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Review
. 2025 Aug;14(4):e70034.
doi: 10.1002/mbo3.70034.

Analyzing the Challenges and Opportunities Associated With Harnessing New Antibiotics From the Fungal Microbiome

Md Sakhawat Hossain  1 , Md Al Amin  1 , Sirajul Islam  1 , Hasan Imam  2 , Liton Chandra Das  1 , Shahin Mahmud  1
Affiliations
Review

Analyzing the Challenges and Opportunities Associated With Harnessing New Antibiotics From the Fungal Microbiome

Md Sakhawat Hossain et al. Microbiologyopen. 2025 Aug.

Abstract

The rapid rise in antibiotic resistance is a critical global health issue, and few new classes of antibiotics have been discovered since 1990 compared to the antibiotic's golden era between 1950 and 1970. However, developing new antimicrobial compounds faces many challenges, improvements in cultivation methods, genetic engineering, and advanced technologies are opening new paths for discovering and producing effective antibiotics. This study focuses on the fungal microbiome as a promising source of new antibiotics. We explored historical developments and advanced genetic techniques to reveal the potential of fungi in antibiotic production. Although isolating and scaling up fungal antibiotic production presents challenges, innovative approaches like in situ separation during fermentation can effectively address these issues. Our research highlights the importance of understanding fungal communication and metabolite sharing to enhance antibiotic yields and the connection of cutting-edge technologies in accelerating the discovery and optimization of antibiotic-producing fungi. By focusing on these technical aspects and fostering teamwork across various fields, this study aims to overcome current obstacles, and advance the development of antibiotic production technologies.

Keywords: antibiotic discovery; fungal metabolite sharing; fungal microbiome; fungal–bacterial interactions; industrial‐scale processes of antibiotics.

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Conflict of interest statement

The authors declare no conflicts of interest.

Figures

Figure 1
Figure 1
Potential approaches for enhancing the heterologous expression of biosynthetic gene clusters (BGCs) in Fungi.
Figure 2
Figure 2
The generalized step‐by‐step process in isolating and discovering novel antibiotic‐producing fungi and characterizing their bioactive compounds.
Figure 3
Figure 3
Procedures for scaling up fungal metabolite production in the biopharmaceutical industry.
Figure 4
Figure 4
Mechanisms of enhanced antibiotic productions in fungi through synthetic molecules and fungal–bacterial interactions.
Figure 5
Figure 5
Integration of advanced technologies for exploring fungal microbiome for novel antibiotic discovery.
See this image and copyright information in PMC

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