Microtiter Plate Cultivation Systems Enable Chemically Diverse Metabolic Footprints During Bacterial Natural Product Discovery

IF 3.5 2区生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Biotechnology and Bioengineering Pub Date : 2025-04-26 DOI:10.1002/bit.29002

Anton Lindig, Georg Hubmann, Stephan Lütz

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引用次数: 0

Abstract

Rediscovery of known structures is a frequent problem in screening for bioactive bacterial natural products (NPs). Highly parallelized microtiter plate cultivation systems (MPCS) can improve the chance to discover novel NPs by testing a multitude of cultivation conditions simultaneously. An in‐depth analysis and comparison of cultivation systems for NP discovery, however, has not been carried out so far. We compared the growth and metabolic footprint of four distinct bacterial species in three MPCS, shake flasks, and stirred tank bioreactors (STR). While the big majority of the cultivation systems provided good growth, we found a considerable divergence in secondary metabolite (SM) formation. The SM space was approximated by the appearance of unique mass features (MFs) in the supernatant extracts throughout the cultivation period. Molecular network analysis was applied to visualize the changes from detected MFs at the molecular level. The cultivation systems had a minor impact on the unicellular growing Bacillus amyloliquefaciens. This impact was more pronounced for the tested filamentous bacteria, resulting in a diversified metabolic footprint. The maximal overlap of 31% of produced MFs indicates a lack of comparability between the cultivation systems, resulting in different entries of growth phases and the formation of associated SMs. The detected SMs and its derivatives exhibited structural modification depending on the cultivation system. A comparison of Streptomyces griseochromogenes NP profile revealed that MPCS yielded less divergent SM formation than shake flasks. Our comprehensive assessment is the first to demonstrate the impact of cultivation systems on the bacterial metabolic footprint, confirming that MPCS provide a robust platform for the parallelization of bacterial cultivations for the discovery of bacterial NPs and accessing the chemical NP space more broadly.

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来源期刊

Biotechnology and Bioengineering 工程技术-生物工程与应用微生物

CiteScore

7.90

自引率

5.30%

发文量

280

审稿时长

2.1 months

期刊介绍： Biotechnology & Bioengineering publishes Perspectives, Articles, Reviews, Mini-Reviews, and Communications to the Editor that embrace all aspects of biotechnology. These include: -Enzyme systems and their applications, including enzyme reactors, purification, and applied aspects of protein engineering -Animal-cell biotechnology, including media development -Applied aspects of cellular physiology, metabolism, and energetics -Biocatalysis and applied enzymology, including enzyme reactors, protein engineering, and nanobiotechnology -Biothermodynamics -Biofuels, including biomass and renewable resource engineering -Biomaterials, including delivery systems and materials for tissue engineering -Bioprocess engineering, including kinetics and modeling of biological systems, transport phenomena in bioreactors, bioreactor design, monitoring, and control -Biosensors and instrumentation -Computational and systems biology, including bioinformatics and genomic/proteomic studies -Environmental biotechnology, including biofilms, algal systems, and bioremediation -Metabolic and cellular engineering -Plant-cell biotechnology -Spectroscopic and other analytical techniques for biotechnological applications -Synthetic biology -Tissue engineering, stem-cell bioengineering, regenerative medicine, gene therapy and delivery systems The editors will consider papers for publication based on novelty, their immediate or future impact on biotechnological processes, and their contribution to the advancement of biochemical engineering science. Submission of papers dealing with routine aspects of bioprocessing, description of established equipment, and routine applications of established methodologies (e.g., control strategies, modeling, experimental methods) is discouraged. Theoretical papers will be judged based on the novelty of the approach and their potential impact, or on their novel capability to predict and elucidate experimental observations.