Devendra Pratap Singh, Gayathri A S, Ramandeep Singh, Narendra M Dixit, Deepak Kumar Saini
{"title":"Multiple input-multiple output (MIMO) designs in two-component signalling systems of Mycobacterium tuberculosis.","authors":"Devendra Pratap Singh, Gayathri A S, Ramandeep Singh, Narendra M Dixit, Deepak Kumar Saini","doi":"10.1093/femsre/fuaf064","DOIUrl":"10.1093/femsre/fuaf064","url":null,"abstract":"<p><p>Two-component systems (TCSs), the primary communication pathways in bacteria, are comprised of two proteins: a signal-sensing histidine kinase (HK) and an output-generating response regulator (RR). Classically, individual TCSs have been viewed as simple input-output systems, in which signal propagate via phosphorylation from the HK to the cognate RR, the latter triggering downstream functions. Emerging evidence suggests that TCSs can also operate through intricate networks, collectively sensing multiple inputs and generating fine-tuned, concerted, diversified, and complex outputs, modulated by several factors such as TCS-dependent cross-talk, additional layers of posttranslational modifications, external protein-based signalling input or adaptor molecules, and small RNAs. In this review, using evidence from mycobacterial TCSs, we discuss how TCSs can function as multiple input-multiple output (MIMO) hubs, thereby serving as signal integration and dispersion units to generate complex adaptive responses tuned by many modulating factors. We also discuss how the MIMO landscape of TCSs drives bacterial adaptation and presents potential strategies for therapeutic intervention.</p>","PeriodicalId":12201,"journal":{"name":"FEMS microbiology reviews","volume":" ","pages":""},"PeriodicalIF":16.9,"publicationDate":"2026-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12757749/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145741779","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Harita Yedavally, Jan Maarten van Dijl, Anna Salvati
{"title":"Nanomedicine applications for the treatment of Staphylococcus aureus infections.","authors":"Harita Yedavally, Jan Maarten van Dijl, Anna Salvati","doi":"10.1093/femsre/fuaf068","DOIUrl":"10.1093/femsre/fuaf068","url":null,"abstract":"<p><p>Staphylococcus aureus is a Gram-positive bacterium capable of infecting multiple types of cells, organs, and tissues in the human body. Treatment can become highly challenging, especially in the case of intracellular infections and upon biofilm formation. Additionally, this pathogen has developed several antimicrobial resistance mechanisms, and resistant strains such as methicillin-resistant S. aureus (MRSA) are among the most difficult to treat. Within this context, nanomedicine can offer novel and more efficient treatments against S. aureus. Here, we first introduce the challenges in the treatment of S. aureus infections, focusing on intracellular infections and biofilms, and challenges associated with the development of resistance. We then provide an overview of the multiple applications of nanomedicine against S. aureus infection and discuss how nanomedicine may overcome the challenges in reaching this pathogen and eliminating it, including potential solutions less prone to generating resistance. Finally, we discuss the current clinical development of antimicrobial nanomedicines, where only one out of 35 completed trials has so far targeted MRSA, indicating that most research is still at the preclinical stage. Challenges in the clinical translation of antimicrobial nanomedicines are discussed, together with strategies to support the development of these promising therapeutic agents.</p>","PeriodicalId":12201,"journal":{"name":"FEMS microbiology reviews","volume":" ","pages":""},"PeriodicalIF":16.9,"publicationDate":"2026-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12802889/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145899733","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Veronika Kuchařová Pettersen, Alise Jany Ponsero, Ching Jian, Alona Riumin, Alexander Kurilshikov, Sabrina John Moyo, Museveni Justine, Claus Klingenberg, Justine Debelius, Mireia Valles-Colomer, Hanna Theodora Noordzij, Alexandra Zhernakova, Katri Korpela, Maria Esteban-Torres, Nele Brusselaers
{"title":"Off to a good start: current gaps and priorities in early-life microbiome research.","authors":"Veronika Kuchařová Pettersen, Alise Jany Ponsero, Ching Jian, Alona Riumin, Alexander Kurilshikov, Sabrina John Moyo, Museveni Justine, Claus Klingenberg, Justine Debelius, Mireia Valles-Colomer, Hanna Theodora Noordzij, Alexandra Zhernakova, Katri Korpela, Maria Esteban-Torres, Nele Brusselaers","doi":"10.1093/femsre/fuag010","DOIUrl":"10.1093/femsre/fuag010","url":null,"abstract":"<p><p>Early-life microbial exposures are essential for optimal development of human physiology. Yet, understanding of the human microbiome during pregnancy and childhood is still far from being complete. To identify knowledge gaps and establish research priorities, a multidisciplinary expert panel used the Delphi method for consensus development and conducted a literature search on early-life microbiome determinants. Responses from 55 researchers from an online survey were analyzed alongside keyword frequency from 20 501 publications. This approach enabled us to categorize existing evidence and highlight areas requiring investigation. While the main routes for mother-to-child bacterial transmission and their contributions to the newborn microbiome have been studied, many gaps remain. Priority areas include non-bacterial microbes, ecological principles of colonization, environmental and social influences, body sites beyond the gut, and factors affecting the maternal microbiome and its effects on the child's microbiome. Significance of factors such as hygiene habits, non-antibiotic medications, and pollution remains to be uncovered. Knowledge is also limited on postnatal microbial sharing via household contacts and shared environments (e.g. family members, peers) and the contribution of these pathways to microbiome assembly. We hope this report will guide and inspire future research into the early-life microbiome as a modifiable factor in reducing disease risk.</p>","PeriodicalId":12201,"journal":{"name":"FEMS microbiology reviews","volume":" ","pages":""},"PeriodicalIF":16.9,"publicationDate":"2026-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13044577/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147389453","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Xueping Li, Di Huang, Ziwei Chen, Luna Cui, Sheng Wang, Tao Wang, Bin Liu, Yutao Liu
{"title":"Pathogenesis and therapeutic strategies in the interaction between gut microbiota and enterohemorrhagic Escherichia coli infection.","authors":"Xueping Li, Di Huang, Ziwei Chen, Luna Cui, Sheng Wang, Tao Wang, Bin Liu, Yutao Liu","doi":"10.1093/femsre/fuag045","DOIUrl":"10.1093/femsre/fuag045","url":null,"abstract":"<p><p>Enterohemorrhagic Escherichia coli (EHEC) is a major foodborne pathogen that causes hemorrhagic colitis and hemolytic uremic syndrome. Increasing evidence indicates that the gut microbiota plays a central role in modulating EHEC pathogenesis through complex metabolic and signaling networks. Beneficial commensals, including Bifidobacterium, Lactobacillus, and segmented filamentous bacteria, contribute to colonization resistance by competing for nutrients and adhesion sites, producing antimicrobial metabolites, and enhancing epithelial barrier integrity. In contrast, certain species such as Bacteroides thetaiotaomicron and Enterococcus faecalis may promote EHEC virulence by altering intestinal nutrient availability or triggering the expression of virulence genes. Microbiota-derived metabolites, including short-chain fatty acids, succinate, indole, riboflavin, nicotinamide, ethanolamine, and L-malate, act as important regulatory signals that connect microbial metabolism with LEE-mediated virulence pathways. Understanding these host-microbe-pathogen interactions provides a mechanistic basis for developing microbiota-targeted interventions such as probiotics, prebiotics, and fecal microbiota transplantation that enhance colonization resistance and attenuate virulence. Integration of AI-based analytics with multi-omics approaches is expected to facilitate the design of personalized, mechanism-driven therapeutic strategies for the control of EHEC infection.</p>","PeriodicalId":12201,"journal":{"name":"FEMS microbiology reviews","volume":" ","pages":""},"PeriodicalIF":16.9,"publicationDate":"2026-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13556468/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148864422","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Mohammad Abdullah Jehad, Lizna M Ali, Vineeta N Pillai, Suresha G Prabhu, Farah Mustafa, Tahir A Rizvi
{"title":"Beyond reverse transcription: molecular mechanisms and emerging paradigms in retroviral replication.","authors":"Mohammad Abdullah Jehad, Lizna M Ali, Vineeta N Pillai, Suresha G Prabhu, Farah Mustafa, Tahir A Rizvi","doi":"10.1093/femsre/fuaf066","DOIUrl":"10.1093/femsre/fuaf066","url":null,"abstract":"<p><p>Retroviruses are exclusive group of positive-sense RNA viruses defined by their ability to reverse transcribe their RNA genome and integrate it into the host's chromosomal DNA. This distinctive replication strategy enables persistent infection and has profoundly shaped our understanding of molecular biology, gene regulation, and evolution. Retroviruses have contributed to landmark discoveries, including the identification of oncogenes, mechanisms of transcriptional control, and the development of gene therapy vectors. This review provides an updated overview of retroviral molecular biology, emphasizing the coordinated steps of the viral life cycle and emerging insights that are reshaping classical models. It explores virion structure, genome organization, and the interplay of cis-acting sequences and trans-acting factors that govern replication. Special focus is given to recent advances in understanding nuclear trafficking of capsids, spatial dynamics of reverse transcription and integration leading to provirus formation, RNA nuclear export, and selective genome packaging. The structural and functional roles of viral proteins, particularly Gag, are discussed in the context of assembly and maturation. By integrating foundational concepts with new discoveries, this review highlights the molecular sophistication of retroviral replication and identifies outstanding questions that guide future research, with implications extending to antiviral strategies, gene therapy, cancer biology, and evolution.</p>","PeriodicalId":12201,"journal":{"name":"FEMS microbiology reviews","volume":" ","pages":""},"PeriodicalIF":12.3,"publicationDate":"2026-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12789967/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145843455","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Miguel Fernandez de Ullivarri, Colin O'Sullivan, R Paul Ross, Colin Hill
{"title":"Killer Peptide: an antibody-derived self-assembling peptide bridging antimicrobial and host-defense mechanisms.","authors":"Miguel Fernandez de Ullivarri, Colin O'Sullivan, R Paul Ross, Colin Hill","doi":"10.1093/femsre/fuag026","DOIUrl":"10.1093/femsre/fuag026","url":null,"abstract":"<p><p>Antimicrobial resistance and persistent biofilm-associated infections continue to drive the search for peptide-based anti-infective agents with mechanisms distinct from conventional antibiotics. Killer Peptide (KP) is an antibody-derived decapeptide originally identified through yeast killer toxin mimicry studies and has emerged as a distinctive example of a multifunctional bioactive peptide. Experimental studies have reported particularly strong antifungal activity, together with activity against selected bacteria, biofilms, viruses, and protozoa, as well as immunomodulatory effects in preclinical models. Mechanistically, KP appears to act through a multistep process involving target-surface recognition, cellular internalization, induction of intracellular stress pathways, and reversible self-assembly into fibrillar structures that may support localized peptide retention. In parallel, KP has been reported to influence innate and adaptive immune responses, suggesting potential host-defense-enhancing properties. In this review, we critically reassess two decades of KP research, covering its molecular origin, structural features, antimicrobial spectrum, mechanisms of action, engineered derivatives, and translational prospects. We also examine current limitations, including the relatively narrow evidence base, incomplete pharmacological characterization, and the need for independent validation across disease models. KP represents a useful conceptual framework for the development of next-generation multifunctional peptides integrating antimicrobial, pathogen-triggered assembly, and immunomodulatory properties.</p>","PeriodicalId":12201,"journal":{"name":"FEMS microbiology reviews","volume":" ","pages":""},"PeriodicalIF":16.9,"publicationDate":"2026-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13285874/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148276720","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Rubén Torres, Begoña Carrasco, Silvia Ayora, Juan C Alonso
{"title":"Mechanisms of chromosomal DNA replication in Escherichia coli and Bacillus subtilis.","authors":"Rubén Torres, Begoña Carrasco, Silvia Ayora, Juan C Alonso","doi":"10.1093/femsre/fuag021","DOIUrl":"10.1093/femsre/fuag021","url":null,"abstract":"<p><p>Faithful DNA replication, which is a highly orchestrated process, is essential in all living organisms to ensure accurate transmission of genetic information to their descendants. In this review, we summarize the molecular mechanisms and dynamics of DNA replication in Escherichia coli and compare them with those of the phylogenetically distant Bacillus subtilis. Although the central features of replication initiation, elongation, termination, and restart are broadly conserved, distinct mechanisms have evolved to adapt each bacterium to its complex environment. This review highlights the players and outlines both the shared and divergent molecular mechanisms governing how the multi-component replication machines, the replisomes, are assembled at the origin of chromosomal replication, oriC, on a circular genome, undergo bidirectional replication elongation, and are ultimately disassembled upon reaching the terminus of replication, ter, region. In response to stress, (a) replication restart mechanism(s) operating at sites other than oriC re-assemble the replisome, allowing unidirectional DNA synthesis to resume, thereby ensuring completion of the cell cycle and maintenance of cell viability.</p>","PeriodicalId":12201,"journal":{"name":"FEMS microbiology reviews","volume":" ","pages":""},"PeriodicalIF":16.9,"publicationDate":"2026-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13220808/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147940798","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Bacterial quorum-sensing systems in cell-cell communication.","authors":"Kai-Zhong Xu, Annadurai Vinothkanna, DanDan Wang, Hongyan Jiang, Zhenbo Xu, Ai-Qun Jia","doi":"10.1093/femsre/fuag020","DOIUrl":"10.1093/femsre/fuag020","url":null,"abstract":"<p><p>Antimicrobial resistance (AMR) and the emergence of multidrug-resistant pathogens necessitate holistic care. Novel antimicrobial drug discovery involves an in-depth assessment of quorum sensing (QS) signaling and cell-cell communication. Bacteria regulate their metabolism to cope with complex host-environmental changes through QS signaling. Previous studies suggest that the social behaviors of bacteria include biofilm formation, virulence, and drug resistance mediated by QS. Over several decades, autoinducer receptors, signaling pathways, and the regulatory networks that control gene expression have corroborated QS signaling molecules. Multiple QS systems and chemical structural diversity signaling molecules have been sporadically reported, but there is no comprehensive review of these findings. This review systematically and comprehensively summarizes the paper, addressing bacterial QS-based cell-cell communication and the potential mechanisms of QS systems in bacterial drug resistance. Furthermore, a status quo update has been established for novel QS systems in the realms of pathogenicity, polymicrobial interactions, and/or AMR patterns. Nevertheless, the applications of QS systems would invoke newer incorporations for futuristic research values. Thus, the complexity and evolutionary insights of QS systems, quorum-sensing signaling molecules, and regulatory mechanisms need a \"cloud\" based repurposing for the design of novel agents in AMR and communication.</p>","PeriodicalId":12201,"journal":{"name":"FEMS microbiology reviews","volume":" ","pages":""},"PeriodicalIF":16.9,"publicationDate":"2026-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13220807/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147873974","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Andriana Grafakou, Cas Mosterd, Simon A Jackson, Paul P de Waal, Noël N M E van Peij, Christian Cambillau, Jennifer Mahony, Douwe van Sinderen
{"title":"Revisiting lactococcal abortive infection-like antiphage systems: diversity, structures, and mechanisms.","authors":"Andriana Grafakou, Cas Mosterd, Simon A Jackson, Paul P de Waal, Noël N M E van Peij, Christian Cambillau, Jennifer Mahony, Douwe van Sinderen","doi":"10.1093/femsre/fuag009","DOIUrl":"10.1093/femsre/fuag009","url":null,"abstract":"<p><p>Lactococcus lactis and Lactococcus cremoris are cornerstone bacterial species employed in the production of fermented dairy products such as cheese. However, the non-sterile dairy processing environment regularly exposes these lactococci to phage infection. To counteract this phage threat, bacteria have evolved a wide range of defence mechanisms, including so-called abortive infection Abi(-like) systems, of which many (AbiA to AbiZ) were originally discovered in Lactococcus. Recent discoveries have expanded the list of Abi-like systems in Lactococcus species. In this review, we focus on systems historically, phenotypically, or mechanistically classified as Abi, critically examine and revisit their antiphage activity spectrum and interference with the phage lytic cycle, as well as mechanistic insights of lactococcal Abi-like systems as obtained through the study of phage escape mutants. Furthermore, we group various Abi-like systems based on structural superimposition and use predicted domain information to explore or expand on their mechanism of action. Finally, we show that despite many Abi-like systems being discovered due to their presence on plasmids, most anti-phage defence systems appear to be chromosomally encoded in sequenced Lactococcus strains. Our findings support the notion that co-evolution of Lactococcus species with their phages, possibly accelerated by the extensive application of these bacteria in dairy fermentations, has resulted in the acquisition of a diverse array of phage defence mechanisms, including Abi-like systems.</p>","PeriodicalId":12201,"journal":{"name":"FEMS microbiology reviews","volume":" ","pages":""},"PeriodicalIF":16.9,"publicationDate":"2026-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13064643/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147354329","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Giovanni Schiesaro, Antonio Di Pietro, Emil Damgaard Jensen
{"title":"The role of fungal G protein-coupled receptors in interspecies cell-cell communication.","authors":"Giovanni Schiesaro, Antonio Di Pietro, Emil Damgaard Jensen","doi":"10.1093/femsre/fuag024","DOIUrl":"10.1093/femsre/fuag024","url":null,"abstract":"<p><p>Fungi occupy a wide range of ecological niches in which they compete or associate with other organisms through the perception of external signals and appropriate cellular responses. Fungal G protein-coupled receptors (GPCRs) are seven-transmembrane domain proteins that mediate the perception of extracellular cues. Despite their critical importance, the majority of fungal GPCRs are currently orphan receptors with unknown ligands and functions. In this review, we summarize the current knowledge on the role of fungal GPCRs in the perception of non-self signals and address persistent inconsistencies in the literature regarding fungal GPCR classification. We propose a refined system that differentiates between characterized, proposed, and uncharacterized GPCRs. Finally, we discuss how synthetic biology tools and experimental work in the native fungal organisms can elucidate the physiological role of fungal GPCRs during interspecies cell-cell communication.</p>","PeriodicalId":12201,"journal":{"name":"FEMS microbiology reviews","volume":" ","pages":""},"PeriodicalIF":16.9,"publicationDate":"2026-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13308352/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147981247","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}