Nature Reviews Gastroenterology & Hepatology, Published online: 14 September 2026; doi:10.1038/s41575-026-01258-wMany compounds not classified as antibiotics can exert antimicrobial activity, with drug–microbiome–host interactions having profound effects on the human microbiome and human health. This Review explores how non-antibiotic compounds exert these antimicrobial effects, highlighting which compounds can influence the microbiome, the underlying mechanisms, and implications for translation and clinical practice.

Nature Microbiology, Published online: 16 September 2026; doi:10.1038/s41564-026-02484-3An engineered non-pathogenic bacterium produces lytic phages and is protective in mouse models of Salmonella infection.

The microbiome plays a significant yet underexplored role in antimicrobial resistance by influencing ecological and evolutionary processes. This Perspective proposes a framework to integrate microbiom...

The TRACS algorithm tracks bacteria, viruses and parasites in metagenomic or population sequencing data, detecting microbial transmission even when multiple strains coexist within a host.

Over three decades, rapid expansion of the transposable element ISL3 has reshaped Enterococcus faecium, which helps to explain this pathogen’s growing clinical threat.

Nature Microbiology - Phylodynamic modelling shows how the changing antibiotic landscape and genetic determinants of resistance shape real-world gonococcal dynamics. Experiments validated that...

The human gut microbiome is important for host health, yet over 60% of gut species remain uncultured and inaccessible to experimental manipulation. He…

A metagenomic survey of babies attending the first year of nursery detected extensive baby-to-baby microbial strain transmission, pointing to social interactions in infancy as crucial drivers of infan...

Enteric infections remain a leading global cause of morbidity, mortality and economic loss, increasingly compounded by the rise of antimicrobial resistance. The gut microbiome — spanning bacteria, ...

Development and application of the integrated linkage disequilibrium score (iLDS) reveals both selective pressures impacting the human gut microbiome and the mechanisms by which gut bacteria adapt to ...

Identifying bacterial interactions that determine susceptibility of human microbiomes to colonisation by pathogenic bacteria has crucial implications for understanding health and disease and, conseque...

Microbiota-derived metabolites serve as key messengers mediating host–microbe and microbe–microbe interactions, often through specialized primary meta…

PhD Project - Nationwide Clostridioides difficile population dynamics. at University of Birmingham, listed on FindAPhD.com

Nature Communications - Here, the authors provide evidence of the biotherapeutic potential of Klebsiella ARO112 for gut inflammatory conditions by showing it accelerates pathobiont clearance and...

Complex prophage integration dynamics, including low-level induction, cross-family host range and transposase-mediated mobilization, challenge existing paradigms and deepen our understanding of phage–...

PhD Project - The overlapping microbiome: ecology, function and resilience beyond species boundaries at University of Bath, listed on FindAPhD.com

The authors investigate the distribution of the aminoglycoside resistance gene npmA in Gram-positive bacteria via a mobile genetic element, highlighting its global presence and cross-species transfer ...

Mathematical modelling and experimental tests reveal principles that govern displacement of a resident strain by an invader in microbial communities.

Bacteria employ a range of competition systems that deliver toxins to inhibit competing strains. This study shows that these systems are particularly important for the ecology of virulent and antibiot...

Authors analyse paired viral and bacterial shotgun metagenomics data from individual honeybee guts, revealing modular, nested phage–bacteria networks, with viral diversity mirroring bacterial strain c...

Competition significantly influences bacterial population dynamics, particularly in how strains interact within and between hosts. This study shows that within-host competition in Streptococcus pneumo...

Here, the authors show that vancomycin-resistant enterococci grow in the antibiotic-treated gut microbiome by utilising enriched nutrients in the presence of reduced concentrations of inhibitory micro...

A long-read metagenomics method empowers faecal microbiota transplantation studies by precisely tracking bacteria from donors to recipients, distinguishing co-existing strains and revealing genomic ch...

Abstract. Microbial communities are frequently organized into complex spatial structures, shaped by intrinsic cellular traits, interactions between communi

Qu et al. present PHLAME, a method to analyze strain composition in metagenomic samples where many strains of the same species coexist. Using PHLAME, they show relationships between strain abundances ...

In this Review, Tonkin-Hill et al. discuss the processes driving bacterial evolution and emergence of pathogenesis within hosts, the importance of understanding within-host genetic diversity, and the ...

About 15,000 pairwise interactions within S. epidermidis from 18 people in 6 families reveal the antagonism and molecular trade-offs that shape the skin microbiota.

Understanding how and why human skin bacteria differ from our closest animal relatives provides crucial insights into human evolution and health. While we have known that human facial skin hosts disti...

The human gut harbors thousands of microbial species, each exhibiting significant inter-individual genetic variability. Although many studies have ass…

Genomic and functional analyses of healthcare-associated vancomycin-resistant Enterococcus faecium reveal that bacteriocin T8 is enriched in emergent lineages and provides a competitive advantage in v...

Accurate nucleotide variant calling is essential in microbial genomics, particularly for outbreak tracking and phylogenetics. This study evaluates variant calls derived from genome assemblies compared...

Much of life on earth is at the mercy of currents and flow. Residence time (τ) estimates how long organisms and resources remain in a system based on the ratio of volume (V) to flow rate (Q). We test...

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npj Biofilms and Microbiomes - Disentangling the feedback loops driving spatial patterning in microbial communities

Abstract. The diffusible toxin ColIb produced by Salmonella enterica serovar Typhimurium SL1344 is a potent inhibitor of Escherichia coli growth. To identi