Mouse gut metagenome
Ontology highlight
ABSTRACT:
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| DRR129364.fastq.gz | Fastqsanger.gz | |||
| DRR129365.fastq.gz | Fastqsanger.gz | |||
| DRR129366.fastq.gz | Fastqsanger.gz | |||
| DRR129367.fastq.gz | Fastqsanger.gz | |||
| DRR129368.fastq.gz | Fastqsanger.gz |
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2025-03-24 | MSV000097426 | MassIVE
Project description:Inappropriate cross talk between mammals and their gut microbiota may trigger intestinal inflammation and drive extra-intestinal immune-mediated diseases. Studies with germ-free or gnotobiotic animals represent the gold standard for research on bacterial-host interaction but they are not readily accessible to the wide scientific community. We aimed at refining a protocol that in a robust manner would deplete murine intestinal microbiota and prove to have significant biologic validity. Previously published protocols for depleting mice of their intestinal microbiota by administering broad-spectrum antibiotics in drinking water were difficult to reproduce. We show that twice daily delivery of antibiotics by gavage depleted mice of their cultivable fecal microbiota and reduced the fecal bacterial DNA load by approximately 400 fold while ensuring the animals’ health. Mice subjected to the protocol for 17 days displayed enlarged ceca, reduced Peyer’s patches and small spleens. Antibiotic treatment significantly reduced the expression of antimicrobial factors and altered the expression of 517 genes in total in the colonic epithelium. Genes involved in cell cycle were significantly altered concomitant with reduced epithelial proliferative activity in situ assessed by Ki-67 expression, suggesting that commensal microbiota drives cellular proliferation in colonic epithelium. We present a robust protocol for depleting mice of their cultivatable intestinal microbiota with antibiotics by gavage and show that the biological effect of this depletion is phenotypic characteristics and epithelial gene expression profile similar to those of germ-free mice. Comparison of genome-wide gene expression of colon intestinal epithelial cells from mice subjected to microbiota depletion protocol against to control mice.
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Project description:Diet plays a major role in altering the composition and function of the gut microbiota. Previously most studies have focused on the effects of fiber, fat, and different amounts of protein on the gut microbiota. In this study we investigated how different sources of protein affect the gut microbiota of mice. We fed conventional and germ-free C57BL/6J mice a series of defined diets where the source of dietary protein was the key difference, which made up twenty or forty percent of the diet. The dietary protein sources used were purified protein. The diets were fed to the same mice for one week each with a fecal sample collected at the end of each week. The diets were fed in this order: standard chow, 20% soy, 20% casein, 20% rice, 40% soy, 20% yeast, 40% casein, 20% pea, 20% egg white protein, 20% chicken bone broth, and lastly at the end of the experiment half of the mice were fed the 20% soy and half the mice the 20% casein diet again as a control. We did not collect fecal samples for the chicken bone broth diet as the diet was stopped prematurely due to diet intolerance. 12 germ-free mice (6 female, 6 male) in four cages were used. 12 mice with a conventional gut microbiota in four cages were used (6 female, 6 male). One germ-free mouse was found dead after diet 5 (20% yeast) and one conventional mouse was sacrificed after the second diet (20% casein). No sample could be collected from one of the conventional mice after the 20% egg white diet.
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Project description:We compared gene expression in the small intestine (ileum) of mice that were either (i) germ-free, (ii) colonized with a conventional mouse cecal microbiota, (iii) colonized with a conventional zebrafish gut microbiota, or (iv) colonized with Pseudomonas aeruginosa PAO1. Experiment Overall Design: Adult germ-free NMRI mice were colonized with either (i) a conventional mouse cecal microbiota harvested from adult Swiss-Webster mice (5 biological replicates), (ii) a conventional zebrafish intestinal microbiota harvested from adult C32 zebrafish (3 biological replicates), or (iii) a culture of Pseudomonas aeruginosa PAO1 (5 biological replicates). 14 days after colonization, total RNA was prepared from the ileum of each animal, with total RNA prepared from adult germ-free NMRI mouse ileum serving as negative controls (5 biological replicates). RNA was used as template to generate cRNA for hybridization to Affymetrix 430 v2 Mouse GeneChips.
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