Abstract
Culturomics-based bacterial diversity studies benefit from the implementation of MALDI-TOF MS to remove genomically redundant isolates from isolate collections. We previously introduced SPeDE, a novel tool designed to dereplicate spectral datasets at an infraspecific level into operational isolation units (OIUs) based on unique spectral features. However, biological and technical variation may result in methodology-induced differences in MALDI-TOF mass spectra and hence provoke the detection of genomically redundant OIUs. In the present study, we used three datasets to analyze to which extent hierarchical clustering and network analysis allowed to eliminate redundant OIUs obtained through biological and technical sample variation and to describe the diversity within a set of spectra obtained from 134 unknown soil isolates. Overall, network analysis based on unique spectral features in MALDI-TOF mass spectra enabled a superior selection of genomically diverse OIUs compared to hierarchical clustering analysis and provided a better understanding of the inter-OIU relationships.
Highlights
In the last decade, there has been a revived interest in the cultivable bacterial diversity from various ecosystems
SPeDE dereplication of the 549 spectra resulted in 35 operational isolation units (OIUs) and yielded at least one OIU reference for 24 of the 25 studied strains (Supplementary Table S2)
We performed hierarchical clustering analysis of the OIU references which visualized the relative distance in the number of unique spectral features (USFs) observed between these references (Figure 1A)
Summary
There has been a revived interest in the cultivable bacterial diversity from various ecosystems. Microorganisms feature a countless repertoire of metabolites and enzymes with industrial potential [1]. In 2015, the global market for microbes and microbial products was estimated at $186.3 billion and had an expected compound annual growth rate of 10.2% up to 2023 [2]. The development of lean but highly diverse microbe libraries permits efficient industrial exploitation [3]. The description and differentiation of both species and strains within a species are of equal importance to environmental monitoring, clinical microbiology, as well as water quality and food safety [4,5]. Long-term maintenance of large culture collections and processing of genomically redundant isolates result in an exponential increase in analysis costs
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