Search Results (878)

Lactic acid bacteria (LAB) are central to food, feed, and health biotechnology, yet their genomes have long resisted rapid, precise manipulation. This review charts the evolution of LAB genome-editing strategies from labor-intensive RecA-dependent double-crossovers to state-of-the-art CRISPR and CRISPR-associated transposase systems. Native homologous recombination, transposon mutagenesis, and phage-derived recombineering opened the door to targeted gene disruption, but low efficiencies and marker footprints limited throughput. Recent phage RecT/RecE-mediated recombineering and CRISPR/Cas counter-selection now enable scar-less point edits, seamless deletions, and multi-kilobase insertions at efficiencies approaching model organisms. Endogenous Cas9 systems, dCas-based CRISPR interference, and CRISPR-guided transposases further extend the toolbox, allowing multiplex knockouts, precise single-base mutations, conditional knockdowns, and payloads up to 10 kb. The remaining hurdles include strain-specific barriers, reliance on selection markers for large edits, and the limited host-range of recombinases. Nevertheless, convergence of phage enzymes, CRISPR counter-selection and high-throughput oligo recombineering is rapidly transforming LAB into versatile chassis for cell-factory and therapeutic applications. Full article

Insects and their bacterial endosymbionts form intricate ecological relationships, yet their role in host–pathogen interactions are not fully elucidated. The small brown planthopper (Laodelphax striatellus), a polyphagous pest of cereal crops, acts as a key vector for rice stripe virus (RSV), a significant threat to rice production. This study aimed to compare the endosymbiont community structures of nonviruliferous and RSV-viruliferous L. striatellus populations using 16S rRNA gene sequencing with high-throughput sequencing technology. Wolbachia was highly dominant in both groups; however, the prevalence of other endosymbionts, specifically Rickettsia and Burkholderia, differed markedly depending on RSV infection. Comprehensive microbial diversity and composition analyses revealed distinct community structures between nonviruliferous and RSV-viruliferous populations, highlighting potential interactions and implications for vector competence and virus transmission dynamics. These findings contribute to understanding virus-insect-endosymbiont dynamics and could inform strategies to mitigate viral spread by targeting symbiotic bacteria. Full article

Dysbiosis is a strategy to control insect pests through disrupting symbiotic bacteria essential for their life cycle. The olive fly, Bactrocera oleae, has been considered a suitable system for dysbiosis, as the insect is strictly dependent on its unique symbiont Candidatus Erwinia dacicola. Here, we review older and recent results from studies of the interaction of the symbiont and its host fly. We then discuss possible methods for disrupting the symbiosis as a means to control the fly. Specifically, we summarize studies using microscopy methods that have investigated in great detail the organs where the bacterium resides and it is always extracellular. Furthermore, we discuss how genome sequences of both host and bacterium can provide valuable resources for understanding the interaction and transcriptomic analyses that have revealed important insights that can be exploited for dysbiosis strategies. We also assess experiments where compounds have been tested against the symbiont. The hitherto limited efficacy in decreasing bacterial abundance suggests that novel molecules and/or new ways for the delivery of agents will be important for successful dysbiosis strategies. Finally, we discuss how gene drive methods could be implemented in olive fly control, though a number of hurdles would need to be overcome. Full article

Porphyra-derived polysaccharides (PPs) are promising prebiotic candidates due to their capacity to modulate gut microbiota and promote host health. However, their interactions with and utilization by probiotic microorganisms remain unclear. In this study, the fermentability of PPs by murine-derived lactic acid bacteria (LAB) strains was investigated, with particular attention to strain-specific metabolic activity, carbohydrate utilization, and potential exopolysaccharide (EPS) production. All tested strains were capable of utilizing PPs to varying extents, with strain A10 exhibiting the highest level of carbohydrate consumption. Notably, strain A5 showed increased mannose concentrations following fermentation, suggesting the biosynthesis of mannose-rich EPSs. HPLC analysis confirmed the presence of high-molecular-weight polysaccharides ranging from 2.6 to 8.1 × 10⁵ Da, indicative of EPS production. FT-IR spectroscopy further revealed spectral features consistent with EPS structures. The antibacterial activity of postbiotic compounds produced by LAB strains fermenting PPs against Escherichia coli and Staphylococcus aureus was observed. These findings demonstrate distinct metabolic adaptations of LAB strains to PPs and emphasize their potential as prebiotic substrates. Full article

Sourdough fermentation, driven by the biochemical activity of lactic acid bacteria (LAB), presents a scientifically promising approach to addressing nutritional limitations in cereal-based staples. This review critically examines both the underlying mechanisms by which LAB enhance the nutritional profile of sourdough and the translational challenges in realizing these benefits. Key improvements explored include enhanced mineral bioavailability (e.g., up to 90% phytate reduction), improved protein digestibility, an attenuated glycemic response (GI ≈ 54 vs. ≈75 for conventional bread), and the generation of bioactive compounds. While in vitro and animal studies extensively demonstrate LAB’s potential to reshape nutrient profiles (e.g., phytate hydrolysis improving iron absorption, proteolysis releasing bioactive peptides), translating these effects into consistent human health outcomes proves complex. Significant challenges hinder this transition from laboratory to diet, including the limited bioavailability of LAB-derived metabolites, high strain variability, and sensitivity to fermentation conditions. Furthermore, interactions with the food matrix and host-specific factors, such as gut microbiota composition, contribute to inconsistent findings. This review highlights methodological gaps, particularly reliance on in vitro or animal models, and the lack of long-term, effective human trials. Although LAB hold significant promise for nutritional improvements in sourdough, translating these findings to validated human benefits necessitates continued efforts in mechanism-driven strain optimization, the standardization of fermentation processes, and rigorous human studies. Full article

Snails at hydrothermal vents rely on symbiotic bacteria for nutrition; however, the specifics of these associations in adapting to such extreme environments remain underexplored. This study investigated the community structure and metabolic potential of bacteria associated with two Indian Ocean vent snails, Chrysomallon squamiferum and Gigantopelta aegis. Using microscopic, phylogenetic, and metagenomic analyses, this study examines bacterial communities inhabiting the foot and gland tissues of these snails. G. aegis exhibited exceptionally low bacterial diversity (Shannon index 0.14–0.18), primarily Gammaproteobacteria (99.9%), including chemosynthetic sulfur-oxidizing Chromatiales using Calvin–Benson–Bassham cycle and methane-oxidizing Methylococcales in the glands. C. squamiferum hosted significantly more diverse symbionts (Shannon indices 1.32–4.60). Its black variety scales were dominated by Campylobacterota (67.01–80.98%), such as Sulfurovum, which perform sulfur/hydrogen oxidation via the reductive tricarboxylic acid cycle, with both Campylobacterota and Gammaproteobacteria prevalent in the glands. The white-scaled variety of C. squamiferum had less Campylobacterota but a higher diversity of heterotrophic bacteria, including Delta-/Alpha-Proteobacteria, Bacteroidetes, and Firmicutes (classified as Desulfobacterota, Pseudomomonadota, Bacteroidota, and Bacillota in GTDB taxonomy). In C. squamiferum, Gammaproteobacteria, including Chromatiales, Thiotrichales, and a novel order “Endothiobacterales,” were chemosynthetic, capable of oxidizing sulfur, hydrogen, or iron, and utilizing the Calvin–Benson–Bassham cycle for carbon fixation. Heterotrophic Delta- and Alpha-Proteobacteria, Bacteroidetes, and Firmicutes potentially utilize organic matter from protein, starch, collagen, amino acids, thereby contributing to the holobiont community and host nutrition accessibility. The results indicate that host species and intra-species variation, rather than the immediate habitat, might shape the symbiotic microbial communities, crucial for the snails’ adaptation to vent ecosystems. Full article

The rise in antibiotic-resistant bacteria has made the management of bacterial diseases increasingly challenging. As a result, bacteriophages have gained attention as a promising alternative to antibiotics for combating bacterial pathogens. However, the usage of phages as biocontrol agents faces many challenges, including environmental stability, delivery efficiency, host specificity, and potential bacterial resistance. Advancements in genetic engineering and nanotechnology have been explored to enhance the stability, efficacy, and adaptability of phage-based treatments. In this review, we discuss the key barriers to the effective implementation of phage therapy and highlight innovative strategies to overcome these challenges. By addressing these limitations, this review aims to provide insights into optimizing phage-based approaches for widespread therapeutic and biocontrol applications. Full article

In this study, the impact of the genomic scaffold on the properties of bacteriophages was investigated by swapping the genomic scaffolds surrounding the tailspike genes between two Przondovirus phages, KP192 and KP195, which infect Klebsiella pneumoniae with different capsular types. A yeast-based transformation-associated recombination cloning technique and subsequent “rebooting” of synthetic phage genomes in bacteria were used to construct the phages. Using Klebsiella strains with K2, K64, and KL111 capsular types, it was shown that the capsular specificity of the synthetic phages is fully consistent with that of the tailspike proteins (tsp). However, the efficiency of plating and the lytic efficiency of these phages strongly depended on the genomic scaffold used and the Klebsiella strain used. Synthetic phages with swapped genomic scaffolds demonstrated superior reproduction efficiency using a number of strains compared to wild-type phages, indicating that some elements of the swapped genomic scaffold enhance phage replication efficiency, presumably by blocking some of the host anti-phage defense systems. Our findings demonstrate that even in the case of closely related phages, the selection of the genomic scaffold used for tsp gene transplantation can have a profound impact on the efficiency of phage propagation on target bacterial strains. Full article

Microbial infections are an escalating global health threat, driven by the alarming rise of antimicrobial resistance (AMR), which has made many conventional antibiotics increasingly ineffective and threatens to reverse decades of medical progress. The rapid emergence and spread of multidrug-resistant bacteria have severely limited treatment options, resulting in increased morbidity, mortality, and healthcare burden worldwide. In response to these challenges, phage therapy is regaining interest as a promising alternative. Bacteriophages, the most abundant biological entities, have remarkable specificity toward their bacterial hosts, enabling them to selectively eliminate pathogenic strains. Phage therapy presents several advantages over conventional antibiotics, which include minimal disruption to the microbiome and a slower rate of resistance development. Among the various sources of phages, the marine environment remains one of the least explored. Given their adaptation to saline conditions, high pressure, and variable nutrient levels, marine bacteriophages mostly exhibit enhanced environmental stability, broader host ranges, and distinct infection mechanisms, thus making them highly promising for therapeutic purposes. This review explores the growing therapeutic potential of marine bacteriophages by examining their ecological diversity, biological characteristics, infection dynamics, and practical applications in microbial disease control. It also deals with emerging strategies such as phage–antibiotic synergy, genetic engineering, and the use of phage-derived enzymes, alongside several challenges that must be addressed to enable clinical translation and regulatory approval. Advancing our understanding and application of marine phages presents a promising path in the global fight against AMR and the development of next-generation antimicrobial therapies. Full article

Phytoplasmas are wall-less, phloem-restricted bacteria responsible for numerous significant plant diseases worldwide. An increasing body of evidence indicates that phytoplasmas can coexist with other pathogens in mixed infections, including various 16Sr group phytoplasmas, ‘Candidatus Liberibacter’ species, viruses, spiroplasmas, fungi, and other difficult-to-culture phloem-limited bacteria. These interactions challenge established views regarding the causes, detection, and management of plant diseases. This review consolidates existing knowledge on the diversity and epidemiology of phytoplasma-related mixed infections, with a particular emphasis on documented co-infections across various host plants and regions, especially in tropical and subtropical areas. Mixed infections affect disease severity, symptom expression, vector behavior, and pathogen dissemination, highlighting the limitations of pathogen-specific diagnostic and control strategies. The necessity for tools to detect multiple pathogens, enhanced understanding of pathogen–pathogen and host–pathogen interactions, and comprehensive surveillance systems is emphasized. Ultimately, breeding for resistance must consider the complexities of natural co-infections to ensure effective protection of crops. Addressing the challenges presented by phytoplasma-related mixed infections is crucial for developing resilient and sustainable plant health strategies in the face of increasing ecological and agricultural pressures. Full article

The growing interest in health-promoting diets has brought fermented foods into the spotlight due to their unique microbial compositions and bioactive metabolites. Fermented foods and their beneficial microbiota are expected to stimulate the overall industry’s expansion over the next few years as their beneficial health effects become established. This narrative review explores the evolving dynamics of fermented food microbiota and their interactions with the gut microenvironment, emphasizing strategic pathways to enhance human health. Fermented foods, both industrially produced and traditionally prepared, serve as carriers of beneficial microorganisms such as lactic acid bacteria, yeasts, and certain fungi that transform food substrates into bioactive compounds including short-chain fatty acids (SCFAs), exopolysaccharides, and bioactive peptides. Simultaneously, their bioactive metabolites are the subject of passionate investigation by the scientific community, uncovering novel beneficial aspects that have not been elucidated until now. These metabolites contribute to improved gut barrier function, modulation of immune responses, and overall metabolic health. Notably, microbial fermentation can reshape the intrinsic properties of food, offering therapeutic potential beyond basic nutrition. The interactions between food-derived microbes and the host gut microbiota suggest a synergistic mechanism influencing gastrointestinal and systemic health outcomes. Nevertheless, there remains a significant gap in the comprehensive evaluation of the existing literature in this specific research area. Further research is needed to standardize fermented food formulations, validate the effects of individual microbial strains, and optimize their application in personalized nutrition and functional food development. Accordingly, this review highlights the association between the microbiota of fermented foods and their metabolites with the gut microenvironment, emphasizing their potential health-promoting properties. Full article

The domestication process not only reduced the allelic diversity of tomato genotypes but also affected the genetic traits associated to microbial recruitment, their composition, and their diversity in different compartments of the plant host. Additionally, this process included the transition from natural to agricultural soils, which differ in nutrient availability, physicochemical properties, and agricultural practices. Therefore, modern cultivars may fail to recruit microbial taxa beneficial to their wild relatives, potentially losing important ecological functions. In this study, we analyzed the phylogenetic relationship and the rhizosphere microbiota of four tomato genotypes, Solanum chilense (wild species), S. lycopersicum var. cerasiforme (Cherry tomato), and the S. lycopersicum landrace ‘Poncho Negro’ and the modern cultivar ‘Cal Ace’, grown in both natural and agricultural soils. Microbial communities were identified using 16S rRNA (bacteria) and ITS2 (fungi) amplicon sequencing, allowing cross-domain taxonomic characterization. While the soil type was the main driver of overall microbial diversity, the host genotype influenced the recruitment of specific microbial taxa, which exhibited different recruitment patterns according to the genetic diversification of Solanum genotypes and soil types. Additionally, co-occurrence network analysis identified two main clusters: first, taxa did not show any preferential associations to particular genotypes or soil types, while the second cluster revealed specific microbial patterns associated to fungal taxa in natural soil and bacterial taxa in agricultural soil. Finally, the functional analysis suggested the loss of specific functions through tomato domestication independently of soil type. These findings highlight the role of the plant genotype as a fine-tuning factor in microbiome assembly, with implications for breeding strategies aimed at restoring beneficial plant–microbe interactions. Full article

Anti-infectives include molecules that target microbes in the context of infection but lack antimicrobial activity under conventional growth conditions. We previously described D66, a small molecule that kills the Gram-negative pathogen Salmonella enterica serovar Typhimurium (S. Typhimurium) within cultured macrophages and murine tissues, with low host toxicity. While D66 fails to inhibit bacterial growth in standard media, the compound is bacteriostatic and disrupts the cell membrane voltage gradient without lysis under growth conditions that permeabilize the outer membrane or reduce efflux pump activity. To gain insights into specific bacterial targets of D66, we pursued two genetic approaches. Selection for resistance to D66 revealed spontaneous point mutations that mapped within the gmhB gene, which encodes a protein involved in the biosynthesis of the lipopolysaccharide core molecule. E. coli and S. Typhimurium gmhB mutants exhibited increased resistance to antibiotics, indicating a more robust barrier to entry. Conversely, S. Typhimurium transposon insertions in genes involved in outer membrane permeability or efflux pump activity reduced fitness in the presence of D66. Together, these observations underscore the significance of the bacterial cell envelope in safeguarding Gram-negative bacteria from small molecules. Full article

The rising prevalence of antibiotic-resistant bacteria demands exploration of alternative antimicrobials. Antimicrobial peptides (AMPs) are a promising group of compounds naturally produced by microorganisms and could serve as potent agents against resistant pathogens. In this study, we evaluated the antimicrobial potential of the cell-free supernatant obtained from Pedobacter silvilitoris—a bacterium originally isolated from decomposing wood—and performed comprehensive genomic screening to uncover novel AMP-encoding genes. The supernatant showed strong inhibitory effects against a diverse selection of pathogens. Scanning electron microscopy (SEM) revealed extensive membrane damage, including pore formation in target bacterial cells, suggesting AMP-mediated activity. A genomic analysis identified 11 candidate AMP genes, named PS_AMP1 to PS_AMP11, based on the significant sequence similarity with known AMPs. Transcriptomic profiling further indicated that several candidates are expressed differentially between the logarithmic and stationary growth phases. Functional assays via gene cloning and peptide synthesis confirmed antimicrobial activity against both Gram-stain-negative and Gram-stain-positive bacteria, with PS_AMP11 emerging as the most effective candidate. Our findings demonstrate that AMPs derived from P. silvilitoris hold substantial promise as alternative antimicrobial agents. Nonetheless, additional structural optimizations may be necessary to fine-tune specificity and to reduce potential host toxicity before clinical deployment. Full article

Protein kinases and phosphatases are essential for post-translational regulation, enabling bacteria to adapt to environmental stresses and modulate virulence. While prior reviews have broadly covered their roles in stress response, antibiotic resistance, and virulence, this article updates specifically on the roles of histidine kinases (HKs) and serine/threonine kinases (STKs) in mediating phage-bacteria interactions. A key aspect is phage-encoded kinases, which hijack bacterial signalling by phosphorylating and disrupting host processes to promote infection. Despite their importance, significant gaps remain in understanding these regulatory networks. This microreview highlights both the unresolved mechanisms and the therapeutic potential of targeting kinase pathways—for instance, by disrupting phage evasion strategies or enhancing phage-based antimicrobial therapies. Full article