Dataset Information

Tracing incorporation of heavy water into proteins for species-specific metabolic activity in complex communities using protein-based stable isotope probing proteomics (Protein-SIP)

ABSTRACT: This dataset was obtained from the authors of Starke et al. (2020, Journal of Proteomics 222: 103791, https://doi.org/10.1016/j.jprot.2020.103791). Sample labels: 1 - High fiber diet inoculum 2 - High protein diet inoculum 3,4,5 - High fiber + unlabeled water 6,7,8 - High protein + unlabeled water 9,10,11 - High fiber + 25% of 99.9 atom% D2O 12,13,14 - High protein + 25% of 99.9 atom% D2O 15,16,17 - High fiber + 25% of 99.0 atom% H218O 18,19,20 - High protein + 25% of 99.0 atom% H218O Direct quote from the original article describing the dataset. “…the impact of specific diets on a defined microbial community derived from a human fecal sample was to be determined. The defined community was chosen to provide a stable in vitro setup that could be useful for future microbiome research. Briefly, the microbial community was grown in a heavy fiber and a heavy protein diet in addition to 25% heavy water, either as D2O or H218O. A dosage of 25% isotopically labeled water was chosen by trial-and-error to yield sufficient incorporation into protein but avoid the reduction of activity of individual organisms. A difference in growth medium formulation, representing a high-fiber diet and a high-protein diet, was utilized to evaluate shifts in microbial activity. We chose to assess these diets because high-protein, low-carbohydrate interventions represent a popular weight-loss strategy and because we expected a strong effect on the synthesis of amino acids by this comparison. After an incubation time of 12 h, the proteins were analyzed for label-free quantitation (metaproteomics) and incorporation of isotopes (protein-SIP), each in triplicates….”

INSTRUMENT(S): Q Exactive

ORGANISM(S): Bacteria

SUBMITTER: Manuel Kleiner

LAB HEAD: Martin von Bergen

PROVIDER: PXD024291 | Pride | 2022-12-30

REPOSITORIES: Pride

ACCESS DATA

Dataset's files

Source:

			Action	DRS
	2017-02-07_RS_Robo_1.msf	Msf
	2017-02-07_RS_Robo_1.pep.xml	Pepxml
	2017-02-07_RS_Robo_1.raw	Raw
	2017-02-07_RS_Robo_10.msf	Msf
	2017-02-07_RS_Robo_10.pep.xml	Pepxml

Items per page:

1 - 5 of 61

Publications

Tracing incorporation of heavy water into proteins for species-specific metabolic activity in complex communities.

Starke Robert R Oliphant Kaitlyn K Jehmlich Nico N Schäpe Stephanie Serena SS Sachsenberg Timo T Kohlbacher Oliver O Allen-Vercoe Emma E von Bergen Martin M

Journal of proteomics 20200423

Stable isotope probing (SIP) approaches are a suitable tool to identify active organisms in bacterial communities, but adding isotopically labeled substrate can alter both the structure and the functionality of the community. Here, we validated and demonstrated a substrate-independent protein-SIP protocol using isotopically labeled water that captures the entire microbial activity of a community. We found that <sup>18</sup>O yielded a higher incorporation rate into peptides and thus comprised a ...[more]

PMID: 32335296

Similar Datasets

Project description:The prevalence of obesity has significantly increased worldwide. Therefore, this study aimed to evaluate the influence of obesity in the proteomic profile of periodontal ligament (PDL) tissues of rat first maxillary molars submitted to orthodontic tooth movement. The study was approved by the Ethical Committee on Animal Experimentation of the Sao Paulo State University, School of Dentistry at Araraquara, Brazil (protocol number 16/2015) and followed the Animal Research: Reporting of In Vivo Experiments guidelines. Therefore, for this study, we used ten male adult Holtzman rats (weight average – 300 g, approximately 8 weeks old). Animals were randomly assigned to one of the following experimental groups: 1 – M group: animals received a standard diet and 75 days after that, the first maxillary molar was randomly selected to be submitted to OTM for 15 days (n=5), and 2 – OM group: animals received a high-fat diet to induce obesity, and 75 days after that the first maxillary molar was randomly selected to be subjected to OTM for 15 days (n=5). All animals were kept under controlled temperature (22-25 °C), receiving water ad libitum with a 12-hour light/dark cycle. To induce obesity, animals of the OM group received a high-fat diet. In contrast to the standard diet (Labina/Purina, Ribeirão Preto, Brazil) administered to the M group. The high-fat diet contained around 3.82 kcal/g and was composed of 27.5 % of standard rat chow plus 25 % of peanuts, 25 % of milk chocolate, and 12.5 % sweet biscuits and contained 20 g of protein, 48 g of carbohydrate, 20 g of total fat, and 4 g of fiber per 100 g of diet. This feed was daily replaced and had started 75 days before baseline (M initiation). The procedure to induce OTM was by a closed coil nickel-titanium spring (Sentalloy, GAC Central Slip, New York, EUA) connected the maxillary first molar and central incisors with a steel wire (CrNi, 0.20 mm, 55.01.208; Morelli, Sorocaba, Brazi). Fifteen days after OTM, animals were euthanized by anesthetic overdose.

Project description:Background: Despite the established relation between energy restriction and metabolic health, the most beneficial nutrient composition of a weight-loss diet is still subject of debate. Objectives: The aim of the study was to examine the additional effects of nutrient quality on top of energy restriction(ER). Methods: A parallel-designed 12-week 25%ER dietary intervention study was conducted. Participants aged 40-70 years with abdominal obesity were randomized over three groups: a 25%ER high nutrient quality diet (n = 40); a 25%ER low nutrient quality diet (n = 40); or a habitual diet (n = 30). Both ER diets were nutritionally adequate, the high nutrient quality ER diet was enriched in monounsaturated and n-3 polyunsaturated fatty acids, fiber, and plant protein and reduced in fructose. Before and after the intervention intra-hepatic lipids, body fat distribution, fasting and postprandial responses to a mixed meal shake challenge test of cardio-metabolic risk factors, lipoproteins, vascular measurements, and adipose tissue transcriptome were assessed. Results: The high quality ER diet (-8.4 ± 3.2) induced 2.1 kg more weight loss (P = 0.007) than the low quality ER diet (-6.3 ± 3.9), reduced fasting serum total cholesterol (P = 0.014) and plasma triglycerides (P < 0.001), promoted an anti-atherogenic lipoprotein profile and induced a more pronounced decrease in adipose tissue gene expression of energy metabolism pathways than the low quality ER diet. Explorative analyses showed that the difference in weight loss between both ER diets were specifically present in insulin sensitive subjects (HOMA-IR ≤ 2.5), in whom the high nutrient quality diet induced 3.9 kg more weight loss than the low nutrient quality diet. Conclusion: A high nutrient quality 25%ER diet is more beneficial for cardiometabolic health than a low nutrient quality 25%ER diet. Overweight insulin sensitive subjects may benefit more from a high than a low nutrient quality ER diet with respect to weight loss, due to potential attenuation of glucose-induced lipid synthesis in adipose tissue. Trial registration: ClinicalTrials.gov NCT02194504.