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Streptococcus pneumoniae adaptation to nutrient deprivation and immune modulation drives upper respiratory tract colonization. 肺炎链球菌对营养剥夺和免疫调节的适应驱动上呼吸道定植。
IF 10.2 1区 环境科学与生态学
ISME Journal Pub Date : 2026-01-14 DOI: 10.1093/ismejo/wrag213
Daan W Arends, Kristin Surmann, Lucille F van Beek, Robert S Jansen, Rob J Mesman, Jeroen D Langereis, Monique van Scherpenzeel, Manuela Gesell Salazar, Uwe Völker, Gerco den Hartog, Marien I de Jonge
{"title":"Streptococcus pneumoniae adaptation to nutrient deprivation and immune modulation drives upper respiratory tract colonization.","authors":"Daan W Arends, Kristin Surmann, Lucille F van Beek, Robert S Jansen, Rob J Mesman, Jeroen D Langereis, Monique van Scherpenzeel, Manuela Gesell Salazar, Uwe Völker, Gerco den Hartog, Marien I de Jonge","doi":"10.1093/ismejo/wrag213","DOIUrl":"10.1093/ismejo/wrag213","url":null,"abstract":"<p><p>Streptococcus pneumoniae is a successful colonizer of the human upper respiratory tract; however, the mechanisms that enable its persistence in this nutrient-limited environment, with numerous immune mechanisms in place, remain enigmatic. Here, we examined how pneumococci adapt to upper respiratory tract conditions and how this affects host interactions. We measured intranasal metal ion and monosaccharide concentrations to create an in vivo-mimicking medium for studying pneumococcal adaptation. Growth in this medium was reduced compared to glucose-rich chemically defined media (CDM). Proteome analysis revealed a shift to galactose as the major carbohydrate source, and decreased levels of fatty acid biosynthesis proteins and pneumolysin, compared to other CDMs. Glycerophosphocholine accumulated extracellularly leading to decreased C-reactive protein and Immunoglobulin M binding to pneumococci. Pneumococci grown in in vivo-mimicking medium, compared to glucose-rich media, were more capable colonizers of primary epithelium and induced less epithelial cytokine release. Together, this shows how pneumococci adapt to the nutrient-limited respiratory environment, modulate epithelial cells, and evade humoral responses to facilitate persistent colonization.</p>","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.2,"publicationDate":"2026-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13561108/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148801033","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Deep-sea anaerobic microbial communities couple degradation of insoluble chitin to extracellular electron transfer. 深海厌氧微生物群落将不溶性甲壳素的降解与细胞外电子转移结合起来。
IF 10.2 1区 环境科学与生态学
ISME Journal Pub Date : 2026-01-14 DOI: 10.1093/ismejo/wrag151
Yamini Jangir, Yongzhao Guo, Stephanie Connon, Sammy Pontrelli, Fabai Wu, Julia Schwartzman, Sujung Lim, Uwe Sauer, Otto X Cordero, Victoria J Orphan
{"title":"Deep-sea anaerobic microbial communities couple degradation of insoluble chitin to extracellular electron transfer.","authors":"Yamini Jangir, Yongzhao Guo, Stephanie Connon, Sammy Pontrelli, Fabai Wu, Julia Schwartzman, Sujung Lim, Uwe Sauer, Otto X Cordero, Victoria J Orphan","doi":"10.1093/ismejo/wrag151","DOIUrl":"10.1093/ismejo/wrag151","url":null,"abstract":"<p><p>Chitin, a major structural component of arthropod exoskeletons, is an abundant carbon and nitrogen source in marine ecosystems. While its degradation is well studied in oxic waters, the microbial processes and interactions that mediate its anaerobic breakdown in deep-sea sediments remain poorly understood. Iron oxides are predicted to be energetically favorable electron acceptors for anaerobic chitin degradation, yet the spatial separation of insoluble substrates and the required microbial partnerships in sediments are not well defined. Here, we used potentiostatically controlled bioelectrochemical reactors poised at +0.22 V vs. Standard Hydrogen Electrode, mimicking iron-reducing conditions, to enrich and characterize a chitin-degrading, metal-reducing microbial community from an anoxic deep-sea whale-fall sediment. Amendment with crystalline chitin generated stable anodic currents, which increased upon addition of chitin-associated metabolites (N-acetylglucosamine, glucose, acetate). 16S rRNA gene sequencing revealed a deep-sea affiliated assemblage dominated by Firmicutes (Vallitalea), Spirochaetota, Gammaproteobacteria, and Desulfobacterota (Trichloromonas). Exoenzyme assays, metabolite profiling, and current measurements confirmed that active chitin degradation provided substrate(s) for extracellular electron transfer (EET). Single-cell analyses using FISH-BONCAT and nanoSIMS showed that Vallitalea (primary degrader) and electrode-respiring Desulfobacterota exhibited highest activity within the electrode biofilm, particularly within ca.10 μm of the surface. We isolated a chitin-degrading Vallitalea sp. and an iron-reducing, electrogenic Trichloromonas sp., and demonstrated that, when reconstituted in co-culture, they cooperatively degrade chitin via acetate cross-feeding coupled to EET. This integrated electrochemical and ecophysiological study reveals microbial interactions linking chitin degradation with iron-oxide respiration in deep-sea sediments and provides a defined electrogenic model community for future syntrophy research.</p>","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.2,"publicationDate":"2026-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13374861/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148260447","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Short-term antagonism between bacteriophages and macrophages decreases with bacteria-phage coevolution. 噬菌体和巨噬细胞之间的短期拮抗作用随着噬菌体的共同进化而减弱。
IF 10.2 1区 环境科学与生态学
ISME Journal Pub Date : 2026-01-14 DOI: 10.1093/ismejo/wrag116
Meaghan Castledine, Zuzanna Szczutkowska, Andrew Matthews, Sarah K Walsh, Rai Lewis, Suzanne Kay, Janet A Willment, Gordon D Brown, Angus Buckling
{"title":"Short-term antagonism between bacteriophages and macrophages decreases with bacteria-phage coevolution.","authors":"Meaghan Castledine, Zuzanna Szczutkowska, Andrew Matthews, Sarah K Walsh, Rai Lewis, Suzanne Kay, Janet A Willment, Gordon D Brown, Angus Buckling","doi":"10.1093/ismejo/wrag116","DOIUrl":"10.1093/ismejo/wrag116","url":null,"abstract":"<p><p>Phage therapy, the use of viruses that infect bacteria (bacteriophages), is a promising complement to antibiotics during the antimicrobial resistance crisis, but treatment success is very variable. A key variable, which likely influences treatment outcomes, is how different immune components interact with bacteriophage, with studies finding neutrophils work synergistically while macrophages work antagonistically with bacteriophage. However, many of these studies characterize interactions and outcomes over short timescales, not considering the potential for the evolution of resistance to bacteriophages which can itself greatly affect treatment outcomes. Here, we measure how macrophages and bacteriophages affect densities and resistance evolution of the pathogen Pseudomonas aeruginosa in vitro. Consistent with previous studies, we find macrophages interact antagonistically with bacteriophages in the short term. However, this antagonism was lost following bacterial population recovery associated with rapidly evolved resistance to bacteriophages. Macrophages resulted in greater net levels of resistance and hindered increases in bacteriophage infectivity, but this did not lead to differences in bacteria-phage population dynamics. This work emphasizes the importance of characterizing the effect of the immune system on phage therapy outcomes over both shorter- and longer- timescales.</p>","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.2,"publicationDate":"2026-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13222528/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147857597","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Abundance-activity decoupling in sulfur-cycling bacteria reflects viral infection types in meromictic lakes. 硫循环细菌丰度-活性解耦反映了分溶湖泊病毒感染类型。
IF 10.2 1区 环境科学与生态学
ISME Journal Pub Date : 2026-01-14 DOI: 10.1093/ismejo/wrag197
Jordan R Walker, Natascha S Varona, Bailey A Wallace, Abelardo Aguilar, Molly D O'Beirne, Josef P Werne, Antoni Luque, William P Gilhooly, Alice Bosco-Santos, Cynthia B Silveira
{"title":"Abundance-activity decoupling in sulfur-cycling bacteria reflects viral infection types in meromictic lakes.","authors":"Jordan R Walker, Natascha S Varona, Bailey A Wallace, Abelardo Aguilar, Molly D O'Beirne, Josef P Werne, Antoni Luque, William P Gilhooly, Alice Bosco-Santos, Cynthia B Silveira","doi":"10.1093/ismejo/wrag197","DOIUrl":"10.1093/ismejo/wrag197","url":null,"abstract":"<p><p>Meromictic lakes serve as analogs of redox-stratified ancient oceans with well-mixed surface waters and anoxic bottoms. In sulfide-rich lakes, purple and green sulfur bacteria (PSB, GSB) dominate the anoxic zones where light penetrates, and their biosignatures can guide interpretations of geologic records. Although PSB and GSB biosignatures indicate presence, they do not directly reflect the community composition of modern analog lakes, posing a challenge for interpretation. Here, we investigate this decoupling by integrating metagenomics, metatranscriptomics, and metaHi-C virus-host linkages with the geochemical profiles of three meromictic lakes. In the phototrophic microbial plates, PSB transcriptional activity far exceeded their abundance (73% of total microbial community activity versus 30% of abundance), whereas GSBs displayed the opposite pattern. Concurrently, PSBs were exclusively associated with temperate viruses and GSBs were targeted by lytic infections. Sulfate-reducing bacteria and viruses encoding genes for sulfate reduction were most active where sulfide concentration was lowest. These results reveal that viral replication strategies are associated with the decoupling between abundance and activity in anoxygenic phototrophs and sulfate reducers. These relationships could accelerate sulfur regeneration, contribute to sustaining phototrophy, and ultimately reflect in the lake's bulk biosignatures.</p>","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.2,"publicationDate":"2026-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13584214/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148632573","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Comment on "A jumbo cyanophage encodes the most comprehensive ribosomal protein set in the known virosphere" by Isaac Meza-Padilla et al. 对Isaac Meza-Padilla等人的“巨型噬藻体编码已知病毒圈中最全面的核糖体蛋白集”的评论。
IF 10.2 1区 环境科学与生态学
ISME Journal Pub Date : 2026-01-14 DOI: 10.1093/ismejo/wrag241
LinXing Chen
{"title":"Comment on \"A jumbo cyanophage encodes the most comprehensive ribosomal protein set in the known virosphere\" by Isaac Meza-Padilla et al.","authors":"LinXing Chen","doi":"10.1093/ismejo/wrag241","DOIUrl":"10.1093/ismejo/wrag241","url":null,"abstract":"","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":"20 1","pages":""},"PeriodicalIF":10.2,"publicationDate":"2026-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13623518/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149082481","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Pseudoalteromonas is a symbiont of marine invertebrates that exhibits broad patterns of phylosymbiosis. 假互单胞菌是一种海洋无脊椎动物的共生体,具有广泛的系统共生模式。
IF 10.2 1区 环境科学与生态学
ISME Journal Pub Date : 2026-01-14 DOI: 10.1093/ismejo/wrag091
Alejandro De Santiago, Shelby Barnes, Tiago José Pereira, Mirayana Marcellino Barros, Lekeah Durden, Min Khant Han, J Cameron Thrash, Holly M Bik
{"title":"Pseudoalteromonas is a symbiont of marine invertebrates that exhibits broad patterns of phylosymbiosis.","authors":"Alejandro De Santiago, Shelby Barnes, Tiago José Pereira, Mirayana Marcellino Barros, Lekeah Durden, Min Khant Han, J Cameron Thrash, Holly M Bik","doi":"10.1093/ismejo/wrag091","DOIUrl":"10.1093/ismejo/wrag091","url":null,"abstract":"<p><p>Despite growing insights into the composition of marine invertebrate microbiomes, our understanding of their ecological and evolutionary patterns remains poor, owing to limited sampling depth and low-resolution datasets. Previous studies have provided conflicting results that both confirm and deny the existence of phylosymbiosis between marine invertebrates and marine bacteria. Here, we investigated potential animal-microbe symbioses in Pseudoalteromonas, a bacterial genus consistently identified as a core microbiome taxon in diverse invertebrates. Using a pangenomic analysis of 236 free-living and invertebrate-associated bacterial strains (including two new nematode-associated isolates generated in this study), we confirm that Pseudoalteromonas is a symbiont with substantial evidence of phylosymbiosis across at least three marine invertebrate phyla (e.g. Nematoda, Mollusca, and Cnidaria). Patterns of symbiosis were consistent irrespective of geography (including in Antarctica), with fluorescence in situ hybridization images from nematodes indicating that bacterial symbionts form biofilms in the mouth and esophagus and are sometimes present in female nematode ovaries exhibiting stunted development. The evolutionary history of Pseudoalteromonas is marked by substantial host-switching and lifestyle transitions, and host-associated genomes suggest that these bacteria are facultative symbionts involved in nutritional symbioses. In marine environments, we hypothesize that horizontally acquired symbionts may have co-evolved with invertebrates, using host mucus as a physical niche and food source, while providing their animal hosts with vitamin B, amino acids, and bioavailable carbon compounds in return.</p>","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.2,"publicationDate":"2026-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13245728/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147724557","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Microbial physiological trait shifts link heavy metal remediation to enhanced soil carbon storage potential. 微生物生理性状变化将重金属修复与提高土壤碳储存潜力联系起来。
IF 10.2 1区 环境科学与生态学
ISME Journal Pub Date : 2026-01-14 DOI: 10.1093/ismejo/wrag250
Rui Xue, Jian Li, Shilin Hu, Jiazhi Ding, Cheng Wang, Wenshun Ke, Chaoran Li, Philippe Corvini, Li Cui
{"title":"Microbial physiological trait shifts link heavy metal remediation to enhanced soil carbon storage potential.","authors":"Rui Xue, Jian Li, Shilin Hu, Jiazhi Ding, Cheng Wang, Wenshun Ke, Chaoran Li, Philippe Corvini, Li Cui","doi":"10.1093/ismejo/wrag250","DOIUrl":"10.1093/ismejo/wrag250","url":null,"abstract":"<p><p>Widespread and chronic heavy metal pollution resulting from industrial activities has compromised the sustainability of soil ecosystems. Increasing and stabilizing soil carbon storage is central to soil development, but how remediation reshapes soil carbon cycling processes during the mitigation of heavy-metal contamination remains unclear. Here, we tracked genome-scale microbial metabolism, community turnover, and phenotype-level physiological responses during a 120-day remediation of heavy metal-contaminated soils with several decades of pollution histories and resolved their dynamic interplay with microbial carbon use efficiency (CUE) and CO2 emissions. We found that heavy-metal stress accelerated microbial respiratory carbon loss from soils, with contaminated soils exhibiting significantly higher cumulative CO₂ emissions than both nearby uncontaminated and remediated soils. Metagenomic profiles were enriched in oxidative-stress defense and metal-detoxification functions, consistent with elevated maintenance costs that may contribute to enhanced respiration. In contrast, remediation significantly reduced soil CO₂ emissions while increasing microbial growth rate and CUE, indicating a shift toward greater soil carbon storage potential. Raman-based in situ monitoring further showed that biomolecules associated with microbial growth, including phospholipids, nucleic acids, and proteins, increased progressively throughout the remediation process. Structural equation modelling further revealed that microbial physiological traits, particularly metabolic activity and intracellular biomolecular content, exerted stronger direct effects on CUE than community traits, including community stability and life-history strategy. These results identify microbial physiological traits as a key link between environmental stress and soil carbon cycling. Together, these findings suggest that remediating heavy metal-contaminated soils may represent an underappreciated pathway for enhancing terrestrial carbon sequestration.</p>","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.2,"publicationDate":"2026-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13657045/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149013101","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Subinhibitory concentrations of antibiotics mediate primary metabolism and shape diverse species interactions among coevolved soil Streptomyces. 抗生素的亚抑制浓度介导了土壤链霉菌的初级代谢,并形成了共同进化的土壤链霉菌之间的多种相互作用。
IF 10.2 1区 环境科学与生态学
ISME Journal Pub Date : 2026-01-14 DOI: 10.1093/ismejo/wrag121
Molly A Kuhs, Zoe A Hansen, Matthew J Michalska-Smith, Julia R Ahlborn, Linda L Kinkel
{"title":"Subinhibitory concentrations of antibiotics mediate primary metabolism and shape diverse species interactions among coevolved soil Streptomyces.","authors":"Molly A Kuhs, Zoe A Hansen, Matthew J Michalska-Smith, Julia R Ahlborn, Linda L Kinkel","doi":"10.1093/ismejo/wrag121","DOIUrl":"10.1093/ismejo/wrag121","url":null,"abstract":"<p><p>Antibiotics produced by soil microbes have provided critical advances in human health, yet their roles within natural soil ecosystems remain poorly understood. Though traditionally viewed as inhibitory weapons, antibiotics at subinhibitory concentrations (SICA) can alter transcription across a wide range of gene targets, with documented impacts on microbial metabolism and hypothesized consequences for community resource competition. However, work to date has focused primarily on SICA outside of the context of coevolved microbial populations. As interest in leveraging the power of microbiomes grows, a deeper understanding of the roles of SICA within natural, cooccurring communities is critical to our ability to both predict and harness microbial dynamics. In this work, we explored the impacts of SICA on the primary metabolism of sympatric populations of soil Streptomyces sourced from high- and low-nutrient soil habitats. Within each population, the effects of six antibiotic compounds at SICA were quantified on both nutrient-use phenotypes and pairwise resource competition. Overall, isolates from low-nutrient soil were found to be more resilient to changes in primary metabolism in the presence of SICA compared to isolates from high-nutrient soil. Across both populations, SICA significantly modified apparent resource competition among coevolved Streptomyces with individual isolates experiencing both increases and decreases in resource use overlap with sympatric partners. The diverse phenotypic shifts observed in this work emphasize that SICA can mediate a broad spectrum of competitive outcomes and highlight the importance of long-term nutrient history in shaping the functional role of antibiotics within microbial communities.</p>","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.2,"publicationDate":"2026-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13285870/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148007459","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Early life nutritional imbalance impairs colonic epithelial regeneration through gut microbiota dysbiosis and metabolic suppression. 生命早期营养失衡通过肠道菌群失调和代谢抑制损害结肠上皮的再生。
IF 10.2 1区 环境科学与生态学
ISME Journal Pub Date : 2026-01-14 DOI: 10.1093/ismejo/wrag135
Yimin Zhuang, Zhiyu Huang, Shuai Liu, Yiming Xu, Guobin Hou, Duo Gao, Tianyu Chen, Boyan Ma, Wen Jiang, Jingtao You, Mengmeng Li, Wei Wang, Shengli Li, Zhijun Cao
{"title":"Early life nutritional imbalance impairs colonic epithelial regeneration through gut microbiota dysbiosis and metabolic suppression.","authors":"Yimin Zhuang, Zhiyu Huang, Shuai Liu, Yiming Xu, Guobin Hou, Duo Gao, Tianyu Chen, Boyan Ma, Wen Jiang, Jingtao You, Mengmeng Li, Wei Wang, Shengli Li, Zhijun Cao","doi":"10.1093/ismejo/wrag135","DOIUrl":"10.1093/ismejo/wrag135","url":null,"abstract":"<p><p>Childhood malnutrition represents a major global health burden that extends beyond caloric deficiency to include dietary imbalance. The early-life gut microbiome functions as a dynamic ecosystem whose structure and metabolic output are intimately linked to host development; yet, how nutritional imbalance disrupts this ecosystem and its integration with the host remains poorly understood. Using an isocaloric but nutrient-imbalanced diet in a mouse model, we recapitulated chronic growth stunting and identified a systemic syndrome comprising growth retardation, oxidative stress, and immunosuppression. Gut microbiota dysbiosis was established as the central mediator of these pathological manifestations. Integrated multi-omics analyses revealed that nutritional imbalance compromised microbial community structure and function, reducing diversity and ecological stability whereas disrupting metabolic activity-particularly short-chain fatty acid production. Through single-cell ribonucleic acid sequencing of colonic epithelium, we demonstrated that these microbial perturbations suppressed host energy metabolism and inhibited the Wnt/β-catenin signaling pathway in regenerative epithelial cells. This resulted in the downregulation of key stem cell regulators LGR5 and ASCL2, ultimately impairing epithelial renewal and manifesting as reduced crypt depth. Our findings reveal a microbiota-dependent mechanism linking dietary imbalance to impaired host development, demonstrating how nutritional stress disrupts gut microbial structure and metabolic output, ultimately compromising epithelial regeneration. This work highlights the importance of considering the gut microbiome as an ecosystem whose homeostasis is fundamental to early-life health.</p>","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.2,"publicationDate":"2026-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13313320/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148058200","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Stable association of a chlamydial symbiont with the freshwater predator hydra suggests broad host potential. 衣原体共生体与淡水捕食者九头蛇的稳定联系表明了广泛的宿主潜力。
IF 10.2 1区 环境科学与生态学
ISME Journal Pub Date : 2026-01-14 DOI: 10.1093/ismejo/wrag104
Angelika Schwarzhans, Justine Boutry, Jácint Tökölyi, Norbert Cyran, Martin Kunert, Matthias Horn, Astrid Collingro
{"title":"Stable association of a chlamydial symbiont with the freshwater predator hydra suggests broad host potential.","authors":"Angelika Schwarzhans, Justine Boutry, Jácint Tökölyi, Norbert Cyran, Martin Kunert, Matthias Horn, Astrid Collingro","doi":"10.1093/ismejo/wrag104","DOIUrl":"10.1093/ismejo/wrag104","url":null,"abstract":"<p><p>Symbiotic associations between microorganisms often involve eukaryotes partnering with microbes for nutrient exchange, protection, and resource acquisition. Bacterial lineages like the Chlamydiota have evolved entirely symbiotic lifestyles, exploiting their eukaryotic hosts for energy, diverse metabolites, and shelter. The study of environmental chlamydiae-outside the well-studied vertebrate host range-has revealed diverging interactions on the mutualism-parasitism spectrum. This highlights their potentially important roles in host-microbe interactions underscoring the relevance of obtaining isolates from diverse environments and hosts. Here, we describe an isolate of a chlamydial symbiont of the freshwater cnidarian Hydra. The symbiont could be isolated and stably maintained in insect cell lines and represents a member of the recently described family-level lineage Chlamydiae Clade III for which we propose the name Endochlamydiaceae. Fluorescence and electron microscopy reveal the symbiont morphology and its endodermal location. Comparative genomics shows the isolate, named Endochlamydia hydrae, encodes a conserved set of genes involved in host invasion, communication, and pathogenicity. Instead of displaying unique genomic adaptations to its animal host, E. hydrae shows signs consistent with ongoing genome reorganisation and streamlining, suggesting a more recent host shift. Screening for closely related 16S rRNA gene sequences in public environmental microbiomes also indicates a broader host range. Moreover, exploration of environmental Hydra oligactis populations revealed they might serve as host for a wider spectrum of chlamydial species. This study highlights the evolutionary success of chlamydiae and their genomic toolkit to infect a wide range of hosts and their ecological significance by interacting with diverse organisms.</p>","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.2,"publicationDate":"2026-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13229535/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147787909","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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