Gut microbiome following long antibiotic course
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB44880 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| assembly.fasta.gz | Fasta.gz | |||
| ERR5919737_1.fastq.gz | Fastqsanger.gz | |||
| ERR5919737_2.fastq.gz | Fastqsanger.gz | |||
| ERR5922430_1.fastq.gz | Fastqsanger.gz | |||
| ERR5922430_2.fastq.gz | Fastqsanger.gz |
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Project description:Antibiotic disruption of the intestinal microbiota may cause susceptibility to pathogens that is resolved by progressive bacterial outgrowth and colonization. Succession is central to ecological theory but not widely documented in studies of the vertebrate microbiome. Here, we study succession in the hamster gut after treatment with antibiotics and exposure to Clostridium difficile. C. difficile infection is typically lethal in hamsters, but protection can be conferred with neutralizing antibodies against the A and B toxins. We compare treatment with neutralizing monoclonal antibodies (mAb) to treatment with vancomycin, which prolongs the lives of animals but ultimately fails to protect them from death. We carried out longitudinal deep sequencing analysis and found distinctive waves of succession associated with each form of treatment. Clindamycin sensitization prior to infection was associated with the temporary suppression of the previously dominant Bacteroidales and the fungus Saccinobaculus in favor of Proteobacteria. In mAb-treated animals, C. difficile proliferated before joining Proteobacteria in giving way to re-expanding Bacteroidales and the fungus Wickerhamomyces. However, the Bacteroidales lineages returning by day 7 were different from those that were present initially, and they persisted for the duration of the experiment. Animals treated with vancomycin showed a different set of late-stage lineages that were dominated by Proteobacteria as well as increased disparity between the tissue-associated and luminal cecal communities. The control animals showed no change in their gut microbiota. These data thus suggest different patterns of ecological succession following antibiotic treatment and C. difficile infection.
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Project description:Long-term dietary intake influences the structure and activity of the trillions of microorganisms residing in the human gut, but it remains unclear how rapidly and reproducibly the human gut microbiome responds to short-term macronutrient change. Here we show that the short-term consumption of diets composed entirely of animal or plant products alters microbial community structure and overwhelms inter-individual differences in microbial gene expression. The animal-based diet increased the abundance of bile-tolerant microorganisms (Alistipes, Bilophila and Bacteroides) and decreased the levels of Firmicutes that metabolize dietary plant polysaccharides (Roseburia, Eubacterium rectale and Ruminococcus bromii). Microbial activity mirrored differences between herbivorous and carnivorous mammals, reflecting trade-offs between carbohydrate and protein fermentation. Foodborne microbes from both diets transiently colonized the gut, including bacteria, fungi and even viruses. Finally, increases in the abundance and activity of Bilophila wadsworthia on the animal-based diet support a link between dietary fat, bile acids and the outgrowth of microorganisms capable of triggering inflammatory bowel disease. In concert, these results demonstrate that the gut microbiome can rapidly respond to altered diet, potentially facilitating the diversity of human dietary lifestyles. RNA-Seq analysis of the human gut microbiome during consumption of a plant- or animal-based diet.
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Project description:Tilmicosin, an antibiotic widely used in animal husbandry to prevent and treat bacterial infections, raises concerns due to its residual accumulation, which impacts both animal health and food safety. In this study, we conducted a comprehensive analysis of tilmicosin clearance patterns in different tissues, assessed physiological impacts through blood biochemistry, and investigated changes in gut microbial composition with 16S rRNA sequencing of the tilmicosin-treated Silkie chickens. Initially, we observed rapid peaks in tilmicosin residues in all tissues within 1 day after treatment, but complete metabolism took longer, extending beyond 9 days. Moreover, tilmicosin treatment significantly decreased serum levels of total bile acid, blood urea nitrogen, and uric acid, while increasing the levels of direct bilirubin, total bilirubin, and glutathione peroxidase at day 3, followed by a decrease from day 5 onwards. The effects of tilmicosin use on microbial composition and diversity lasted for an extended period, with the relative abundance of Proteobacteria remaining significantly different between the control and tilmicosin-treated groups at 120 days. Additionally, correlation analysis revealed a strong positive correlation between Mucispirillum_schaedleri and tilmicosin residue in all tissues, while Parabbacteroide_distasonis, Faecalibacterium_prausnitzii, and others exhibited negative correlations with tilmicosin residue. Overall, our study indicates a significant correlation between intestinal microbes and antibiotic residues, providing a theoretical basis for guiding the withdrawal period after antibiotic use.
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Project description:Intervention 1: ?1st Arm: Short course radiotherapy with 25 Gy in 5 fractions with concurrent chemotherapy regimen including Capecitabine 625mg/m2/bid for 5 days and Oxaliplatin 50mg/m2/day for 1 day then one cycle chemotherapy with XELOX regimen (Capecitabine 1000mg/m2/bid for 14 days and Oxaliplatin 130mg/m2/day for 1 day) 3 - 4 weeks after completion of radiotherapy then surgery at least 8 weeks after the radiotherapy last session. Intervention 2: 2nd Arm (Control): Long course radiotherapy with 50 Gy in 25 fractions with concurrent Capecitabine 825mg/m2/bid for 5 days each week then one cycle chemotherapy with XELOX regimen (Capecitabine 1000mg/m2/bid for 14 days and Oxaliplatin 130mg/m2/day for 1 day) 3 - 4 weeks after completion of radiotherapy then surgery at least 8 weeks after the radiotherapy last session.;Treatment - Drugs;Treatment - Drugs;?1st Arm: Short course radiotherapy with 25 Gy in 5 fractions with concurrent chemotherapy regimen including Capecitabine 625mg/m2/bid for 5 days and Oxaliplatin 50mg/m2/day for 1 day then one cycle chemotherapy with XELOX regimen (Capecitabine 1000mg/m2/bid for 14 days and Oxaliplatin 130mg/m2/day for 1 day) 3 - 4 weeks after completion of radiotherapy then surgery at least 8 weeks after the radiotherapy last session.;2nd Arm (Control): Long course radiotherapy with 50 Gy in 25 fractions with concurrent Capecitabine 825mg/m2/bid for 5 days each week then one cycle chemotherapy with XELOX regimen (Capecitabine 1000mg/m2/bid for 14 days and Oxaliplatin 130mg/m2/day for 1 day) 3 - 4 weeks after completion of radiotherapy then surgery at least 8 weeks after the radiotherapy last session.
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