[HTML][HTML] Considerations for constructing a protein sequence database for metaproteomics

JA Blakeley-Ruiz, M Kleiner - Computational and structural biotechnology …, 2022 - Elsevier
Mass spectrometry-based metaproteomics has emerged as a prominent technique for
interrogating the functions of specific organisms in microbial communities, in addition to total …

'Multi-omics' data integration: applications in probiotics studies

ID Kwoji, OA Aiyegoro, M Okpeku, MA Adeleke - npj Science of Food, 2023 - nature.com
The concept of probiotics is witnessing increasing attention due to its benefits in influencing
the host microbiome and the modulation of host immunity through the strengthening of the …

Metaproteomics to understand how microbiota function: The crystal ball predicts a promising future

J Armengaud - Environmental Microbiology, 2023 - Wiley Online Library
In the medical, environmental, and biotechnological fields, microbial communities have
attracted much attention due to their roles and numerous possible applications. The study of …

[HTML][HTML] Enhancing phosphorus removal of photogranules by incorporating polyphosphate accumulating organisms

LM Trebuch, J Sohier, S Altenburg, BO Oyserman… - Water Research, 2023 - Elsevier
Photogranules are a novel wastewater treatment technology that can utilize the sun's energy
to treat water with lower energy input and have great potential for nutrient recovery …

The astounding exhaustiveness and speed of the Astral mass analyzer for highly complex samples is a quantum leap in the functional analysis of microbiomes

T Dumas, R Martinez Pinna, C Lozano, S Radau… - Microbiome, 2024 - Springer
Background By analyzing the proteins which are the workhorses of biological systems,
metaproteomics allows us to list the taxa present in any microbiota, monitor their relative …

[HTML][HTML] Meta-omics profiling of full-scale groundwater rapid sand filters explains stratification of iron, ammonium and manganese removals

F Corbera-Rubio, M Laureni, N Koudijs, S Müller… - Water Research, 2023 - Elsevier
Rapid sand filters (RSF) are an established and widely applied technology for groundwater
treatment. Yet, the underlying interwoven biological and physical-chemical reactions …

Physiological and stoichiometric characterization of ethanol-based chain elongation in the absence of short-chain carboxylic acids

MT Allaart, BB Fox, IHMS Nettersheim, M Pabst… - Scientific Reports, 2023 - nature.com
Hexanoate is a valuable chemical that can be produced by microorganisms that convert
short-chain-to medium-chain carboxylic acids through a process called chain elongation …

[HTML][HTML] Metalloenzymes play major roles to achieve high-rate nitrogen removal in N-damo communities: Lessons from metaproteomics

S Quiton-Tapia, A Trueba-Santiso, JM Garrido… - Bioresource …, 2023 - Elsevier
Nitrite-driven anaerobic methane oxidation (N-damo) is a promising biological process to
achieve carbon–neutral wastewater treatment solutions, aligned with the sustainable …

Deep learning-driven fragment ion series classification enables highly precise and sensitive de novo peptide sequencing

D Klaproth-Andrade, J Hingerl, Y Bruns… - Nature …, 2024 - nature.com
Unlike for DNA and RNA, accurate and high-throughput sequencing methods for proteins
are lacking, hindering the utility of proteomics in applications where the sequences are …

[HTML][HTML] Predicting the impact of temperature on metabolic fluxes using resource allocation modelling: Application to polyphosphate accumulating organisms

T Páez-Watson, MCM van Loosdrecht, SA Wahl - Water Research, 2023 - Elsevier
The understanding of microbial communities and the biological regulation of its members is
crucial for implementation of novel technologies using microbial ecology. One poorly …