Novel approaches toward preferential detection of viable cells using nucleic acid amplification techniques
Andreas Nocker,Anne K. Camper +1 more
TLDR
This article elaborates on possible future directions for microbial viability assessment using nucleic acid-modifying compounds in combination with DNA- (and potentially RNA-) amplification technologies.Abstract:
This article elaborates on possible future directions for microbial viability assessment using nucleic acid-modifying compounds in combination with DNA- (and potentially RNA-) amplification technologies Bacteria were traditionally considered viable when they could be cultured, whereas today's viability concept is based on the presence of some form of metabolic activity, responsiveness, RNA transcripts that tend to degrade rapidly after cell death, or of an intact membrane The latter criterion was the focus of recent approaches to limit detection to intact cells using ethidium monoazide or propidium monoazide Membrane integrity must, however, be considered as a very conservative criterion for microbial viability The new concept presented here aims at limiting nucleic acid-based detection to cells with an active metabolism, which might be a more appropriate viability criterion To selectively detect only cells with metabolic and respiratory activity (while excluding inactive dead cells from detection), we suggest the use of 'activity-labile compounds' In addition to their potential usefulness for viability assessment, these new compounds could also be beneficial for selectively amplifying nucleic acids of cells that have metabolic activities of interest This preferential detection of microorganisms with certain metabolic capabilities is referred to as 'molecular enrichment' in distinction to 'growth enrichment'read more
Citations
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Nucleic acid-based approaches to investigate microbial-related cheese quality defects
Daniel J. O'Sullivan,Linda Giblin,Paul L.H. McSweeney,Jeremiah J. Sheehan,Paul D. Cotter,Paul D. Cotter +5 more
TL;DR: The DNA-based methods that are available to detect/quantify spoilage bacteria, and relevant metabolic pathways in cheeses are reviewed and it is highlighted how these strategies can be employed to improve cheese quality and reduce the associated economic burden on cheese processors.
Journal ArticleDOI
Considering fungal:bacterial dominance in soils – Methods, controls, and ecosystem implications
TL;DR: Many of the potential reasons why expectations related to fungal:bacterial dominance were not met are explored, highlighting areas where future research, especially furthering a basic understanding of the ecology of bacteria and fungi, is needed.
Journal ArticleDOI
Critical review on biofilm methods
Joana Azeredo,Nuno F. Azevedo,Romain Briandet,Nuno Cerca,Tom Coenye,Ana Rita Costa,Mickaël Desvaux,Giovanni Di Bonaventura,Michel Hébraud,Zoran Jaglic,Miroslava Kačániová,Susanne Knøchel,Anália Lourenço,Filipe Mergulhão,Rikke Louise Meyer,George Nychas,Manuel Simões,Odile Tresse,Claus Sternberg +18 more
TL;DR: This review aims at helping scientists in finding the most appropriate and up-to-date methods to study their biofilms by giving a critical perspective, highlighting the advantages and limitations of several methods.
Journal ArticleDOI
Who is who in litter decomposition? Metaproteomics reveals major microbial players and their biogeochemical functions
Thomas Schneider,Katharina M. Keiblinger,Emanuel Schmid,Katja Sterflinger-Gleixner,Günther Ellersdorfer,Bernd Roschitzki,Andreas Richter,Andreas Richter,Leo Eberl,Sophie Zechmeister-Boltenstern,Kathrin Riedel +10 more
TL;DR: Fungi were found to be the main producers of extracellular hydrolytic enzymes, with no bacterial hydrolases being detected by the metaproteomics approach, providing evidence that the litter nutrient content and the stoichiometry of C:N:P affect the decomposer community structure and activity.
Journal ArticleDOI
A Basic Guide to Real Time PCR in Microbial Diagnostics: Definitions, Parameters, and Everything.
Petr Kralik,Matteo Ricchi +1 more
TL;DR: This basic guide will help to orient beginners and users of qPCR in the use of this powerful technique.
References
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