Journal ArticleDOI
Compendium of specialized metabolite biosynthetic diversity encoded in bacterial genomes
Athina Gavriilidou,Satria A. Kautsar,Nestor Zaburannyi,Daniel Krug,Rolf Müller,Marnix H. Medema,Nadine Ziemert +6 more
TLDR
The authors analyzed ~170,000 bacterial genomes and ~47,000 metagenome assembled genomes using a modified BiG-SLiCE and the new clust-o-matic algorithm.Abstract:
Bacterial specialized metabolites are a proven source of antibiotics and cancer therapies, but whether we have sampled all the secondary metabolite chemical diversity of cultivated bacteria is not known. We analysed ~170,000 bacterial genomes and ~47,000 metagenome assembled genomes (MAGs) using a modified BiG-SLiCE and the new clust-o-matic algorithm. We estimate that only 3% of the natural products potentially encoded in bacterial genomes have been experimentally characterized. We show that the variation in secondary metabolite biosynthetic diversity drops significantly at the genus level, identifying it as an appropriate taxonomic rank for comparison. Equal comparison of genera based on relative evolutionary distance revealed that Streptomyces bacteria encode the largest biosynthetic diversity by far, with Amycolatopsis, Kutzneria and Micromonospora also encoding substantial diversity. Finally, we find that several less-well-studied taxa, such as Weeksellaceae (Bacteroidota), Myxococcaceae (Myxococcota), Pleurocapsa and Nostocaceae (Cyanobacteria), have potential to produce highly diverse sets of secondary metabolites that warrant further investigation. read more
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MIBiG 3.0: a community-driven effort to annotate experimentally validated biosynthetic gene clusters
Barbara R. Terlouw,Kai Blin,Jorge C. Navarro-Muñoz,Nicole Avalon,Marc G. Chevrette,Susan Egbert,Sanghoon Lee,David Meijer,Michael J J Recchia,Zachary L. Reitz,Jeffrey A. van Santen,Nelly Selem-Mojica,Thomas Tørring,Liana Zaroubi,Mohammad Alanjary,Gajender Aleti,César Aguilar,Suhad A.A. Al-Salihi,Hannah E. Augustijn,J. Abraham Avelar-Rivas,Luis A Avitia-Domínguez,Francisco Barona-Gómez,Jordan Bernaldo-Agüero,Vincent A. Bielinski,Friederike Biermann,Thomas C. Booth,Victor J Carrion Bravo,Raquel Castelo-Branco,Fernanda O. Chagas,Pablo Cruz-Morales,Chao Du,Katherine R. Duncan,Athina Gavriilidou,Damien Gayrard,Karina Gutiérrez-García,Kristina Haslinger,Eric J. N. Helfrich,Justin J. J. van der Hooft,Afif Pranaya Jati,Edward Kalkreuter,Nikolaos Kalyvas,Kyo Bin Kang,Satria A. Kautsar,Won Ki Kim,Aditya M. Kunjapur,Yong-Xin Li,Geng-Min Lin,Catarina Isabel Mateus Loureiro,Joris J. R. Louwen,Nico L L Louwen,George Lund,John E. Parra,Benjamin Philmus,Bita Pourmohsenin,Lotte J U Pronk,Adriana Rego,D A B Rex,Serina L. Robinson,L. R. Rosas-Becerra,Eve T. Roxborough,Michelle Schorn,D. J. Scobie,Kumar Saurabh Singh,Nika S. Sokolova,Xiaoyu Tang,Daniel W. Udwary,Aruna Vigneshwari,Kristiina Vind,Sophie P J M Vromans,Valentin Waschulin,Sam E Williams,Jaclyn M. Winter,Thomas Wittek,Huali Xie,Dong Yang,Jing-Dong Yu,Mitja M Zdouc,Zhen Zheng,Jérôme Collemare,Roger G. Linington,Tilmann Weber,Marnix H. Medema +81 more
TL;DR: The Minimum Information about a Biosynthetic Gene Clustering (MIBiG) as discussed by the authors is a standardised data format that describes the minimally required information to uniquely characterise a BGC.
Journal ArticleDOI
Fighting antibiotic resistance—strategies and (pre)clinical developments to find new antibacterials
Sebastian Walesch,Joy Birkelbach,Gwenaëlle Jézéquel,F. P. Jake Haeckl,Julian D. Hegemann,Thomas Hesterkamp,Anna K. H. Hirsch,Peter Hammann,Rolf Müller +8 more
TL;DR: In this article , the challenges, advancements and current standing of the clinical and pre-clinical antibacterial research pipeline are highlighted and strategies for rejuvenating the discovery process and advocate for renewed and enthusiastic investment in the discovery pipeline.
Journal ArticleDOI
Microbiome composition modulates secondary metabolism in a multispecies bacterial community
Marc G. Chevrette,Chris S. Thomas,Amanda Hurley,Natalia Rosario-Meléndez,Krishnan P. Sankaran,Yixing Tu,Austin W. Hall,S.B. Magesh,Jo Handelsman +8 more
TL;DR: Results from this model community show that bacterial BGC expression and chemical output depend on the identity and biosynthetic capacity of coculture partners, suggesting community composition and microbiome interactions may shape the regulation of secondary metabolism in nature.
Journal ArticleDOI
Antiphage small molecules produced by bacteria - beyond protein-mediated defenses.
TL;DR: A review of small molecule-based defense strategies against phage infection, with a focus on the antiphage molecules described recently, can be found in this paper , where the authors highlight the ecological significance of these strategies.
Journal ArticleDOI
Native metabolomics identifies the rivulariapeptolide family of protease inhibitors
Daniel Petras,Dion K Dickman +1 more
TL;DR: A scalable native metabolomics approach that integrates non-targeted liquid chromatography tandem mass spectrometry and detection of protein binding via native mass spectra was developed in this article .
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