A practical guide to amplicon and metagenomic analysis of microbiome data

YX Liu, Y Qin, T Chen, M Lu, X Qian, X Guo… - Protein & cell, 2021 - academic.oup.com
Advances in high-throughput sequencing (HTS) have fostered rapid developments in the
field of microbiome research, and massive microbiome datasets are now being generated …

Mining genomes to illuminate the specialized chemistry of life

MH Medema, T de Rond, BS Moore - Nature Reviews Genetics, 2021 - nature.com
All organisms produce specialized organic molecules, ranging from small volatile chemicals
to large gene-encoded peptides, that have evolved to provide them with diverse cellular and …

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 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 …

BiG-FAM: the biosynthetic gene cluster families database

SA Kautsar, K Blin, S Shaw, T Weber… - Nucleic acids …, 2021 - academic.oup.com
Computational analysis of biosynthetic gene clusters (BGCs) has revolutionized natural
product discovery by enabling the rapid investigation of secondary metabolic potential within …

Bioinformatic prospecting and synthesis of a bifunctional lipopeptide antibiotic that evades resistance

Z Wang, B Koirala, Y Hernandez, M Zimmerman… - Science, 2022 - science.org
Emerging resistance to currently used antibiotics is a global public health crisis. Because
most of the biosynthetic capacity within the bacterial kingdom has remained silent in …

Evolution and diversity of assembly-line polyketide synthases: Focus review

A Nivina, KP Yuet, J Hsu, C Khosla - Chemical reviews, 2019 - ACS Publications
Assembly-line polyketide synthases (PKSs) are among the most complex protein
machineries known in nature, responsible for the biosynthesis of numerous compounds …

The antiSMASH database version 3: increased taxonomic coverage and new query features for modular enzymes

K Blin, S Shaw, SA Kautsar, MH Medema… - Nucleic acids …, 2021 - academic.oup.com
Microorganisms produce natural products that are frequently used in the development of
antibacterial, antiviral, and anticancer drugs, pesticides, herbicides, or fungicides. In recent …

BiG-SLiCE: A highly scalable tool maps the diversity of 1.2 million biosynthetic gene clusters

SA Kautsar, JJJ van der Hooft, D de Ridder… - …, 2021 - academic.oup.com
Background Genome mining for biosynthetic gene clusters (BGCs) has become an integral
part of natural product discovery. The> 200,000 microbial genomes now publicly available …

Engineering living and regenerative fungal–bacterial biocomposite structures

RM McBee, M Lucht, N Mukhitov, M Richardson… - Nature Materials, 2022 - nature.com
Engineered living materials could have the capacity to self-repair and self-replicate, sense
local and distant disturbances in their environment, and respond with functionalities for …