Project description:In this study, we studied the fibrolytic potential of the rumen microbiota in the rumen of 6 lambs separated from their dams from 12h of age and artificially fed with milk replacer (MR) and starter feed from d8, in absence (3 lambs) or presence (3 lambs) of a combination of the live yeast Saccharomyces cerevisiae CNCM I-1077 and selected yeast metabolites. The fibrolytic potential of the rumen microbiota of the lambs at 56 days of age was analyzed with a DNA microarray (FibroChip) targeting genes coding for 8 glycoside hydrolase (GH) families.
Project description:<p>Antibiotics were once used in animal production to improve productivity and resistance to pathogenic microbiota. However, due to its negative effects, the search for a new class of substances that can replace its efficacy has become one of the urgent problems to be solved. Plant essential oils (EOs) as a natural feed additive can maintain microbiota homeostasis and improve animal performance. However, its specific mechanism of action needs to be further investigated. Therefore, we added different doses of essential oil of Zanthoxylum bungeanum (EOZB) to the diets of Small Tail Han Sheep hybrid male lambs (STH lambs) to evaluate the effect of EOZB on rumen enzyme activity, rumen microbiology and its metabolites in STH lambs. Twenty STH lambs were randomly divided into four groups (n = 5/group) and provided with the same diet. The dietary treatments were as follows: basal diet (BD) group; BD+EOZB 5 mL/kg group; BD+EOZB 10 mL/kg group; BD+EOZB 15 mL/kg group. We found that EOZB 10 ml/kg helped to increase rumen pectinase (P<0.05) and lipase (P<0.05) activities. Microbial 16S rRNA gene analysis showed that EOZB significantly altered the abundance of rumen microbiota (P<0.05). LC/GC-MS metabolomic analysis showed that the addition of EOZB produced a total of 1073 differential metabolites, with 58 differential metabolites remaining after raising the screening criteria. These differential metabolites were mainly enriched in glycerophospholipid metabolism, choline metabolism in cancer, retrograde endocannabinoid signaling, benzoxazinoid biosynthesis, and protein digestion and absorption. Correlation analysis showed that some rumen microbiota were significantly correlated with differential metabolite and enzyme activities.</p>
Project description:Dwelling in the gut of herbivores, anaerobic gut fungi (AGF) have evolved several strategies to efficiently degrade unpretreated biomass. Their genomes encode a diverse array of carbohydrate-active enzymes (CAZymes), yet exceedingly few of these enzymes have been validated. Here, we developed a predictive bioinformatic pipeline to both annotate novel putative CAZymes and validate their activity through heterologous expression. 173 fungal proteins from Piromyces finnis associated with biomass degradation were synthesized and expressed in E. coli, and 9.8% were soluble with expression levels exceeding 5% of total proteome. Among the 17 heterologously expressed proteins, a combination of sequence and structure-based homology annotation identified many multifunctional proteins having catalytic domains, such as glycoside hydrolase (GH) and carbohydrate esterase (CE), fused with repetitive dockerins. Screening across three cellulose and hemicellulose substates experimentally verified six predicted functions. One promising enzyme, celsome_012, exhibited robust and optimized activity against beechwood xylan at 37°C and pH 6.4, producing five-times more products than other recombinant proteins screened here. Overall, this study represents the first large-scale screening campaign of putative AGF CAZymes, highlighting proteins amenable to E. coli overexpression, integrating advanced sequence and structural annotation, and identifying a robust, novel fungal xylanase for detailed biochemical characterization.
Project description:Transcriptomics was performed on batch cultivations of A. niger grown on three monosaccharides and three complex carbohydrates with defined compositions as to allow the detection of cross-induction if present, and for demonstration of how enzyme interaction graphics can be used to visualize the global transcription response. Batch cultivations of A. niger were grown in shake-flasks on one of three monosaccharides (arabinose, glucose, xylose) or one of three complex carbohydrates (arabinan, starch, xylan). Three replicates were performed for each monosaccharide and complex carbohydrate, except for starch, where two replicates were performed.
Project description:Because of the central role of the liver in numerous physiological processes and its possible relation with quality carcass traits in suckling lambs, and considering that female lambs have higher carcass fatness levels, this experiment has analyzed the liver transcriptome of 12 suckling lambs (slaughter age: +/- 25 days), including six males and six females. RNA was extracted from the liver tissue of the lambs at the time of slaughter following a standard protocol. The RNA integrity value was calculated using the Agilent 2,100 Bioanalyzer equipment (Agilent Technologies, CA, USA). cDNA libraries were sequenced to a minimum depth of 30 million paired-end reads, generating 150 bp stranded paired-end reads using an Illumina Novaseq 6,000 system.
Project description:Samples of perirenal fat tissue from 8 Assaf breed suckling lambs. These animals were selected from a larger group of 17 Assaf suckling lambs for which carcass traits were measured. The 8 selected lambs were those showing the highest and the lowest values, from the larger group, for the percentage of perirenal and cavitary fat relative to the half carcass weight. Hence, considering the values for this trait, we defined the High-PF group (n = 4; average: 3.23 ± 0,.47) and the Low-PF group (n = 4; 1.65 ± 0,.16), respectively.
Project description:Our group has developed an extra-uterine environment for newborn development (EXTEND) using an ovine model, that aims to mimic the womb to improve short and long-term health outcomes associated with prematurity. This study’s objective was to determine the histologic and transcriptomic consequences of EXTEND on the brain. Histology and RNA-sequencing was conducted on brain tissue from three cohorts of lambs: control pre-term (106-107 days), control late pre-term (127 days), and experimental lambs who were born pre-term and supported on EXTEND until late pre-term age (125-128 days). Bioinformatic analysis determined differential gene expression among the three cohorts and across four different brain tissue sections: basal ganglia, cerebellum, hippocampus, and motor cortex. There were no clinically relevant histological differences between the control late pre-term and EXTEND ovine brain tissues. RNA-sequencing demonstrated that there was greater differential gene expression between the control pre-term lambs and EXTEND lambs than between the control late pre-term lambs and EXTEND lambs. Our study demonstrates that the use of EXTEND to support pre-term lambs until they reach late pre-term gestational age results in brain tissue gene expression that more closely resembles that of the lambs who reached late pre-term gestation within their maternal sheep’s womb than that of the lambs who were born prematurely.