Carolyn A Miller, Enrico Pirotta, Sharon Grim, Michael J Moore, John W Durban, Peter L Tyack, Holly Fearnbach, Samantha G M Leander, Amy R Knowlton, Amy M Warren, Monica A Zani, Regina Asmutis-Silvia, Heather M Pettis, Amy Apprill
As important members of the marine ecosystem, baleen whales are frequently managed and protected, but methodology to assess their health remains limited. Recent technological advances, such as the use of drones, support the non-invasive collection of promising health-associated data, including respiratory exhalant microbiota. Here, we considered five health metrics paired with respiratory exhalant samples to examine the utility of characterizing respiratory microorganisms for health diagnostics of North Atlantic right whales (Eubalaena glacialis), one of the most endangered baleen whale species. In 2016–2024, we used drones to collect 103 exhalant samples from 85 individuals to examine the associated microbiome, using amplicon sequencing methods targeting bacteria and archaea. The health status of sampled whales was characterized using an index of body condition derived from full-body vertical drone images, three qualitative assessments obtained from photo-identification imagery, and an existing health and vital rates model. Using an elastic net penalized regression approach, we demonstrate significant relationships between these health metrics and respiratory-associated microorganisms. Bacterial taxa that significantly contributed to the model for the body condition index differed between the thinnest and most robust males in the dataset. The thin whale harbored taxa belonging to the same genus as mammalian pathogens, Clostridium and Peptoniphilus, whereas the robust whale harbored taxa commonly observed in lipid-rich environments, Sediminispirochaeta and Candidatus Gracilibacteria. These differences warrant further investigation into the mechanisms by which bacteria contribute to whale health. Our findings demonstrate the utility of non-invasive multi-metric health models that include respiratory exhalant microbiota for whale health assessment and management.
{"title":"Respiratory microbiomes reflect whale health","authors":"Carolyn A Miller, Enrico Pirotta, Sharon Grim, Michael J Moore, John W Durban, Peter L Tyack, Holly Fearnbach, Samantha G M Leander, Amy R Knowlton, Amy M Warren, Monica A Zani, Regina Asmutis-Silvia, Heather M Pettis, Amy Apprill","doi":"10.1093/ismejo/wraf231","DOIUrl":"https://doi.org/10.1093/ismejo/wraf231","url":null,"abstract":"As important members of the marine ecosystem, baleen whales are frequently managed and protected, but methodology to assess their health remains limited. Recent technological advances, such as the use of drones, support the non-invasive collection of promising health-associated data, including respiratory exhalant microbiota. Here, we considered five health metrics paired with respiratory exhalant samples to examine the utility of characterizing respiratory microorganisms for health diagnostics of North Atlantic right whales (Eubalaena glacialis), one of the most endangered baleen whale species. In 2016–2024, we used drones to collect 103 exhalant samples from 85 individuals to examine the associated microbiome, using amplicon sequencing methods targeting bacteria and archaea. The health status of sampled whales was characterized using an index of body condition derived from full-body vertical drone images, three qualitative assessments obtained from photo-identification imagery, and an existing health and vital rates model. Using an elastic net penalized regression approach, we demonstrate significant relationships between these health metrics and respiratory-associated microorganisms. Bacterial taxa that significantly contributed to the model for the body condition index differed between the thinnest and most robust males in the dataset. The thin whale harbored taxa belonging to the same genus as mammalian pathogens, Clostridium and Peptoniphilus, whereas the robust whale harbored taxa commonly observed in lipid-rich environments, Sediminispirochaeta and Candidatus Gracilibacteria. These differences warrant further investigation into the mechanisms by which bacteria contribute to whale health. Our findings demonstrate the utility of non-invasive multi-metric health models that include respiratory exhalant microbiota for whale health assessment and management.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-11-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145478420","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}
Hylke H Kortenbosch, Bo Briggeman, Francisca Reyes Marquez, Ben Auxier, Sytze de Bruin, Bas J Zwaan, Eveline Snelders
Humans are exposed to the mould Aspergillus fumigatus via inhalation, and infections are increasingly resistant to triazole-class antifungals. Ecologically, this fungus is a ubiquitous saprotroph found in terrestrial environments. Although triazole-resistant A. fumigatus is found in large quantities in specific agricultural environments; it is not clear how much these contribute to the overall exposure of individuals to antifungal resistance. Triazoles are also used to protect a wide range of products unrelated to agriculture, and therefore, it could not be excluded that the resistance observed in agricultural settings may be the result of selection beyond agricultural sources. In the case of A. fumigatus genomics cannot reliably link resistant isolates to specific environmental sources. Therefore, we used a spatial sampling approach to measure population trends in triazole resistance. We conducted a large-scale, unbiased air sampling throughout the Netherlands using a citizen science approach. We find that $sim $4$%$ of over 60K screened colonies are resistant to clinical triazoles. Modelling resistance data with spatial land-use data shows that agricultural land use, particularly flower bulbs and greenhouses, can predict peaks in antifungal resistance in airborne A. fumigatus in the Netherlands. Furthermore, genotyping resistant isolates suggests land-use-associated niche differentiation between two dominant resistance haplotypes, with only one of the two showing a significant association with agricultural land use. By linking triazole resistance to land use, this work informs necessary policy-driven changes to reduce human exposure to antifungal-resistant A. fumigatus, and suggests that similar spatial patterns in antifungal resistance may occur in other agriculture-associated fungi as well.
{"title":"Land use drives drug resistance in an airborne human fungal pathogen","authors":"Hylke H Kortenbosch, Bo Briggeman, Francisca Reyes Marquez, Ben Auxier, Sytze de Bruin, Bas J Zwaan, Eveline Snelders","doi":"10.1093/ismejo/wraf246","DOIUrl":"https://doi.org/10.1093/ismejo/wraf246","url":null,"abstract":"Humans are exposed to the mould Aspergillus fumigatus via inhalation, and infections are increasingly resistant to triazole-class antifungals. Ecologically, this fungus is a ubiquitous saprotroph found in terrestrial environments. Although triazole-resistant A. fumigatus is found in large quantities in specific agricultural environments; it is not clear how much these contribute to the overall exposure of individuals to antifungal resistance. Triazoles are also used to protect a wide range of products unrelated to agriculture, and therefore, it could not be excluded that the resistance observed in agricultural settings may be the result of selection beyond agricultural sources. In the case of A. fumigatus genomics cannot reliably link resistant isolates to specific environmental sources. Therefore, we used a spatial sampling approach to measure population trends in triazole resistance. We conducted a large-scale, unbiased air sampling throughout the Netherlands using a citizen science approach. We find that $sim $4$%$ of over 60K screened colonies are resistant to clinical triazoles. Modelling resistance data with spatial land-use data shows that agricultural land use, particularly flower bulbs and greenhouses, can predict peaks in antifungal resistance in airborne A. fumigatus in the Netherlands. Furthermore, genotyping resistant isolates suggests land-use-associated niche differentiation between two dominant resistance haplotypes, with only one of the two showing a significant association with agricultural land use. By linking triazole resistance to land use, this work informs necessary policy-driven changes to reduce human exposure to antifungal-resistant A. fumigatus, and suggests that similar spatial patterns in antifungal resistance may occur in other agriculture-associated fungi as well.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"28 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-11-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145472858","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 human nasal microbiome can serve as a reservoir for pathogens. In particular, the opportunistic pathogen Staphylococcus aureus can be a member of the nasal microbiome increasing the risk of subsequent infections. The nasal carriage of S. aureus is known to be positively and negatively impacted by non-pathogenic species, suggesting interactions between the pathogen and commensals, but the underlying molecular mechanism remains largely unclear. Herein we demonstrate that S. aureus competes with nasal commensals for the coenzyme biotin. Biotin is crucial for all living organisms and we show that depletion of biotin impairs S. aureus growth and membrane integrity. We found the nasal cavity to be a biotin-limited environment, suggesting competition for the coenzyme within the microbiome. For some nasal commensals and S. aureus, we observed biotin prototrophy and all strains released biotin into the environment. In contrast, other commensals and especially coagulase-negative staphylococci (CoNS) were found to be biotin auxotrophs and strongly reliant on prototrophic strains under biotin-limited conditions. We show that high-affinity biotin uptake systems are used by prototrophic and auxotrophic strains alike and represent crucial factors to optimize competitive fitness of species in co-culture. Together, our data show that biotin-mediated interactions occur between the species of the human nasal microbiome and provide evidence for interspecies competition and co-dependency.
{"title":"Competitive fitness of Staphylococcus aureus against nasal commensals depends on biotin biosynthesis and acquisition.","authors":"Kevser Bilici,David Gerlach,Laura Camus,Simon Heilbronner","doi":"10.1093/ismejo/wraf248","DOIUrl":"https://doi.org/10.1093/ismejo/wraf248","url":null,"abstract":"The human nasal microbiome can serve as a reservoir for pathogens. In particular, the opportunistic pathogen Staphylococcus aureus can be a member of the nasal microbiome increasing the risk of subsequent infections. The nasal carriage of S. aureus is known to be positively and negatively impacted by non-pathogenic species, suggesting interactions between the pathogen and commensals, but the underlying molecular mechanism remains largely unclear. Herein we demonstrate that S. aureus competes with nasal commensals for the coenzyme biotin. Biotin is crucial for all living organisms and we show that depletion of biotin impairs S. aureus growth and membrane integrity. We found the nasal cavity to be a biotin-limited environment, suggesting competition for the coenzyme within the microbiome. For some nasal commensals and S. aureus, we observed biotin prototrophy and all strains released biotin into the environment. In contrast, other commensals and especially coagulase-negative staphylococci (CoNS) were found to be biotin auxotrophs and strongly reliant on prototrophic strains under biotin-limited conditions. We show that high-affinity biotin uptake systems are used by prototrophic and auxotrophic strains alike and represent crucial factors to optimize competitive fitness of species in co-culture. Together, our data show that biotin-mediated interactions occur between the species of the human nasal microbiome and provide evidence for interspecies competition and co-dependency.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"85 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-11-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145440831","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}
Microbial communities are crucial in host adaptation to stressors, particularly in dynamic ecosystems. In aquatic environments, Daphnia magna is ideal for studying host-microbiome interactions due to its ecological importance and sensitivity. Adaptation to toxins, such as those produced by cyanobacteria, may involve both host and microbial gene repertoires. Yet, the influence of microbiota composition and function on host performance remains poorly understood. Because epigenetic mechanisms such as DNA methylation regulate gene expression and mediate adaptive responses, we also investigated whether these associations are reflected in DNA methylation levels. To address this, we conducted a fully factorial transplant experiment using microbiota-depleted Daphnia colonised with microbiota from the same or different genotype, previously exposed to toxic or non-toxic diets, or left uncolonised. We assessed life-history traits, microbial composition (16S rRNA genes), functional profiles (whole-genome-resequencing), and DNA methylation (colorimetric quantification). Daphnia fed non-toxic diets grew larger and reproduced more. Increased methylation occurred when microbiota donors differed from the host genotype and was strongest under toxic diet. Dysbiosis and reduced performance were noted in individuals colonised with toxic-diet microbiota from another genotype, where Limnohabitans spp. was reduced or absent. Signs of hormesis emerged when Daphnia received microbiota from their own genotype reared on non-toxic diets. DNA methylation of both host and microbiota was associated with functional pathways, including increased mitochondrial fatty acid biosynthesis. These findings highlight the importance of host-microbiota matching and microbial environmental history in shaping host performance and epigenetic responses, emphasizing the need to consider host-microbe-environment interactions in evolutionary and ecological studies.
{"title":"Host-microbiota matching and epigenetic modulation drive Daphnia magna responses to cyanobacterial stress.","authors":"Karen Bisschop,Naina Goel,Manon Coone,Isabel Vanoverberghe,Anna Greffe,Jana Asselman,Ellen Decaestecker","doi":"10.1093/ismejo/wraf247","DOIUrl":"https://doi.org/10.1093/ismejo/wraf247","url":null,"abstract":"Microbial communities are crucial in host adaptation to stressors, particularly in dynamic ecosystems. In aquatic environments, Daphnia magna is ideal for studying host-microbiome interactions due to its ecological importance and sensitivity. Adaptation to toxins, such as those produced by cyanobacteria, may involve both host and microbial gene repertoires. Yet, the influence of microbiota composition and function on host performance remains poorly understood. Because epigenetic mechanisms such as DNA methylation regulate gene expression and mediate adaptive responses, we also investigated whether these associations are reflected in DNA methylation levels. To address this, we conducted a fully factorial transplant experiment using microbiota-depleted Daphnia colonised with microbiota from the same or different genotype, previously exposed to toxic or non-toxic diets, or left uncolonised. We assessed life-history traits, microbial composition (16S rRNA genes), functional profiles (whole-genome-resequencing), and DNA methylation (colorimetric quantification). Daphnia fed non-toxic diets grew larger and reproduced more. Increased methylation occurred when microbiota donors differed from the host genotype and was strongest under toxic diet. Dysbiosis and reduced performance were noted in individuals colonised with toxic-diet microbiota from another genotype, where Limnohabitans spp. was reduced or absent. Signs of hormesis emerged when Daphnia received microbiota from their own genotype reared on non-toxic diets. DNA methylation of both host and microbiota was associated with functional pathways, including increased mitochondrial fatty acid biosynthesis. These findings highlight the importance of host-microbiota matching and microbial environmental history in shaping host performance and epigenetic responses, emphasizing the need to consider host-microbe-environment interactions in evolutionary and ecological studies.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"112 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-11-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145433853","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}
Xuhui Huang,Emily E Chase,Brittany N Zepernick,Robbie M Martin,Lauren E Krausfeldt,Helena L Pound,Hanqi Wu,Zheng Zheng,Steven W Wilhelm
Cyanobacterial blooms dominated by Microcystis spp. pose significant ecological challenges, including the release of toxins and disruption of aquatic food webs. Although Microcystis can exist as free-living single cells or within dense mucilaginous colonies, the drivers and consequences of colony formation remain unclear. Here, we integrated metatranscriptomic datasets from two Microcystis bloom events in Lake Taihu, China, to analyze and to support findings on the functional differences between colonial and single-cell Microcystis. Our results confirmed colony expression profiles were disproportionately enriched in Microcystis transcripts compared to other prokaryotic taxa. This pattern exhibits Black Queen-like dynamics, where Microcystis assumes greater metabolic and defensive roles while associated bacteria reduce their transcriptional activity. Concomitantly, viral infection strategies diverged by Microcystis community morphology: colony-associated cells expressed lysogeny-associated genes, whereas single cells exhibited increased signatures of lytic infection. These data are consistent with the hypothesis that Microcystis colonies foster conditions favorable to lysogen formation-likely due to local high cell densities and the resulting advantage of superinfection immunity-whereas solitary cells experience stronger lytic pressure. On a broader scale, our findings refine the understanding of bloom dynamics by identifying how community morphological states coincide with distinct host-virus interactions. Cumulatively, this work underscores the importance of colony formation in shaping Microcystis ecology and highlights the need for further mechanistic studies to disentangle the complex interplay between phage infection modes, colony formation, and microbial community structure.
{"title":"Contrasting viral infection strategies for single cell and colonial Microcystis populations consistent with Black Queen dynamics.","authors":"Xuhui Huang,Emily E Chase,Brittany N Zepernick,Robbie M Martin,Lauren E Krausfeldt,Helena L Pound,Hanqi Wu,Zheng Zheng,Steven W Wilhelm","doi":"10.1093/ismejo/wraf244","DOIUrl":"https://doi.org/10.1093/ismejo/wraf244","url":null,"abstract":"Cyanobacterial blooms dominated by Microcystis spp. pose significant ecological challenges, including the release of toxins and disruption of aquatic food webs. Although Microcystis can exist as free-living single cells or within dense mucilaginous colonies, the drivers and consequences of colony formation remain unclear. Here, we integrated metatranscriptomic datasets from two Microcystis bloom events in Lake Taihu, China, to analyze and to support findings on the functional differences between colonial and single-cell Microcystis. Our results confirmed colony expression profiles were disproportionately enriched in Microcystis transcripts compared to other prokaryotic taxa. This pattern exhibits Black Queen-like dynamics, where Microcystis assumes greater metabolic and defensive roles while associated bacteria reduce their transcriptional activity. Concomitantly, viral infection strategies diverged by Microcystis community morphology: colony-associated cells expressed lysogeny-associated genes, whereas single cells exhibited increased signatures of lytic infection. These data are consistent with the hypothesis that Microcystis colonies foster conditions favorable to lysogen formation-likely due to local high cell densities and the resulting advantage of superinfection immunity-whereas solitary cells experience stronger lytic pressure. On a broader scale, our findings refine the understanding of bloom dynamics by identifying how community morphological states coincide with distinct host-virus interactions. Cumulatively, this work underscores the importance of colony formation in shaping Microcystis ecology and highlights the need for further mechanistic studies to disentangle the complex interplay between phage infection modes, colony formation, and microbial community structure.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-11-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145433856","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}
Fangze Gui,Yusufjon Gafforov,Juan Ignacio Vílchez,Jiangtao Zhao,Zhonghua Ma,Tianxing Lv,Mengcen Wang
Chemical communication, a universal mode among the interactive members within dynamic plant-microbiome systems, fundamentally drives coevolutionary trajectories. Emerging evidence suggests the critical role of epigenetic regulation in chemical communication, though its mechanistic insights are yet not well understood, a gap that has limited the precise mining of microbiomes function in modern agriculture. Here, we synthesize recent findings from chemistry to epigenetics to illuminate the overlooked epigenetic landscape in plant-microbiome chemical communication. Revisiting the traditional plant-pathogen interaction model and a more complex ternary model involving the plant resident microbiota, we not only present knowledge gaps but also critically dissect the paradoxical roles of resident microbiota by proposing four chemo-epigenetic patterns that fine-tune the interactions among plants, resident microbiota and pathogens. Further, Intelligent Click Chemistry (ICC), an innovative interdisciplinary strategy integrating click chemistry and artificial intelligence, is proposed and discussed, with the aim of unraveling the complex chemo-epigenetic events underlying plant-microbiome chemical communication. Untangling the epigenetic landscape underpinning plant-microbiome chemical communication would enable the strategic and precise exploitation of beneficial microbial traits and suppression of detrimental interactions for sustainable agriculture.
{"title":"Epigenetic landscape underlying plant-microbiome chemical communication.","authors":"Fangze Gui,Yusufjon Gafforov,Juan Ignacio Vílchez,Jiangtao Zhao,Zhonghua Ma,Tianxing Lv,Mengcen Wang","doi":"10.1093/ismejo/wraf249","DOIUrl":"https://doi.org/10.1093/ismejo/wraf249","url":null,"abstract":"Chemical communication, a universal mode among the interactive members within dynamic plant-microbiome systems, fundamentally drives coevolutionary trajectories. Emerging evidence suggests the critical role of epigenetic regulation in chemical communication, though its mechanistic insights are yet not well understood, a gap that has limited the precise mining of microbiomes function in modern agriculture. Here, we synthesize recent findings from chemistry to epigenetics to illuminate the overlooked epigenetic landscape in plant-microbiome chemical communication. Revisiting the traditional plant-pathogen interaction model and a more complex ternary model involving the plant resident microbiota, we not only present knowledge gaps but also critically dissect the paradoxical roles of resident microbiota by proposing four chemo-epigenetic patterns that fine-tune the interactions among plants, resident microbiota and pathogens. Further, Intelligent Click Chemistry (ICC), an innovative interdisciplinary strategy integrating click chemistry and artificial intelligence, is proposed and discussed, with the aim of unraveling the complex chemo-epigenetic events underlying plant-microbiome chemical communication. Untangling the epigenetic landscape underpinning plant-microbiome chemical communication would enable the strategic and precise exploitation of beneficial microbial traits and suppression of detrimental interactions for sustainable agriculture.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"35 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-11-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145433854","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}
This study reports the isolation and characterization of Bacteriovorax sp. As-1, a predatory bacterium recovered from the gut of oxytetracycline-treated juvenile rainbow trout (Oncorhynchus mykiss). Phylogenetic and genomic analysis indicate it is closely related to Bacteriovorax stolpii DSM 12778T, although genomic metrics suggest it represents a new species. Like other Bdellovibrio-and-like organisms, Bacteriovorax sp. As-1 exhibits predatory activity against Aeromonas salmonicida, significantly reducing its prey viability by nearly six orders of magnitude. However, whole genome sequencing revealed the presence of multiple antibiotic resistance genes, including those previously associated with decreased susceptibility to tetracyclines, aminoglycosides, sulfonamides, and fluoroquinolones, located within genomic islands, and flanked by insertion sequences, suggesting acquisition via horizontal gene transfer. In addition to these, mutations were also detected in gyrA gene that confer resistance to ciprofloxacin. Phenotypic assays confirmed Bacteriovorax sp. As-1 has increased antibiotic resistance as compared to Bx. stolpii DSM 12778T. This study presents a natural predatory strain carrying IS-linked ARG clusters consistent with horizontal gene transfer, highlighting their potential role as reservoirs of resistance determinants in antibiotic-enriched environments.
{"title":"Acquisition of Novel Antibiotic Resistance Genes by the Bacterial Predator Bacteriovorax sp. As-1.","authors":"Fathrinah Binti Kohadie,Young-Ung Heo,Wonsik Mun,Sumin Choi,Sinseong Park,Yoonhang Lee,Do-Hyung Kim,Robert J Mitchell","doi":"10.1093/ismejo/wraf245","DOIUrl":"https://doi.org/10.1093/ismejo/wraf245","url":null,"abstract":"This study reports the isolation and characterization of Bacteriovorax sp. As-1, a predatory bacterium recovered from the gut of oxytetracycline-treated juvenile rainbow trout (Oncorhynchus mykiss). Phylogenetic and genomic analysis indicate it is closely related to Bacteriovorax stolpii DSM 12778T, although genomic metrics suggest it represents a new species. Like other Bdellovibrio-and-like organisms, Bacteriovorax sp. As-1 exhibits predatory activity against Aeromonas salmonicida, significantly reducing its prey viability by nearly six orders of magnitude. However, whole genome sequencing revealed the presence of multiple antibiotic resistance genes, including those previously associated with decreased susceptibility to tetracyclines, aminoglycosides, sulfonamides, and fluoroquinolones, located within genomic islands, and flanked by insertion sequences, suggesting acquisition via horizontal gene transfer. In addition to these, mutations were also detected in gyrA gene that confer resistance to ciprofloxacin. Phenotypic assays confirmed Bacteriovorax sp. As-1 has increased antibiotic resistance as compared to Bx. stolpii DSM 12778T. This study presents a natural predatory strain carrying IS-linked ARG clusters consistent with horizontal gene transfer, highlighting their potential role as reservoirs of resistance determinants in antibiotic-enriched environments.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"22 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-11-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145433822","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}
Silvia Abbà,Liam D Adair,Francesca Barbero,Luca P Casacci,Iljia Dukovski,Francisca Font,Tom Hawtrey,Elizabeth J New,Jukkrit Nootem,Pramsak Patawanich,Lukas Patten,Marco Polin,Daniel Segrè,Nian Kee Tan,Irene Stefanini
Saccharomyces cerevisiae relies on social wasps (e.g., Vespa crabro, Polistes spp.) for dispersal and genetic mixing. Unlike most natural environments, wasp intestines provide conditions that support yeast survival, sporulation, spore germination, and mating. This study explores the mechanisms at the basis of this process by examining the wasp gut environment and yeast responses. Molecular analyses based on yeast deletion collection and transcriptomics showed that yeast sporulates in the crop, spores germinate in the gut, and cells ferment in the gut. The crop and gut differ chemically: the gut has more sugars, a higher pH, and (in workers) greater viscosity. In vitro tests confirmed yeast survival in both environments, with faster germination in gut-like conditions. Computational models based on these physicochemical traits matched the experimental results. The data obtained provide fundamental insights into yeast progression towards mating within wasps' intestines and suggest a possible relation between yeast alcoholic fermentation and wasps' alcohol tolerance, thereby enhancing our understanding of the S. cerevisiae-social wasp association.
{"title":"Wasp intestinal cues drive yeast toward outbreeding strategies.","authors":"Silvia Abbà,Liam D Adair,Francesca Barbero,Luca P Casacci,Iljia Dukovski,Francisca Font,Tom Hawtrey,Elizabeth J New,Jukkrit Nootem,Pramsak Patawanich,Lukas Patten,Marco Polin,Daniel Segrè,Nian Kee Tan,Irene Stefanini","doi":"10.1093/ismejo/wraf243","DOIUrl":"https://doi.org/10.1093/ismejo/wraf243","url":null,"abstract":"Saccharomyces cerevisiae relies on social wasps (e.g., Vespa crabro, Polistes spp.) for dispersal and genetic mixing. Unlike most natural environments, wasp intestines provide conditions that support yeast survival, sporulation, spore germination, and mating. This study explores the mechanisms at the basis of this process by examining the wasp gut environment and yeast responses. Molecular analyses based on yeast deletion collection and transcriptomics showed that yeast sporulates in the crop, spores germinate in the gut, and cells ferment in the gut. The crop and gut differ chemically: the gut has more sugars, a higher pH, and (in workers) greater viscosity. In vitro tests confirmed yeast survival in both environments, with faster germination in gut-like conditions. Computational models based on these physicochemical traits matched the experimental results. The data obtained provide fundamental insights into yeast progression towards mating within wasps' intestines and suggest a possible relation between yeast alcoholic fermentation and wasps' alcohol tolerance, thereby enhancing our understanding of the S. cerevisiae-social wasp association.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145411535","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}
Sai Yang,Jiawei Zhang,Yafei Ou,Wenxiao Liu,Xinru Tian,Li-Jun Hou,Hong-Po Dong
Aerobic methanotrophs encode a hydroxylamine oxidoreductase, which facilitates the oxidation of ammonia to nitrite or nitric oxide, potentially leading to nitrous oxide production. Aerobic methane oxidation has been documented in shallow marine waters or the water column of the open ocean. However, little is known about the distribution pattern of marine aerobic methanotrophs containing hydroxylamine oxidoreductase and their contribution to marine nitrous oxide emissions. Here, by analyzing global marine metagenomes, we show that hydroxylamine oxidoreductase-containing aerobic methanotrophs were widely distributed across diverse marine habitats, with higher abundances in methane seep systems and estuary regions than in other environments. Among these, aerobic methanotrophs belonging to Gammaproteobacteria were the most widely distributed and abundant functional group. We also identified a second order within Gammaproteobacteria (Ga0077536) potentially capable of aerobic methanotrophy, and a complete repertoire of denitrification genes in a gammaproteobacterial methanotroph, expanding the phylogenetic and functional diversity of marine aerobic methanotrophs. By using enrichments of estuarine methanotrophs in combination with 15N stable isotope tracing and metatranscriptomic analysis, we indicate that marine aerobic methanotrophs take part in ammonia oxidation and nitrous oxide production. The ammonia oxidation can persist for approximately 6 days, and the nitrous oxide produced is at least partially derived from the hydroxylamine oxidation. Given the prevalence of denitrification genes in aerobic methanotrophs, methane oxidation may also be coupled to NOx- reduction under anoxic marine conditions, potentially contributing to nitrous oxide production. The intrinsic nature of aerobic methanotrophs could partially offset the mitigation of global warming achieved through the methane consumption.
{"title":"Ammonia oxidation by aerobic methanotrophs as a source of marine nitrous oxide.","authors":"Sai Yang,Jiawei Zhang,Yafei Ou,Wenxiao Liu,Xinru Tian,Li-Jun Hou,Hong-Po Dong","doi":"10.1093/ismejo/wraf242","DOIUrl":"https://doi.org/10.1093/ismejo/wraf242","url":null,"abstract":"Aerobic methanotrophs encode a hydroxylamine oxidoreductase, which facilitates the oxidation of ammonia to nitrite or nitric oxide, potentially leading to nitrous oxide production. Aerobic methane oxidation has been documented in shallow marine waters or the water column of the open ocean. However, little is known about the distribution pattern of marine aerobic methanotrophs containing hydroxylamine oxidoreductase and their contribution to marine nitrous oxide emissions. Here, by analyzing global marine metagenomes, we show that hydroxylamine oxidoreductase-containing aerobic methanotrophs were widely distributed across diverse marine habitats, with higher abundances in methane seep systems and estuary regions than in other environments. Among these, aerobic methanotrophs belonging to Gammaproteobacteria were the most widely distributed and abundant functional group. We also identified a second order within Gammaproteobacteria (Ga0077536) potentially capable of aerobic methanotrophy, and a complete repertoire of denitrification genes in a gammaproteobacterial methanotroph, expanding the phylogenetic and functional diversity of marine aerobic methanotrophs. By using enrichments of estuarine methanotrophs in combination with 15N stable isotope tracing and metatranscriptomic analysis, we indicate that marine aerobic methanotrophs take part in ammonia oxidation and nitrous oxide production. The ammonia oxidation can persist for approximately 6 days, and the nitrous oxide produced is at least partially derived from the hydroxylamine oxidation. Given the prevalence of denitrification genes in aerobic methanotrophs, methane oxidation may also be coupled to NOx- reduction under anoxic marine conditions, potentially contributing to nitrous oxide production. The intrinsic nature of aerobic methanotrophs could partially offset the mitigation of global warming achieved through the methane consumption.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"82 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-10-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145411462","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}
Yunhua Zhang,Wujia Mo,Keyi Chen,Yichen Ding,Kaikai Mao,Hu Wan,Jizhong Zhou,Feng Ju
The fall armyworm, Spodoptera frugiperda, is a major global agricultural pest, known for its rapid evolution of insecticide resistance. Although host genetic adaptation contributes to this trait, the role of gut symbiont-mediated metabolic pathways in promoting resistance remains poorly understood. Here, we show that besides direct biodegradation, a generalist symbiont Enterococcus casseliflavus EMBL-3 indirectly promotes chlorantraniliprole resistance by compensating for tryptophan deficiency in a maize-based diet. Metabolomics and isotope tracing identify EMBL-3 as the primary producer of tryptophan, which is subsequently converted by co-resident microbes to indoleacetic acid. Indoleacetic acid activates the aryl hydrocarbon receptor, leading to upregulation of UDP-glucuronosyltransferase, a detoxification enzyme essential for chlorantraniliprole resistance, as confirmed by CRISPR/Cas9 knockout. This tripartite EMBL-3-indoleacetic acid-UDP-glucuronosyltransferase axis defines a hierarchical symbiont-host metabolic network driving chlorantraniliprole resistance. Our findings provide a framework and targets for disrupting pest adaptability by targeting critical symbiont metabolic nodes, positioning microbiome-mediated detoxification as a universal vulnerability in resistant pests.
{"title":"Cooperative Microbial Metabolism Enhances Tryptophan-Mediated Insecticide Detoxification in the Fall Armyworm.","authors":"Yunhua Zhang,Wujia Mo,Keyi Chen,Yichen Ding,Kaikai Mao,Hu Wan,Jizhong Zhou,Feng Ju","doi":"10.1093/ismejo/wraf237","DOIUrl":"https://doi.org/10.1093/ismejo/wraf237","url":null,"abstract":"The fall armyworm, Spodoptera frugiperda, is a major global agricultural pest, known for its rapid evolution of insecticide resistance. Although host genetic adaptation contributes to this trait, the role of gut symbiont-mediated metabolic pathways in promoting resistance remains poorly understood. Here, we show that besides direct biodegradation, a generalist symbiont Enterococcus casseliflavus EMBL-3 indirectly promotes chlorantraniliprole resistance by compensating for tryptophan deficiency in a maize-based diet. Metabolomics and isotope tracing identify EMBL-3 as the primary producer of tryptophan, which is subsequently converted by co-resident microbes to indoleacetic acid. Indoleacetic acid activates the aryl hydrocarbon receptor, leading to upregulation of UDP-glucuronosyltransferase, a detoxification enzyme essential for chlorantraniliprole resistance, as confirmed by CRISPR/Cas9 knockout. This tripartite EMBL-3-indoleacetic acid-UDP-glucuronosyltransferase axis defines a hierarchical symbiont-host metabolic network driving chlorantraniliprole resistance. Our findings provide a framework and targets for disrupting pest adaptability by targeting critical symbiont metabolic nodes, positioning microbiome-mediated detoxification as a universal vulnerability in resistant pests.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"33 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-10-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145351794","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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