New developments in RiPP discovery, enzymology and engineering

M Montalbán-López, TA Scott, S Ramesh… - Natural product …, 2021 - pubs.rsc.org
Covering: up to June 2020 Ribosomally-synthesized and post-translationally modified
peptides (RiPPs) are a large group of natural products. A community-driven review in 2013 …

An introduction to the analysis of shotgun metagenomic data

TJ Sharpton - Frontiers in plant science, 2014 - frontiersin.org
Environmental DNA sequencing has revealed the expansive biodiversity of microorganisms
and clarified the relationship between host-associated microbial communities and host …

Programmed DNA destruction by miniature CRISPR-Cas14 enzymes

LB Harrington, D Burstein, JS Chen, D Paez-Espino… - Science, 2018 - science.org
CRISPR-Cas systems provide microbes with adaptive immunity to infectious nucleic acids
and are widely employed as genome editing tools. These tools use RNA-guided Cas …

Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life

DH Parks, C Rinke, M Chuvochina, PA Chaumeil… - Nature …, 2017 - nature.com
Challenges in cultivating microorganisms have limited the phylogenetic diversity of currently
available microbial genomes. This is being addressed by advances in sequencing …

Clustering huge protein sequence sets in linear time

M Steinegger, J Söding - Nature communications, 2018 - nature.com
Metagenomic datasets contain billions of protein sequences that could greatly enhance
large-scale functional annotation and structure prediction. Utilizing this enormous resource …

Protein structure determination using metagenome sequence data

S Ovchinnikov, H Park, N Varghese, PS Huang… - Science, 2017 - science.org
Despite decades of work by structural biologists, there are still~ 5200 protein families with
unknown structure outside the range of comparative modeling. We show that Rosetta …

Uncovering Earth's virome

D Paez-Espino, EA Eloe-Fadrosh, GA Pavlopoulos… - Nature, 2016 - nature.com
Viruses are the most abundant biological entities on Earth, but challenges in detecting,
isolating, and classifying unknown viruses have prevented exhaustive surveys of the global …

IMG/M: integrated genome and metagenome comparative data analysis system

IMA Chen, VM Markowitz, K Chu… - Nucleic acids …, 2016 - academic.oup.com
Abstract The Integrated Microbial Genomes with Microbiome Samples (IMG/M: https://img.
jgi. doe. gov/m/) system contains annotated DNA and RNA sequence data of (i) archaeal …

Recurring patterns in bacterioplankton dynamics during coastal spring algae blooms

H Teeling, BM Fuchs, CM Bennke, K Krüger, M Chafee… - elife, 2016 - elifesciences.org
A process of global importance in carbon cycling is the remineralization of algae biomass by
heterotrophic bacteria, most notably during massive marine algae blooms. Such blooms can …

Nutritional preferences of human gut bacteria reveal their metabolic idiosyncrasies

M Tramontano, S Andrejev, M Pruteanu… - Nature …, 2018 - nature.com
Bacterial metabolism plays a fundamental role in gut microbiota ecology and host–
microbiome interactions. Yet the metabolic capabilities of most gut bacteria have remained …