In immunocompetent hosts, Salmonella enterica serovar Typhimurium typically causes transient intestinal blooms with acute diarrhoea, followed by asymptomatic systemic carriage with intermittent reactivation. Inflammation elicited by bistable expression of type III secretion systems and pathogen-associated signals shapes Salmonella pathogenesis in both the intestine and systemic tissues. Inflammation is a two-sided coin that, over time, can either benefit or harm the host, microbiota and Salmonella. The host deploys the inflammasome, hypoxia and reactive oxygen and nitrogen species in both intestinal and systemic tissues, but the effectors of these responses are cell-specific and tissue-specific. Salmonella fine-tunes its metabolism and virulence programmes in response to chemical and physical cues derived from the microbiota and from heterogeneous host cells that vary in embryonic origin, architecture and activation states. Similar to its host, Salmonella undergoes coordinated virulence, metabolic, redox and energetic reprogramming with outcomes tailored to specific host cells and tissues. Paradoxically, Salmonella often exploits common signalling and metabolic pathways to support rapid growth in the gut lumen and in the cytosol of enterocytes while sustaining an energy-conserving and metabolic-conserving survival strategy in viscera. In this Review, I discuss current perspectives of how the dynamic interplay between microbial competition, host defences and Salmonella countermeasures determines the outcome of infection ranging from acute gastroenteritis to quiescent chronic infection.

Despite a tremendous body of literature on environmental Actinomycetota, their role in the human gut remains poorly understood. In this Review, we highlight the representative species Eggerthella lenta, which has emerged as a major player in the gut microbiota and is increasingly amenable to mechanistic dissection. We discuss the unique metabolic niche of this asaccharolytic obligate anaerobe, including growth on amino acids and short-chain fatty acids, versatile anaerobic respiratory capacity, and the extensive biotransformation of endogenous, diet-derived and pharmaceutical small molecules. E. lenta is associated with a wide range of chronic diseases in humans and sufficient to exacerbate disease in preclinical models, prompting a renewed consideration of the pathogenic potential of this common member of the gut microbiota. Further mechanistic dissection coupled with the development of microbiome-editing tools is essential to understand E. lenta and its multifaceted contributions to gut microbial ecology and host pathophysiology.

The global rise of antibiotic resistance has rekindled interest in bacteriophages (phages) as alternative therapeutics. Here, we isolated and characterized a novel Escherichia coli phage, Ec_Ou_ZC1, from the family Drexlerviridae, genus Tunavirus, sharing 94.72% genomic identity with Escherichia phage phiD2-2. Ec_Ou_ZC1 encodes an orphan methyltransferase and a Cor superinfection exclusion (SIE) protein. Heterologous expression of Cor blocked all tested FhuA-dependent Drexlerviridae phages (Ec_Ou_ZC1, T1, Bas03, Bas12, Bas13) but not T4 or T7, confirming family-specific SIE through FhuA receptor inactivation. Plaque assays against four antiviral STAND (Avs) systems revealed differential susceptibility within Drexlerviridae: Bas03 (Braunvirinae) was sensitive to SeAvs3, while Ec_Ou_ZC1, Bas05, Bas12, Bas13, and T1 (Tempevirinae and Tunavirinae) resisted all four systems, suggesting that Avs resistance depends on specific genomic features. Species-level phylogenetic analyses using concatenated single-copy orthologs robustly resolved evolutionary relationships within Tunavirus, separating Escherichia- and Shigella-infecting phages and providing a framework for predicting host range of new isolates.

The depletion of soil organic matter (SOM) represents one of the most conspicuous hallmarks of Mollisol degradation in Northeast China. This study focuses on typical black soil with high, medium, and low fertility levels to investigate the responses of soil properties and microbial communities to varying soil fertility. We observed a significant decline in the Soil Quality Index (SQI) and key enzyme activities from high to low fertility levels, which mirrored the synchronous depletion of soil carbon fractions (SOM, POC, and MBC). Our results indicated that while microbial alpha diversity peaked in soils with medium fertility, overarching network complexity was highest in environments with high fertility. Compositionally, this robust community structure was primarily associated with significant increases in the abundance of Actinobacterota and Mortierellomycota. Furthermore, network analysis identified specific keystone taxa, including Gemmatimonadaceae, Roseiflexaceae, Penicillium, and Trichoderma, which are closely associated with efficient nutrient cycling and enhanced disease resistance. This study elucidates the microbial taxa associated with high-fertility soils. And by elucidating these underlying microbial associations, this study provides a solid theoretical foundation for restoring degraded black soils through targeted microbiome regulation. Ultimately, our findings highlight promising avenues for developing novel soil conservation technologies centered on core functional microorganisms.