Research articles

Construction and analysis of 2,901 promoter–GFP fusions in Salmonella reveal dynamic, heterogeneous transcriptional activity, including roles for manganese homeostasis and Entner–Doudoroff carbon metabolism in promoting intramacrophage growth and survival of bacteria.

Using a cohort of nearly 1,000 genetically diverse mice undergoing dietary restriction over the lifespan, the authors reveal numerous insights into the interactions between the gut microbiome, host genome, diet, health and longevity.

Biochemical characterization of 66 carbohydrate-active enzymes from the gut microorganism Akkermansia muciniphila reveals that these enzymes can break down a range of host glycans, including mucin, which they degrade to completion.

Transcriptomics of gene expression in Plasmodium falciparum liver-stage parasites reveals transcriptional regulation, metabolic pathways and antigen expression, facilitating vaccine and drug target identification.

Samples from over 4,000 bats representing 40 different species yield 8,176 viral metagenomes that expand RNA virus diversity and decipher environmental and anthropogenic factors influencing bat viral ecology.

A 471-metagenome time series from Lake Mendota in Wisconsin, USA, reveals seasonal and decadal shifts in bacterial functional and ecological dynamics, especially in response to environmental extremes.

A long-term metagenomic time series reveals how viruses impact diversity, ecological dynamics and evolution of freshwater microbiomes.

Thousands of metagenome-assembled genomes from the Vanishing Glaciers project showcase the interactions between prokaryotes, algae, fungi and viruses in glacier-fed stream environments.

Metabolomic analysis of bile after infection by enteric bacteria in mice reveals composition changes including increased itaconate levels that promote intestinal homeostasis and reduce Vibrio cholerae colonization.

Genome sequence mining and computational analyses lead to the discovery and functional characterization of conserved bacterial toxins with activity against bacteria and fungi.

Using shotgun metagenomics, cultivation and metabolic modelling, the authors construct the Salmon Microbial Genome Atlas as a resource for future studies on sustainable aquaculture.

Deep mutational scanning of the azole antifungals drug target Erg11 provides an extensive catalogue of resistance mutations and reveals that resistance to azoles can arise through a large set of mutations that will probably lead to azole pan-resistance without a fitness cost.

The leaf microbiome compositions of 267 Arabidopsis thaliana populations across Europe reveal associations with climate and plant genetics.

A combination of metagenomic sequencing and fungal cultivation were used to establish a multi-kingdom collection of 33,804 microbial genomes from the human vaginal microbiome.

This study presents an extensive global compendium of metagenomically derived sequences that will serve as a foundation for understanding the role of viruses in soil ecosystems.

A single-cell transcriptomic resource of 174,531 microbial cells across 2,534 species allows the detection of single-cell-level functional roles in the rumen microbiome.

Integration of differential and conventional RNA sequencing and transposon mutant fitness data for Bacteroides thetaiotaomicron grown under 15 different conditions provides an expression atlas, expands the regulatory RNA repertoire and reveals that the small RNA MasB regulates susceptibility to tetracyclines.

A DNA barcoding approach enables discrimination between bacterial strains that could not be distinguished with conventional microbial marker gene amplicon sequencing techniques.

WISH-tags can be used in combination with quantitative polymerase chain reaction or next-generation sequencing to decipher population dynamics at the strain level within plant and mammalian microbiotas.

Metabolic engineers and synthetic biologists can produce recombinant proteins at scale without royalty payments, or strain distribution constraints, using OPENPichia.