MALDI-TOF MS as a Novel Tool for Dereplication and Characterization of Microbiota in Bacterial Diversity Studies

Differentiation of environmental aquatic bacterial isolates by MALDI-TOF MS

“…Grouping of environmental isolates from unknown environments is essential in biodiversity studies where large numbers of strains need to be isolated on different growth media, particularly since easily isolated organisms constitute a minor fraction of total bacterial community in environmental samples (Dieckmann et al, 2005). MALDI-TOF MS was found a powerful tool for a high-throughput dereplication of environmental samples, a process of recognizing identical isolates at a specific taxonomic level and grouping them accordingly (Ichiki et al, 2008;Ghyselinck et al, 2011), Dereplication involves rapid screening of all isolates in order to recongnize and eliminate those that represent the same taxon (Spitaels et al, 2016). Today, MALDI-TOF MS is used as a dereplication tool for grouping isolates at the species level, while groups of spectra are generated mostly using algorithms based on the presence or absence of peaks, or on peak intensities (Spitaels et al, 2016).…”

“…MALDI-TOF MS was found a powerful tool for a high-throughput dereplication of environmental samples, a process of recognizing identical isolates at a specific taxonomic level and grouping them accordingly (Ichiki et al, 2008;Ghyselinck et al, 2011), Dereplication involves rapid screening of all isolates in order to recongnize and eliminate those that represent the same taxon (Spitaels et al, 2016). Today, MALDI-TOF MS is used as a dereplication tool for grouping isolates at the species level, while groups of spectra are generated mostly using algorithms based on the presence or absence of peaks, or on peak intensities (Spitaels et al, 2016). For dereplication purposes it was first used on bacteria isolated from marine sponges (Dieckmann et al, 2005), and was also successfully applied in extreme surroundings, such as hypersaline environments, where it was used for dereplication of halophilic prokaryotes (Munoz et al, 2011;Viver et al, 2015).…”

“…For dereplication purposes it was first used on bacteria isolated from marine sponges (Dieckmann et al, 2005), and was also successfully applied in extreme surroundings, such as hypersaline environments, where it was used for dereplication of halophilic prokaryotes (Munoz et al, 2011;Viver et al, 2015). MALDI-TOF MS has the capacity to simplify both identification and dereplication, as mass spectra of isolates that cannot be identified directly can be clustered, and representative bacteria can be subjected to further polyphasic identification (Spitaels et al, 2016;Kopcakova et al, 2014).…”

“…For example, MALDI-TOF MS was used to differentiate pathogenic and non-pathogenic Leptospira strains, by categorizing the super reference spectra and the major spectra projection dendrogram into groups, thus proving an important tool in surveillance of this omnipresent and zoonotic organism (Xiao et al, 2015). Furthermore, MALDI-TOF MS not only facilitates the detection of novel species, but can also reveal taxonomic anomalies (Spitaels et al, 2016;Wieme et al, 2014).…”

Physiology of Acetic Acid Bacteria and Their Role in Vinegar and Fermented Beverages

“…MALDI-TOF is not however suitable for differentiation at the strain level due to a strong effect of the growth medium used on the proteomic profile of the strains (Wieme et al, 2014). However, efforts to minimize the effect of the growth medium, with the potential to enable inter-strain discrimination, have been applied in some studies; for instance, subculturing of isolates under investigation multiple times on the same, defined agar medium prior to MALDI-TOF analysis (De Roos, Verce, et al, 2018;Spitaels, Wieme, & Vandamme, 2016).…”