[HTML][HTML] NanoSIMS for biological applications: current practices and analyses

J Nuñez, R Renslow, JB Cliff, CR Anderton - Biointerphases, 2018 - pubs.aip.org
Secondary ion mass spectrometry (SIMS) has become an increasingly utilized tool in
biologically relevant studies. Of these, high lateral resolution methodologies using the …

[HTML][HTML] Challenges and perspectives of metaproteomic data analysis

R Heyer, K Schallert, R Zoun, B Becher, G Saake… - Journal of …, 2017 - Elsevier
In nature microorganisms live in complex microbial communities. Comprehensive taxonomic
and functional knowledge about microbial communities supports medical and technical …

Rational design of a microbial consortium of mucosal sugar utilizers reduces Clostridiodes difficile colonization

FC Pereira, K Wasmund, I Cobankovic… - Nature …, 2020 - nature.com
Many intestinal pathogens, including Clostridioides difficile, use mucus-derived sugars as
crucial nutrients in the gut. Commensals that compete with pathogens for such nutrients are …

Metabolic heterogeneity and cross-feeding within isogenic yeast populations captured by DILAC

S Kamrad, C Correia-Melo, L Szyrwiel, SK Aulakh… - Nature …, 2023 - nature.com
Genetically identical cells are known to differ in many physiological parameters such as
growth rate and drug tolerance. Metabolic specialization is believed to be a cause of such …

Identification of syntrophic acetate-oxidizing bacteria in anaerobic digesters by combined protein-based stable isotope probing and metagenomics

F Mosbæk, H Kjeldal, DG Mulat, M Albertsen… - The ISME …, 2016 - academic.oup.com
Inhibition of anaerobic digestion through accumulation of volatile fatty acids occasionally
occurs as the result of unbalanced growth between acidogenic bacteria and methanogens …

Autotrophic and mixotrophic metabolism of an anammox bacterium revealed by in vivo 13C and 2H metabolic network mapping

CE Lawson, GHL Nuijten, RM de Graaf… - The ISME …, 2021 - academic.oup.com
Anaerobic ammonium-oxidizing (anammox) bacteria mediate a key step in the
biogeochemical nitrogen cycle and have been applied worldwide for the energy-efficient …

[HTML][HTML] Characterisation of cellulose-degrading organisms in an anaerobic digester

JS Poulsen, N de Jonge, WV Macêdo, FR Dalby… - Bioresource …, 2022 - Elsevier
The recalcitrant nature of lignocellulosic biomass hinders efficient exploitation of this fraction
for energy production. A better understanding of the microorganisms able to convert plant …

A complete and flexible workflow for metaproteomics data analysis based on MetaProteomeAnalyzer and Prophane

H Schiebenhoefer, K Schallert, BY Renard, K Trappe… - Nature protocols, 2020 - nature.com
Metaproteomics, the study of the collective protein composition of multi-organism systems,
provides deep insights into the biodiversity of microbial communities and the complex …

Mycelial nutrient transfer promotes bacterial co-metabolic organochlorine pesticide degradation in nutrient-deprived environments

N Khan, E Muge, FJ Mulaa, B Wamalwa… - The ISME …, 2023 - academic.oup.com
Biotransformation of soil organochlorine pesticides (OCP) is often impeded by a lack of
nutrients relevant for bacterial growth and/or co-metabolic OCP biotransformation. By …

Challenges and promise at the interface of metaproteomics and genomics: an overview of recent progress in metaproteogenomic data analysis

H Schiebenhoefer, T Van Den Bossche… - Expert Review of …, 2019 - Taylor & Francis
Introduction: The study of microbial communities based on the combined analysis of
genomic and proteomic data–called metaproteogenomics–has gained increased research …