mSphere最新文献

{"title":"Characterization of the ligand binding pocket of the virulence regulator Rns, a member of the AraC/XylS family of transcription factors.","authors":"Jessica D Tolbert, Kacey M Talbot, Christopher M Bollinger, F Jon Kull, George P Munson, Charles R Midgett","doi":"10.1128/msphere.00115-25","DOIUrl":"10.1128/msphere.00115-25","url":null,"abstract":"<p><p>Diarrheal disease caused by Gram-negative enteric pathogens, such as enterotoxigenic <i>Escherichia coli</i> (ETEC), <i>Vibrio cholerae</i>, <i>Shigella</i> spp., and <i>Salmonella</i> spp., is a leading cause of morbidity and mortality of children, especially in low resource nations. While progress has been made in reducing this burden, there remains a need to develop effective therapies. Recently, we determined the structure of Rns, a member of the AraC/XylS family that regulates the expression of pili and other virulence factors in ETEC. The structure revealed decanoic acid bound between the N- and C-terminal domains. To test the hypothesis that bound decanoic acid directly inhibits Rns, we identified amino acid side chains predicted to be necessary for ligand binding. Removal of the positive side chains of R75 and H20 rendered Rns insensitive to fatty acid inhibition. Additionally, mutations designed to block decanoic acid binding also produced a variant Rns that was fatty acid insensitive. We also observed that this variant is structurally more flexible than wildtype Rns bound to decanoic acid, suggesting that fatty acid binding contributes to structural rigidity. These studies demonstrate that Rns binding pocket residues are critical for binding fatty acids, which result in inhibition of DNA binding and support our hypothesis that fatty acids must bind in the binding pocket to inhibit other AraC regulators. Further work by us and others suggests that inhibition of AraC virulence regulators by fatty acids is a common paradigm among many bacterial pathogens. Therefore, understanding the molecular basis of inhibition lays the groundwork for the development of small molecule therapeutics targeting enteric disease.</p><p><strong>Importance: </strong>As antimicrobial resistance increases, it is critical to develop new strategies to combat these infections. One area of concern is bacteria that cause intestinal disease such as <i>Salmonella</i> species, <i>Vibrio cholerae</i>, <i>Shigella</i> species, and enterotoxigenic <i>Escherichia coli</i> (ETEC). ETEC is a leading cause of travelers' diarrheal disease and a leading cause of mortality for children under 5 years old. To cause disease, ETEC requires the gene regulator Rns. Our previous work found that Rns was inhibited by a fatty acid. Here, we identify key features in the protein that are required for not only binding fatty acids but also for responding to them. This was done through a combination of microbiological as well as structural techniques of altered Rns proteins that can no longer bind fatty acid. Understanding how Rns is inhibited will lead to new ideas about how to target this class of proteins without causing antimicrobial resistance.</p>","PeriodicalId":19052,"journal":{"name":"mSphere","volume":" ","pages":"e0011525"},"PeriodicalIF":3.1,"publicationDate":"2025-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12379584/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144699108","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":"Challenges and innovations in resistance, remediation, and regulation: key findings from the spring 2025 ASM Theobald Smith Society meeting.","authors":"Lily Lumkong, Brian Nyiro, Sammi Russo, Isabella Westervelt, Raymond F Sullivan, Jeffrey M Boyd, Valerie J Carabetta, Srujana S Yadavalli, Jennifer S Sun","doi":"10.1128/msphere.00374-25","DOIUrl":"10.1128/msphere.00374-25","url":null,"abstract":"<p><p>The annual spring meeting for the Theobald Smith Society was held in May 2025 on the campus of Rutgers University-New Brunswick, as part of a 2-day celebration of microbiology discovery in New Jersey. A total of 140 branch members from across New Jersey attended the meeting, composed of undergraduate, graduate, and postdoctoral trainees, faculty members, and government and industry professionals. This report highlights the breadth and diversity of research conducted by members of the American Society for Microbiology in the Theobald Smith Society and celebrates their groundbreaking discoveries.</p>","PeriodicalId":19052,"journal":{"name":"mSphere","volume":" ","pages":"e0037425"},"PeriodicalIF":3.1,"publicationDate":"2025-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12379591/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144775865","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":"The impact of tropodithietic acid on microbial physiology under varying culture complexities.","authors":"Olesia Shlakhter, Sergey Malitsky, Einat Segev","doi":"10.1128/msphere.00138-25","DOIUrl":"10.1128/msphere.00138-25","url":null,"abstract":"<p><p>Understanding marine bacterial physiology under environmentally relevant conditions requires the study of biotic interactions across systems of varying complexities. Here, we examine how the capability of <i>Phaeobacter inhibens</i> bacteria to produce tropodithietic acid (TDA), a secondary metabolite, influences microbial physiology and interactions. Our systematic approach, which includes progressing from bacterial monocultures to co-cultures and tri-cultures involving algal hosts, allows us to evaluate the impact of the <i>tdaB</i> gene and the TDA metabolite on microbial interactions. Our findings show that deleting the <i>tdaB</i> gene resulted in no detectable TDA production and affected bacteria-bacteria interactions in co-culture but not in tri-cultures with the algal host. Additionally, our data reveal that algal death was delayed in cultures containing <i>P. inhibens</i> Δ<i>tdaB</i> mutants compared to those with wild-type bacteria, although no TDA was detected in these tri-cultures. The findings of our study highlight the importance of microbial complexity in the study of bacterial physiology and point to the understudied role of TDA in microbial interactions.IMPORTANCELaboratory model systems enable controlled studies of marine microbial processes; however, the microbial complexity of the culture can influence the outcome. In this study, we employ a systematic approach to assess the impact of the bacterial ability to produce the antibiotic TDA in laboratory cultures with varying microbial complexities (from bacterial monocultures to bacterial co-cultures and algal-bacterial tri-cultures). Our findings demonstrate altered effects of the <i>tdaB</i> gene deletion with increasing microbial complexity, showing distinct impacts on microbial fitness. Since antibiotics like TDA mediate microbial interactions, it is important to examine them within ecologically relevant model systems that reflect inter- and intra-trophic interactions, including bacteria-bacteria and algae-bacteria relationships. Overall, our study highlights the importance of accounting for culture complexity when designing laboratory experiments to investigate microbial interactions and the compounds that mediate them.</p>","PeriodicalId":19052,"journal":{"name":"mSphere","volume":" ","pages":"e0013825"},"PeriodicalIF":3.1,"publicationDate":"2025-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12379602/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144659686","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":"Limitations of repurposing ceftazidime for <i>Stenotrophomonas maltophilia</i>: a cautionary perspective.","authors":"Madhumathi Irulappan, Balaji Veeraraghavan","doi":"10.1128/msphere.00384-25","DOIUrl":"10.1128/msphere.00384-25","url":null,"abstract":"","PeriodicalId":19052,"journal":{"name":"mSphere","volume":" ","pages":"e0038425"},"PeriodicalIF":3.1,"publicationDate":"2025-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12379587/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144775866","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":"The development of functional opsonophagocytic assays to evaluate antibody responses to <i>Klebsiella pneumoniae</i> capsular antigens.","authors":"Robert Lawrence, Emma Bownes, Marina Johnson, Heather Fox, Drew Huff, Ivan Olave, Anup Datta, David Goldblatt, Nathalie Karaky","doi":"10.1128/msphere.00176-25","DOIUrl":"10.1128/msphere.00176-25","url":null,"abstract":"<p><p><i>Klebsiella pneumoniae</i> is one of the leading causes of nosocomial infections in low- and middle-income countries (LMICs), with a high mortality rate among the immunocompromised. With increasing antibiotic resistance, there is an urgent need for preventive measures such as vaccines, but none are currently licensed for use. In order to evaluate natural immunity and assess the immunogenicity of novel vaccines, we set out to develop functional assays that effectively measure the immune response of <i>K. pneumoniae</i> anti-capsular antibodies <i>in vitro</i>. Serotypes KL2, KL15, KL25, KL62, and KL102 were targeted as these are five of the most prevalent and invasive strains, particularly in LMIC settings, and are putative vaccine antigens. Opsonophagocytic killing assays (OPAs) for each serotype were developed and qualified. Serotype-specific IgG from vaccinated rabbit sera and human sera was used to demonstrate <i>in vitro</i> antibody and complement-mediated killing for all serotypes tested, whereas cross-reactivity between each serotype was minimal by competitive analyses. These assays act as a platform to allow further serological evaluation of natural immunity and the performance of <i>K. pneumoniae</i> vaccines. Understanding the function of vaccine-induced antibodies, as well as natural IgG induced by exposure to <i>K. pneumoniae</i>, will be crucial to determine correlates of protection and aid in the path to licensure of a <i>K. pneumoniae</i> vaccine.IMPORTANCE<i>K. pneumoniae</i> is a pathogen that causes serious infections such as pneumonia and sepsis globally. The increasing prevalence of antibiotic resistance in this pathogen has complicated treatment efforts, highlighting the need for preventive therapeutic strategies such as vaccination. However, no licensed vaccines are currently available. Standardized assays to assess the immunogenicity of new vaccines are crucial for vaccine development and evaluation of other therapeutics. Therefore, we have developed assays that can assess the functionality of antibodies, which can be used to evaluate the potential of novel <i>K. pneumoniae</i> conjugate vaccines, and inform which antibodies are most effective for preventing disease.</p>","PeriodicalId":19052,"journal":{"name":"mSphere","volume":" ","pages":"e0017625"},"PeriodicalIF":3.1,"publicationDate":"2025-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12306171/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144275405","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":"Dynamics of amylopectin granule accumulation during the course of chronic <i>Toxoplasma</i> infection is linked to intra-cyst bradyzoite replication.","authors":"Aashutosh Tripathi, Ryan W Donkin, Joy S Miracle, Robert D Murphy, Matthew S Gentry, Abhijit Patwardhan, Anthony P Sinai","doi":"10.1128/msphere.00205-25","DOIUrl":"10.1128/msphere.00205-25","url":null,"abstract":"<p><p>The contribution of amylopectin granules (AG), a branched chain storage homopolymer of glucose, to the maintenance and progression of the chronic <i>Toxoplasma gondii</i> infection has remained undefined. Here, we describe the role of AG in the physiology of encysted bradyzoites using a purpose-developed imaging-based application, AmyloQuant, which permitted the quantification of relative levels of AG within <i>in vivo</i>-derived tissue cysts during the initiation and maturation of chronic infection. Our findings establish that AG are dynamic, exhibiting considerable heterogeneity among tissue cysts at all post-infection time points examined. Quantification of relative steady-state AG levels within tissue cysts reveals a previously unrecognized temporal cycle involving both phases of AG accumulation and utilization over the first 6 weeks of the chronic infection. This AG cycle is temporally coordinated with overall bradyzoite mitochondrial activity. In addition, the staging of AG levels is defined by a period of low accumulation, leading into a phase of high accumulation, followed by apparent rapid utilization associated with a coordinated burst of intra-cyst bradyzoite replication. These findings suggest that AG may represent a key component in the licensing of bradyzoite replication, intimately linking stored metabolic potential to the course of the chronic infection, thereby extending the impact of AG beyond the previously assigned role in transmission. These findings force a fundamental reassessment of the chronic <i>Toxoplasma</i> infection, highlighting the critical need to address the temporal progression of this crucial stage in the parasite life cycle.IMPORTANCEAmylopectin granules (AG) represent a storage polymer of glucose within <i>Toxoplasma gondii</i> bradyzoites, the life cycle stage associated with the chronic infection. In this study, we report on the development of AmyloQuant, an image-based application, to investigate the levels and distribution of AG within encysted bradyzoites in the murine brain with the progression of the chronic infection. Quantification reveals that AG, although heterogeneous both within and across tissue cysts, exhibit a previously unrecognized temporal cycle that is linked to the overall mitochondrial activity and the capacity to replicate <i>in vivo</i>. This confirms that encysted bradyzoites, long considered dormant, retain considerable metabolic activity, with AG playing a potentially critical role in defining and perhaps licensing the progression of this life-long persistent infection.</p>","PeriodicalId":19052,"journal":{"name":"mSphere","volume":" ","pages":"e0020525"},"PeriodicalIF":3.1,"publicationDate":"2025-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12306163/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144258521","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":"The <i>Plasmodium falciparum</i> homolog of Vps16 interacts with the core members of the Vps-C tethering complex.","authors":"Florian Lauruol, Thomas Galaup, Alexandra Bourgeois, Audrey Sergerie, Dave Richard","doi":"10.1128/msphere.00287-25","DOIUrl":"10.1128/msphere.00287-25","url":null,"abstract":"<p><p>The organelles of the apical complex (rhoptries, micronemes, and dense granules) are critical for erythrocyte invasion by the malaria parasite <i>Plasmodium falciparum</i>. Though they have essential roles in the parasite lifecycle, the mechanisms behind their biogenesis are still poorly defined. The Class C Vps proteins Vps11, Vps16, Vps18, and Vps33 constitute the core of the CORVET and HOPS complexes implicated in vesicle tethering and fusion in the eukaryotic endolysosomal system. Work in the model apicomplexan <i>Toxoplasma gondii</i> has revealed that TgVps11 is essential for the generation of the apical complex. <i>P. falciparum</i> possesses all four subunits of the Vps-C complex, and recent work has shown that some of its components were critical for host-cell cytosol trafficking and the biogenesis of the apical complex. We here show that the <i>P. falciparum</i> ortholog of Vps16, a member of the Vps-C complex, is expressed throughout the asexual erythrocytic cycle and that it is potentially associated with the Golgi apparatus and the rhoptries in schizont stage parasites. We then demonstrate by immunoprecipitation and mass spectrometry that PfVps16 interacts with all the members of the canonical Vps-C complex along with the Vps3 CORVET component. Interestingly, three uncharacterized <i>Plasmodium</i>-specific proteins are also found as interactors of PfVps16, and structural predictions revealed that two of them possess folds commonly found in proteins present in membrane tethering complexes. These findings suggest that <i>P. falciparum</i> may possess both conserved and parasite-specific features within its endosomal tethering machinery.IMPORTANCEThe malaria parasite relies on special compartments to invade red blood cells. These are key to the parasite's ability to infect, but how these are generated is not well known. In eukaryotic cells, certain protein assemblies, called tethering complexes, help move and fuse small transport vesicles, which is important for building and maintaining organelles. <i>Plasmodium falciparum</i> possesses some of these proteins, and recent studies suggest they play an important role in building its infection machinery and transporting material inside the parasite. We found that the malaria parasite possesses additional components associated with the typical tethering proteins and that these are not found in other eukaryotes. These results suggest that <i>P. falciparum</i> uses both common and unique tools to create the cellular machinery it needs to infect red blood cells. We propose that the <i>Plasmodium</i>-specific components might represent interesting targets for the development of antimalarials with potentially reduced side effects since they are not present in humans.</p>","PeriodicalId":19052,"journal":{"name":"mSphere","volume":" ","pages":"e0028725"},"PeriodicalIF":3.1,"publicationDate":"2025-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12306165/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144584375","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":"The pre-mRNA splicing modulator pladienolide B inhibits <i>Cryptococcus neoformans</i> germination and growth.","authors":"Sierra L Love, Megan C McKeon, Henrik Vollmer, Joshua C Paulson, Nanami Oshimura, Olivia Valentine, Sébastien C Ortiz, Christina M Hull, Aaron A Hoskins","doi":"10.1128/msphere.00248-25","DOIUrl":"10.1128/msphere.00248-25","url":null,"abstract":"<p><p><i>Cryptococcus neoformans</i> is an opportunistic fungal pathogen responsible for life-threatening infections, particularly in immunocompromised individuals. The limitations of current antifungal therapies due to toxicity and the emergence of resistance highlight the need for novel treatment strategies and targets. <i>C. neoformans</i> has an intron-rich genome, and pre-mRNA splicing is required for expression of the vast majority of its genes. In this study, we investigated the efficacy of a human splicing inhibitor, pladienolide B (PladB), as an antifungal against <i>C. neoformans</i>. PladB inhibited the growth of <i>C. neoformans</i> in liquid culture and spore germination. The potency of PladB could be increased by simultaneous treatment with either FK506 or clorgyline. This combination treatment resulted in significant reductions in fungal growth and prevented spore germination. Transcriptomic analysis revealed that PladB inhibits splicing in <i>C. neoformans</i> and results in widespread intron retention. In combination with FK506, this resulted in downregulation of or intron retention in transcripts from processes vital for cellular growth, including translation, transcription, and RNA processing. Together, these results suggest that targeting RNA splicing pathways could be a promising antifungal strategy and that the effectiveness of splicing inhibitors as antifungals can be increased by co-administering drugs such as FK506.IMPORTANCEFungal infections, like those caused by <i>Cryptococcus neoformans</i>, can turn deadly for many patients. New treatments and therapeutic targets are needed to combat these pathogens. One potential target is the pre-mRNA processing pathway, which is required for expression of nearly all protein-coding genes in <i>C. neoformans</i>. We have determined that a pre-mRNA splicing inhibitor can inhibit both <i>C. neoformans</i> growth and germination and that the potency of this drug can be increased when used in combination with other molecules. This work provides evidence that targeting steps in pre-mRNA processing may be an effective antifungal strategy and avenue for the development of new medicines.</p>","PeriodicalId":19052,"journal":{"name":"mSphere","volume":" ","pages":"e0024825"},"PeriodicalIF":3.1,"publicationDate":"2025-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12306170/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144476112","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":"Novel lineages of bacteria with reduced genomes from the gut of farm animals.","authors":"Shahjahon Begmatov, Alexey V Beletsky, Andrey V Mardanov, Anastasia P Lukina, Liubov B Glukhova, Olga V Karnachuk, Nikolai V Ravin","doi":"10.1128/msphere.00294-25","DOIUrl":"10.1128/msphere.00294-25","url":null,"abstract":"<p><p>Genome reduction and associated metabolic deficiencies have been described in various lineages of parasitic and symbiotic microorganisms that obtain essential nutrients from their partners, and in some free-living microorganisms that inhabit stable environments. The animal gut is a relatively stable ecosystem, characterized by an abundance of organic substances and a high concentration of microorganisms, which provides favorable conditions for the survival of microorganisms with reduced genomes. Metagenomic analysis of 49 samples of feces of farm animals (cows, sheep, yaks, and horses) revealed uncultured lineages of bacteria with reduced genomes (<1 Mbp): family UBA1242 (<i>Christensenellales</i>, <i>Firmicutes</i>), order Rs-D84 (<i>Alphaproteobacteria</i>), and family UBA9783 (<i>Opitutales</i>, <i>Verrucomicrobiota</i>), defined in genome-taxonomy database. Analysis of the genomes showed that these bacteria lacked pathways for the biosynthesis of amino acids, nucleotides, lipids, and many other essential metabolites. The UBA9783 genomes encoded a near-complete Embden-Meyerhof glycolytic pathway and the non-oxidative phase of the pentose phosphate pathway, while in UBA1242 and Rs-D84, these pathways are incomplete. All bacteria are limited to fermentative metabolism and lack aerobic and anaerobic respiratory pathways. All UBA9783 and some Rs-D84 genomes encoded F₀F₁-type ATP synthase and pyrophosphate-energized proton pump; they also can import and utilize peptides and some amino acids. While UBA9783 bacteria could thrive as specialized free-living organisms in the organic-rich gut environment, the UBA1242 and Rs-D84 lineages appear to have adopted the lifestyle of an obligate symbiont/parasite, obtaining metabolites from other cells.IMPORTANCEThe microbiota of the animal gastrointestinal tracts is a complex community of microorganisms which interact in a synergistic or antagonistic relationship and play key nutritional and metabolic roles. However, despite its importance, the gut microbiota of farm animals, especially its uncultured majority, remains largely unexplored. We performed a metagenomic analysis of the gut microbiome of farm animals and characterized three uncultured lineages of bacteria with reduced genomes (<1 Mbp) from the phyla <i>Firmicutes</i>, <i>Proteobacteria</i>, and <i>Verrucomicrobiota</i>. These bacteria were predicted to possess key metabolic deficiencies such as the inability to synthesize essential cell metabolites, suggesting their adaptation to the lifestyle of a symbiont/parasite, or a scavenger obtaining nutrients from the organic-rich gut environment. This study shows that genome reduction with metabolic specialization and adaptation to a partner-dependent lifestyle occurred through convergent evolution in several phylogenetically distant lineages of gut microbiota.</p>","PeriodicalId":19052,"journal":{"name":"mSphere","volume":" ","pages":"e0029425"},"PeriodicalIF":3.1,"publicationDate":"2025-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12306168/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144528957","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":"NLP-like deep learning aided in identification and validation of thiosulfinate tolerance clusters in diverse bacteria.","authors":"Brendon K Myers, Anuj Lamichhane, Brian H Kvitko, Bhabesh Dutta","doi":"10.1128/msphere.00023-25","DOIUrl":"10.1128/msphere.00023-25","url":null,"abstract":"<p><p>Allicin tolerance (<i>alt</i>) clusters in phytopathogenic bacteria, which provide resistance to thiosulfinates like allicin, are challenging to find using conventional approaches due to their varied architecture and the paradox of being vertically maintained within genera despite likely being horizontally transferred. This results in significant sequential diversity that further complicates their identification. Natural language processing (NLP), like techniques such as those used in DeepBGC, offers a promising solution by treating gene clusters like a language, allowing for identifying and collecting gene clusters based on patterns and relationships within the sequences. We curated and validated <i>alt</i>-like clusters in <i>Pantoea ananatis</i> 97-1R, <i>Burkholderia gladioli</i> pv. <i>gladioli</i> FDAARGOS 389, and <i>Pseudomonas syringae</i> pv. tomato DC3000. Leveraging sequences from the RefSeq bacterial database, we conducted comparative analyses of gene synteny, gene/protein sequences, protein structures, and predicted protein interactions. This approach enabled the discovery of several novel <i>alt</i>-like clusters previously undetectable by other methods, which were further validated experimentally. Our work highlights the effectiveness of NLP-like techniques for identifying underrepresented gene clusters and expands our understanding of the diversity and utility of <i>alt</i>-like clusters in diverse bacterial genera. This work demonstrates the potential of these techniques to simplify the identification process and enhance the applicability of biological data in real-world scenarios.IMPORTANCEThiosulfinates, like allicin, are potent antifeedants and antimicrobials produced by <i>Allium</i> species and pose a challenge for phytopathogenic bacteria. Phytopathogenic bacteria have been shown to utilize an allicin tolerance (<i>alt</i>) gene cluster to circumvent this host response, leading to economically significant yield losses. Due to the complexity of mining these clusters, we applied techniques akin to natural language processing to analyze Pfam domains and gene proximity. This approach led to the identification of novel <i>alt</i>-like gene clusters, showcasing the potential of artificial intelligence to reveal elusive and underrepresented genetic clusters and enhance our understanding of their diversity and role across various bacterial genera.</p>","PeriodicalId":19052,"journal":{"name":"mSphere","volume":" ","pages":"e0002325"},"PeriodicalIF":3.1,"publicationDate":"2025-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12306174/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144317517","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}