Metaproteomic Profiling of the Secretome of a Granule‐forming Ca. Accumulibacter Enrichment DOI Creative Commons
Berdien van Olst,

Simon A. Eerden,

Nella A. Eštok

et al.

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

Published: March 11, 2025

ABSTRACT Extracellular proteins are supposed to play crucial roles in the formation and structure of biofilms aggregates. However, often little is known about these proteins, particular for microbial communities. Here, we use two advanced metaproteomic approaches study extracellular proteome a granular Candidatus Accumulibacter enrichment as proxy communities that form solid granules, such those used biological wastewater treatment. Limited proteolysis whole granules metaproteome isolation from culture's supernatant successfully classified over 50% identified protein biomass be secreted. Moreover, structural sequence‐based classification 387 corresponding secreted biomass, with characteristics could aid aggregates, including filamentous, beta‐barrel containing, cell surface proteins. While various aggregate‐forming originated Ca . Accumulibacter, some associated other taxa. This suggests not only range different but also multiple organisms contribute biofilm formation. Therefore, obtained data provides resource exploring potentially support stability biofilms, whereas demonstrated can applied explore general.

Language: Английский

Metaproteomics Beyond Databases: Addressing the Challenges and Potentials of De Novo Sequencing DOI Open Access
Tim Van Den Bossche, Denis Beslic, Sam van Puyenbroeck

et al.

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

Published: Jan. 31, 2025

Metaproteomics enables the large-scale characterization of microbial community proteins, offering crucial insights into their taxonomic composition, functional activities, and interactions within environments. By directly analyzing metaproteomics offers phenotypes roles individual members play in diverse ecosystems. Although database-dependent search engines are commonly used for peptide identification, they rely on pre-existing protein databases, which can be limiting complex, poorly characterized microbiomes. De novo sequencing presents a promising alternative, derives sequences from mass spectra without requiring database. Over time, this approach has evolved manual annotation to advanced graph-based, tag-based, deep learning-based methods, significantly improving accuracy identification. This Viewpoint explores evolution, advantages, limitations, future opportunities de metaproteomics. We highlight recent technological advancements that have improved its potential detecting unsequenced species providing deeper communities.

Language: Английский

Citations

1
Metaproteomic Profiling of the Secretome of a Granule‐forming Ca. Accumulibacter Enrichment DOI Creative Commons
Berdien van Olst,

Simon A. Eerden,

Nella A. Eštok

et al.

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

Published: March 11, 2025

ABSTRACT Extracellular proteins are supposed to play crucial roles in the formation and structure of biofilms aggregates. However, often little is known about these proteins, particular for microbial communities. Here, we use two advanced metaproteomic approaches study extracellular proteome a granular Candidatus Accumulibacter enrichment as proxy communities that form solid granules, such those used biological wastewater treatment. Limited proteolysis whole granules metaproteome isolation from culture's supernatant successfully classified over 50% identified protein biomass be secreted. Moreover, structural sequence‐based classification 387 corresponding secreted biomass, with characteristics could aid aggregates, including filamentous, beta‐barrel containing, cell surface proteins. While various aggregate‐forming originated Ca . Accumulibacter, some associated other taxa. This suggests not only range different but also multiple organisms contribute biofilm formation. Therefore, obtained data provides resource exploring potentially support stability biofilms, whereas demonstrated can applied explore general.

Language: Английский

Citations

0