Construction of Protein Sequence Databases for Metaproteomics: A Review of the Current Tools and Databases DOI
Muzaffer Arıkan,

Başak Atabay

Journal of Proteome Research, Journal Year: 2024, Volume and Issue: unknown

Published: Oct. 25, 2024

In metaproteomics studies, constructing a reference protein sequence database that is both comprehensive and not overly large critical for the peptide identification step. Therefore, availability of well-curated databases tools custom construction essential to enhance performance analyses. this review, we first provide an overview by presenting concise historical background, outlining typical experimental bioinformatics workflow, emphasizing crucial step metaproteomics. We then delve into current available building such databases, highlighting their individual approaches, utility, advantages limitations. Next, examine existing detailing scope relevance in research. Then, practical recommendations metaproteomics, along with challenges area. conclude discussion anticipated advancements, emerging trends, future directions

Language: Английский

The Landscape and Perspectives of the Human Gut Metaproteomics DOI Creative Commons

Zhong-Zhi Sun,

Zhibin Ning, Daniel Figeys

et al.

Molecular & Cellular Proteomics, Journal Year: 2024, Volume and Issue: 23(5), P. 100763 - 100763

Published: April 10, 2024

The human gut microbiome is closely associated with health and diseases. Metaproteomics has emerged as a valuable tool for studying the functionality of by analyzing entire proteins present in microbial communities. Recent advancements liquid chromatography tandem mass spectrometry (LC-MS/MS) techniques have expanded detection range metaproteomics. However, overall coverage proteome metaproteomics still limited. While metagenomics studies revealed substantial diversity functional potential microbiome, few summarized studied landscape metaproteomics.In this paper, we current re-analyzing identification results from fifteen published studies. We quantified limited high proportion annotation metaproteomics-identified proteins. conducted preliminary comparison between view identifying key areas consistency divergence. Based on metaproteomics, discuss feasibility using to study functionally unknown propose whole workflow peptide-centric analysis. Additionally, suggest enhancing analysis refining taxonomic classification calculating confidence scores, well developing tools interaction taxonomy function.

Language: Английский

Citations

11
AI in microbiome‐related healthcare DOI Creative Commons
Niklas Probul,

Zihua Huang,

Christina C. Saak

et al.

Microbial Biotechnology, Journal Year: 2024, Volume and Issue: 17(11)

Published: Nov. 1, 2024

Abstract Artificial intelligence (AI) has the potential to transform clinical practice and healthcare. Following impressive advancements in fields such as computer vision medical imaging, AI is poised drive changes microbiome‐based healthcare while facing challenges specific field. This review describes state‐of‐the‐art use of microbiome‐related It points out limitations across topics data handling, modelling safeguarding patient privacy. Furthermore, we indicate how these current shortcomings could be overcome future discuss influence opportunities increasingly complex on

Language: Английский

Citations

4
Database selection for shotgun metaproteomic of low-diversity dairy microbiomes DOI Creative Commons
Vinícius da Silva Duarte, Luiza de Paula Dias Moreira, Siv Skeie

et al.

International Journal of Food Microbiology, Journal Year: 2024, Volume and Issue: 418, P. 110706 - 110706

Published: April 15, 2024

The metaproteomics field has recently gained more and interest as a valuable tool for studying both the taxonomy function of microbiomes, including those used in food fermentations. One crucial step pipeline is selecting database to obtain high-quality taxonomical functional information from microbial communities. best strategies described building protein databases using sample-specific or study-specific obtained metagenomic sequencing. While this true high-diversity microbiomes (such gut soil), there still lack validation different construction low-diversity such found fermented dairy products where starter cultures containing few species are used. In study, we assessed performance various applied on two cheese production commercial analyzed by LC-MS/MS. Substantial differences were detected between strategies, terms number peptides proteins identified spectra was achieved metagenomic-derived databases. However, extensive constructed high available online genomes similar annotation metaproteome compared Our results indicate that, case use publically construct can be considered an alternative metagenome-derived

Language: Английский

Citations

3
Critical steps in an environmental metaproteomics workflow DOI Creative Commons
Daniel J. Nebauer, Leanne A. Pearson, Brett A. Neilan

et al.

Environmental Microbiology, Journal Year: 2024, Volume and Issue: 26(5)

Published: May 1, 2024

Abstract Environmental metaproteomics is a rapidly advancing field that provides insights into the structure, dynamics, and metabolic activity of microbial communities. As still maturing, it lacks consistent workflows, making challenging for non‐expert researchers to navigate. This review aims introduce workflow environmental metaproteomics. It outlines standard practices sample collection, processing, analysis, offers strategies overcome unique challenges presented by common matrices such as soil, freshwater, marine environments, biofilms, sludge, symbionts. The also highlights bottlenecks in data analysis are specific samples suggestions obtain high‐quality datasets. includes recent benchmarking studies descriptions software packages specifically built analysis. article written without assuming reader's familiarity with single‐organism proteomic accessible those new proteomics or mass spectrometry general. primer improve accessibility this exciting technology empower tackle ambitious research questions. While primarily resource field, should be useful established looking streamline troubleshoot their experiments.

Language: Английский

Citations

3
A single microfluidic device for multi-omics analysis sample preparation DOI
R. Ranjith Kumar, Iman Haddad, Massamba Ndiaye

et al.

Lab on a Chip, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 1, 2025

The ChipFilter device is suited to prepare microorganism samples for parallel proteomic and genomic analyses, which particularly relevant in the case of low-abundant drastically reduces sampling bias.

Language: Английский

Citations

0
Metaproteomic portrait of the healthy human gut microbiota DOI Creative Commons
Alessandro Tanca, Antonio Palomba, Giovanni Fiorito

et al.

npj Biofilms and Microbiomes, Journal Year: 2024, Volume and Issue: 10(1)

Published: June 28, 2024

Gut metaproteomics can provide direct evidence of microbial functions actively expressed in the colonic environments, contributing to clarify role gut microbiota human physiology. In this study, we re-analyzed 10 fecal datasets healthy individuals from different continents and countries, with aim identifying stable variable defining contribution specific bacterial taxa main metabolic pathways. The "core" metaproteome included 182 83 pathways that were identified all analyzed. Several enzymes involved glucose pyruvate metabolism, along glutamate dehydrogenase, acetate kinase, elongation factors G Tu DnaK, proteins lowest abundance variability cohorts under study. On contrary, chemotaxis, response stress cell adhesion among most functions. Random-effect meta-analysis correlation trends between taxa, revealed key ecological molecular associations within microbiota. biological processes was also investigated, finding Faecalibacterium is genus top contributor anti-inflammatory butyrate production Active other mucosal immunomodulators facilitating host tolerance observed, including Roseburia flagellin lipopolysaccharide biosynthetic by members Bacteroidota. Our study provides a detailed picture microbiota, unveil its functional mechanisms relationship nutrition, immunity, environmental stressors.

Language: Английский

Citations

2
NovoLign: metaproteomics by sequence alignment DOI Creative Commons
Hugo B.C. Kleikamp,

Ramon van der Zwaan,

Ramon van Valderen

et al.

ISME Communications, Journal Year: 2024, Volume and Issue: 4(1)

Published: Jan. 1, 2024

Abstract Tremendous advances in mass spectrometric and bioinformatic approaches have expanded proteomics into the field of microbial ecology. The commonly used spectral annotation method for metaproteomics data relies on database searching, which requires sample-specific databases obtained from whole metagenome sequencing experiments. However, creating these is complex, time-consuming, prone to errors, potentially biasing experimental outcomes conclusions. This asks alternative that can provide rapid orthogonal insights data. Here, we present NovoLign, a de novo pipeline performs sequence alignment sequences complete enables taxonomic profiling complex communities evaluates coverage searches. Furthermore, NovoLign supports creation reference searching ensure comprehensive coverage. We assessed false positive annotations using wide range silico data, including pure strains, laboratory enrichment cultures, synthetic communities, environmental communities. In summary, employs large-scale enable profiling, evaluation outcomes, databases. publicly available via: https://github.com/hbckleikamp/NovoLign.

Language: Английский

Citations

2
Metagenomic/Metaproteomic Investigation of the Microbiota in Dongbei Suaicai, a Traditional Fermented Chinese Cabbage DOI Creative Commons
Yamin Zhang, Haiyang Yan,

Xiangxiu Xu

et al.

Fermentation, Journal Year: 2024, Volume and Issue: 10(4), P. 185 - 185

Published: March 28, 2024

Dongbei Suaicai (DBSC) has a complicated microbial ecosystem in which the composition and metabolism of communities during process have not been well explored. Here, combined metagenomic metaproteomic technology was used to reveal taxonomic metabolic profiles DBSC. The results showed that firmicutes proteobacteria were prevalent bacteria phylum Pseudomonas, while Weissella, Pediococcus, Leuconostoc genus. vital pathways involved glycolysis/gluconeogenesis [path: ko00010], as pyruvate ko00620], fructose mannose Ko00051], glycine, serine threonine Ko00260]. Moreover, key proteins (dps, fliC, tsf, fusA, atpD, metQ, pgi, tpiA, eno, alaS, bglA, tktA, gor, pdhD, aceE, gnd) related metabolized enriched fermentation. This study will aid facilitating understanding fermentation mechanisms

Language: Английский

Citations

1
Orthrus: an AI-powered, cloud-ready, and open-source hybrid approach for metaproteomics DOI Creative Commons
Yun Chiang, Matthew J. Collins

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Nov. 15, 2024

Abstract While metaproteomics provides invaluable insight into microbial communities and functions, significant bioinformatics challenges persist due to data complexity the limitations of database searching. We introduce Orthrus , a hybrid approach combining transformer-based de novo sequencing ( Casanovo ) searching with rescoring Sage + Mokapot ). Benchmarking against PEAKS ® 11 MaxQuant MetaNovo demonstrates high peptide outputs, taxonomic diversity, proteome coverage. is Python-based accessible all via Google Colaboratory.

Language: Английский

Citations

1
Insights on Wet and Dry Workflows for Human Gut Metaproteomics DOI Creative Commons
Valeria Marzano, Stefano Levi Mortera, Lorenza Putignani

et al.

PROTEOMICS, Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 30, 2024

The human gut microbiota (GM) is a community of microorganisms that resides in the gastrointestinal (GI) tract. Recognized as critical element health, functions GM extend beyond GI well-being to influence overall systemic health and susceptibility disease. Among other omic sciences, metaproteomics highlights additional facets make it highly valuable discipline study GM. Indeed, allows protein inventory complex microbial communities. Proteins with associated taxonomic membership function are identified quantified from their constituent peptides by liquid chromatography coupled mass spectrometry analyses querying specific databases (DBs). aim this review was compile comprehensive information on metaproteomic studies GM, focus bacterial component, assist newcomers understanding methods types research conducted field. outlines key steps metaproteomic-based study, such extraction, DB selection, bioinformatic workflow. importance standardization emphasized. In addition, list previously published provided hints for researchers interested investigating role disease states.

Language: Английский

Citations

1