Current Understanding of Human Metaproteome Association and Modulation

Ezzeldin, Shahd; El-Wazir, Aya; Enany, Shymaa; Muhammad, Abdelrahman; Johar, Dina; Osama, Aya; Ahmed, Eman; Shikshaky, Hassan; Magdeldin, Sameh

doi:10.1021/acs.jproteome.9b00301

Cited by 9 publications

(7 citation statements)

References 94 publications

(251 reference statements)

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“…Metaproteomics based on liquid chromatography–tandem mass spectrometry (LC-MS/MS) has shown the capability to provide deep function information regarding the dynamic host-microbiota interactions 2 , 5 , 6 . Due to the extreme complexity and heterogeneity of gut metaproteome, accurate protein identification and quantification in metaproteome is still a severe challenge compared to the conventional proteomics of a single organism.…”

Section: Introductionmentioning

confidence: 99%

Data-independent acquisition boosts quantitative metaproteomics for deep characterization of gut microbiota

Zhao

Yang

et al. 2023

npj Biofilms Microbiomes

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Metaproteomics can provide valuable insights into the functions of human gut microbiota (GM), but is challenging due to the extreme complexity and heterogeneity of GM. Data-independent acquisition (DIA) mass spectrometry (MS) has been an emerging quantitative technique in conventional proteomics, but is still at the early stage of development in the field of metaproteomics. Herein, we applied library-free DIA (directDIA)-based metaproteomics and compared the directDIA with other MS-based quantification techniques for metaproteomics on simulated microbial communities and feces samples spiked with bacteria with known ratios, demonstrating the superior performance of directDIA by a comprehensive consideration of proteome coverage in identification as well as accuracy and precision in quantification. We characterized human GM in two cohorts of clinical fecal samples of pancreatic cancer (PC) and mild cognitive impairment (MCI). About 70,000 microbial proteins were quantified in each cohort and annotated to profile the taxonomic and functional characteristics of GM in different diseases. Our work demonstrated the utility of directDIA in quantitative metaproteomics for investigating intestinal microbiota and its related disease pathogenesis.

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Section: Introductionmentioning

confidence: 99%

Data-independent acquisition boosts quantitative metaproteomics for deep characterization of gut microbiota

Zhao

Yang

et al. 2023

npj Biofilms Microbiomes

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“…As the color change originating from the enzyme-like activity of Mn:N-CDs can be easily observed with the naked eye, it is advantageous to apply them in colorimetric sensor systems. In recent years, numerous research groups have examined the metabolism of the human microbiome and its relevance to diseases [41][42][43][44], and information about the composition of the microbiome or its metabolites can be quite helpful for understanding their relevance [45]. GABA is not only a representative metabolite released in the metabolic process of the microbiome but also an inhibitory neurotransmitter that acts on the central nervous system of mammals [45][46][47].…”

Section: Resultsmentioning

confidence: 99%

Highly Enhanced Enzymatic Activity of Mn-Induced Carbon Dots and Their Application as Colorimetric Sensor Probes

2021

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Nanomaterial-based enzyme mimetics (nanozymes) have attracted significant interest because of their lower cost and higher stability compared to natural enzymes. In this study, we focused on improving the enzymatic properties of metal induced N-doped carbon dots (N-CDs), which are nanozymes of interest, and their applications for sensory systems. For this purpose, Mn(acetate)2 was introduced during the synthetic step of N-doped carbon dots, and its influence on the enzymatic properties of Mn-induced N-CDs (Mn:N-CDs) was investigated. Their chemical structure was analyzed through infrared spectroscopy and X-ray photoelectron spectrometry; the results suggest that Mn ions lead to the variation in the population of chemical bonding in Mn:N-CDs, whereas these ions were not incorporated into N-CD frameworks. This structural change improved the enzymatic properties of Mn:N-CDs with respect to those of N-CDs when the color change of a 3,3′,5,5′-tetramethylbenzidine/H2O2 solution was examined in the presence of Mn:N-CDs and N-CDs. Based on this enhanced enzymatic property, a simple colorimetric system with Mn:N-CDs was used for the detection of γ-aminobutyric acid, which is an indicator of brain-related disease. Therefore, we believe that Mn:N-CDs will be an excellent enzymatic probe for the colorimetric sensor system.

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“…Additionally, regarding host proteins, T1D patients exhibited an increased expression of mucin-2 and a reduction in elastase 3A expression with respect to healthy individuals, suggesting both an increased mucin synthesis in charge of gastrointestinal epithelium protection and a reduction in exocrine pancreas functionality (Table 2). [5][6][7][8][9][10][11][12][13][14][15][16][17][18][19][20][21][22] and observed a significant depletion of the genus Enterococcus in T1D subjects with high levels of HbA1c compared with healthy individuals. In this study, the metaproteomics was used to investigate the urinary proteome alterations in T1D subjects compared to their healthy siblings.…”

Section: Metaproteome Alteration In T1dmentioning

confidence: 91%

“…We are here referring to pathologies mainly featured by an imbalance in the Bacteroidetes/Firmicutes ratio [5]. Some species belonging to these phyla are responsible for the production of short chain fatty acids (SCFAs), such as butyrate, propionate, and Nutrients 2022, 14, 47 2 of 17 acetate [6]. The imbalance in these phyla abundance can impact gut epithelial integrity, leading to an increased permeability and undermining the immune homeostasis and the inflammatory response [7].…”

Section: Introductionmentioning

confidence: 99%

Metaproteomics Approach and Pathway Modulation in Obesity and Diabetes: A Narrative Review

et al. 2021

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Low-grade inflammatory diseases revealed metabolic perturbations that have been linked to various phenotypes, including gut microbiota dysbiosis. In the last decade, metaproteomics has been used to investigate protein composition profiles at specific steps and in specific healthy/pathologic conditions. We applied a rigorous protocol that relied on PRISMA guidelines and filtering criteria to obtain an exhaustive study selection that finally resulted in a group of 10 studies, based on metaproteomics and that aim at investigating obesity and diabetes. This batch of studies was used to discuss specific microbial and human metaproteome alterations and metabolic patterns in subjects affected by diabetes (T1D and T2D) and obesity. We provided the main up- and down-regulated protein patterns in the inspected pathologies. Despite the available results, the evident paucity of metaproteomic data is to be considered as a limiting factor in drawing objective considerations. To date, ad hoc prepared metaproteomic databases collecting pathologic data and related metadata, together with standardized analysis protocols, are required to increase our knowledge on these widespread pathologies.

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Current Understanding of Human Metaproteome Association and Modulation

Cited by 9 publications

References 94 publications

Data-independent acquisition boosts quantitative metaproteomics for deep characterization of gut microbiota

Data-independent acquisition boosts quantitative metaproteomics for deep characterization of gut microbiota

Highly Enhanced Enzymatic Activity of Mn-Induced Carbon Dots and Their Application as Colorimetric Sensor Probes

Metaproteomics Approach and Pathway Modulation in Obesity and Diabetes: A Narrative Review

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