Proteomics: An In‐Depth Review on Recent Technical Advances and Their Applications in Biomedicine

Medicinal Research Reviews, Год журнала: 2025, Номер unknown

Опубликована: Янв. 9, 2025

ABSTRACT Proteins hold pivotal importance since many diseases manifest changes in protein activity. Proteomics techniques provide a comprehensive exploration of structure, abundance, and function biological samples, enabling the holistic characterization overall organisms. Nowadays, breadth emerging methodologies proteomics is unprecedentedly vast, with constant optimization technologies sample processing, data collection, analysis, its scope application steadily transitioning from bench to clinic. Here, we offer an insightful review technical developments applications biomedicine over past 5 years. We focus on profound contributions profiling disease spectra, discovering new biomarkers, identifying promising drug targets, deciphering alterations conformation, unearthing protein–protein interactions. Moreover, summarize cutting‐edge potential breakthroughs pipeline principal challenges proteomics. Based these, aspire broaden applicability inspire researchers enhance our understanding complex systems by utilizing such techniques.

Язык: Английский

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Considerations for constructing a protein sequence database for metaproteomics

Computational and Structural Biotechnology Journal, Год журнала: 2022, Номер 20, С. 937 - 952

Опубликована: Янв. 1, 2022

Mass spectrometry-based metaproteomics has emerged as a prominent technique for interrogating the functions of specific organisms in microbial communities, addition to total community function. Identifying proteins by mass spectrometry requires matching spectra fragmented peptide ions database protein sequences corresponding sample. This sequence determines which can be identified from measurement, and such taxonomic functional information that inferred measurement. Thus, construction directly impacts outcome any study. Several factors, source curation, need considered during maximize accurate identifications traceable species origin. In this review, we provide an overview existing strategies relevant studies have sought test validate these strategies. Based on review literature our experience decision tree best practices choosing implementing

Язык: Английский

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Isolation and Cultivation of Human Gut Microorganisms: A Review

Microorganisms, Год журнала: 2023, Номер 11(4), С. 1080 - 1080

Опубликована: Апрель 20, 2023

Microbial resources from the human gut may find use in various applications, such as empirical research on microbiome, development of probiotic products, and bacteriotherapy. Due to “culturomics”, number pure bacterial cultures obtained has significantly increased since 2012. However, there is still a considerable microbes be isolated cultured. Thus, improve efficiency obtaining microbial gut, some constraints current methods, labor burden, culture condition, targetability, need optimized. Here, we overview general knowledge recent culturomics for microorganisms. Furthermore, discuss optimization several parts including sample collection, processing, isolation, cultivation, which strategies.

Язык: Английский

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Dietary protein source strongly alters gut microbiota composition and function

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Апрель 5, 2024

The source of protein in a persons diet affects their total life expectancy. However, the mechanisms by which dietary sources differentially impact human health and expectancy are poorly understood. Dietary choices have major impacts on composition function intestinal microbiota that ultimately mediate host health. This raises possibility outcomes based might be driven interactions between gut microbiota. In this study, we determine effects seven different mice. We apply an integrated metagenomics-metaproteomics approach to simultaneously investigate these microbiotas function. abundances measured metaproteomics can provide microbial species abundances, evidence for phenotype members molecular level because proteins allow us infer metabolic physiological processes used community. showed significantly altered overall Different led changes abundance amino acid degrading involved degradation glycosylations protein. particular, brown rice egg white increased enzymes bacteria usually associated with mucus barrier. These results show change metabolism, could implications context mediated diseases.

Язык: Английский

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Broad-spectrum anti-inflammatory and antioxidant therapy of inflammatory-storm actuated diseases via programmable self-derived cryo-dead neutrophils

Chemical Engineering Journal, Год журнала: 2025, Номер unknown, С. 160643 - 160643

Опубликована: Фев. 1, 2025

Язык: Английский

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Large Quantities of Bacterial DNA and Protein in Common Dietary Protein Source Used in Microbiome Studies

PROTEOMICS, Год журнала: 2025, Номер unknown

Опубликована: Фев. 21, 2025

ABSTRACT Diet has been shown to greatly impact the intestinal microbiota. To understand role of individual dietary components, defined diets with purified components are frequently used in diet‐microbiota studies. Defined use casein as protein source. Previous work indicated that contains microbial DNA potentially impacting results microbiome Other diet‐based microbially derived molecules may measurements, such proteins detected by metaproteomics, have not determined for casein. Additionally, other sources studies characterized their content. We metagenomics and metaproteomics identify quantify a casein‐based diet better potential impacts on metagenomic metaproteomic further tested six additional an integrated metagenomic–metaproteomic approach found contaminating is unique within set was identified sources. also illustrate contribution diet‐derived analysis stool samples from germ‐free mice (GF) conventional microbiota (CV) following consumption non‐casein protein. This study highlights confounding factor must be considered through evaluation itself given study.

Язык: Английский

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Microbial genomics and genome sequencing approaches

Elsevier eBooks, Год журнала: 2025, Номер unknown, С. 3 - 20

Опубликована: Янв. 1, 2025

Язык: Английский

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High-throughput workflow for cultivation and characterization of gut microbiota strains with anti-inflammatory properties and metabolite signature associated with gut-brain communication

Scientific Reports, Год журнала: 2025, Номер 15(1)

Опубликована: Март 13, 2025

The gut microbiota is deeply interconnected with the brain, a phenomenon often referred to as gut-brain axis. Dysfunction in microbiota-gut-brain axis can cause various neurological and psychiatric disorders associated chronic inflammation dysbiosis. Therefore, cultivation of anaerobic human strains, characterization their safety status immunomodulatory potential could contribute deciphering molecular mechanisms underlying communication revealed biotherapeutic potential. However, poor cultivability members, makes research into physiological role challenging. Hence, we report high-throughput workflow based on targeted linked metagenome sequencing, combined bioinformatic search for members anti-inflammatory properties which produce most important microbial metabolites that affect brain function. With this approach, isolated 147 bacterial 41 were characterized 12 strains showing immunosuppressive features ability producing metabolites. Through established best growing conditions essential cultivation, archiving, phenotyping, bacteria microbiota-gut-brain-axis research, probiotic 7 extremely oxygen-sensitive strains.

Язык: Английский

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Advances in the clinical use of metaproteomics

Expert Review of Proteomics, Год журнала: 2023, Номер 20(4-6), С. 71 - 86

Опубликована: Май 30, 2023

ABSTRACTIntroduction Investigating the taxonomic and functional composition of human microbiomes can aid in understanding disease etiologies, diagnosis, therapy monitoring for several diseases, including inflammatory bowel or obesity. One method microbiome is metaproteomics, which assesses microbial proteins thus enables study host–microbiome interactions. This advantage led to increased interest metaproteome analyses significant developments introduce this into a clinical context.Areas covered review summarizes recent progress from technical side an application-related point view.Expert opinion Numerous publications imply massive potential metaproteomics impact health care. However, key challenges standardization validation experimental bioinformatic workflows accurate quantification methods must be overcome.KEYWORDS: Bioinformaticsmass spectrometryhuman microbiomeproteomicshost–pathogen interactionsanalytic sample preparation methodsmetaproteome Article highlights covers findings regarding all elements metaproteomic wet-lab workflow, starting with handling, through cell lysis, protein extraction, purification, digestion LC-MS/MS measurements.Strategies handling studies, e.g. database construction annotation, are acquired literature.The exploring interactions highlighted by summary discoveries obtained studies diseases like disease, cancer, covid-19.We identified agreements on bioinformatical metadata standards as use context.We propose that will have application diagnostics, investigation drug–microbiome interactions, personalized healthcare.Author contributionsAll authors relevant literature beyond search methodology, contributed defining concept scope review, provided expertise identification future research directions challenges. All critical feedback, helped structure manuscript, messages highlight. L Knipper workflow original articles Supplementary Table 1. M Wolf took lead writing manuscript designed figures, input authors. R Heyer supervised project. approved final version published.Declaration interestThe no affiliations financial involvement any organization entity conflict subject matter materials discussed manuscript. includes employment, consultancies, honoraria, stock ownership options, expert testimony, grants patents received pending, royalties.Reviewer disclosuresPeer reviewers other relationships disclose.Supplemental dataSupplemental data article accessed online at https://doi.org/10.1080/14789450.2023.2215440.Additional informationFundingThis paper was not funded.

Язык: Английский

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Metabolic handoffs between multiple symbionts may benefit the deep-sea bathymodioline mussels

ISME Communications, Год журнала: 2023, Номер 3(1)

Опубликована: Май 20, 2023

Bathymodioline mussels rely on thiotrophic and/or methanotrophic chemosynthetic symbionts for nutrition, yet, secondary heterotrophic are often present and play an unknown role in the fitness of organism. The bathymodioline Idas that thrive gas seeps sunken wood Mediterranean Sea Atlantic Ocean, host at least six symbiont lineages co-occur. These include primary methane- sulfur-oxidizing gammaproteobacteria, symbionts, Methylophagaceae, Nitrincolaceae Flavobacteriaceae, whose physiology metabolism obscure. Little is known about if how these interact or exchange metabolites. Here we curated metagenome-assembled genomes modiolaeformis used genome-centered metatranscriptomics metaproteomics to assess key functions. Methylophagaceae a methylotrophic autotroph, as it encoded expressed ribulose monophosphate Calvin-Benson-Bassham cycle enzymes, particularly RuBisCO. ASP10-02a likely fuels its with nitrogen-rich macromolecules may provide holobiont vitamin B12. Urechidicola (Flavobacteriaceae) degrade glycans remove NO. Our findings indicate flexible associations allow expanding range substrates environmental niches, via new metabolic functions handoffs.

Язык: Английский

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