Nature Microbiology, Published online: 02 October 2026; doi:10.1038/s41564-026-02500-6Multiomic experiments using defined and native gut communities reveal that complex dietary glycans mediate the dominance of Prevotellaceae in non-industrialized gut metagenomes through signalling-mediated cross-feeding with Enterobacteriaceae.

In this Review, Schubert and Hardt explore the metabolic strategies that Enterobacteriaceae use to establish themselves in the gut, and how they adapt to inflammatory conditions in this environment.

El Mouali and Tawk et al. characterize the oxygen-tolerance response in the human gut-residing bacterium Segatella copri. They identified a subset of strains that acquired an additional oxygen regulat...

El Mouali and Tawk et al. characterize the oxygen-tolerance response in the human gut-residing bacterium Segatella copri. They identified a subset of strains that acquired an additional oxygen regulat...

HZI-Studie identifiziert funktionelle Unterschiede in Segatella-Stämmen aus verschiedenen Regionen der Welt

El Mouali and Tawk et al. characterize the oxygen-tolerance response in the human gut-residing bacterium Segatella copri. They identified a subset of strains that acquired an additional oxygen regulat...

Title: Assistant Professor x6 (111522-0426). Application Deadline: . Position Type: Permanent

Phages employ diverse counter-defense strategies to overcome bacterial immune systems. Here, the authors reveal that the phage homing nuclease SegB facilitates immune evasion by promoting the segmenta...

Can specific HIV drugs heal the gut? For late-stage patients, viral suppression isn't enough to stop chronic inflammation. Our 2-year trial reveals that dolutegravir, unlike darunavir, profoundly restores the gut microbiome, offering a new pathway to long-term health and reduced inflammation.

Uropathogenic Escherichia coli infection of a murine prostate organoid model reveals a bacterial FimH–host prostatic acid phosphatase adhesin-receptor interaction enabling invasion and replication wit...

Nature Reviews Microbiology, Published online: 05 January 2026; doi:10.1038/s41579-025-01268-6In this Review, Hajjar, Mars and Kashyap discuss the role of the microbiome in cancer development and progression and in treatment response. They also consider the potential of the microbiome as a therapeutic target and as a prognostic and predictive biomarker, and outline major knowledge gaps in the field.

Abstract. Salmonella virulence chiefly relies upon two major pathogenicity islands, SPI-1 and SPI-2, which enable host cell invasion and intracellular surv

Machine learning methods have emerged as promising tools to predict antimicrobial resistance (AMR) and uncover resistance determinants from genomic data. This study shows that sampling biases driven b...

To cause disease, pathogens must express their virulence genes at the right time and in proper levels. Here, we establish that a small RNA (sRNA) restricts the activation of a regulator critical for t...

Abstract. Two-dimensional drawing of nucleic acid structures, particularly RNA structures, is fundamental to the communication of nucleic acids research. H

Abstract. The Indri indri is a critically endangered lemur species that has not successfully been maintained or bred under human care. Investigating this l

Analyzing readouts of inflammaging across four cohorts, Franck and colleagues identify strong variation and observe that inflammaging, in its known form, primarily emerges in industrialized—but not nonindustrialized—populations.

Research on horizontal gene transfer (HGT) has surged over the past two decades, revealing its critical role in accelerating evolutionary rates, facil…

Abstract. Bacteriophages with RNA genomes are among the simplest biological entities on Earth. Since their discovery in the 1960s, they have been used as i

Microbial life has dominated Earth’s history but left a sparse fossil record, greatly hindering our understanding of evolution in deep time. However, bacterial metabolism has left signatures in the ge...

Nature Communications - Acute systemic immune activation may affect gut-luminal colonisation dynamics. Here, the authors show that LPS exposure in mice elevates gut-luminal oxygen species levels,...

‘Fast Facts: The Gut Microbiome’, though pithy and concise, is amazingly comprehensive and takes the reader through all major aspects of the human gut micr

Diener et al. present a method that allows the estimation of dietary intake from human stool by detecting food-derived DNA in faecal metagenomes.

The early evolution of microbial respiration under low-oxygen conditions is still incompletely understood. Here, the authors analyzed the genomics of filamentous geothermal communities and showed that...

Abstract. Micromix is a flexible web platform for sharing and integrating microbial omics data, including RNA sequencing and transposon-insertion sequencin

Split-And-pool Metagenomic Plot-sampling sequencing (SAMPL-seq) can be applied to complex microbial communities to reveal spatial co-localization of microbes at the micron scale.

Gut microbiota-derived succinate promotes CitC succinyltransferase-dependent succinylation of PurR to alleviate T3SS repression and promote virulence in enterohaemorrhagic Escherichia coli and Citroba...

A cross-sectional study from four African countries shows the importance of investigating the gut microbiome in previously under-represented populations and provides a framework for equitable microbio...

Single-cell decisions made in complex environments underlie many bacterial phenomena. Image-based transcriptomics approaches offer an avenue to study such behaviors, yet these approaches have been hin...

Typhoid fever is a systemic infection caused by Salmonella enterica serovar Typhi ( S. Typhi) invasion from the gut lumen. Transmission between people occurs through ingestion of contaminated food and...

Here, using metagenomics, the authors show that the gut m...

Objectives This work aimed to resolve the conflicting reports on Prevotellaceae abundance in the development of rheumatoid arthritis (RA) and to observe structural, functional and temporal changes in…

The Human Microbiome Compendium is a unified database of publicly available human gut microbiome 16S samples, built with the integrated data from hundreds of independent projects. The compendium is us...

Microbiome science is a multi-disciplinary field, but classical microbiologists are needed to ensure advances are grounded in our understanding of basic microbiological concepts.

Antimicrobial resistance (AMR) poses a growing threat to human health. Increasingly, genome sequencing is being applied for the surveillance of bacterial pathogens, producing a wealth of data to train...

El Mouali et al. characterized the RNA landscape of the human gut-residing bacteria Segatella copri using in vitro and gut-derived samples. They identified a small RNA regulator essential for gut colo...