Cecal metabolome of specific-pathogen-free mice fed with five distinct rodent diets with varying fiber content and source.
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus Musculus
TISSUE(S): Cecum
PROVIDER: ST002170 | MetabolomicsWorkbench |
REPOSITORIES: MetabolomicsWorkbench
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| mwtab | Other |
Items per page: 5 1 - 1 of 1 |
Similar Datasets
Project description: Not available
| ST002171 | MetabolomicsWorkbench
Project description:IntroductionFeeding a Bones and Raw Food (BARF) diet has become an increasing trend in canine nutrition. Bones and Raw Food diets contain a high amount of animal components like meat, offal, and raw meaty bones, combined with comparatively small amounts of plant ingredients like vegetables and fruits as well as different sorts of oil and supplements. While many studies have focused on transmission of pathogens via contaminated meat and on nutritional imbalances, only few studies have evaluated the effect of BARF diets on the fecal microbiome and metabolome. The aim of the study was to investigate differences in the fecal microbiome and the metabolome between dogs on a BARF diet and dogs on a commercial diet (canned and dry dog food).MethodsNaturally passed fecal samples were obtained from 27 BARF and 19 commercially fed dogs. Differences in crude protein, fat, fiber, and NFE (Nitrogen-Free Extract) between diets were calculated with a scientific nutrient database. The fecal microbiota was analyzed by 16S rRNA gene sequencing and quantitative PCR assays. The fecal metabolome was analyzed in 10 BARF and 9 commercially fed dogs via untargeted metabolomics approach.ResultsDogs in the BARF group were fed a significantly higher amount of protein and fat and significantly lower amount of NFE and fiber. There was no significant difference in alpha-diversity measures between diet groups. Analysis of similarity (ANOSIM) revealed a significant difference in beta-diversity (p < 0.01) between both groups. Linear discriminant analysis effect size (LefSe) showed a higher abundance of Lactobacillales, Enterobacteriaceae, Fusobacterium and, Clostridium in the BARF group while conventionally fed dogs had a higher abundance of Clostridiaceae, Erysipelotrichaceae, Ruminococcaceae, and Lachnospiraceae. The qPCR assays revealed significantly higher abundance of Escherichia coli (E. coli) and Clostridium (C.). perfringens and an increased Dysbiosis Index in the BARF group. Principal component analysis (PCA) plots of metabolomics data showed clustering between diet groups. Random forest analysis showed differences in the abundance of various components, including increased 4-hydroxybutryric acid (GBH) and 4-aminobutyric acid (GABA) in the BARF group. Based on univariate statistics, several metabolites were significantly different between diet groups, but lost significance after adjusting for multiple comparison. No differences were found in fecal bile acid concentrations, but the BARF group had a higher fecal concentration of cholesterol in their feces compared to conventionally fed dogs.ConclusionMicrobial communities and metabolome vary significantly between BARF and commercially fed dogs.
| S-EPMC6093636 | biostudies-literature
Project description: Not available
| ST002172 | MetabolomicsWorkbench
Project description:Growing broiler chickens of the Cobb500 strain were used to determine the effects on intestinal microbiota composition of a protein-free (PF) diet as compared to a diet based in casein (CAS) as the only protein source. CAS was formulated to contain the same amount of protein (190 g kg-1) as a commercial Maize-soy diet which was used as a practical reference. The ileal AA flow (g kg-1 dry matter intake) was significantly higher (P < 0.001) than PF in birds fed protein containing diets (CAS or Maize-soy). Taken as a whole (discriminant and ANOSIM analysis), the intestinal (ileal and caecal contents and ileal tissue) microbiota composition of PF and CAS were significantly (P < 0.001) different from Maize-soy and not different from each other in some cases. RT-qPCR and sequencing analysis of the ileal and caecal microbiota revealed significant (P < 0.05) differences in a number of bacterial groups between broilers fed PF, CAS or Maize-soy diets. The main result was that the lack of protein in the intestinal medium of PF birds resulted in a drop of Lactobacillus spp. counts (on average, 43 in PF vs 1,734 in the Maize-soy diet) and increased Enterobacteriaceae (on average, 419 in PF vs 172 in the Maize-soy diet) and other potentially pathogenic bacterial groups (in both intestinal contents and tissue). Thus, the lack of protein in the intestinal medium of PF birds resulted in a microbiota composition compatible with a pro-inflammatory state, and this effect was somewhat less marked in birds fed CAS. The results reported here suggest that the adverse effects on microbiota composition in broilers fed CAS were less marked than in those fed PF, which would be in line with a preferential use of a highly digestible protein containing diet to determine endogenous AA excretion instead of a PF diet.
| S-EPMC11530906 | biostudies-literature
Project description:Diets containing higher-amylose-content starches were proved to have some beneficial effects on monogastric animals, such as promoting the proliferation of intestinal probiotics. However, current research on the effects of diets with different starch sources on animals at the extraintestinal level is still very limited. We hypothesized that diets with different starch sources may affect lipid-related gene expression and metabolism in the liver of pigs. This study aimed to use adult pig models to evaluate the effects of diets with different starch sources (tapioca starch, TS; pea starch, PS) on the liver gene expressions and metabolism. In total, 48 growing pigs were randomly assigned to the TS and PS diets with 8 replicate pens/group and 3 pigs per pen. On day 44 of the experiment, liver samples were collected for metabolome and transcriptome analysis. Metabolome data suggested that different starch sources affected (p < 0.05) the metabolic patterns of liver. Compared with the TS diet, the PS diet increased (p < 0.05) some unsaturated fatty acids and several amino acids or peptide levels in the liver of pigs. Moreover, transcriptome data indicated the PS diets elevated (p < 0.05) fatty acid β-oxidation-related gene expression in the liver of pigs, and reduced (p < 0.05) unsaturated fatty acid metabolism-related gene expression. The results of quantitative real-time PCR confirmed that the PS diet upregulated (p < 0.05) the expression of acyl-CoA dehydrogenase very long chain (ACADVL), carnitine palmitoyl transferase (CPT) 1A, and malonyl-CoA decarboxylase (MLYCD), and downregulated (p < 0.05) the expression level of cytochrome P450 2U1 (CYP2U1) and aldehyde dehydrogenase 1B1 (ALDH1B1) in the liver. In addition, the results of a Mantel test indicated the muscle fatty acids were significantly closely correlated (p < 0.05) with liver gene expressions and metabolites. In summary, these findings suggest that diets containing higher amylose starches improved the lipid degradation and the unsaturated fatty acid levels in pig livers, and thus can generate some potential beneficial effects (such as anti-inflammatory and antioxidant) on pig health.
| S-EPMC11591517 | biostudies-literature
Project description:to detect gut microbiota Raw sequence reads
| PRJNA669439 | ENA
Project description:In this study, a comparative, untargeted metabolomics approach was applied to compare urinary metabolite profiles of rats fed irradiated and non-irradiated diets. γ-Irradiated and non-irradiated NIH 7001 diet was given orally to animals beginning 5 days after exposure to the carcinogen N-methyl-N-nitrosourea and continued for 120 days. There was a 36% reduction in mammary tumor incidence in rats consuming the γ-irradiated diet, compared to rats receiving the non-irradiated form of the same diet. Urine samples from rats fed with γ-irradiated and non-irradiated diets were analyzed using nanoLC-MS/MS on a Q-TOF mass spectrometer, collecting positive and negative ion data. Data processing involved feature detection and alignment with MS-DIAL, normalization, mean-centering and Pareto scaling, and univariate and multivariate statistical analysis using MetaboAnalyst, and pathway analysis with Mummichog. Unsupervised Principal Component Analysis and supervised Partial Least Squares-Discriminant Analysis of both negative and positive ions revealed separation of the two groups. The top 25 metabolites from variable importance in projection scores >1 showed their contributions in discriminating urines the γ-irradiated diet fed group from non-irradiated control diet group. Consumption of the γ-irradiated diet led to alteration of several gut microbial metabolites such as phenylacetylglycine, indoxyl sulfate, kynurenic acid, hippurate and betaine in the urine. This study provides insights into metabolic changes in rat urine in response to a γ-irradiated diet which may be associated with mammary cancer prevention.
| S-EPMC9608802 | biostudies-literature
Project description:This study was designed to evaluate the effects of dietary coated sodium butyrate (CSB) on the intestinal antioxidant, immune function, and cecal microbiota of laying hens. A total of 720 52-week-old Huafeng laying hens were randomly allocated into five groups and fed a basal diet supplemented with CSB at levels of 0 (control), 250 (S250), 500 (S500), 750 (S750), and 1000 (S1000) mg/kg for eight weeks. The results revealed that CSB supplementation quadratically decreased the malondialdehyde content and increased the superoxide dismutase activity of the jejunum as well as the total antioxidative capacity activity of the ileum (p < 0.05). Dietary CSB supplementation linearly decreased the diamine oxidase and D-lactic acid content of the serum (p < 0.05). Compared with the control group, the addition of CSB resulted in linear and/or quadratic effects on the mRNA expression of inflammatory cytokines TNF-α, IL-6, and IL-10 in the jejunum and ileum (p < 0.05). The short-chain fatty acid concentrations increased quadratically as supplemental CSB improved (p < 0.05). Additionally, dietary CSB levels had no effect on microbial richness estimators, but ameliorated cecal microbiota by raising the abundance of probiotics and lowering pathogenic bacteria enrichment. In conclusion, our results suggest that dietary supplementation with CSB could improve the intestinal health of laying hens via positively influencing the antioxidant capacity, inflammatory cytokines, short-chain fatty acids, and gut microbiota. In this study, 500 mg/kg CSB is the optimal supplement concentration in the hens’ diet.
| S-EPMC8908843 | biostudies-literature
Project description:chicken cecal content Raw sequence reads
| PRJNA797199 | ENA
Project description:16S amplicon sequencing of chicken cecal content
| PRJNA1080234 | ENA