Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

RM Bowers, NC Kyrpides, R Stepanauskas… - Nature …, 2017 - nature.com
We present two standards developed by the Genomic Standards Consortium (GSC) for
reporting bacterial and archaeal genome sequences. Both are extensions of the Minimum …

Fungal secondary metabolism: regulation, function and drug discovery

NP Keller - Nature Reviews Microbiology, 2019 - nature.com
One of the exciting movements in microbial sciences has been a refocusing and
revitalization of efforts to mine the fungal secondary metabolome. The magnitude of …

antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline

K Blin, S Shaw, K Steinke, R Villebro… - Nucleic acids …, 2019 - academic.oup.com
Secondary metabolites produced by bacteria and fungi are an important source of
antimicrobials and other bioactive compounds. In recent years, genome mining has seen …

MIBiG 3.0: a community-driven effort to annotate experimentally validated biosynthetic gene clusters

BR Terlouw, K Blin, JC Navarro-Munoz… - Nucleic acids …, 2023 - academic.oup.com
With an ever-increasing amount of (meta) genomic data being deposited in sequence
databases,(meta) genome mining for natural product biosynthetic pathways occupies a …

MIBiG 2.0: a repository for biosynthetic gene clusters of known function

SA Kautsar, K Blin, S Shaw… - Nucleic acids …, 2020 - academic.oup.com
Fueled by the explosion of (meta) genomic data, genome mining of specialized metabolites
has become a major technology for drug discovery and studying microbiome ecology. In …

antiSMASH 4.0—improvements in chemistry prediction and gene cluster boundary identification

K Blin, T Wolf, MG Chevrette, X Lu… - Nucleic acids …, 2017 - academic.oup.com
Many antibiotics, chemotherapeutics, crop protection agents and food preservatives
originate from molecules produced by bacteria, fungi or plants. In recent years, genome …

Pathogen-induced activation of disease-suppressive functions in the endophytic root microbiome

VJ Carrión, J Perez-Jaramillo, V Cordovez, V Tracanna… - Science, 2019 - science.org
Microorganisms living inside plants can promote plant growth and health, but their genomic
and functional diversity remain largely elusive. Here, metagenomics and network inference …

Streptomyces: The biofactory of secondary metabolites

K Alam, A Mazumder, S Sikdar, YM Zhao… - Frontiers in …, 2022 - frontiersin.org
Natural products derived from microorganisms serve as a vital resource of valuable
pharmaceuticals and therapeutic agents. Streptomyces is the most ubiquitous bacterial …

BAGEL4: a user-friendly web server to thoroughly mine RiPPs and bacteriocins

AJ van Heel, A de Jong, C Song, JH Viel… - Nucleic acids …, 2018 - academic.oup.com
Interest in secondary metabolites such as RiPPs (ribosomally synthesized and
posttranslationally modified peptides) is increasing worldwide. To facilitate the research in …

A computational framework to explore large-scale biosynthetic diversity

JC Navarro-Muñoz, N Selem-Mojica… - Nature chemical …, 2020 - nature.com
Genome mining has become a key technology to exploit natural product diversity. Although
initially performed on a single-genome basis, the process is now being scaled up to mine …