The ISME JournalPub Date : 2025-08-13DOI: 10.1093/ismejo/wraf163
Julia Mougin,Yannick Labreuche,Viviane Boulo,David Goudenège,Jamal Saad,Gaelle Courtay,Jacqueline Le Grand,Oriane Chevalier,Juliette Pouzadoux,Caroline Montagnani,Marie-Agnès Travers,Bruno Petton,Delphine Destoumieux-Garzón
{"title":"Antibiotic Use in Oyster Hatcheries Promotes Rapid Spread of a Highly Transferable and Modular Resistance Plasmid in Vibrio.","authors":"Julia Mougin,Yannick Labreuche,Viviane Boulo,David Goudenège,Jamal Saad,Gaelle Courtay,Jacqueline Le Grand,Oriane Chevalier,Juliette Pouzadoux,Caroline Montagnani,Marie-Agnès Travers,Bruno Petton,Delphine Destoumieux-Garzón","doi":"10.1093/ismejo/wraf163","DOIUrl":"https://doi.org/10.1093/ismejo/wraf163","url":null,"abstract":"Plasmids play a key role in the horizontal gene transfer of antibiotic resistance genes, particularly in aquaculture where ARG-carrying Vibrio bacteria are frequently detected. Given the expansion of global aquaculture and its reliance on antibiotics, we investigated how these practices influence the emergence, dynamics, and spread of ARGs, focusing on Magallana gigas hatcheries - the world's most widely farmed shellfish. Among the three antibiotics tested, only chloramphenicol led to a pronounced selection and dissemination of chloramphenicol-resistant Vibrio isolates. Resistance was mediated by catA2, located in a highly modular, insertion sequence- and transposase-rich region of a conjugative plasmid, alongside tet(B). This plasmid was closely related to emerging pAQU-type plasmids unreported in Europe. pAQU-MAN, derived from Marine ANtimicrobial resistance, is a low-copy, highly transferable plasmid that rapidly spread throughout the hatchery following CHL treatment. Though naturally found in commensal Vibrio, it exhibited a broad host range, transferring efficiently to both oyster- and human-pathogenic Vibrio strains, as well as to E. coli, with high conjugation rates. Additionally, it remained stable in Vibrio hosts and was transmitted from oyster parents to progenies, even in the absence of antibiotic. It eventually disappeared from the microbial community associated to adults. Our findings highlight that antibiotic use in oyster hatcheries can select for highly modular and transferable multidrug-resistant plasmids, posing a risk of environmental dissemination, although their limited persistence in juvenile oyster reduces the likelihood of transmission to humans. We discuss the human and ecological factor driving pAQU-MAN spread and control in aquaculture settings.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"19 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-08-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144825733","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The ISME JournalPub Date : 2025-08-13DOI: 10.1093/ismejo/wraf175
Baofei Yan,Xian Zheng,Danya Lu,Ting Li,Xi Chen,Zhitao Shao,Tingming Fu
{"title":"Silibinin-drived microbiota enrich (R)-2,3-dihydroxy-isovalerate and ameliorate colitis via the GAT-3/RARβ/RORγt axis.","authors":"Baofei Yan,Xian Zheng,Danya Lu,Ting Li,Xi Chen,Zhitao Shao,Tingming Fu","doi":"10.1093/ismejo/wraf175","DOIUrl":"https://doi.org/10.1093/ismejo/wraf175","url":null,"abstract":"Microbiota-associated factors are increasingly recognized as significant contributors to the progression of ulcerative colitis, and microbial modulation has emerged as an effective therapy for this condition. The herbal compound silibinin has demonstrated properties that modulate gut microbiota. Herein, we investigated the response of gut microbiota to silibinin in ameliorating colitis, using a mouse model of colitis coupled with antibiotic exposure. Results indicated that antibiotic pretreatment negated the benefits of silibinin in mice with colitis. Furthermore, fecal microbiota transplantation involving silibinin-modulated gut microbiota further substantiated the gut microbiota-dependent effects of silibinin. Within the metabolic profiles of silibinin-regulated microbiota, we identified that Alistipes-associated (R)-2,3-dihydroxy-isovalerate exhibited the most pronounced anti-inflammatory effects in vitro and demonstrated protective effects against colitis. Moreover, (R)-2,3-dihydroxy-isovalerate reinstated the protective effects of silibinin in mice with colitis under antibiotic exposure. These effects were primarily mediated via the targeting of the colonic GABA transporter 3 by (R)-2,3-dihydroxy-isovalerate. We further revealed that the retinoic acid receptor β and the retinoid-related orphan nuclear receptor γt may mediate the impact of silibinin-derived microbiota and (R)-2,3-dihydroxy-isovalerate on colitis. Additionally, the knockdown of colonic GABA transporter 3 diminished the impact of silibinin on the GABA transporter 3/retinoic acid receptor β/retinoid-related orphan nuclear receptor γt axis and colitis. Our findings highlight that (R)-2,3-dihydroxy-isovalerate, enriched from microbiota derived from silibinin, can target the GABA transporter 3/retinoic acid receptor β/retinoid-related orphan nuclear receptor γt axis, which is essential for anti-colitis properties of silibinin-regulated microbiota.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"27 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-08-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144825735","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The ISME JournalPub Date : 2025-08-13DOI: 10.1093/ismejo/wraf176
Matthew C Gaines,Michail N Isupov,Mathew McLaren,Risat Ul Haque,Alejandra Recalde,Rafael Bargiela,Vicki A M Gold,Sonja-Verena Albers,Peter N Golyshin,Olga V Golyshina,Bertram Daum
{"title":"Unusual cell surfaces, pili, and archaella of Thermoplasmatales archaea.","authors":"Matthew C Gaines,Michail N Isupov,Mathew McLaren,Risat Ul Haque,Alejandra Recalde,Rafael Bargiela,Vicki A M Gold,Sonja-Verena Albers,Peter N Golyshin,Olga V Golyshina,Bertram Daum","doi":"10.1093/ismejo/wraf176","DOIUrl":"https://doi.org/10.1093/ismejo/wraf176","url":null,"abstract":"Archaea of the order Thermoplasmatales push the boundaries of our current knowledge of prokaryotic life. They show distinct cellular plasticity, heterogenous cell morphologies, and lack a paracrystalline S-layer. As the S-layer has previously been implicated in acting as a stator scaffold for filaments driving cellular propulsion, particularly archaella, we asked whether the absence of an S-layer precludes the formation of functional archaella or pili in Thermoplasmatales. Using cryoEM, we investigated the two Thermoplasmatales species Cuniculiplasma divulgatum and Oxyplasma meridianum. We found that these species indeed generate pili and archaella, and that the latter likely function in cellular propulsion. Whereas C. divulgatum produces pili with terminal hooks using a unique assembly machinery, O. meridianum generates wide, \"barbed\" archaella with an unusually high degree of glycosylation. Our results show that, for the generation of functional archaella and pili, a canonical S-layer is not necessary.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"746 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-08-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144825734","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The ISME JournalPub Date : 2025-08-12DOI: 10.1093/ismejo/wraf080
Xingyao Ye, Xiaojun Niu, Dongqing Zhang, Mengyu Lv, Ling Li, Qiang Liu, Deye Chen, Yu Lin, Zhiquan Yang, Yi Zhang
{"title":"Cyanuric acid in Paramecium secretions is an efficient quorum sensing inducer","authors":"Xingyao Ye, Xiaojun Niu, Dongqing Zhang, Mengyu Lv, Ling Li, Qiang Liu, Deye Chen, Yu Lin, Zhiquan Yang, Yi Zhang","doi":"10.1093/ismejo/wraf080","DOIUrl":"https://doi.org/10.1093/ismejo/wraf080","url":null,"abstract":"Quorum sensing is a process of bacterial chemical communication via extracellular signal molecules known as autoinducers, allowing synchronized collective behavior changes related to population density. However, the ecological significance of quorum sensing in multi-species communities, particularly coexisting with predators, remains unaddressed. In this study, we discovered that cyanuric acid (CA), a compound secreted by the widespread protozoan Paramecium, significantly influences the LuxR-type quorum sensing in Pseudomonas aeruginosa PAO1. Exogenous CA acts as a substitute for autoinducers known as N-acyl homoserine lactones in activating LasR/RhlR regulators that involve promiscuous ligand-receptor interactions, and exerts a specific restoring effect on the PAO1-ΔlasI/ΔrhlI mutant. Further, the inductive capabilities of CA were harnessed to expedite the start-up of the anammox process, substantially enhancing the aggregation and dynamics of the anammox consortium. Treating with 500 nM CA led to a 76.3% increase in anammox bacteria abundance compared to the control, resulting in exceptional nitrogen removal rates of 1.42 g N·L−1·d−1 within 54 days. This study unveils a mode of interspecies information transfer across trophic levels in aquatic organismal communities through CA-stimulated quorum sensing.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"26 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-08-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144825288","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The ISME JournalPub Date : 2025-08-12DOI: 10.1093/ismejo/wraf166
Diego Garfias-Gallegos, Carlos J Pardo-De la Hoz, Diane L Haughland, Nicolas Magain, Blanka Aguero, Jolanta Miadlikowska, François Lutzoni
{"title":"Central metabolism and development are rewired in lichenized cyanobacteria","authors":"Diego Garfias-Gallegos, Carlos J Pardo-De la Hoz, Diane L Haughland, Nicolas Magain, Blanka Aguero, Jolanta Miadlikowska, François Lutzoni","doi":"10.1093/ismejo/wraf166","DOIUrl":"https://doi.org/10.1093/ismejo/wraf166","url":null,"abstract":"Nostoc cyanobacteria are among the few organisms capable of fixing both carbon and nitrogen. These metabolic features are essential for the cyanolichen symbiosis, where Nostoc supplies both carbon (as glucose) and nitrogen (as ammonium) to a cyanolichen-forming fungal partner. This nutrient flow was established by seminal biochemical studies published in the 20th century. Since then, cyanolichen metabolism has received little attention, and the molecular mechanisms that underlie the physiology of lichenized Nostoc remain mostly unknown. Here, we aimed to elucidate the genomic and transcriptional changes that enable Nostoc’s metabolic role in cyanolichens. We used comparative genomics across 243 genomes of Nostoc s. lat. Coupled with metatranscriptomic experiments using Peltigera cyanolichens. We found that genes for photoautotrophic carbon fixation are upregulated in lichenized Nostoc. This likely results in a higher rate of carbon fixation that allows Nostoc to provide carbon to the fungal partner while meeting its own metabolic needs. We also found that the transfer of ammonium from Nostoc to the lichen-forming fungus is facilitated by two molecular mechanisms: (i) transcriptional downregulation of glutamine synthetase, the key enzyme responsible for ammonium assimilation in Nostoc; and (ii) frequent losses of a putative high-affinity ammonium permease, which likely reduces Nostoc’s capacity to recapture leaked ammonium. Finally, we found that the development of motile hormogonia is downregulated in lichenized Nostoc, which resembles the repression of motility in Nostoc symbionts after they colonize symbiotic cavities of their plant hosts. Our results pave the way for a revival of cyanolichen ecophysiology in the omics era.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"20 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-08-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144825289","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The ISME JournalPub Date : 2025-08-12DOI: 10.1093/ismejo/wraf171
Karla Iveth Aguilera-Campos, Julie Boisard, Viktor Törnblom, Jon Jerlström-Hultqvist, Ada Behncké-Serra, Elena Aramendia Cotillas, Courtney Weir Stairs
{"title":"Anaerobic breviate protist survival in microcosms depends on microbiome metabolic function.","authors":"Karla Iveth Aguilera-Campos, Julie Boisard, Viktor Törnblom, Jon Jerlström-Hultqvist, Ada Behncké-Serra, Elena Aramendia Cotillas, Courtney Weir Stairs","doi":"10.1093/ismejo/wraf171","DOIUrl":"https://doi.org/10.1093/ismejo/wraf171","url":null,"abstract":"Anoxic and hypoxic environments serve as habitats for diverse microorganisms, including unicellular eukaryotes (protists) and prokaryotes. To thrive in low-oxygen environments, protists and prokaryotes often establish specialized metabolic cross-feeding associations, such as syntrophy, with other microorganisms. Previous studies show that the breviate protist Lenisia limosa engages in a mutualistic association with a denitrifying Arcobacter bacterium based on hydrogen exchange. Here, we investigate if the ability to form metabolic interactions is conserved in other breviates by studying five diverse breviate microcosms and their associated bacteria. We show that five laboratory microcosms of marine breviates live with multiple hydrogen-consuming prokaryotes that are predicted to have different preferences for terminal electron acceptors using genome-resolved metagenomics. Protist growth rates vary in response to electron acceptors depending on the make-up of the prokaryotic community. We find that the metabolic capabilities of the bacteria and not their taxonomic affiliations determine protist growth and survival and present new potential protist-interacting bacteria from the Arcobacteraceae, Desulfovibrionaceae, and Terasakiella lineages. This investigation uncovers potential nitrogen and sulfur cycling pathways within these bacterial populations, hinting at their roles in syntrophic interactions with the protists via hydrogen exchange.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"8 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-08-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144825071","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The ISME JournalPub Date : 2025-08-12DOI: 10.1093/ismejo/wraf170
Cody S Madsen, Jeffrey A Kimbrel, Patrick Diep, Dante P Ricci
{"title":"Synthetic communities as a model for determining interactions between a biofertilizer chassis organism and native microbial consortia","authors":"Cody S Madsen, Jeffrey A Kimbrel, Patrick Diep, Dante P Ricci","doi":"10.1093/ismejo/wraf170","DOIUrl":"https://doi.org/10.1093/ismejo/wraf170","url":null,"abstract":"Biofertilizers are critical for sustainable agriculture since they can replace ecologically disruptive chemical fertilizers while improving the trajectory of soil and plant health. Yet, for improving deployment, the persistence of biofertilizers within native soil consortia must be elucidated and enhanced. We describe a high-throughput, modular, and automation-friendly in vitro approach to screen for biofertilizer persistence within soil-derived consortia after co-cultivation with stable synthetic soil microbial communities (SynComs) obtained through a top-down cultivation process. We profiled ~1200 SynComs isolated from various soil sources and cultivated in divergent media types, and detected significant phylogenetic diversity (e.g., Shannon index >4) and richness (observed richness >400) across these communities. We observed high reproducibility in SynCom community structure from common soil and media types, which provided a testbed for assessing biofertilizer persistence within representative native consortia. Furthermore, we demonstrated the screening method described herein can be coupled with microbial engineering to efficiently identify soil-derived SynComs where an engineered biofertilizer organism (i.e. Bacillus subtilis) persists. Accordingly, we discovered that B. subtilis persisted in approximately 10% of SynComs that generally followed the diversity-invasion principle. Additionally, our approach enables analysis of the ecological impact of B. subtilis inoculation on SynCom structure and profile alterations in community diversity and richness associated with the presence of a genetically modified model bacterium. Ultimately, this work establishes a modular pipeline that could be integrated into a variety of microbiology/microbiome-relevant workflows or related applications that would benefit from assessing persistence and interaction of a specific organism of interest with native consortia.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"12 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-08-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144825292","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The ISME JournalPub Date : 2025-08-12DOI: 10.1093/ismejo/wraf152
Sonia García Méndez, Stien Mertens, Arne Temmerman, Helena Van den Eynde, Margo Vermeersch, Lena Vlaminck, Olivier Berteloot, Judith Van Dingenen, Alexander Clarysse, Annick De Keyser, Serge Beullens, Ilse de Baenst, Niranjana Roy, Quinten De Paepe, Jan Michiels, Isabel Roldan-Ruiz, Joke Pannecoucque, Anne Willems, Steven Maere, Sofie Goormachtig
{"title":"Fast track to environmentally adapted rhizobia for growing soybean at northern latitudes using citizen science","authors":"Sonia García Méndez, Stien Mertens, Arne Temmerman, Helena Van den Eynde, Margo Vermeersch, Lena Vlaminck, Olivier Berteloot, Judith Van Dingenen, Alexander Clarysse, Annick De Keyser, Serge Beullens, Ilse de Baenst, Niranjana Roy, Quinten De Paepe, Jan Michiels, Isabel Roldan-Ruiz, Joke Pannecoucque, Anne Willems, Steven Maere, Sofie Goormachtig","doi":"10.1093/ismejo/wraf152","DOIUrl":"https://doi.org/10.1093/ismejo/wraf152","url":null,"abstract":"Soybean serves as a crucial source of plant-based protein for human diets. Recently, there is a growing incentive to extend the range of this crop to more northern latitudes, in order to enable profitable soybean production in Europe. To reach economic yields, soybean requires inoculation with symbiotic, diazotrophic rhizobial bacteria. However, the performance of commercial inocula is often variable under local conditions. Here, we present the citizen science project “Soy in 1,000 Gardens”, a large-scale trapping experiment for isolating local soybean-nodulating rhizobia in Flanders, Belgium. We identified two locally isolated Bradyrhizobium strains performing at least as well as commercial strain B. diazoefficiens G49 in local field trials. Additionally, we found that nutrient content, microbial alpha diversity, and the presence of arbuscular mycorrhizal fungi in the soil were correlated with nodulation. Finally, we report a correlation between low bacterial alpha diversity and red nodule interior, and identified Tardiphaga as a dominant colonizer of red nodules.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"16 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-08-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144824914","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The ISME JournalPub Date : 2025-08-11DOI: 10.1093/ismejo/wraf172
David Kneis,Magali de la Cruz Barron,Diala Konyali,Valentin Westphal,Patrick Schröder,Kathi Westphal-Settele,Jens Schönfeld,Dirk Jungmann,Thomas Ulrich Berendonk,Uli Klümper
{"title":"Ecology-based approach to predict no-effect antibiotic concentrations for minimizing environmental selection of resistance.","authors":"David Kneis,Magali de la Cruz Barron,Diala Konyali,Valentin Westphal,Patrick Schröder,Kathi Westphal-Settele,Jens Schönfeld,Dirk Jungmann,Thomas Ulrich Berendonk,Uli Klümper","doi":"10.1093/ismejo/wraf172","DOIUrl":"https://doi.org/10.1093/ismejo/wraf172","url":null,"abstract":"Selection for antibiotic resistance has been demonstrated at low, environmentally relevant antibiotic concentrations. The concept of minimum selective concentrations (MSC) has been adopted in environmental regulation to define maximum permissible antibiotic concentrations. Such empirically determined MSC values often fail to reflect the complexity of natural communities, where susceptibility and resistance-associated fitness costs vary widely across species. To address this limitation, computational approaches have been developed to predict no-effect concentrations for selection of antibiotic resistance (PNECres) from routinely collected minimum inhibitory concentration (MIC) data. However, these approaches, using assessment factors to convert MICs to PNECres, often lack a strong ecological basis, undermining confidence in their predictions. Here, we propose a simple but biologically consistent framework to derive PNECres values by integrating MIC data with probabilistic estimates of resistance-related fitness costs. We demonstrate mathematically and empirically that for typical high-level resistances, the MSC/MIC ratio is approximately equal to the resistance cost, allowing for cost-based estimation of MSCs. In experimental validation across 26 strain-antibiotic combinations, 66% of computed MSCs deviated by less than factor two from empirical values. Leveraging these findings, we explored the general distribution of fitness costs of resistance determinants to establish a cost-based probabilistic model for replacing conventional fixed assessment factors. When applied to current MIC databases, our framework suggests that regulatory environmental threshold concentrations should be lowered by at least one order of magnitude to guard against selection for antibiotic resistance. Our approach offers a feasible and biologically transparent alternative for deriving PNECres values in environmental risk assessment.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"12 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-08-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144825736","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The ISME JournalPub Date : 2025-08-11DOI: 10.1093/ismejo/wraf174
Logan D Moore,Matthew J Ballinger
{"title":"Evolution of specialized toxin arsenals in a bacterial symbiont of arthropods.","authors":"Logan D Moore,Matthew J Ballinger","doi":"10.1093/ismejo/wraf174","DOIUrl":"https://doi.org/10.1093/ismejo/wraf174","url":null,"abstract":"Bacteria commonly deploy toxic proteins that act with specificity on target molecules to support invasion and improve survival in competitive environments. Many toxin-encoding bacteria have evolved into host-associated defensive partnerships, in which they use toxins to improve host survival during infection. The stability of these relationships requires that symbiont toxins target diverse parasites while minimizing damage to the host. We investigate the specificity of a group of ribosome-targeting toxins (RIPs) encoded by heritable Spiroplasma symbionts that contribute to defense against parasite infection in fruit fly hosts. Using E. coli to express five divergent copies of this toxin, we show that distantly related members of the family all retain the ability to inactivate ribosomes by adenine cleavage at the α-sarcin/ricin loop, the enzymatic hallmark of RIPs. However, when exposed to live insect and fungal cells, ribosome inactivation varies across the five toxins, suggesting cellular recognition or localization play a role in target specificity. To identify toxin domains required for specificity, we removed rapidly evolving \"accessory\" domains from two toxins. Both truncated toxins exhibit significantly increased activity on purified ribosomes in vitro, suggesting one role of accessory domains is to reduce toxicity, which may help protect hosts from collateral damage. One of the truncated toxins also showed significantly reduced inactivation of cellular ribosomes in vivo, indicating a role for accessory domains in cell specificity. Together, these data reveal a mechanism for symbiont discrimination between hosts and parasites and highlight how dynamic toxin evolution can contribute to stability and novelty in defensive symbiosis.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"7 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-08-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144825737","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}