The dawn of the revolution that will allow us to precisely describe how microbiomes function

Journal of Proteomics, Journal Year: 2025, Volume and Issue: 316, P. 105430 - 105430

Published: March 11, 2025

The community of microorganisms inhabiting a specific environment, such as the human gut - including bacteria, fungi, archaea, viruses, protozoa, and others is known microbiota. A holobiont, in turn, refers to an integrated ecological unit where microbial communities function interact with their host, thus more integrative concept. To understand processes involved, diversity present must be identified molecular components quantified, especially proteins. Indeed, proteins through roles catalytic units, structural components, signaling molecules are main drivers biological processes. Metagenomics has significantly expanded what we know about genetic material microbiota, revealing functional potential; metabolomics delivers overall snapshot metabolites produced by community. But metaproteomics offers complementary approach explore microbiome holobiont functionality focusing on active pathways from each taxon. Significant recent advances high-resolution tandem mass spectrometry have greatly catalog peptide sequences accessible sample, creating conditions for unprecedented taxonomical profiling, while also providing accurate biomass quantification, detailed protein characterization, greater capacity monitor abundance distinguish host biomarkers. By integrating artificial intelligence into pipeline, extended datasets can now efficiently mined gain comprehensive view complex systems, paving way next-generation metaproteomics. In this perspective, I discuss transformative potential methodology. We cusp remarkable omic revolution that promises uncover intricate workings microbiomes producing vast array new knowledge multiple applications. SIGNIFICANCE: Metaproteomics provides powerful lens investigate identifying quantifying within Recent breakthroughs dramatically repertoire detectable per sample. This progress enables taxonomic resolution identification, precise monitoring, unique identification commentary, delve distinctive features make tool. advancements argue primary challenge analyzing samples shifting data acquisition interpretation. With integration intelligence, believe poised become next Big Thing research, unlocking profound insights ecosystem dynamics.

Language: Английский

Evaluation of imputation and imputation-free strategies for differential abundance analysis in metaproteomics data

Briefings in Bioinformatics, Journal Year: 2025, Volume and Issue: 26(2)

Published: March 1, 2025

Abstract For metaproteomics data derived from the collective protein composition of dynamic multi-organism systems, proportion missing values and dimensions exceeds that observed in single-organism experiments. Consequently, evaluations differential analysis strategies other mass spectrometry (MS) (such as proteomics metabolomics) may not be directly applicable to data. In this study, we systematically evaluated five imputation methods [sample minimum, quantile regression, k-nearest neighbors (KNN), Bayesian principal component (bPCA), random forest (RF)] six imputation-free (moderated t-test, two-part Wilcoxon test, semiparametric abundance analysis, with Bayes shrinkage estimation variance method, Mixture) for simulated metaproteomic datasets based on both data-dependent acquisition MS experiments emerging data-independent The simulation comprised 588 scenarios by considering impacts sample size, fold change between case control, value ratio at nonrandom. Compared methods, KNN, bPCA, RF performed poorly a high missingness large size resulted false-positive risk. We made empirical recommendations balance sensitivity control false positives. moderated t-test was optimal low ratio. test recommended small or comprehensive our study can provide guidance metaproteomics.

Language: Английский

A Non‐Metaproteomics Researchers’ View on Metaproteomics in Microbiome Research

PROTEOMICS, Journal Year: 2025, Volume and Issue: unknown

Published: April 27, 2025

ABSTRACT Metaproteomics, an emerging field among the omic techniques, holds great promise for unraveling function of microbiomes in host health and our environment. Metaproteomics can also be a valuable addition to multiomics studies microbiome, complementing genome‐resolved metagenomics, metatranscriptomics, metabolomics. The potential advancements from metaproteomics research touch breadth disciplines, including ecology, biochemistry, immunology, medical microbiology, cell physiology, medicine, could lead both fundamental applied discoveries. However, there are significant roadblocks widespread adoption microbiome researchers. In this Viewpoint article, we highlight pivotal role by showcasing its advantages, exploring opportunities overcome challenges, paving way broader as mainstream technique. We hope that recommendations provided article will inspire new, beneficial collaborations between proteomics experts, algorithm infrastructure developers, biochemists, biologists, microbiologists, enabling construction knowledge base have immediate direct impact on

Language: Английский