posted on 2024-01-08, 20:33authored byYixuan Huang, Bhagyashree N. Swarge, Winfried Roseboom, Jurre D. Bleeker, Stanley Brul, Peter Setlow, Gertjan Kramer
Reliable and comprehensive multi-omics analysis is essential
for
researchers to understand and explore complex biological systems more
completely. Bacillus subtilis (B. subtilis) is a model organism for Gram-positive spore-forming bacteria, and
in-depth insight into the physiology and molecular basis of spore
formation and germination in this organism requires advanced multilayer
molecular data sets generated from the same sample. In this study,
we evaluated two monophasic methods for polar and nonpolar compound
extraction (acetonitrile/methanol/water; isopropanol/water, and 60%
ethanol) and two biphasic methods (chloroform/methanol/water, and
methyl tert-butyl ether/methanol/water) on coefficients of variation
of analytes, identified metabolite composition, and the quality of
proteomics profiles. The 60% EtOH protocol proved to be the easiest
in sample processing and was more amenable to automation. Collectively,
we annotated 505 and 484 metabolites and identified 1665 and 1562
proteins in B. subtilis vegetative
cells and spores, respectively. We also show differences between vegetative
cells and spores from a multi-omics perspective and demonstrate that
an integrative multi-omics analysis can be implemented from one sample
using the 60% EtOH protocol. The results obtained by the 60% EtOH
protocol provide comprehensive insight into differences in the metabolic
and protein makeup of B. subtilis vegetative
cells and spores.