In this study, authors show that human gut microbiome composition and microbial genomes vary strongly across five industrialized countries, with diet microbiome links that are partly shared but largely population-specific.

Antimicrobial resistance is often inferred from resistance genes and susceptibility phenotypes measured under standardized conditions. We argue that for many resistance genes, resistance is better vie...

Nature Microbiology, Published online: 17 September 2026; doi:10.1038/s41564-026-02471-8In vivo silencing of genes in E. coli strains using CRISPRi reveals specific genetic factors and metabolic adaptations that influence colonization in the mouse gut under variable physiological conditions.

Micronutrient deficiencies are common during infancy, particularly in settings with a high burden of infectious diseases. At the same time, the developing infant gut microbiota is a key determinant of susceptibility to infection from both resident pathobionts and incoming enteric pathogens. Recent human and experimental studies suggest that micronutrients regulate this developing microbial ecosystem in a highly context-dependent manner, with effects varying according to developmental stage, nutritional status, intestinal location, and environmental exposure. In this review, we synthesise current evidence linking micronutrient-microbiota interactions to microbial competition and metabolism, epithelial barrier integrity, and mucosal immunity, and discuss how these interactions may shape susceptibility to enteric and invasive bacterial infections during infancy.

Here the authors propose guidance on the process of establishing a state-of-the-art collection of microorganisms, including project planning, strain deposition and the naming of new taxa.

## Seerave & MVIF Symposium: The Microbiome in Cancer Immunotherapy ## The gut microbiome is a modifiable determinant of response to immune checkpoint inhibitors, yet it remains one of the most underr...

## Seerave & MVIF Symposium: The Microbiome in Cancer Immunotherapy ## The gut microbiome is a modifiable determinant of response to immune checkpoint inhibitors, yet it remains one of the most underr...

## Seerave & MVIF Symposium: The Microbiome in Cancer Immunotherapy ## The gut microbiome is a modifiable determinant of response to immune checkpoint inhibitors, yet it remains one of the most underr...

## Seerave & MVIF Symposium: The Microbiome in Cancer Immunotherapy ## The gut microbiome is a modifiable determinant of response to immune checkpoint inhibitors, yet it remains one of the most underr...

The maternal gut microbiome is a predictor of infant eczema.

Nature Reviews Gastroenterology & Hepatology, Published online: 03 August 2026; doi:10.1038/s41575-026-01229-1In this Consensus Statement, an international panel of experts provides recommendations to harmonize metadata, sampling, analysis and end points in gut microbiome-based clinical research.

Here, Buyanbadrakh et al. systematically map growth interactions among gut bacteria, revealing predominantly inhibitory effects, and identifying extracellular vesicles and pH modulation as mechanisms ...

Baertschi et al. demonstrate that microbiota transplantation functions as a selective ecological filter. Although donor species frequently appear, only specific lineages achieve stable strain integrat...

Nature Microbiology, Published online: 29 July 2026; doi:10.1038/s41564-026-02434-zLipidomics and proteomics in mice colonized with variable gut microbiota reveal an important role of gut microbes in restricting lipid uptake via triggering Myd88 signalling and the degradation of phosphatidylcholine in bile.

Agus, A., Clément, K. & Sokol, H. Gut microbiota-derived metabolites as central regulators in metabolic disorders. Gut 70, 1174–1182 (2021). Rinninella, E. et al. What is the healthy gut microbiota composition? A changing ecosystem across age, environment, diet, and diseases. Microorganisms 7, 14 (2019). Das, B. & Nair, G. B. Homeostasis and dysbiosis of the gut microbiome in health and disease. J. Biosci. 44, 117 (2019). Schult, D. et al. Gut bacterial dysbiosis and instability is associated with the onset of complications and mortality in COVID-19. Gut Microbes 14, 2031840 (2022). He, Y. et al. Effects of dietary fiber on human health. Food Sci. Hum. Wellness 11, 1–10 (2022). Tanes, C. et al. Role of dietary fiber in the recovery of the human gut microbiome and its metabolome. Cell Host Microbe 29, 394–407 (2021). Cantu-Jungles, T. M. & Hamaker, B. R. New view on dietary fiber selection for predictable shifts in gut microbiota. mBio 11, e02179-19 (2020). Oliver, A. et al. High-fiber, whole-food dietary intervention alters the human gut microbiome but not fecal short-chain fatty acids. mSystems 6, 10–1128 (2021). Koh, A., De Vadder, F., Kovatcheva-Datchary, P. & Bäckhed, F. From dietary fiber to host physiology: short-chain fatty acids as...

You can see AI everywhere except in the productivity statistics

Nature Microbiology, Published online: 17 July 2026; doi:10.1038/s41564-026-02422-3Environmental stress shifts microbial composition towards species with high growth rates, providing community-wide protection.

Some new articles in the reading list. I’ll probably do a little break for those during the summer holidays. Have a good one! (a) Microbiome and population health Genomic landscape of the human vagina...

YouTube video by Microbiome Virtual International Forum

By taking into account the impacts of species presence, absence and potential interactions, synthetic soil microbial consortia are designed to degrade the toxic environmental contaminant bisphenol-A.

Taxonomically and functionally distinct communities assemble on cellulose and its monomer, glucose. Although single carbon sources were provided, high and comparable diversity was maintained in both ...

Pekel, Karcher, et al. present the largest gut microbiome meta-analysis of colorectal cancer to date, integrating 6,779 amplicon and shotgun sequencing profiles. They establish a robust microbiome sig...

Nature Microbiology asked members of the Global Grants for Gut Health Colloquium about the impact artificial intelligence is having on their microbiome research.

Biological communities are complex, dynamic systems that underpin ecosystem functionality, yet their long-term dynamics and predictability remain p...

A randomized, single-blind, parallel-group, phase 1b clinical trial compared fecal microbiota transplant or a 15-strain live biotherapeutic product (MTC01) derived from the same donor and found similar efficacy and engraftment between treatments.

Nature Microbiology, Published online: 01 June 2026; doi:10.1038/s41564-026-02378-4Engineered Bacteroides thetaiotaomicron, Btbots, use a genetic AND circuit to sense nitric oxide and deoxycholic acid as inflammatory signal in the gut to release therapeutic molecules, TFF3 and IL-35, that alleviate colitis in mice.