Phages are a valuable resource for the genetic engineering of Streptomyces antibiotic-producing bacteria. Indeed, a few integrative vectors based on phage integrase are available to insert transgenes at specific genomic loci. Chromosome conformation captures previously demonstrated that the Streptomyces linear chromosome is organized in two spatial compartments: the central compartment encompassing the most conserved and highly expressed genes in exponential phase, and the terminal compartments enriched in poorly conserved sequences including specialized metabolite biosynthetic gene clusters. This study introduces a new integrative tool based on a recently described phage, Samy, which specifically targets the terminal compartment of its native host chromosome. Samy is related to PhiC31 phage and, like the latter, encodes a serine integrase. Whereas PhiC31 targets a site generally located near the origin of replication, the Samy integration site is one of the farthest known attB sites from it. We demonstrated that the Samy integrase efficiently mediates the specific integration of a non-replicating plasmid in six Streptomyces strains from distinct clades. Bioinformatic analyses revealed that the Samy-attB site is rather conserved and located in the terminal compartment of most Streptomyces chromosomes. Finally, heterologous expression of the albonoursin biosynthetic gene cluster from the Samy-, PhiC31-, and R4-attB sites yields quantitatively equivalent levels of production, though qualitative differences were observed. Altogether, these results demonstrate that the att-int Samy system expands Streptomyces genetic engineering tools by enabling targeted integration in the terminal chromosomal compartment.

Intracellular bacterial pathogens can cause high levels of morbidity and mortality in humans. Host immune responses that protect against these infections include pyroptosis, a form of lytic cell death caused by the insertion of large gasdermin (GSDM) pores into the host plasma membrane. Here we review recent advances in our understanding of how the five GSDM proteins, GSDMA–E, are activated by distinct signalling pathways. Pyroptosis can both eliminate intracellular niches and release cytosolic interleukin-1 family cytokines that further prime host immune responses against the invading pathogen. Because pyroptosis targets microbes, host-adapted intracellular pathogens have evolved strategies to efficiently subvert it. However, environmental pathogens fail to evade, making pyroptosis a potent barrier against infection. We summarize recent findings for the host-adapted bacterial pathogens Shigella flexneri, Salmonella enterica serovar Typhimurium and Mycobacterium tuberculosis, contrasted with the environmental bacteria Burkholderia thailandensis and Chromobacterium violaceum. This Review discusses recent advances in our understanding of how gasdermins are activated by distinct signalling pathways and summarizes recent findings from host-adapted bacterial pathogens contrasted with environmental bacteria.

High-yielding recombinant protein expression systems often face challenges due to the metabolic burden caused by the competition for cellular resources, resulting in reduced growth and, hence, limiting their industrial applicability. Furthermore, industrial recombinant protein production is also affected by the occurrence of oxygen gradients, which is a prevalent issue in large-scale bioreactors. These gradients create a heterogeneous environment in the bioreactor, which affects cell growth and metabolism, having severe consequences on the process performance. Both these factors alter cellular physiology and metabolism, thereby affecting recombinant protein yields. Understanding metabolic adaptations to these stress conditions is crucial for uncovering the underlying cellular mechanisms, which can direct further optimization of the recombinant strains. In this study, we aimed to explore the combined response of the central metabolism of E. coli to metabolic burden and microaerobic conditions. Two recombinant protein-producing E. coli BL21 strains carrying XylS/Pm vectors with low (A2-mCh) and medium plasmid copy numbers (A3-mCh), and producing mCherry protein, were studied by introducing oxygen limitation. Central metabolite pools were analyzed by three targeted LC–MS/MS methods, using the isotope dilution strategy for absolute quantification. Both recombinant strains exhibited different levels of metabolic burden, with the strain possessing a higher plasmid copy number showing more pronounced growth retardation and a stronger impact on metabolite pools. Both strains, however, showed a similar response to oxygen limitation, with significant adaptations in the central metabolite pools. The low plasmid copy number strain showed an increase in the concentration of lower glycolytic and tricarboxylic acid cycle metabolites, while the pools of upper glycolytic and pentose phosphate pathways and nucleoside phosphates were mostly unaffected. However, a more extreme response was seen in A3-mCh, where the majority of the metabolite pools were increased. Oxygen limitation caused lower metabolic activity, but the energy charge and redox balance were maintained, and no negative effect was observed on mCherry production rates. This study provides insights into metabolic adaptations in E. coli BL21 recombinant strains, having quite robust mechanisms to maintain intracellular metabolic homeostasis during both internal and external perturbations.

Anthropogenic nitrogen enrichment is widely expected to suppress symbiotic nitrogen fixation in terrestrial ecosystems. Nevertheless, observed symbiotic nitrogen fixation responses remain incompletely explained by exogenous nitrogen inputs, climate, and edaphic factors. In this meta-analysis, we integrate 908 globally distributed field measurements to identify the key predictors that improve simulation of symbiotic nitrogen fixation responses to nitrogen enrichment. On average, symbiotic nitrogen fixation declines by 33.0% upon nitrogen enrichment, with the reduction being more pronounced in non-croplands than croplands. Models considering only environmental factors overestimate symbiotic nitrogen fixation decline relative to observations. The better performance of plant traits like plant growth and biomass allocation (shoot:root ratio) partially buffer symbiotic nitrogen fixation suppression under nitrogen enrichment. Integrating both environmental factors and plant performance traits improves predictive accuracy of symbiotic nitrogen fixation responses by 42.7% and brings the simulated symbiotic nitrogen fixation reductions into close agreement with observations. The alterations in plant performance traits are thus critical for explaining variability in terrestrial symbiotic nitrogen fixation responses, and incorporating plant trait dynamics in Earth System Models can quantitatively partition the compensatory symbiotic nitrogen fixation supported by nitrogen-fixing plant growth from the direct negative impact of nitrogen inputs. Anthropogenic nitrogen enrichment reduces symbiotic nitrogen fixation, but environmental factors alone cannot explain this response. This meta-analysis shows that integrating both environmental factors and plant performance traits improves the predictive accuracy of symbiotic nitrogen fixation responses by 42.7%.

Antibiotic resistance is a growing global health threat. Although antibiotic activity is well studied in homogeneous liquid cultures, many infections are caused by spatially structured multicellular populations where consumption of scarce nutrients establishes strong spatial variations in their abundance. These nutrient variations have long been hypothesized to help bacterial populations tolerate antibiotics, since liquid culture studies link antibiotic tolerance to metabolic activity, and thus, local nutrient availability. Here, we test this hypothesis by visualizing cell death in structured E. coli populations exposed to select nutrients and antibiotics. We find that nutrient availability acts as a bottleneck to antibiotic killing, causing death to propagate through the population as a traveling front. By integrating our measurements with biophysical theory and simulations, we establish quantitative principles that explain how collective nutrient consumption can limit the progression of this “death front,” protecting a population from a nominally deadly antibiotic dose. While increasing nutrient supply can overcome this bottleneck, in some cases, excess nutrient unexpectedly promotes the regrowth of resistant cells. Altogether, this work provides a key step toward predicting and controlling antibiotic treatment of spatially structured bacterial populations, yielding biophysical insights into collective behavior and guiding strategies for effective antibiotic stewardship. In this work, authors provide evidence that bacteria in spatially structured populations protect each other from antibiotics through collective nutrient consumption, creating ‘death fronts’ that sweep through the colony– explaining why infections often survive treatments that work in lab tests.

With antimicrobial resistance emerging as a top global health concern, new approaches to prevent and treat infections are urgently needed. Antimicrobial peptides are recognized as a promising alternative to conventional antibiotics. Considering the costly, labor-intensive, and time-consuming nature of wet lab screening, in recent years, proteomics research has increasingly relied on in silico methods to predict physicochemical, structural, and biological properties of candidate peptides. Here, we present the AMPSeek protocol to enable scientists to screen peptides and predict their potential antimicrobial activity, toxicity, and associated three-dimensional structure with a single command. The AMPSeek framework integrates AMPlify, tAMPer, and LocalColabFold, scales efficiently with increasing sample size, and produces an interactive HyperText Markup Language report to facilitate result interpretation. We provide step-by-step instructions for installing and running AMPSeek on a ten-peptide test set, along with two additional datasets (n = 20 and n = 100; mean peptide length ≈121.3) to demonstrate AMPSeek's near-linear scalability.

Intestinal motility is a function of the enteric nervous system involving secretion of the excitatory neurotransmitter acetylcholine (ACh). Although gut commensal bacteria are key regulators of intestinal physiology, the molecular mechanisms underlying microbial influence on intestinal peristalsis and constipation remain unclear. Here we report a link between microbial nitrogen metabolism and intestinal motility regulation via ammonia production. We observed compensatory elevation of intestinal ammonia levels and urease activity in mouse models of intestinal dysmotility, induced by ACh deficiency, and in patients with constipation. Ammonia supplementation or intervention in mice with the urease-positive Lysinibacillus fusiformis isolated from patient stool, or engineered urease-expressing bacteria, effectively restored colonic ACh levels. In vitro, ammonia upregulated the expression of voltage-gated calcium channels on enteric neurons, driving Ca2+ influx to potentiate ACh secretion. Our study reveals a microbial compensatory mechanism that responds to fluctuating ACh levels in the intestine and provides microbial targets for intestinal motility disorders. Intestinal motility defects caused by lower acetylcholine levels in the gut are compensated by bacteria that generate ammonia from urea which facilitates the release of acetylcholine via upregulation of voltage-gated channels on enteric neurons.