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Activity-based protein profiling of the mouse gut microbiome in response to high or low fiber diets

ABSTRACT: Gastrointestinal content of mice fed high or low fiber diets was labeled with the GH2c-ABP. 3x replicates of each diet, 2x littermates per diet. 12 total mice.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Environmental Samples

TISSUE(S): Gut

SUBMITTER: Matthew Monroe

LAB HEAD: Aaron Wright

PROVIDER: PXD018644 | Pride | 2022-08-11

REPOSITORIES: Pride

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Dataset's files

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			Action	DRS
	FiberStudy_A_Hi_GH_QEP_20July18_Wally_18-02-10.mgf	Mgf
	FiberStudy_A_Hi_GH_QEP_20July18_Wally_18-02-10.pride.mgf.gz	Mgf
	FiberStudy_A_Hi_GH_QEP_20July18_Wally_18-02-10.raw	Raw
	FiberStudy_A_Hi_GH_QEP_20July18_Wally_18-02-10_msgfplus.mzid.gz	Mzid
	FiberStudy_A_Hi_GHwPI_QEP_20July18_Wally_18-02-10.mgf	Mgf

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Publications

Activity-based protein profiling identifies alternating activation of enzymes involved in the bifidobacterium shunt pathway or mucin degradation in the gut microbiome response to soluble dietary fiber.

Killinger Bryan J BJ Whidbey Christopher C Sadler Natalie C NC DeLeon Adrian J AJ Munoz Nathalie N Kim Young-Mo YM Wright Aaron T AT

NPJ biofilms and microbiomes 20220720 1

While deprivation of dietary fiber has been associated with adverse health outcomes, investigations concerning the effect of dietary fiber on the gut microbiome have been largely limited to compositional sequence-based analyses or utilize a defined microbiota not native to the host. To extend understanding of the microbiome's functional response to dietary fiber deprivation beyond correlative evidence from sequence-based analyses, approaches capable of measuring functional enzymatic activity are ...[more]

PMID: 35858888

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Changes in the liver transcriptome of farmed Atlantic salmon (Salmo salar) fed diets based on terrestrial alternatives to fish meal and fish oil

Project description:After a 14-week feeding trial, Atlantic salmon fed a diet based on animal by-product meal and vegetable oil (ABP) showed lower growth rates compared to others fed an FM/FO-based diet (MAR). Interestingly, feeding a vegetable meal/oil-based diet (VEG) resulted in growth rates similar to the FM/FO-based diet. A 44K microarray experiment conducted on liver total RNA samples from these three dietary groups identified 46 genes related to metabolic and growth-relevant pathways, 25 immune-related, and 12 related to oxidation-reduction processes.

2018-10-16 | GSE106604 | GEO

Transcriptome response to change in ploidy level in Arabidopsis

Project description:By reciprocally crossing 2x and 4x C24 ecotype plants, we have generated 4 types of offspring with various ploidy (2x; 3x; 4x) or parent-of-origin genome dosage (3x from 4xper2x; 3x from 2xper4x). For each offspring generated, total RNA was extracted using Trizol from 8 seedlings 9 days after germination (developmental stage1.02, 2 leaves). Sample names: DIP diploid TET tetraploid TFE triploid female excess TME triplod male excess Experimenter name: Olivier Garnier Experimenter phone: 00-353-21-490-4028 Experimenter address: Plant molecular genetics lab, Dpt of Biochemistry, UCC Experimenter address: Lee Maltings Prospect row Experimenter zip/postal_code: Cork Experimenter country: Ireland Keywords: strain_or_line_design

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Transcription profiling of Arabipdosis C24 plants with different ploidy levels

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Project description:Transcriptional profiling of adipose tissue comparing three diets with different levels of replacement of fish oil for vegetable oils. Juvenile gilthead sea bream (Sparus aurata L.) of 16 g initial mean body weight were distributed into 9 fibreglass tanks (500 l) in groups of 60 fish at the research experimental facilities of IATS. Each group received (from May 23rd to September 19th) one of the three experimental diets nominally CTRL, 66VO and VO. All diets were based on plant proteins and dietary oil was either Scandinavian FO (CTRL diet) or a blend of vegetable oils, replacing the 66% (66VO diet) and 100% (VO diet) of FO. Four samples, using a control diet (CTRL) as reference and double color hybridization and dye swap with the other two (66VO, VO)

2015-05-09 | E-GEOD-21766 | biostudies-arrayexpress

To determine transcriptome of gnotobiotic mice fed fiber-rich and fiber-free diets

Project description:Despite accepted health benefits of dietary fiber, little is known about the mechanisms by which fiber deprivation impacts the gut microbiota and alters disease risk. Using a gnotobiotic model, in which mice were colonized with a synthetic human gut microbiota, we elucidated the functional interactions between dietary fiber, the gut microbiota and the colonic mucus barrier, which serves as a primary defence against pathogens. We show that during chronic or intermittent dietary fiber deficiency, the gut microbiota resorts to host-secreted mucus glycoproteins as a nutrient source, leading to erosion of the colonic mucus barrier. Dietary fiber deprivation promoted greater epithelial access and lethal colitis by the mucosal pathogen, Citrobacter rodentium, but only in the presence of a fiber-deprived microbiota that is pushed to degrade the mucus layer. Our work reveals intricate pathways linking diet, gut microbiome and intestinal barrier dysfunction, which could be exploited to improve health using dietary therapeutics. Germ-free mice (Swiss Webster) were colonized with synthetic human gut microbiota comprising of 14 species belonging to five different phyla (names of bacterial species: Bacteroides thetaiotaomicron, Bacteroides ovatus, Bacteroides caccae, Bacteroides uniformis, Barnesiella intestinihominis, Eubacterium rectale, Marvinbryantia formatexigens, Collinsella aerofaciens, Escherichia coli HS, Clostridium symbiosum, Desulfovibrio piger, Akkermansia muciniphila, Faecalibacterium prausnitzii and Roseburia intestinalis). These mice were fed either a fiber-rich diet or a fiber-free diet for about 6 weeks. The mice were then sacrificed and their cecal tissues were immediately flash frozen for RNA extraction. The extracted RNA was subjected to microarray analysis based on Mouse Gene ST 2.1 strips using the Affy Plus kit. Expression values for each gene were calculated using robust multi-array average (RMA) method.

2016-11-21 | GSE79067 | GEO

Effects of the differential K+ diets on mouse kidney cortex tissue

Project description:In this project, we investigated the global proteome alteration in mouse kidney cortex tissues after differential K+ diet treatments. TMTpro labeling strategy was used to obtain protein quantification information from LC-MS based proteomic analysis.

2023-05-10 | PXD035354 | Pride

Transcription profiling of mouse livers from animals fed four different diets

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2009-04-08 | E-GEOD-6297 | biostudies-arrayexpress

Transcription profiling of brains of mice fed four different diets for a 2-week duration

2009-09-23 | E-GEOD-6285 | biostudies-arrayexpress

Transcription profiling of Arabidopsis to compare change in ploidy level

Project description:By reciprocally crossing 2x and 4x C24 ecotype plants, we have generated 4 types of offspring with various ploidy (2x; 3x; 4x) or parent-of-origin genome dosage (3x from 4xper2x; 3x from 2xper4x). For each offspring generated, total RNA was extracted using Trizol from 8 seedlings 9 days after germination (developmental stage1.02, 2 leaves). Sample names:; DIP diploid; TET tetraploid; TFE triploid female excess; TME triplod male excess; Experimenter name: Olivier Garnier; Experimenter phone: 00-353-21-490-4028; Experimenter address: Plant molecular genetics lab, Dpt of Biochemistry, UCC; Experimenter address: Lee Maltings Prospect row; Experimenter zip/postal_code: Cork; Experimenter country: Ireland Experiment Overall Design: 11 samples were used in this experiment

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