Impact of Organic and Conventional Husbandry Systems on the Gut Microbiome and Resistome in Pigs
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PROVIDER: PRJEB94130 | ENA |
REPOSITORIES: ENA
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Project description:Improper use of antibiotics in swine could reduce commensal bacteria and possibly increase pathogen infections via the gut resistome. This study aimed to compare the metaproteomic profiles of gut resistome and related metabolism in the cecal microbiota of fattening pigs raised under antibiotic-free (ABF) conditions with those of ordinary industrial pigs (CTRL).
2023-10-09 | PXD037218 | JPOST Repository
Project description:The aim of this study was to investigate the microbial composition, and the profiles of antimicrobial resistance genes (ARGs, resistome) and mobile genetic elements (mobilome) of retail chicken carcasses originated from conventional intensive production systems (CO), certified antimicrobial-free intensive production systems (AF), and certified organic production systems with restricted antimicrobial use (OR). DNA samples were collected from 72 chicken carcasses according to a cross-sectional study design. Shot-gun metagenomics was performed by means of Illumina high throughput DNA sequencing followed by downstream bioinformatic analyses. Gammaproteobacteria was the most abundant bacterial class in all groups. Although CO, AF, and OR did not differ in terms of alpha- and beta-microbial diversity, the abundance of some taxa differed significantly across the groups, including spoilage-associated organisms such as Pseudomonas and Acinetobacter. The co-resistome comprised 29 ARGs shared by CO, AF and OR, including genes conferring resistance to beta-lactams (blaACT-8, 10, 13, 29; blaOXA-212;blaOXA-275 and ompA), aminoglycosides (aph(3')-IIIa, VI, VIa and spd), tetracyclines (tet KL (W/N/W and M), lincosamides (inu A,C) and fosfomycin (fosA). ARGs were significantly less abundant (P < 0.05) in chicken carcasses from AF and OR compared with CO. Regarding mobile genetic elements (MGEs), transposases accounted for 97.2% of the mapped genes. A higher abundance (P = 0.037) of MGEs was found in CO compared to OR. There were no significant differences in ARGs or MGEs diversity among groups according to the Simpson´s index. In summary, retail frozen chicken carcasses from AF and OR systems show similar ARGs, MGEs and microbiota profiles compared with CO, even though the abundance of ARGs and MGEs was higher in chicken carcasses from CO, probably due to a higher selective pressure.
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Project description:Soil metagenome with poultry litter in conventional and organic production systems Genome sequencing and assembly
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Project description:Soil microbiome from organic cropping systems Raw sequence reads
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Project description:Fat is an important energy store in animals, especially pigs, because of their high fat deposition ability. In animal husbandry, fat content is closely related to animal's lean meat rate and other important economic traits. Long-chain non-coding RNA regulates numerous biological processes, including lipid metabolism. Resveratrol (RES) has been reported to have anti-obesity effects. However, it is unclear whether RES can control fat deposition in pigs by regulating the activities of long-chain non-coding RNAs (lncRNA). The aim of this study was to examine the expression of lncRNA in subcutaneous fat tissues of pigs fed RES-supplemented diet. A total of 12 Duroc × Landrace × Yorkshire hybrid pigs were randomly assigned to two diets, the control diet and the experimental diet containing 400 mg/kg RES. At the end of the study, RNA sequencing was carried out, and the results indicated the expression of lncRNA in the adipose tissues of pigs from the two groups. A total of 499 lncRNAs were identified. Eighty-two (82) differentially expressed genes, including 5 lncRNAs and 77 mRNAs, were also identified. We also observed that the lncRNAs, MSTRG.12490 and MSTRG.13223 targeted the mRNAs, THBS4 and SFPR2, respectively. Results of Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses showed that the differentially expressed genes were mainly involved in adipocytokine signaling pathway, Wnt signaling pathway, PI3K-Akt signaling pathway, and MAPK signaling pathway, which are associated with glycolipid metabolism.Results from this study contributes to the knowledge of the genes and pathways involved in fat metabolism in pigs and the role of RES in the diet of pigs.
2022-05-26 | GSE203574 | GEO
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Project description:Metagenomic investigations have the potential to provide unprecedented insights into microbial ecologies, such as those relating to antimicrobial resistance (AMR). We characterized the microbial resistome in livestock operations raising cattle conventionally (CONV) or without antibiotic exposures (RWA) using shotgun metagenomics. Samples of feces, wastewater from catchment basins, and soil where wastewater was applied were collected from CONV and RWA feedlot and dairy farms. After DNA extraction and sequencing, shotgun metagenomic reads were aligned to reference databases for identification of bacteria (Kraken) and antibiotic resistance genes (ARGs) accessions (MEGARes). Differences in microbial resistomes were found across farms with different production practices (CONV vs. RWA), types of cattle (beef vs. dairy), and types of sample (feces vs. wastewater vs. soil). Feces had the greatest number of ARGs per sample (mean = 118 and 79 in CONV and RWA, respectively), with tetracycline efflux pumps, macrolide phosphotransferases, and aminoglycoside nucleotidyltransferases mechanisms of resistance more abundant in CONV than in RWA feces. Tetracycline and macrolide-lincosamide-streptogramin classes of resistance were more abundant in feedlot cattle than in dairy cow feces, whereas the β-lactam class was more abundant in dairy cow feces. Lack of congruence between ARGs and microbial communities (procrustes analysis) suggested that other factors (e.g., location of farms, cattle source, management practices, diet, horizontal ARGs transfer, and co-selection of resistance), in addition to antimicrobial use, could have impacted resistome profiles. For that reason, we could not establish a cause-effect relationship between antimicrobial use and AMR, although ARGs in feces and effluents were associated with drug classes used to treat animals according to farms' records (tetracyclines and macrolides in feedlots, β-lactams in dairies), whereas ARGs in soil were dominated by multidrug resistance. Characterization of the "resistance potential" of animal-derived and environmental samples is the first step toward incorporating metagenomic approaches into AMR surveillance in agricultural systems. Further research is needed to assess the public-health risk associated with different microbial resistomes.
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Project description:We sequenced mRNA from subcuteneous adipose tissue of 36 pigs (12 Low, 12 Mean and 12 High) to investigate expression profiling of obesity (porcine model). Uploaded RNAseq data on the first 12 samples (from titles 1_SusScrofa to 12_SusScrofa) are LOW obese pigs, the middle 12 samples (from titles 13_SusScrofa to 24_SusScrofa) are MEDIUM obese pigs and the last 12 samples (from titles 24_SusScrofa to 36_SusScrofa) are HIGH obese pigs. These 3 categories based on an aggregate Obesity Index (OI) values and calculated using a multi-trait Estimated Breeding Value (EBV) and Selection Index methods combining nine obesity and obesity-related (OOR) phenotypes into a single value representative of the genetic predisposition to obesity. in Human studies, this is somewhat equivalent to combined multi-trait, weighted Polygenic Risk Scores (PRS) for obesity. That is, they are predicted based on genetic / genomic information and several correlated phenotypes using Mixed Models / BLUP. For more information on Obesity Index, refer to Frontiers in Genetics (2014), Sec. Systems Biology, Vol. 5. https://doi.org/10.3389/fgene.2014.00214
2015-01-15 | GSE61271 | GEO