent t-test. The result of correlation analysis shows that all the four variables have large positive correlations with each other indicating a strong and significant relationship between them. From the regression analysis undertaken, CG, SR, and SA together explained 52.3 percent of the RMPs and CG emerged as the most influential variable that impacts the RMPs. The independent t-test carried out shows that there were significant differences in the CG and SA between the local and foreign Islamic banks. However, there were no significant differences between the two types of the bank in relation to SR and RMPs. The study has contributed to the body of knowledge and is beneficial to academicians, industry players, regulators, and other stakeholders.

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