Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Digestion-resistant proteins support the healthy metabolite profiles associated with plant-based diets

ABSTRACT: Plant-based diets are known to increase healthy phenol metabolites (hippuric acid and 3-phenylpropionate) while decreasing inflammatory phenols (cresol sulfate and phenol sulfate), but there is not yet a mechanistic understanding for how plant-based diets differentially regulate these metabolites. Here, through isotope tracing studies, we show cresol and phenol sulfate primarily come from bacterial digestion of secreted protein. Through careful dietary studies, we show gut microbial access to fiber decreases secreted protein contribution and overall concentrations of these inflammatory phenols. Additionally, plant proteins increase hippuric acid and 3-phenylpropionate. Plant proteins are resistant to mammalian digestion, which increases gut microbial access to dietary protein. This increase in protein fuels production of healthy phenols regardless of the fiber or fat composition of the diet. Our data establish digestion-resistant plant protein as a modulator of microbiome metabolism. Together, fiber and digestion-resistant protein supports the healthy metabolite profiles associated with plant-based diets.

INSTRUMENT(S):

ORGANISM(S): Gut Metagenome Mus Musculus (mouse)

TISSUE(S): Cecum, Cecum Mucosa

SUBMITTER: Felix Keber

LAB HEAD: Martin Wühr

PROVIDER: PXD066561 | Pride | 2026-07-06

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	45941_ORC_02637_JA01xx_Phe_Microbiome_isotope_Phe_20ppm_1iT_C125.mzid	Mzid
	45943_ORC_02638_JA01xx_Phe_Microbiome_isotope_Phe_20ppm_1iT_C125.mzid	Mzid
	45945_ORC_02639_JA01xx_Phe_Microbiome_isotope_Phe_20ppm_1iT_C125.mzid	Mzid
	45946_ORC_02640_JA01xx_Phe_Microbiome_isotope_Phe_20ppm_1iT_C125.mzid	Mzid
	ORC_02637.raw	Raw

Items per page:

1 - 5 of 13

Similar Datasets

Lipids accumulation in nitrogen and phosphorus-limited yeast is caused by less growth-related dilution

Project description:Oleaginous yeasts are used commercially to produce oleochemicals and hold potential also for biodiesel production. In response to nitrogen or phosphorous limitation, oleaginous yeast accumulate triacylglycerol. Previous work has investigated potential mechanisms by which nutrient limitation induces lipid biosynthesis without verifying whether lipid biosynthesis flux is actually enhanced. Here we show, using 13C-glucose tracing, that in nitrogen or phosphorous limitation, lipid accumulation occurs without consistent increases in biosynthetic flux. Instead, the main driver of increased lipid pools is decreased growth-related dilution. This conclusion holds across two divergent oleaginous yeasts: Rhodotorula toruloides and Yarrowia lipolytica. Quantitative proteomics shows a substantial proteome reallocation in response to nitrogen and phosphorous limitation, with ribosomal proteins strongly down regulated, while lipid biosynthetic enzymes are preserved but not consistently upregulated in absolute quantity. Thus, nutrient limitation, rather than triggering greatly enhanced lipid synthesis, results in roughly sustained lipid enzyme levels and biosynthetic flux. Due to slower lipid dilution by cell division, this suffices to drive marked lipid accumulation.

2025-08-27 | PXD063019 | Pride

The potent biodegrading actinomycete Rhodococcus opacus 1CP: Relating aromatic compound metabolism with whole-genome and transcriptome data

Project description:The genus Rhodococcus comprises numerous strains recognized for pollutant degradation, secondary metabolite production including biosurfactant, lignin breakdown, or utilization of volatile organic compounds. Often gene redundancies and evolution of alternative pathways are attributed to such characteristics. Rhodococcus opacus 1CP initially isolated as a chlorophenol degrading strain was found to be a model organism comprising several such features. In this study, we analyzed the genome and transcriptome and demonstrated that the strain 1CP undergo three different routes of ortho, meta, and side chain attack in degrading aromatic compounds. The wild type strain, single or double knock-out mutant of phenol hydroxylases, well compensated the loss and chooses the classical ortho-route to attack substituted phenols, while the triple knock-out mutant takes the meta-pathway to act on p-cresol indicating that this pathway serves as a reserve in strain 1CP. Growth of 1CP in phenol, p-cresol and styrene induces several gene clusters that are associated in lignin metabolization. Catechol, protocatechuate, and phenylacetic acid are major key intermediates that are funneled into central pathways which enable the strain 1CP to degrade acetophenone, benzoate, phenol, 2-phenylethanol, and styrene. Strain 1CP has an alternative option with the modified ortho-cleavage pathway which enables it to degrade 2-chlorophenol. Interestingly, in almost all cases, redundant genes were identified, but only in minor cases as phenol hydroxylases, they were found to be active and simultaneously involved in metabolic activities. The transcriptome and kinetic data showed that the redundant styrene-oxide isomerase is upregulated and involved in styrene degradation.

2026-03-27 | GSE294731 | GEO

Transcriptome Analysis of Common Carp (Cyprinus carpio) Fed with Animal and Plant Diets

Project description:purpose?To elucidate the relationship of utilization different type of diets in fish method?enzyme activity determination and transcriptome sequencing were performed in common carp fed with single animal diet group (group AD), plant diet group (group PD) and mix diets group (group MD). Group MD as control group results? 916 and 1296 differentially expressed genes were identified between group AD vs MD and PD vs MD. Protein digestion and absorption, bile secretion, hematopoietic cell lineage and intestinal immune network for IgA production pathways were significantly differentially expressed between common carp fed with single type of diet and mix diets. Conclusion?common carp fed with mix diets had stronger immunity than common carp fed with single type of diets.

2019-01-19 | GSE125366 | GEO

Project description:Phenol inhibition on anaerobic digestion

| PRJNA865089 | ENA

Effect of Plant and Animal Proteins on Biomarkers of Colorectal Cancer and Type 2 Diabetes in Healthy Adults (ScenoProt)

Project description:The aim of this study is to investigate the effects of dietary plant and animal proteins on gut metabolism and markers for colorectal cancer as well as blood protein metabolites and markers for type 2 diabetes in healthy adults. The study participants will be stratified into three groups with different protein composition in diets: 1) animal 70%/plant 30%; 2) animal 50%/plant 50% and 3) animal 30%/plant 70%. The participants will get part of their diet as ready foods or raw material to promote their compliance. The participants will also get personal advice for their diets. Blood, stool and urine samples will be collected in the beginning and in the end of the 12 week intervention, as well as phenotype measures like BMI, blood pressure and body composition. The participants will also fill food diary before and in the end of the intervention.

| 2248500 | ecrin-mdr-crc

LL_phenol

Project description:Anaerobic digestion of phenol rich influent

| PRJEB28103 | ENA

The role of dietary fiber in microglial transcriptome

Project description:To understand how dietary fiber affects microglial transcriptome at early stage, we fed mice diets releasing different amount of fiber and profiled microglia at 3 weeks. We found that fiber significantly altered the transcriptomic signature of microglia.

2023-09-08 | GSE186210 | GEO

Anaerobic membrane bioreactor treating phenol and p-cresol

Project description:Anaerobic membrane bioreactor treating phenol and p-cresol Raw sequence reads

| PRJNA1296805 | ENA

Proteomic characterization of the Pseudomonas sp. strain phDV1 response to monocyclic aromatic compounds

Project description:The degradation of aromatic compounds comprises an important step in the removal of pollutants and re-utilization of plastics and other non-biological polymers. Here we set out to study Pseudomonas sp. strain phDV1, a gram-negative bacterium that was selected for its ability to degrade aromatic compounds. In order to understand how the aromatic compounds and their degradation products are reintroduced in the metabolism of the bacteria and the systematic/metabolic response of the bacterium to the new carbon source, the proteome of this strain was analysed in the presence of succinate, phenol and o-, m-, p-cresol as sole carbon source. We then applied label-free quantitative proteomics to monitor overall proteome remodeling during metabolic adaptation to different carbon sources. As a reference proteome, we grew the bacteria in succinate and then compared the respective proteomes of bacteria grown on phenol and different cresols. In total, we identified 2295 proteins; 1908 proteins were used for quantification between different growth conditions. We found that 70, 100, 150 and 155 proteins were significantly differentially expressed in cells were grown in phenol, o-, m- and p-cresol-containing medium, respectively. The carbon source affected the synthesis of enzymes related to aromatic compound degradation, and in particular, the enzyme involved in the meta-pathway of monocyclic aromatic compounds degradation. In addition, proteins involved in the production of polyhydroxyalkanoate (PHA), an attractive biomaterial, showed higher expression levels in the presence of monocyclic aromatic compounds.Our results provide for the first time comprehensive information on the proteome response of this strain to monocyclic aromatic compounds.

2020-10-22 | PXD021237 | Pride

The Formation of Phenol and Indole Flavor Substances in Stinky Tofu Brine Based on Metabolism of Aromatic Amino Acids

Project description:<p>Understanding the formation mechanism of the flavor compounds in stinky tofu brine is crucial for controlling the flavor quality of Changsha stinky tofu. Dynamic changes in associated bacteria, enzymes, and differential metabolites in the metabolic pathway of aromatic amino acids in brine were investigated. Results showed that phenol (0.39-89.96 µg/mL), p-cresol (0.19-389.62 µg/mL), indole (1.14-242.97 µg/mL), 3-methylindole (0.14-3.00 µg/mL) were the key flavor substances of brine. The main associated bacteria Clostridiales bacterium SYSU GA17129, Aneurinibacillus aneurinilyticus, and Anaerosalibacter massiliensis were significantly positively correlated with key flavor substances (P < 0.05). The main associated enzymes were transaminase, decarboxylase, and lyase. In summary, phenol and p-cresol were formed by the metabolism of tyrosine and phenylalanine through five reaction chains, and indole and 3-methylindole were formed by the metabolism of tryptophan through one and three reaction chains, respectively.</p>

2026-03-20 | MTBLS2849 | MetaboLights

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data