Biosynthetic potential of the global ocean microbiome
Lucas Paoli,Hans-Joachim Ruscheweyh,Clarissa C. Forneris,Florian Hubrich,Satria A. Kautsar,Agneya Bhushan,Alessandro Lotti,Quentin Clayssen,Guillem Salazar,Alessio Milanese,Charlotte I. Carlström,Chrysa Papadopoulou,Dan Gehrig,Mikhail Karasikov,Harun Mustafa,Martin Larralde,Laura M. Carroll,Pablo Sánchez,Ahmed A. Zayed,Dylan R. Cronin,Silvia G. Acinas,Peer Bork,Chris Bowler,Tom O. Delmont,Josep M. Gasol,Alvar D. Gossert,André Kahles,Matthew B. Sullivan,Patrick Wincker,Georg Zeller,Serina L. Robinson,Jörn Piel,Shinichi Sunagawa +32 more
TLDR
This paper investigated the diversity and novelty of biosynthetic gene clusters in the ocean by integrating around 10,000 microbial genomes from cultivated and single cells with more than 25,000 newly reconstructed draft genomes from more than 1,000 seawater samples.Abstract:
Abstract Natural microbial communities are phylogenetically and metabolically diverse. In addition to underexplored organismal groups 1 , this diversity encompasses a rich discovery potential for ecologically and biotechnologically relevant enzymes and biochemical compounds 2,3 . However, studying this diversity to identify genomic pathways for the synthesis of such compounds 4 and assigning them to their respective hosts remains challenging. The biosynthetic potential of microorganisms in the open ocean remains largely uncharted owing to limitations in the analysis of genome-resolved data at the global scale. Here we investigated the diversity and novelty of biosynthetic gene clusters in the ocean by integrating around 10,000 microbial genomes from cultivated and single cells with more than 25,000 newly reconstructed draft genomes from more than 1,000 seawater samples. These efforts revealed approximately 40,000 putative mostly new biosynthetic gene clusters, several of which were found in previously unsuspected phylogenetic groups. Among these groups, we identified a lineage rich in biosynthetic gene clusters (‘ Candidatus Eudoremicrobiaceae’) that belongs to an uncultivated bacterial phylum and includes some of the most biosynthetically diverse microorganisms in this environment. From these, we characterized the phospeptin and pythonamide pathways, revealing cases of unusual bioactive compound structure and enzymology, respectively. Together, this research demonstrates how microbiomics-driven strategies can enable the investigation of previously undescribed enzymes and natural products in underexplored microbial groups and environments. read more
Citations
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Journal ArticleDOI
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
Mirusviruses link herpesviruses to giant viruses
Morgan Gaïa,Lingjie Meng,Eric Pelletier,Patrick Forterre,Chiara Vanni,Antonio Fernandez-Guerra,Olivier Jaillon,Patrick Wincker,Hiroyuki Ogata,Mart Krupovic,Tom O. Delmont +10 more
TL;DR: This paper carried out a phylogeny-guided genome-resolved metagenomic survey of the sunlit oceans and discovered plankton-infecting relatives of herpesviruses that form a putative new phylum dubbed Mirusviricota.
Peer ReviewDOI
Plankton-infecting relatives of herpesviruses clarify the evolutionary trajectory of giant viruses
Morgan Gaïa,Lingjie Meng,Eric Pelletier,Patrick Forterre,Chiara Vanni,Antonio Fernandez-Guerra,Olivier Jaillon,Patrick Wincker,Hiroyuki Ogata,Mart Krupovic,Tom O. Delmont +10 more
TL;DR: A phylogeny-guided genome-resolved metagenomic survey of the sunlit oceans exposed a major, previously undescribed clade of large eukaryotic DNA viruses which exposed a putative new phylum dubbed ‘Mirusviricota’, which provides missing links in the evolution of both animal herpesviruses from tailed prokaryotic viruses and giant varidnaviruses from smaller relatives.
Journal ArticleDOI
MAGNETO: An Automated Workflow for Genome-Resolved Metagenomics
TL;DR: MAGNETO is presented, an automated workflow dedicated to MAG reconstruction, which includes a fully-automated coassembly step informed by optimal clustering of metagenomic distances, and implements complementary genome binning strategies, for improving MAG recovery.
Journal ArticleDOI
proGenomes3: approaching one million accurately and consistently annotated high-quality prokaryotic genomes
Anthony Fullam,Ivica Letunic,Thomas Schmidt,Quinten R Ducarmon,Nicolai Karcher,Supriya Khedkar,Michael Kuhn,Martin Larralde,Oleksandr M. Maistrenko,Lukas Malfertheiner,Alessio Milanese,Joaão F. Matias Rodrigues,Claudia Sanchis-López,Christian Schudoma,Damian Szklarczyk,Shinichi Sunagawa,Georg Zeller,Jaime Huerta-Cepas,Christian von Mering,Peer Bork,Daniel R. Mende +20 more
TL;DR: Progenomes3 as mentioned in this paper is a database of 907 388 high-quality genomes containing 4 billion genes that passed stringent criteria and have been consistently annotated using multiple functional and taxonomic databases including mobile genetic elements and biosynthetic gene clusters.
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Biosynthetic potential of the global ocean microbiome
Lucas Paoli,Hans-Joachim Ruscheweyh,Clarissa C. Forneris,Florian Hubrich,Satria A. Kautsar,Agneya Bhushan,Alessandro Lotti,Quentin Clayssen,Guillem Salazar,Alessio Milanese,Charlotte I. Carlström,Chrysa Papadopoulou,Dan Gehrig,Mikhail Karasikov,Harun Mustafa,Martin Larralde,Laura M. Carroll,Pablo Sánchez,Ahmed A. Zayed,Dylan R. Cronin,Silvia G. Acinas,Peer Bork,Chris Bowler,Tom O. Delmont,Josep M. Gasol,Alvar D. Gossert,André Kahles,Matthew B. Sullivan,Patrick Wincker,Georg Zeller,Serina L. Robinson,Jörn Piel,Shinichi Sunagawa +32 more