The ISME Journal最新文献

{"title":"Muribaculum intestinale restricts Salmonella Typhimurium colonization by converting succinate to propionate","authors":"Zhenyu Wang, Shuaishuai Kang, Zhenhua Wu, Xiaoyi Liu, Xiangyu Zhang, Yujun Wu, Yang Wen, Xingjian Zhou, Guolong Zhang, Junjun Wang, Dandan Han","doi":"10.1093/ismejo/wraf069","DOIUrl":"https://doi.org/10.1093/ismejo/wraf069","url":null,"abstract":"Insufficient dietary fiber intake is associated with dysbiosis and compromised colonization resistance to enteric infections. However, a detailed understanding of the relationship between dietary fiber insufficiency and colonization resistance remains elusive. Our study aimed to delineate the impact of fiber deprivation on gut microbiome and colonization resistance in a murine model with Salmonella Typhimurium infection. Our findings indicate that dietary fiber deprivation resulted in impaired colonization resistance and depletion of commensal bacteria Muribaculaceae. By combining dietary switch, FMT, and genomic analysis, we identify Muribaculum intestinale as a candidate bacterium, capable of converting succinate into propionate. Oral administration of Muribaculum intestinale augmented colonization resistance to Salmonella Typhimurium, accompanied by succinate reduction and propionate elevation. Dietary supplementation of propionate, but not succinate, enhanced colonization resistance to Salmonella Typhimurium in mice consuming a fiber-free diet. Taken together, our research identified a crucial metabolic pathway encoded by gut microbiome underlying colonization resistance, providing an intervention strategy for combatting enteric infections among Western diet-consuming populations.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"123 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-04-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143847178","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}

{"title":"Heat-induced Stress Modulates Cell Surface Glycans and Membrane Lipids of Coral Symbionts","authors":"Giada Tortorelli, Sabrina L Rosset, Clarisse E S Sullivan, Sarah Woo, Erika C Johnston, Nia Symone Walker, Joshua R Hancock, Carlo Caruso, Alyssa C Varela, Kira Hughes, Christian Martin, Robert A Quinn, Crawford Drury","doi":"10.1093/ismejo/wraf073","DOIUrl":"https://doi.org/10.1093/ismejo/wraf073","url":null,"abstract":"The susceptibility of corals to environmental stress is determined by complex interactions between host genetic variation and the Symbiodiniaceae family community. We exposed genotypes of Montipora capitata hosting primarily Cladocopium or Durusdinium symbionts to ambient conditions and an eight-day heat stress. Symbionts’ cell surface glycan composition differed between genera and was significantly affected by temperature and oxidative stress. The metabolic profile of coral holobionts was primarily shaped by symbionts identity, but was also strongly responsive to oxidative stress. At peak temperature stress, betaine lipids in Cladocopium were remodeled to more closely resemble the abundance and saturation state of Durusdinium symbionts, which paralleled a larger metabolic shift in Cladocopium. Exploring how Symbiodiniaceae members regulate stress and host-symbiont affinity helps identify the traits contributing to coral resilience under climate change.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"10 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-04-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143847104","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}

{"title":"Fungal-mediated soil aggregation as a mechanism for carbon stabilization","authors":"Steven P C de Goede, S Emilia Hannula, Boris Jansen, Elly Morriën","doi":"10.1093/ismejo/wraf074","DOIUrl":"https://doi.org/10.1093/ismejo/wraf074","url":null,"abstract":"Soils can potentially be turned into net carbon sinks for atmospheric carbon to offset anthropogenic greenhouse gas emissions. Occlusion of soil organic carbon (SOC) in soil aggregates is a key mechanism which temporarily protects it from decomposition by soil organisms. Filamentous fungi are recognized for their positive role in the formation and stabilization of aggregates. In this review we assess the current knowledge of the contribution of fungi to soil aggregation, and set a new research agenda to quantify fungal-mediated aggregation across different climates and soils. Our review highlights three main knowledge gaps: (1) the lack of quantitative data and mechanistic understanding of aggregate turnover under field conditions, (2) lack of data on the biochemical and biological mechanisms by which filamentous fungi influence soil aggregation, and (3) uncharacterized contribution of soil fungi across environments. Adopting a trait-based approach to increase the level of mechanistic understanding between fungal diversity and soil structure seems promising, but will need additional experiments in which fungal diversity is manipulated by either removal through sieving or dilution, or addition through using synthetic communities of cultured fungi. We stress the importance of integrating ecological and physicochemical perspectives for accurate modeling of soil aggregation and SOC cycling, which is needed to successfully predict the effects of land management strategies.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"30 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-04-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143847106","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}

{"title":"Promiscuous and genome-wide recombination underlies the sequence-discrete species of the SAR11 lineage in the deep ocean","authors":"Jianshu Zhao, Maria Pachiadaki, Roth E Conrad, Janet K Hatt, Laura A Bristow, Luis M Rodriguez-R, Ramon Rossello-Mora, Frank J Stewart, Konstantinos T Konstantinidis","doi":"10.1093/ismejo/wraf072","DOIUrl":"https://doi.org/10.1093/ismejo/wraf072","url":null,"abstract":"Surveys of microbial communities (metagenomics) or isolate genomes have revealed sequence-discrete species. That is, members of the same species show >95% Average Nucleotide Identity (ANI) of shared genes among themselves vs. <83% ANI to members of other species while genome pairs showing between 83-95% ANI are comparatively rare. In these surveys, aquatic bacteria of the ubiquitous SAR11 clade (Class Alphaproteobacteria) are an outlier and often do not exhibit discrete species boundaries, suggesting the potential for alternate modes of genetic differentiation. To explore evolution in SAR11, we analyzed high-quality, single-cell amplified genomes (SAGs) and companion metagenomes from an oxygen minimum zone (OMZ) in the Eastern Tropical Pacific Ocean, where the SAR11 make up ~20% of the total microbial community. Our results show that SAR11 do form several sequence-discrete species, but their ANI range of discreteness is shifted to lower identities between 86-91%, with intra-species ANI ranging between 91-100%. Measuring recent gene exchange among these genomes based on a recently developed methodology revealed higher frequency of homologous recombination within compared to between species that affects sequence evolution at least twice as much as diversifying point mutation across the genome. Recombination in SAR11 appears to be more promiscuous compared to other prokaryotic species, likely due to the deletion of universal genes involved in the mismatch repair, and has facilitated the spreading of adaptive mutations within the species (gene sweeps), further promoting the high intra-species diversity observed. Collectively, these results implicate rampant, genome-wide homologous recombination as the mechanism of cohesion for distinct SAR11 species.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"108 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-04-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143847108","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}

{"title":"Within-host competition causes pathogen molecular evolution and perpetual microbiota dysbiosis","authors":"Emily J Stevens, Jingdi D Li, Tobias E Hector, Georgia C Drew, Kim Hoang, Samuel T E Greenrod, Steve Paterson, Kayla C King","doi":"10.1093/ismejo/wraf071","DOIUrl":"https://doi.org/10.1093/ismejo/wraf071","url":null,"abstract":"Pathogens newly invading a host must compete with resident microbiota. This. within-host microbial warfare could lead to more severe disease outcomes or constrain the evolution of virulence. By passaging a widespread pathogen (Staphylococcus aureus) and a native microbiota community across populations of nematode hosts, we show that the pathogen displaced microbiota and reduced species richness, but maintained its virulence across generations. Conversely, pathogen populations and microbiota passaged in isolation caused more host harm relative to their respective no-host controls. For the evolved pathogens, this increase in virulence was partly mediated by enhanced biofilm formation and expression of the global virulence regulator agr. Whole genome sequencing revealed shifts in the mode of selection from directional (on pathogens evolving in isolation) to fluctuating (on pathogens evolving in host microbiota). This approach also revealed that competitive interactions with the microbiota drove early pathogen genomic diversification. Metagenome sequencing of the passaged microbiota shows that evolution in pathogen-infected hosts caused a significant reduction in community stability (dysbiosis), along with restrictions on the co-existence of some species based on nutrient competition. Our study reveals how microbial competition during novel infection could determine the patterns and processes of evolution with major consequences for host health.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"70 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-04-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143847107","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}

{"title":"Tetrahymena predation drives adaptive evolution of Salmonella by disrupting O-antigen biosynthesis and upregulating transcriptional regulator csgD","authors":"Hao Huang, Jinzhu Geng, Yuhao Dong, Chen Yuan, Gang Li, Meng Nie, Jingjing Guo, Yongjie Liu","doi":"10.1093/ismejo/wraf070","DOIUrl":"https://doi.org/10.1093/ismejo/wraf070","url":null,"abstract":"Protozoan predation is increasingly understood to be one of the main environmental factors driving bacterial virulence evolution and adaptation strategies. In this study, we reveal the adaptive evolution of Salmonella Enteritidis in phenotypic and genomic traits after passage through Tetrahymena thermophila. We identified a beneficial and fixed mutation that occurs at the coding region of rfbP, encoding the undecaprenyl-phosphate galactosephosphotransferase, and demonstrated that almost all observed phenotypic changes caused by selection pressure, including enhanced biofilm formation and reduced bacterial motility, are related to the early termination of RfbP protein translation. This mutation blocks the lipopolysaccharide O antigen synthesis, and leads to upregulation of the transcriptional factor csgD, which plays a central role in regulating Salmonella adaptation to the adverse environment. Our findings underscore the selective pressure from Tetrahymena as a pivotal driver of adaptive evolution in Salmonella, elucidating the nexus between adaptation to protozoan predation and augmented environmental persistence. This investigation advances our understanding of the ecological role of protozoan predation in the natural selection of bacterial communities.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"6 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-04-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143827683","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}

{"title":"Episomal virus maintenance enables bacterial population recovery from infection and promotes virus-bacterial coexistence","authors":"Rodrigo Sanchez-Martinez, Akash Arani, Mart Krupovic, Joshua S Weitz, Fernando Santos, Josefa Anton","doi":"10.1093/ismejo/wraf066","DOIUrl":"https://doi.org/10.1093/ismejo/wraf066","url":null,"abstract":"Viruses are ubiquitous in aquatic environments with total densities of virus-like particles often exceeding 107/ml in surface marine oligotrophic waters. Hypersaline environments harbor elevated prokaryotic population densities of 108/ml that coexist with viruses at even higher densities, approaching 1010/ml. The presence of high densities of microbial populations and viruses challenge traditional explanations of top-down control exerted by viruses. At close to saturation salinities, prokaryotic populations are dominated by Archaea and the bacterial genus Salinibacter. In this work we examine the episomal maintenance of a virus within a Salinibacter ruber host. We found that infected cultures of Sal. ruber M1 developed a population-level resistance and underwent systematic and reproducible recovery post infection that was counter-intuitively dependent on the multiplicity of infection, where higher viral pressures led to better host outcomes. Furthermore, we developed a nonlinear population dynamics model that successfully reproduced the qualitative features of the recovery. Together, experiments and models suggest that episomal virus maintenance and lysis inhibition enable host-virus co-existence at high viral densities. Our results emphasize the ecological importance of exploring a spectrum of viral infection strategies beyond the conventional binary of lysis or lysogeny.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"21 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-04-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143822824","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}

{"title":"Adaptive survival strategies of rumen microbiota with solid diet deficiency in early life cause epithelial mitochondrial dysfunction","authors":"Shiqiang Yu, Yuting Fu, Jinrui Qu, Kai Zhang, Weiyun Zhu, Shengyong Mao, Junhua Liu","doi":"10.1093/ismejo/wraf064","DOIUrl":"https://doi.org/10.1093/ismejo/wraf064","url":null,"abstract":"With extreme nutritional substrate deficiency, the adaptive responses of the gastrointestinal microbiota and host metabolism are largely unknown. Here, we successfully established a microbial substrate deficiency model in the rumen without solid diet introduction in neonatal lambs. In the absence of solid diet, we observed a reduction in the Simpson Index of rumen bacteria, along with a marked decline in the abundance of keystone microorganisms such as Prevotella, Selenomonas, Megasphaera, and Succiniclasticum, indicating a simplified microbial interaction network. Additionally, more urea and NH3-N production facilitated microbial efficient nitrogen utilization to prioritize ammonia as a nitrogen source for survival, reallocating energy to overcome nutritional limitations and sustain their viability. In addition, enriched microorganisms (Methanosarcina, Methanomicrobium, Methanobrevibacter, and Methanobacterium) promoted hydrogen removal and the growth of nitrogen-producing microorganisms (Pecoramyces, Piromyces, Caecomyces, and Orpinomyces). It also reinforced the glutamate-glutamine pathway, as evidenced by the higher expression of glnA, GLUL, gdhA, ureAB, suggesting enhanced internal cycling of nitrogen for microbial survival. This selfish microbial survival strategy deprived the host of adequate volatile fatty acids for energy metabolism, resulting in the downregulation of rumen epithelial cell cycle proteins (CCNB1, CCNE), abnormal mitochondrial morphology, and reduced mitochondrial DNA copy number and ATP production. Overall, these findings revealed the adaptive survival strategies of rumen microbiota with solid diet deficiency in early life, which caused alterations in epithelial cell mitochondrial function.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"377 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-04-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143790189","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}

{"title":"Phage-phage competition and biofilms affect interactions between two virulent bacteriophages and Pseudomonas aeruginosa","authors":"Magdalena Bürkle, Imke H E Korf, Anne Lippegaus, Sebastian Krautwurst, Christine Rohde, Chantal Weissfuss, Geraldine Nouailles, Xavière Menatong Tene, Baptiste Gaborieau, Jean-Marc Ghigo, Jean-Damien Ricard, Andreas C Hocke, Kai Papenfort, Laurent Debarbieux, Martin Witzenrath, Sandra-Maria Wienhold, Gopinath Krishnamoorthy","doi":"10.1093/ismejo/wraf065","DOIUrl":"https://doi.org/10.1093/ismejo/wraf065","url":null,"abstract":"Virulent bacteriophages (or phages) are viruses that specifically infect and lyse a bacterial host. When multiple phages co-infect a bacterial host, the extent of lysis, dynamics of bacteria-phage and phage-phage interactions are expected to vary. The objective of this study is to identify the factors influencing the interaction of two virulent phages with different Pseudomonas aeruginosa growth states (planktonic, an infected epithelial cell line, and biofilm) by measuring the bacterial time-kill and individual phage replication kinetics. A single administration of phages effectively reduced P. aeruginosa viability in planktonic conditions and infected human lung cell cultures, but phage-resistant variants subsequently emerged. In static biofilms, the phage combination displayed initial inhibition of biofilm dispersal, but sustained control was achieved only by combining phages and meropenem antibiotic. In contrast, adherent biofilms showed tolerance to phage and/or meropenem, suggesting a spatio-temporal variation in the phage-bacterial interaction. The kinetics of adsorption of each phage to P. aeruginosa during single- or co-administration were comparable. However, the phage with the shorter lysis time depleted bacterial resources early and selected a specific nucleotide polymorphism that conferred a competitive disadvantage and cross-resistance to the second phage. The extent and strength of this phage-phage competition and genetic loci conferring phage resistance, are, however, P. aeruginosa genotype dependent. Nevertheless, adding phages sequentially resulted in their unimpeded replication with no significant increase in bacterial host lysis. These results highlight the interrelatedness of phage-phage competition, phage resistance and specific bacterial growth state (planktonic/biofilm) in shaping the interplay among P. aeruginosa and virulent phages.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"16 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-04-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143790190","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}

{"title":"Longitudinal dynamics and cross-domain interactions of eukaryotic populations in wastewater treatment plants","authors":"Yue Huang, Xuemei Mao, Xiawan Zheng, Yuxiang Zhao, Dou Wang, Mengying Wang, Yiqiang Chen, Lei Liu, Yulin Wang, Martin F Polz, Tong Zhang","doi":"10.1093/ismejo/wraf058","DOIUrl":"https://doi.org/10.1093/ismejo/wraf058","url":null,"abstract":"Activated sludge is a large reservoir of novel microorganisms and microbial genetic diversity. While much attention has been given to the profile and functions of prokaryotes, the eukaryotic diversity remains largely unexplored. In this study, we analyzed longitudinal activated sludge samples spanning 13 years from the largest secondary wastewater treatment plants in Hong Kong, unveiling a wealth of eukaryotic taxa and 681 856 non-redundant protein-coding genes, the majority (416044) of which appeared novel. Ciliophora was the most dominant phylum with a significant increase after a transient intervention (bleaching event). Our metagenomic analysis reveals close linkage and covariation of eukaryotes, prokaryotes, and prokaryotic viruses (phages), indicating common responses to environmental changes such as transient intervention and intermittent fluctuations. Furthermore, high-resolution cross-domain relationships were interpreted by S-map, demonstrating a predatory role of Arthropoda, Ascomycota, Mucoromycota, and Rotifera. This high-resolution profile of microbial dynamics expands our knowledge on yet-to-be-cultured populations and their cross-domain interactions and highlights the ecological importance of eukaryotes in the activated sludge ecosystem.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"108 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143782690","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}