The need to innovate sample collection and library generation in microbial drug discovery: a focus on academia

Abstract

This viewpoint discusses limitations of sample collection and microbial strain library generation practices, and will offer suggestions to innovate these areas.

Genome-guided discovery of natural products through multiplexed low coverage whole-genome sequencing of soil Actinomycetes on Oxford Nanopore Flongle

“…In summary, multiplexed low coverage sequencing of Actinomycetes genomes on Flongle is a promising option for the genome-guided discovery of natural products. Numerous research laboratories house valuable bacterial strain collections (29)(30)(31)(32)(33)(34). Limited by the costs of large-scale long read sequencing, genome sequencing of natural product producing bacteria usually occurs on a strain-by-strain basis {Sun, 2021 #295;Li, 2021 #316;Yang, 2021 #317;Braesel, 2018 #326}.…”

Solid-Phase Extraction Embedded Dialysis (SPEED), an Innovative Procedure for the Investigation of Microbial Specialized Metabolites

“…This area of research, especially in the field of metabolites from micro-organisms, was accelerated by the development of genome-based technologies [ 1 , 2 ]. The era of drug lead discovery from culturable bacteria is not nearing its end, however its success relies on researchers’ ability to innovate in strategies used to collect samples from the environment [ 3 ] and methods used to trap specialized metabolites from culture media [ 4 ]. Nevertheless, one of the major persisting drawbacks is the isolation of sufficient quantities of compounds to carry out chemical and biological investigations.…”

Metabolomic Analysis of The Chemical Diversity of South Africa Leaf Litter Fungal Species Using an Epigenetic Culture-Based Approach

“…Microorganisms are known to be a rich source of new bioactive molecules with a wide range of biotechnological applications in the pharmaceutical, agrochemical and cosmetic industries. The rediscovery of already known structures, the usual low production yields and the difficulty in activating cryptic biosynthetic gene clusters (BGCs) under laboratory conditions are some of the limitations to exploit their huge chemical production capability [ 1 , 2 , 3 ]. Recent advances in laboratory automation and detection technologies, such as chromatography coupled to mass spectrometry, have contributed to the rapid and efficient generation of large libraries of natural products [ 2 , 3 , 4 ].…”

“…The rediscovery of already known structures, the usual low production yields and the difficulty in activating cryptic biosynthetic gene clusters (BGCs) under laboratory conditions are some of the limitations to exploit their huge chemical production capability [ 1 , 2 , 3 ]. Recent advances in laboratory automation and detection technologies, such as chromatography coupled to mass spectrometry, have contributed to the rapid and efficient generation of large libraries of natural products [ 2 , 3 , 4 ]. Moreover, different approaches through the variations in nutritional and culturing factors have been extensively applied in order to exploit the biosynthetic potential revealed from genome-based studies [ 5 , 6 , 7 ].…”