Katalin Demeter, Domenico Savio, Alexander K T Kirschner, Georg H Reischer, Stoimir Kolarevic, Juraj Parajka, Julia Derx, Stefan Jakwerth, Christian Wurzbacher, Alfred P Blaschke, Robert L Mach, Günter Blöschl, Andreas H Farnleitner, Alexander Eiler
Modelling bacterial dynamics in large river systems is crucial for predicting continental-scale ecosystem functioning under anthropogenic pressures. Although the River Continuum and Metacommunity concepts have provided theoretical frameworks, quantitative parameters necessary for microbial macroecological models remain scarce. Here, we present results from two whole-river surveys, conducted six years apart along 2600 km of the Danube River. Using bacterial secondary production, cell counts, and 16S rRNA gene amplicon sequencing, we quantified carbon, cell, phylotype, and diversity turnover along the river. Carbon incorporation per cell declined with water travel time by 6,000 - 21,000 atoms per hour. Bacterial cells multiplied every eight days, resulting in four to six doublings during downstream transport. Growth responses at the level of individual phylotypes differed up to a hundredfold from these bulk community estimates. Bacterial diversity dynamics were dominated by phylotype turnover rather than phylotype loss. Turnover ranged 0.92 to 0.96 across the river, indicating an almost complete replacement of phylotypes with 2–11% of headwater-associated ASVs persisting under base-flow conditions. Richness declined gradually downstream at a rate of approximately 0.13 ASVs per hour. Variations in bacterial secondary production, cell abundance, and observed ASVs were best explained by models combining hydrological and water quality parameters, whereas beta diversity followed a gradual development primarily structured by water travel time. Together, these results identify water travel time as the key integrative parameter governing microbial macroecological dynamics along large rivers, with environmental conditions fine-tuning local responses. These models can help predict changes in microbial diversity and functioning under anthropogenic alterations.
{"title":"Hydrological regime of a continental river system predicts bacterial macroecological patterns","authors":"Katalin Demeter, Domenico Savio, Alexander K T Kirschner, Georg H Reischer, Stoimir Kolarevic, Juraj Parajka, Julia Derx, Stefan Jakwerth, Christian Wurzbacher, Alfred P Blaschke, Robert L Mach, Günter Blöschl, Andreas H Farnleitner, Alexander Eiler","doi":"10.1093/ismejo/wrag013","DOIUrl":"https://doi.org/10.1093/ismejo/wrag013","url":null,"abstract":"Modelling bacterial dynamics in large river systems is crucial for predicting continental-scale ecosystem functioning under anthropogenic pressures. Although the River Continuum and Metacommunity concepts have provided theoretical frameworks, quantitative parameters necessary for microbial macroecological models remain scarce. Here, we present results from two whole-river surveys, conducted six years apart along 2600 km of the Danube River. Using bacterial secondary production, cell counts, and 16S rRNA gene amplicon sequencing, we quantified carbon, cell, phylotype, and diversity turnover along the river. Carbon incorporation per cell declined with water travel time by 6,000 - 21,000 atoms per hour. Bacterial cells multiplied every eight days, resulting in four to six doublings during downstream transport. Growth responses at the level of individual phylotypes differed up to a hundredfold from these bulk community estimates. Bacterial diversity dynamics were dominated by phylotype turnover rather than phylotype loss. Turnover ranged 0.92 to 0.96 across the river, indicating an almost complete replacement of phylotypes with 2–11% of headwater-associated ASVs persisting under base-flow conditions. Richness declined gradually downstream at a rate of approximately 0.13 ASVs per hour. Variations in bacterial secondary production, cell abundance, and observed ASVs were best explained by models combining hydrological and water quality parameters, whereas beta diversity followed a gradual development primarily structured by water travel time. Together, these results identify water travel time as the key integrative parameter governing microbial macroecological dynamics along large rivers, with environmental conditions fine-tuning local responses. These models can help predict changes in microbial diversity and functioning under anthropogenic alterations.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"8 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146098307","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}
Diego Javier Jiménez,Ramona Marasco,Júnia Schultz,Carlos Andrés Díaz Rodríguez,Juan Nogales,Luis Miguel Rodriguez-R,Jörg Overmann,Alexandre Soares Rosado
Despite advances in sequencing, microbial genomics, and cultivation techniques, the vast majority of prokaryotic species remain uncultured, which is a persistent bottleneck in microbiology and microbial ecology. This perspective outlines a conceptual framework to improve the transition from genome-resolved metagenomics to the targeted isolation of yet-uncultured prokaryotic taxa. The proposed framework integrates the induced reshaping of microbiomes, genome-based inferences of physiological and phenotypic traits, culture media design, and targeted culturomics, enabling hypothesis-driven cultivation. In addition, this manuscript addresses the critical limitations in the field, including the sequence-to-function gap, and emphasizes the synergistic potential of experimental microbiology, microbial ecology, metagenomics, and artificial intelligence (AI)-based predictions to enhance rational and actionable roadmaps for discovering and cultivating novel prokaryotic lineages.
{"title":"Discovery and cultivation of prokaryotic taxa in the age of metagenomics and artificial intelligence.","authors":"Diego Javier Jiménez,Ramona Marasco,Júnia Schultz,Carlos Andrés Díaz Rodríguez,Juan Nogales,Luis Miguel Rodriguez-R,Jörg Overmann,Alexandre Soares Rosado","doi":"10.1093/ismejo/wrag012","DOIUrl":"https://doi.org/10.1093/ismejo/wrag012","url":null,"abstract":"Despite advances in sequencing, microbial genomics, and cultivation techniques, the vast majority of prokaryotic species remain uncultured, which is a persistent bottleneck in microbiology and microbial ecology. This perspective outlines a conceptual framework to improve the transition from genome-resolved metagenomics to the targeted isolation of yet-uncultured prokaryotic taxa. The proposed framework integrates the induced reshaping of microbiomes, genome-based inferences of physiological and phenotypic traits, culture media design, and targeted culturomics, enabling hypothesis-driven cultivation. In addition, this manuscript addresses the critical limitations in the field, including the sequence-to-function gap, and emphasizes the synergistic potential of experimental microbiology, microbial ecology, metagenomics, and artificial intelligence (AI)-based predictions to enhance rational and actionable roadmaps for discovering and cultivating novel prokaryotic lineages.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"74 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146073219","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}
Huiyu Chuai,Gen Li,Luchen Tao,Lei Ouyang,Ruihan Ruan,Zhong Wei,Joann Whalen,Uffe N Nielsen,Ting Liu,Huixin Li
Trait-mediated interactions across trophic levels drive trophic cascades in macroecological systems, yet their relevance in microbially dominated soil ecosystems remains underexplored. We combined a regional field survey with controlled experiments using a defined 122-strain synthetic bacterial community and bacterivorous nematodes to test whether faunal predation reorganizes root-associated microbiomes to suppress soilborne disease. Field observations showed that sites with stronger nematode-Pseudomonadota associations had lower bacterial wilt incidence. In controlled experiments, nematode predation selectively enriched Pseudomonadota in the rhizosphere and reduced Ralstonia solanacearum populations and disease incidence. Preferential grazing drove this enrichment: Pseudomonadota constituted over 95% of sequences in nematode guts, and focal taxa showed moderate antagonism, small cell size, and high metabolic activity. Together, these results identify Pseudomonadota as key bridging taxa in cross-trophic interactions. Trait-linked responses to predation contribute to pathogen suppression and suggest a biocontrol framework that integrates microbial traits with trophic connectivity.
{"title":"Pseudomonadota bridge cross-trophic interactions to suppress plant pathogens.","authors":"Huiyu Chuai,Gen Li,Luchen Tao,Lei Ouyang,Ruihan Ruan,Zhong Wei,Joann Whalen,Uffe N Nielsen,Ting Liu,Huixin Li","doi":"10.1093/ismejo/wrag011","DOIUrl":"https://doi.org/10.1093/ismejo/wrag011","url":null,"abstract":"Trait-mediated interactions across trophic levels drive trophic cascades in macroecological systems, yet their relevance in microbially dominated soil ecosystems remains underexplored. We combined a regional field survey with controlled experiments using a defined 122-strain synthetic bacterial community and bacterivorous nematodes to test whether faunal predation reorganizes root-associated microbiomes to suppress soilborne disease. Field observations showed that sites with stronger nematode-Pseudomonadota associations had lower bacterial wilt incidence. In controlled experiments, nematode predation selectively enriched Pseudomonadota in the rhizosphere and reduced Ralstonia solanacearum populations and disease incidence. Preferential grazing drove this enrichment: Pseudomonadota constituted over 95% of sequences in nematode guts, and focal taxa showed moderate antagonism, small cell size, and high metabolic activity. Together, these results identify Pseudomonadota as key bridging taxa in cross-trophic interactions. Trait-linked responses to predation contribute to pathogen suppression and suggest a biocontrol framework that integrates microbial traits with trophic connectivity.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"30 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146056917","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}
Andrea Catacora-Grundy,Netanel Kramer,Sofie Lindegaard Jakobsen,Michael Kühl,Johan Decelle,Daniel Wangpraseurt
Light availability plays a central role in shaping the photophysiology and energy metabolism of photosymbiotic organisms such as reef-building corals. Although light varies greatly within coral colonies, the effects of this spatial heterogeneity on the subcellular organization and energy storage of symbiotic algae (Symbiodiniaceae) remain poorly understood. Here, we combined microscale measurements of light and oxygen across both light-exposed upper regions and shaded basal regions of a Favites abdita colony with three-dimensional cellular imaging using Focused Ion Beam Scanning Electron Microscopy (FIB-SEM). Our multi-scale approach revealed subcellular heterogeneity among symbiont populations, suggesting different cell cycle stages and physiological states across a spatial stratification in the coral. Subcellular morphometrics revealed that symbiont cells at the top of the colony were twice more voluminous than those at the shaded base with similar plastid volume occupancy. Compared to symbionts at the top of the colony, symbionts in the basal region accumulated nearly three times more starch relative to their cell volume. These findings show that light gradients within coral colonies shape symbiont morphology and energy storage patterns, with important implications for coral stress tolerance and resilience.
{"title":"Intra-colony light gradients drive variation in coral symbiont morphology and carbon storage.","authors":"Andrea Catacora-Grundy,Netanel Kramer,Sofie Lindegaard Jakobsen,Michael Kühl,Johan Decelle,Daniel Wangpraseurt","doi":"10.1093/ismejo/wrag006","DOIUrl":"https://doi.org/10.1093/ismejo/wrag006","url":null,"abstract":"Light availability plays a central role in shaping the photophysiology and energy metabolism of photosymbiotic organisms such as reef-building corals. Although light varies greatly within coral colonies, the effects of this spatial heterogeneity on the subcellular organization and energy storage of symbiotic algae (Symbiodiniaceae) remain poorly understood. Here, we combined microscale measurements of light and oxygen across both light-exposed upper regions and shaded basal regions of a Favites abdita colony with three-dimensional cellular imaging using Focused Ion Beam Scanning Electron Microscopy (FIB-SEM). Our multi-scale approach revealed subcellular heterogeneity among symbiont populations, suggesting different cell cycle stages and physiological states across a spatial stratification in the coral. Subcellular morphometrics revealed that symbiont cells at the top of the colony were twice more voluminous than those at the shaded base with similar plastid volume occupancy. Compared to symbionts at the top of the colony, symbionts in the basal region accumulated nearly three times more starch relative to their cell volume. These findings show that light gradients within coral colonies shape symbiont morphology and energy storage patterns, with important implications for coral stress tolerance and resilience.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"42 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146056919","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}
Remi Gschwind,Mehdi Bonnet,Anna Abramova,Victor Hugo Jarquín-Díaz,Marcus Wenne,Ulrike Löber,Nicolas Godron,Ioannis D Kampouris,Faina Tskhay,Fouzia Nahid,Chloé Debroucker,Maximilien Bui-Hai,Inès El Aiba,Uli Klümper,Thomas U Berendonk,Sofia K Forslund-Startceva,Rabaab Zahra,Johan Bengtsson-Palme,Etienne Ruppé
Antibiotic resistance poses a global public health threat, which can originate from the transfer of environmental antibiotic resistance genes to pathogenic bacteria, as highlighted by the "One Health" framework. Cefiderocol is a siderophore cephalosporin recently introduced in clinical practice which displays a "Trojan Horse" mechanism, utilizing bacterial iron transportation systems for cell entry. Although it is only used as a last-line antibiotic, resistance has already been observed in clinical isolates. Yet, cefiderocol resistance genes are difficult to monitor as resistance mechanisms remain mostly undescribed in antibiotic resistance gene databases and therefore uncharacterized in the environment. To address this critical gap, we applied functional metagenomics to diverse environmental samples (wastewater, freshwater, and soil) from France, Germany, Sweden, and Pakistan. Four antibiotic resistant genes were identified as responsible for increased cefiderocol minimum inhibitory concentrations to clinically-relevant levels (ranging from 1 to 4 mg/L), including ꞵ-lactamases (VEB-3, OXA-372 homolog, and YbxI homolog) and a partial penicillin-binding protein homolog. None of these genes had been previously reported as a cefiderocol resistance gene. Three out of four had their closest homologs in pathogenic bacteria. The blaVEB-3 gene was associated with a mobile genetic element and distributed across all wastewater metagenomes analyzed in this study. We therefore highlight the critical need for functional metagenomics, to characterize previously uncharacterized last-line antibiotic resistance mechanisms which will be used to enrich antibiotic resistance gene databases and thereby improving antibiotic resistance surveillance in all One Health compartments.
{"title":"Cefiderocol resistance genes identified in environmental samples using functional metagenomics.","authors":"Remi Gschwind,Mehdi Bonnet,Anna Abramova,Victor Hugo Jarquín-Díaz,Marcus Wenne,Ulrike Löber,Nicolas Godron,Ioannis D Kampouris,Faina Tskhay,Fouzia Nahid,Chloé Debroucker,Maximilien Bui-Hai,Inès El Aiba,Uli Klümper,Thomas U Berendonk,Sofia K Forslund-Startceva,Rabaab Zahra,Johan Bengtsson-Palme,Etienne Ruppé","doi":"10.1093/ismejo/wrag010","DOIUrl":"https://doi.org/10.1093/ismejo/wrag010","url":null,"abstract":"Antibiotic resistance poses a global public health threat, which can originate from the transfer of environmental antibiotic resistance genes to pathogenic bacteria, as highlighted by the \"One Health\" framework. Cefiderocol is a siderophore cephalosporin recently introduced in clinical practice which displays a \"Trojan Horse\" mechanism, utilizing bacterial iron transportation systems for cell entry. Although it is only used as a last-line antibiotic, resistance has already been observed in clinical isolates. Yet, cefiderocol resistance genes are difficult to monitor as resistance mechanisms remain mostly undescribed in antibiotic resistance gene databases and therefore uncharacterized in the environment. To address this critical gap, we applied functional metagenomics to diverse environmental samples (wastewater, freshwater, and soil) from France, Germany, Sweden, and Pakistan. Four antibiotic resistant genes were identified as responsible for increased cefiderocol minimum inhibitory concentrations to clinically-relevant levels (ranging from 1 to 4 mg/L), including ꞵ-lactamases (VEB-3, OXA-372 homolog, and YbxI homolog) and a partial penicillin-binding protein homolog. None of these genes had been previously reported as a cefiderocol resistance gene. Three out of four had their closest homologs in pathogenic bacteria. The blaVEB-3 gene was associated with a mobile genetic element and distributed across all wastewater metagenomes analyzed in this study. We therefore highlight the critical need for functional metagenomics, to characterize previously uncharacterized last-line antibiotic resistance mechanisms which will be used to enrich antibiotic resistance gene databases and thereby improving antibiotic resistance surveillance in all One Health compartments.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"2 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146056918","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}
Jiao Xi, Hanxiang Tao, Ziyi Zhang, Biyao Lian, Wei Sun, Yang Zhang, Shuhai Bu, Xiaojun Yang, Xun Qian
Driven by wildlife conservation and economic demands, captive breeding has expanded globally, intensifying wildlife–human interactions. In specialty animal breeding, particularly for species with short domestication histories and underdeveloped breeding protocols, clinically important antibiotics are commonly misused, posing potential ecological and health risks that remain largely unexplored. We collected fecal samples from three groups of musk deer (Moschus berezovskii): those exposed to clinically important antibiotics, those not exposed for six months, and wild musk deer, and analyzed their microbiomes and resistomes using metagenomic and culture-based methods. We found that captivity significantly expanded and reshaped the fecal resistome of musk deer. The antibiotic-exposed musk deer harbored a significantly higher diversity and abundance of antibiotic resistance genes (ARGs) compared to those non-exposed to antibiotics and wild deer. We observed a higher abundance of clinically important ARGs within Enterobacteriaceae in fecal samples of captive musk deer. This observation was further supported by the antibiotic susceptibility profiles of 124 Escherichia coli strains isolated from antibiotic-exposed musk deer. Seven identical mobile genetic element-associated ARGs were detected in distinct bacterial hosts across fecal samples from musk deer and farm workers, indicating potential conjugative transfer between the two groups. Our results suggest that captive breeding of specialty animals is an overlooked but significant reservoir for disseminating clinically important ARGs, and underscore the transmission risk at the animal–human interface.
{"title":"Captive breeding of specialty animals represents an overlooked yet critical reservoir for spreading antibiotic resistance genes","authors":"Jiao Xi, Hanxiang Tao, Ziyi Zhang, Biyao Lian, Wei Sun, Yang Zhang, Shuhai Bu, Xiaojun Yang, Xun Qian","doi":"10.1093/ismejo/wrag009","DOIUrl":"https://doi.org/10.1093/ismejo/wrag009","url":null,"abstract":"Driven by wildlife conservation and economic demands, captive breeding has expanded globally, intensifying wildlife–human interactions. In specialty animal breeding, particularly for species with short domestication histories and underdeveloped breeding protocols, clinically important antibiotics are commonly misused, posing potential ecological and health risks that remain largely unexplored. We collected fecal samples from three groups of musk deer (Moschus berezovskii): those exposed to clinically important antibiotics, those not exposed for six months, and wild musk deer, and analyzed their microbiomes and resistomes using metagenomic and culture-based methods. We found that captivity significantly expanded and reshaped the fecal resistome of musk deer. The antibiotic-exposed musk deer harbored a significantly higher diversity and abundance of antibiotic resistance genes (ARGs) compared to those non-exposed to antibiotics and wild deer. We observed a higher abundance of clinically important ARGs within Enterobacteriaceae in fecal samples of captive musk deer. This observation was further supported by the antibiotic susceptibility profiles of 124 Escherichia coli strains isolated from antibiotic-exposed musk deer. Seven identical mobile genetic element-associated ARGs were detected in distinct bacterial hosts across fecal samples from musk deer and farm workers, indicating potential conjugative transfer between the two groups. Our results suggest that captive breeding of specialty animals is an overlooked but significant reservoir for disseminating clinically important ARGs, and underscore the transmission risk at the animal–human interface.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"88 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-01-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146056026","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}
Na Han,Xianhui Peng,Tingting Zhang,Yujun Qiang,Xiuwen Li,Wen Zhang
Plasmids are key vectors for disseminating antibiotic resistance genes, yet their diversity and dynamics in the healthy human gut microbiome remain largely unexplored. Using fecal metagenomes from two cohorts (n = 498 samples), we constructed a comprehensive atlas of the healthy human gut plasmidome. We observed a polarization: while 97.4% of 19 151 plasmid clusters exhibited low prevalence (<5%), we identified 17 plasmid clusters detected in >30% of individuals. Among these, plasmid pGut1 emerged as a paradigm of a stealth vector. Prevalent globally (>50% in independent cohorts), pGut1 possesses a minimal 4-kb conserved backbone ensuring stability and a hypervariable region acting as a "plug-and-play" module. We documented 40 distinct cargo inserts, including multiple antibiotic resistance genes like cfr(C), erm(B), and aphA, across individuals, within individuals over time, and even within single fecal samples, validated by single-cell and Nanopore sequencing. Screening 2.3 million bacterial genomes revealed pGut1 in 93 strains across 49 genera and 2 phyla, including pathogenic Clostridioides difficile and three distinct Salmonella enterica strains. This suggests potential repeated cross-species transmission events, equipping pathogens with new antibiotic resistance genes. Our study exposes a hidden reservoir of highly adaptable, multi-host plasmids like pGut1 silently propagating antibiotic resistance genes in healthy populations. These plasmids, pre-adapted for cross-boundary dissemination, may pose a threat for fueling multidrug-resistant pathogens.
{"title":"Hidden reservoir of highly adaptable multi-host plasmids that propagate antibiotic genes in healthy human populations.","authors":"Na Han,Xianhui Peng,Tingting Zhang,Yujun Qiang,Xiuwen Li,Wen Zhang","doi":"10.1093/ismejo/wrag004","DOIUrl":"https://doi.org/10.1093/ismejo/wrag004","url":null,"abstract":"Plasmids are key vectors for disseminating antibiotic resistance genes, yet their diversity and dynamics in the healthy human gut microbiome remain largely unexplored. Using fecal metagenomes from two cohorts (n = 498 samples), we constructed a comprehensive atlas of the healthy human gut plasmidome. We observed a polarization: while 97.4% of 19 151 plasmid clusters exhibited low prevalence (<5%), we identified 17 plasmid clusters detected in >30% of individuals. Among these, plasmid pGut1 emerged as a paradigm of a stealth vector. Prevalent globally (>50% in independent cohorts), pGut1 possesses a minimal 4-kb conserved backbone ensuring stability and a hypervariable region acting as a \"plug-and-play\" module. We documented 40 distinct cargo inserts, including multiple antibiotic resistance genes like cfr(C), erm(B), and aphA, across individuals, within individuals over time, and even within single fecal samples, validated by single-cell and Nanopore sequencing. Screening 2.3 million bacterial genomes revealed pGut1 in 93 strains across 49 genera and 2 phyla, including pathogenic Clostridioides difficile and three distinct Salmonella enterica strains. This suggests potential repeated cross-species transmission events, equipping pathogens with new antibiotic resistance genes. Our study exposes a hidden reservoir of highly adaptable, multi-host plasmids like pGut1 silently propagating antibiotic resistance genes in healthy populations. These plasmids, pre-adapted for cross-boundary dissemination, may pose a threat for fueling multidrug-resistant pathogens.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"36 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-01-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146021688","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}
Daniel Martak, Thibault Bourdin, Benoit Valot, Audrey Laboissière, Frédéric Lirussi, Xavier Bertrand, Edward Topp, Didier Hocquet
Antimicrobial resistance (AMR) is a serious global health threat, yet the drivers of its spread among humans are not fully understood. Antibiotics can enter the human gastrointestinal tract through the food chain, leading to the presence of low concentrations in the gut microbiota. However, the role of such traces in promoting the implantation of drug-resistant pathogens in the gut microbiota has never been explored in a controlled experimental setting. Using an in vitro model of the human gut microbiota, we tested whether traces of 19 antibiotics used in both human and veterinary medicine, alone or in combination, lead to the enrichment of Gram-negative pathogens producing extended-spectrum β-lactamases or carbapenemases. 28 strains of Gram-negative pathogens epidemic in humans (10 Escherichia coli, 6 Klebsiella pneumoniae, 5 Enterobacter hormaechei, 4 Acinetobacter baumannii, 3 Pseudomonas aeruginosa) were tested. We found that antibiotics at levels similar to those measured in the feces of healthy individuals (fluoroquinolones, 1–100 μg L−1; trimethoprim, 100 μg L−1; a mixture of fifteen veterinary antibiotics, 10–20 μg L−1) enriched the human gut microbiota with those resistant pathogens. Overall, the present study indicates that dietary consumption of some antibiotics can result in concentrations in the human colon sufficiently high to favor the implantation of exogenous antibiotic-resistant pathogens. These findings highlight the need to reassess permissible antibiotic concentrations in food and critically evaluate agricultural practices contributing to the contamination of animal- and plant-based products.
{"title":"Foodborne antibiotics enrich human gut microbiota with pathogens producing extended-spectrum β-lactamases and carbapenemases","authors":"Daniel Martak, Thibault Bourdin, Benoit Valot, Audrey Laboissière, Frédéric Lirussi, Xavier Bertrand, Edward Topp, Didier Hocquet","doi":"10.1093/ismejo/wrag008","DOIUrl":"https://doi.org/10.1093/ismejo/wrag008","url":null,"abstract":"Antimicrobial resistance (AMR) is a serious global health threat, yet the drivers of its spread among humans are not fully understood. Antibiotics can enter the human gastrointestinal tract through the food chain, leading to the presence of low concentrations in the gut microbiota. However, the role of such traces in promoting the implantation of drug-resistant pathogens in the gut microbiota has never been explored in a controlled experimental setting. Using an in vitro model of the human gut microbiota, we tested whether traces of 19 antibiotics used in both human and veterinary medicine, alone or in combination, lead to the enrichment of Gram-negative pathogens producing extended-spectrum β-lactamases or carbapenemases. 28 strains of Gram-negative pathogens epidemic in humans (10 Escherichia coli, 6 Klebsiella pneumoniae, 5 Enterobacter hormaechei, 4 Acinetobacter baumannii, 3 Pseudomonas aeruginosa) were tested. We found that antibiotics at levels similar to those measured in the feces of healthy individuals (fluoroquinolones, 1–100 μg L−1; trimethoprim, 100 μg L−1; a mixture of fifteen veterinary antibiotics, 10–20 μg L−1) enriched the human gut microbiota with those resistant pathogens. Overall, the present study indicates that dietary consumption of some antibiotics can result in concentrations in the human colon sufficiently high to favor the implantation of exogenous antibiotic-resistant pathogens. These findings highlight the need to reassess permissible antibiotic concentrations in food and critically evaluate agricultural practices contributing to the contamination of animal- and plant-based products.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"68 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146044820","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}
Chen Zhang, Siavash Atashgahi, Tom N P Bosma, Hauke Smidt
Marine sediments harbour diverse organohalide-respiring bacteria (OHRB), but their functional roles and metabolic interactions remains poorly understood. To investigate these interactions, we obtained and characterized a debrominating consortium from Aarhus Bay marine sediments. The consortium transformed 2,6-dibromophenol (2,6-DBP) to phenol under sulfate-reducing conditions, with bacterial growth demonstrating respiratory energy conservation. Metagenomic analysis and binning revealed five new species-level populations (>85% complete, <3% contaminated) dominated by Desulforhopalus (bin.5). Critically, bin.5 encodes a thiolytic tetrachloro-p-hydroquinone (TPh-) reductive dehalogenase (RDase), previously characterized only in aerobic bacteria, representing evidence of this enzyme functioning in a strictly anaerobic sulfate-reducing bacterium. Two additional populations (Desulfoplanes bin.3 and Marinifilaceae bin.4) encoded two and one putative respiratory corrinoid-dependent RDase, respectively. Transcription of all four RDase genes was rapidly induced upon 2,6-DBP addition, indicating multi-population response. Acetylene inhibited debromination post-transcriptionally without affecting RDase gene transcription, or sulfate metabolism, confirming RDase-mediated catalysis. Genome analysis indicated bin.5 encodes a near-complete vitamin B12 biosynthesis pathway (lacking only cbiJ, which can be bypassed through alternative reductases), consistent with debromination activity independent of exogenous B12 addition. Comparative genomics identified Marinifilum and Ancylomarina as candidate OHRB taxa, substantially expanding known phylogenetic diversity of marine organohalide respirers. This work reveals previously unrecognized biochemical versatility in anaerobic dehalogenation and demonstrates metabolic self-sufficiency enabling organohalide respiration in oligotrophic marine sediments.
{"title":"Organohalide respiration by a Desulforhopalus -dominated community","authors":"Chen Zhang, Siavash Atashgahi, Tom N P Bosma, Hauke Smidt","doi":"10.1093/ismejo/wrag007","DOIUrl":"https://doi.org/10.1093/ismejo/wrag007","url":null,"abstract":"Marine sediments harbour diverse organohalide-respiring bacteria (OHRB), but their functional roles and metabolic interactions remains poorly understood. To investigate these interactions, we obtained and characterized a debrominating consortium from Aarhus Bay marine sediments. The consortium transformed 2,6-dibromophenol (2,6-DBP) to phenol under sulfate-reducing conditions, with bacterial growth demonstrating respiratory energy conservation. Metagenomic analysis and binning revealed five new species-level populations (&gt;85% complete, &lt;3% contaminated) dominated by Desulforhopalus (bin.5). Critically, bin.5 encodes a thiolytic tetrachloro-p-hydroquinone (TPh-) reductive dehalogenase (RDase), previously characterized only in aerobic bacteria, representing evidence of this enzyme functioning in a strictly anaerobic sulfate-reducing bacterium. Two additional populations (Desulfoplanes bin.3 and Marinifilaceae bin.4) encoded two and one putative respiratory corrinoid-dependent RDase, respectively. Transcription of all four RDase genes was rapidly induced upon 2,6-DBP addition, indicating multi-population response. Acetylene inhibited debromination post-transcriptionally without affecting RDase gene transcription, or sulfate metabolism, confirming RDase-mediated catalysis. Genome analysis indicated bin.5 encodes a near-complete vitamin B12 biosynthesis pathway (lacking only cbiJ, which can be bypassed through alternative reductases), consistent with debromination activity independent of exogenous B12 addition. Comparative genomics identified Marinifilum and Ancylomarina as candidate OHRB taxa, substantially expanding known phylogenetic diversity of marine organohalide respirers. This work reveals previously unrecognized biochemical versatility in anaerobic dehalogenation and demonstrates metabolic self-sufficiency enabling organohalide respiration in oligotrophic marine sediments.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"51 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146048042","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}
Guillaume Chesneau, Alba Noel, Dimitri Bréard, Alice Boulanger, Martial Briand, Sophie Bonneau, Chrystelle Brin, Marion Fischer-Le Saux, Yujia Liu, Andrew Hendrickson, Torben Nielsen, Alain Sarniguet, David Guilet, Adam Arkin, Lauren Lui, Matthieu Barret
The seed is a habitat with limited resources and space. Although it is widely accepted that microbial competition is a key driver of the assembly of seed-associated microbial communities, the underlying mechanisms of this competition are not well understood. The initial objective of this work was to assess the importance of contact-independent microbial competition between the phytopathogenic bacterium Xanthomonas campestris pv. campestris 8004 (Xcc8004) and 30 strains representative of the bacterial populations most commonly associated with radish (Raphanus sativus) seeds. We identified Pseudomonas lactucae CFBP 13502 as a potent inhibitor of Xcc8004, mediated by exometabolites, specifically induced by certain seed-borne strains. Transcriptomic analysis linked this inducible activity to the upregulation of a gene cluster encoding a lipopeptide siderophore. Targeted gene deletion in P. lactucae CFBP 13502 confirmed that this cluster is essential for antagonism against Xcc8004. Furthermore, iron supplementation abolished this inhibitory effect, strongly supporting iron chelation as the underlying mechanism. Through comparative metabolomics, we elucidated the structure of a family of lipopeptide siderophores, produced by P. lactucae CFBP 13502, which we named lactuchelins. Our findings provide molecular evidence of competitive exclusion mechanisms at the seed microbiome interface, highlighting lactuchelins as a promising avenue for the development of seed-based biocontrol strategies against seed-borne phytopathogens.
{"title":"Lactuchelins represent lipopeptide siderophores produced by Pseudomonas lactucae that inhibit Xanthomonas campestris","authors":"Guillaume Chesneau, Alba Noel, Dimitri Bréard, Alice Boulanger, Martial Briand, Sophie Bonneau, Chrystelle Brin, Marion Fischer-Le Saux, Yujia Liu, Andrew Hendrickson, Torben Nielsen, Alain Sarniguet, David Guilet, Adam Arkin, Lauren Lui, Matthieu Barret","doi":"10.1093/ismejo/wrag003","DOIUrl":"https://doi.org/10.1093/ismejo/wrag003","url":null,"abstract":"The seed is a habitat with limited resources and space. Although it is widely accepted that microbial competition is a key driver of the assembly of seed-associated microbial communities, the underlying mechanisms of this competition are not well understood. The initial objective of this work was to assess the importance of contact-independent microbial competition between the phytopathogenic bacterium Xanthomonas campestris pv. campestris 8004 (Xcc8004) and 30 strains representative of the bacterial populations most commonly associated with radish (Raphanus sativus) seeds. We identified Pseudomonas lactucae CFBP 13502 as a potent inhibitor of Xcc8004, mediated by exometabolites, specifically induced by certain seed-borne strains. Transcriptomic analysis linked this inducible activity to the upregulation of a gene cluster encoding a lipopeptide siderophore. Targeted gene deletion in P. lactucae CFBP 13502 confirmed that this cluster is essential for antagonism against Xcc8004. Furthermore, iron supplementation abolished this inhibitory effect, strongly supporting iron chelation as the underlying mechanism. Through comparative metabolomics, we elucidated the structure of a family of lipopeptide siderophores, produced by P. lactucae CFBP 13502, which we named lactuchelins. Our findings provide molecular evidence of competitive exclusion mechanisms at the seed microbiome interface, highlighting lactuchelins as a promising avenue for the development of seed-based biocontrol strategies against seed-borne phytopathogens.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"101 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-01-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145986545","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}
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