The ISME Journal最新文献

{"title":"Bacterial transmission within social groups shapes the underexplored gut microbiome in the lemur Indri indri.","authors":"Francisca Labisa-Morais,Daria Valente,Aitor Blanco-Míguez,Paolo Manghi,Albert Garcia-Valiente,Harilala Andriamaniraka,Federica Armanini,Francesco Asnicar,Chiara De Gregorio,Davide Golzato,Serena Manara,Monica Modesto,Elisa Piperni,Michal Punčochář,Donatella Scarafile,Valeria Torti,Luigimaria Borruso,Paola Mattarelli,Cristina Giacoma,Camillo Sandri,Caterina Spiezio,Nicola Segata,Mireia Valles-Colomer","doi":"10.1093/ismejo/wraf136","DOIUrl":"https://doi.org/10.1093/ismejo/wraf136","url":null,"abstract":"The Indri indri is a critically endangered lemur species that has not successfully been maintained or bred under human care. Investigating this lemur's virtually unexplored gut microbiome will deepen our understanding of the species' health determinants and inform conservation efforts. Through metagenomic assembly and integration into an updated reference database, we found the I. indri faecal microbiome remains largely uncultivated (cultivated species representing <0.1% relative abundance) and is largely specific to this primate species. After reconstructing 342 metagenome-assembled genomes encompassing 48 candidate species from a total of 22 samples (18 of which newly sequenced), we substantially improved microbiome mappability to 85% on average and found evidence for a proportionally large core microbiome. Social group membership emerged as the main determinant of both their taxonomic and functional gut microbiome composition. Using strain-level profiling, we detected extensive microbiome transmission within social groups, suggesting physical interaction is key in promoting microbiome acquisition. Strain sharing rates were highest between mothers and their offspring. Intergroup strain sharing was minimal and inversely correlated with geographical distance, aligning with the rare intergroup interactions and stable territory occupancy coupled with ongoing habitat fragmentation. No evidence of microbiome acquisition through geophagy was detected. These findings underscore the profound influence of social structure on microbiome transmission and composition in I. indri, and highlight the importance of considering social dynamics into research and conservation strategies.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"20 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144700994","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":"Comparative genome analysis reveals broad phylogenetic and functional diversity within the order Nitrospirales.","authors":"Linnea F M Kop,Hanna Koch,Daan Speth,Claudia Lüke,Eva Spieck,Mike S M Jetten,Holger Daims,Sebastian Lücker","doi":"10.1093/ismejo/wraf151","DOIUrl":"https://doi.org/10.1093/ismejo/wraf151","url":null,"abstract":"Nitrification, a key process in the nitrogen cycle, involves the oxidation of ammonia to nitrite and nitrate by a diverse group of chemolithoautotrophic microorganisms. The order Nitrospirales (referred to in literature as the genus Nitrospira), which includes both nitrite-oxidizing and complete ammonia-oxidizing bacteria, plays a central role in this process. We sequenced the genomes of nine Nitrospirales members, incorporating genomes from previously unsequenced taxonomic Nitrospirales lineages. A comprehensive genomic analysis of these new Nitrospirales was conducted, which included an examination of their habitat distribution, phylogenetic diversity, and functional capabilities. This was complemented by the construction of and comparison to a database of 446 non-redundant, high-quality Nitrospirales genomes. Our phylogenomic analysis uncovered the presence of additional unclassified lineages and provided a comparison between genome-based and 16S rRNA gene-based taxonomies. Whereas some Nitrospirales lineages seem to exhibit habitat preferences, others are found across a wide variety of ecosystems, suggesting a broad niche spectrum. This capacity to adapt to different environmental conditions is also reflected in the high variability and modularity of the respiratory chain and nitrogen assimilation mechanisms. Additionally, we found evidence of quorum sensing systems in species beyond lineage II, implying a broader ecological role for this communication mechanism within the Nitrospirales. Finally, we identified a set of conserved genes unique to nitrite oxidoreductase-containing Nitrospirales, providing insights into the emergence of this functional group. In conclusion, our study emphasizes the adaptability of the various nitrifying classes of the order Nitrospirales to diverse environments and reveals the presence of new taxonomic lineages.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"678 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144684281","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":"Eco-evolutionary robustness of wild bacterial communities to experimental perturbation.","authors":"Duhita G Sant,Thomas P Smith,Edgar L Y Wong,Juli Cohen,Kayla C King,Thomas Bell,Timothy G Barraclough","doi":"10.1093/ismejo/wraf144","DOIUrl":"https://doi.org/10.1093/ismejo/wraf144","url":null,"abstract":"Most knowledge about bacterial evolution and ecological interactions comes from laboratory studies. One difference between the wild and most laboratory experiments is the diversity of bacterial taxa present. Understanding how wild bacteria respond to perturbation therefore requires consideration of how ecological sorting, colonization, and genetic changes of constituent species interact. Ecological sorting of species might reduce evolutionary rates and make communities robust to disturbance, or it could amplify selection pressures and lead to unstable co-evolutionary cascades. Even estimates of basic rates of ecological sorting, dispersal, and genetic change are rare. Here, we addressed these knowledge gaps by liming wild decomposer communities living in beech tree holes and tracking ecological and evolutionary responses for 12 weeks. Overall, tree hole communities were extremely robust to liming involving short-term pulses up to 4 pH units and long-term increases up to 2 pH units. Species diversity and composition displayed significant but small changes in treatment tree holes compared to control ones. New bacterial taxa colonized at a low rate that did not vary with liming. Genetic changes in the frequency of single nucleotide polymorphisms in metagenome assembled genomes occurred at rates that were both comparable to and correlated with ecological changes in the same metagenome assembled genomes, but the rate of genetic changes did not vary between limed and control tree holes. Analysis of rates of genetic change estimated low effective population size (~104) and generation times of roughly 1 day. Our study provides estimates of rates of ecological and evolutionary processes in wild bacterial communities, which displayed remarkable robustness to our experimental perturbation.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"15 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144684275","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":"Absolute abundance unveils Basidiobolus as a cross-domain bridge indirectly bolstering gut microbiome homeostasis.","authors":"Mitra Ghotbi,Jason E Stajich,Jason W Dallas,Alexander J Rurik,Chloe Cummins,Lluvia Vargas-Gastélum,Marjan Ghotbi,Joseph W Spatafora,Kian Kelly,N Reed Alexander,Kylie C Moe,Kimberly C Syring,Leila Shadmani,Julissa Perez-Marron,Donald M Walker","doi":"10.1093/ismejo/wraf150","DOIUrl":"https://doi.org/10.1093/ismejo/wraf150","url":null,"abstract":"The host microbiome is integral to metabolism, immune function, and pathogen resistance. Yet, reliance on relative abundance in microbiome studies introduces compositional biases that obscure ecological interpretation, while the absence of robust tools for absolute abundance quantification has limited biological discovery. Here, we apply absolute abundance profiling to uncover host-specific microbial patterns across herpetofauna orders that are masked in relative abundance data. Relative and absolute abundance-derived bacterial and fungal microbiomes exhibit divergent profiles shaped by compositional bias and multifactorial effects. Absolute abundance identified key genera, Lactococcus, Parabacteroides and Cetobacterium in salamanders, and Basidiobolus and Mortierella in lizards, turtles, snakes, and tortoises, that consistently emerged as core taxa, revealing host-associated patterns previously obscured by compositional constraints. In closely related Desmognathus species, where environmental and phylogenetic variation was minimized, absolute abundance enabled finer resolution of microbiome dynamics and significantly reduced false discovery rates. Absolute abundance-based network analyses further revealed distinct keystone taxa between the relative and absolute abundance datasets. Despite low redundancy, Basidiobolus exhibited high network betweenness, efficiency, and degree, suggesting its role as a key connector between microbial modules and a contributor to overall network robustness. This predicted structural role aligns with Burt's structural hole theory, which suggests that nodes linking otherwise disconnected modules occupy influential network positions. These findings underscore the value of absolute abundance in resolving microbial dynamics and supporting meaningful interpretation of host-microbiome associations. This advance is made possible by DspikeIn, a flexible wet-lab and computational framework that enhances ecological resolution and cross-study comparability.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"10 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144669574","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":"Novel viruses of Haloquadratum walsbyi expand the known archaeal virosphere of hypersaline environments.","authors":"Judith Villamor,María Dolores Ramos-Barbero,Mercedes Moreno-Paz,Cristian Villena Alemany,Manuel Martínez-García,Víctor Parro,Josefa Antón,Fernando Santos","doi":"10.1093/ismejo/wraf149","DOIUrl":"https://doi.org/10.1093/ismejo/wraf149","url":null,"abstract":"Solar salterns represent unique systems with low diversity microbial communities that serve as an excellent model for studying the evolution and ecology of archaeal viruses and the interactions with their hosts. This is particularly relevant for the extremely abundant \"square\" archaeon Haloquadratum walsbyi, for which isolated viruses have remained elusive despite the fact that this microbe governs the salt-saturated ponds of most solar salterns worldwide. In this work, we have used cutting-edge imaging techniques, based on virusFISH, and a combination of -omic techniques, at both population and single-cell levels, to provide an in-depth characterization of the Hqr. walsbyi virosphere. Our analyses have led to the identification of a new subfamily of tailed low-GC dsDNA viruses, which we propose to name \"Haloquadravirinae\", with host assignment confirmed by virusFISH in natural samples. Haloquadraviruses can represent more than 50% of the viral community in solar saltern viromes and infect nearly 40% of square cells in natural environments. The genetic imprint of these viruses, which are globally distributed in hypersaline environments, has provided insights into the structure of their virions and their potential life strategy. Along with the identification of other virus-like elements associated with Hqr. walsbyi through single-cell genomics, this work expands our current understanding of the archaeal virosphere.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"95 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144645897","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":"Distinct lactate utilization strategies drive niche differentiation between two co-existing Megasphaera species in the rumen microbiome.","authors":"Cameron R Strachan,Connor M Bowers,Byung-Chul Kim,Tea Movsesijan,Viktoria Neubauer,Anna J Mueller,Xiaoqian A Yu,Fátima C Pereira,Veronika Nagl,Johannes Faas,Martin Wagner,Qendrim Zebeli,Paul J Weimer,Pieter Candry,Martin F Polz,Christopher E Lawson,Evelyne Selberherr","doi":"10.1093/ismejo/wraf147","DOIUrl":"https://doi.org/10.1093/ismejo/wraf147","url":null,"abstract":"Lactate utilization mitigates rumen acidosis and is associated with decreased methane production in the rumen. While several lactate utilization pathways exist across different microbial species in the rumen, how they are metabolically differentiated remains unclear. Here, we show that the key lactate-utilizing species Megasphaera hexanoica and Megasphaera elsdenii display distinct growth strategies based on their fermentative end products. This allows them to co-exist and play distinct metabolic roles, which appear particularly relevant in the early stages of rumen development, as both species are highly enriched in the calf. Specifically, M. hexanoica is more strongly associated with rumen microbiome states that involve increased lactate utilization and preferentially runs reverse beta-oxidation (termed chain elongation) to produce butyrate and medium-chain fatty acids from lactate. As M. elsdenii instead utilizes lactate via the acrylate pathway to produce propionate, we leverage Enzyme Cost Minimization to predict how this pathway relates to a distinct growth strategy. We find that M. elsdenii maximizes growth rate when lactate transiently accumulates, which contrasts M. hexanoica's invariably high-yield strategy. This trade-off, which is supported by the analysis of growth kinetics, metabolic flux, and bioreactors simulating the rumen microbiome, ultimately contributes to co-existence on lactate and may have driven niche differentiation. Lastly, we demonstrate how lactate utilization in the Megasphaera is threatened by toxins widespread in feed, which points to dietary interventions to support calf health.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"9 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-07-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144622007","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":"New lineage of scuticociliates dominates the ciliate community and bacterivory in hypolimnetic waters of a freshwater reservoir","authors":"Karel Šimek, Usman Asghar, Bettina Sonntag, Vojtěch Kasalický, Tanja Shabarova, Indranil Mukherjee","doi":"10.1093/ismejo/wraf148","DOIUrl":"https://doi.org/10.1093/ismejo/wraf148","url":null,"abstract":"Deep, cold, and dark hypolimnia represent the largest volume of water in freshwater lakes with limited occurrences of phototrophs. However, the presence of prokaryotes supports populations of bacterivorous ciliates and heterotrophic nanoflagellates (HNF). Nevertheless, protistan bacterivory rates and the major hypolimnetic ciliate bacterivores are poorly documented. We conducted a high frequency sampling (three-times a week) in the oxic hypolimnion of a stratified mesoeutrophic reservoir during summer, characterized by stable physicochemical conditions and low water temperature. Using fluorescently labeled bacteria we estimated that ciliates and HNF contributed, on average, 30% and 70% to aggregated protistan bacterivory, respectively, and collectively removed about two thirds of daily hypolimnetic prokaryotic production. The ciliate community was analyzed by the quantitative protargol staining method. One scuticociliate morphotype dominated the hypolimnetic ciliate community, accounting for 82% of total ciliates and over 98% of total ciliate bacterivory, with average cell-specific uptake rate of 202 prokaryotes per hour. Moreover, long-amplicon sequencing revealed that the scuticociliate belongs to an unidentified clade closely related to the Ctedoctematidae and Eurystomatellidae families. The high-resolution sampling, microscopic, and sequencing methods allowed uncovering indigenous microbial food webs in the hypolimnetic environment and revealed a functional simplification of ciliate communities, dominated by a new bacterivorous scuticociliate lineage.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"699 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-07-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144612907","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":"Understanding Prokaryotic Adaptation through Advanced DNA Methylation Detection Techniques.","authors":"Ziming Chen,Chian Teng Ong,Elizabeth M Ross","doi":"10.1093/ismejo/wraf143","DOIUrl":"https://doi.org/10.1093/ismejo/wraf143","url":null,"abstract":"DNA methylation, a versatile epigenetic modification in prokaryotes, is a crucial regulator of various biological activities, such as genome defence, gene expression, and DNA repair. The most common DNA methylation form in prokaryotes is N6-methyladenine, where a methyl group is added to the adenine. Orphan and restriction-modification system methylases constitute the main methylation systems in prokaryotes. Prokaryotes can adapt to environmental fluctuations through orphan methylase regulation and phase variation of restriction-modification systems, which generate diversified methylomes that modulate the expression of genes. Modern sequencing techniques, including single-molecule real-time sequencing and Nanopore sequencing, enable the characterization of several methylation patterns simultaneously and facilitate the study of prokaryotic epigenomics. This review introduces the prokaryotic DNA methylation systems and prokaryotic adaptation through DNA methylation. Finally, we summarize the current sequencing techniques capable of characterizing methylation forms applicable to prokaryotes and their future perspectives.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"43 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144586698","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":"Endophytic commensal bacteria capitalize on the AvrPto-FER pathway to enhance proliferation during early stages of pathogen invasion.","authors":"Yi Zhang,Dan Hu,Hong-Xia Sun,Jia Chen,Jia-Hao Yang,Xin-Mei Li,Xiu-Shan Li,Yan Chen,Feng Yu","doi":"10.1093/ismejo/wraf145","DOIUrl":"https://doi.org/10.1093/ismejo/wraf145","url":null,"abstract":"Leaves typically harbor a community of pre-existing beneficial and commensal bacteria that contribute to plant health. When pathogens invade, plants employ a series of strategies to response to the invasion, including the modulation of the microbial community structure. However, it remains unclear how commensal bacteria respond to pathogen at the early stage, and whether this response is specifically regulated. Here, we show that infection of Arabidopsis thaliana leaves by the pathogen Pseudomonas syringae pv. tomato DC3000 leads to a significant increase in the population of commensal bacteria, characterized by enrichment of Gammaproteobacteria and Alphaproteobacteria, alongside a reduction in Firmicutes and Betaproteobacteria. This cascade of events specifically occurs because AvrPto, an effector secreted by Pst DC3000, targets and inhibits the host receptor kinase FER, resulting in suppression of FER-mediated pattern-triggered immunity via the previously identified RIPK-RBOHD module. This specific suppression via FER pathway creates a condition that facilitates rapid proliferation of pre-existing commensal bacteria during early pathogen invasion. Our work provides a paradigm for the study of the interaction and ecological generality between commensal bacteria and pathogens with spatiotemporal patterns.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"689 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144586631","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":"High life history diversity within a single genus of algal viruses","authors":"Eva J P Lievens, Irina V Agarkova, David D Dunigan, James L Van Etten, Lutz Becks","doi":"10.1093/ismejo/wraf146","DOIUrl":"https://doi.org/10.1093/ismejo/wraf146","url":null,"abstract":"Microbial viruses are key players in aquatic ecosystems, where they control host populations and affect nutrient flow. The impact of these viruses can be understood through their life history traits, which are used to parameterize ecological models and infer evolutionary strategies. However, most existing data on microbial virus traits come from highly divergent strains. Very little is known about the trait diversity of closely related viruses, opening the critical question: can unknown viral traits be extrapolated from those of known strains? To answer this question, we quantified the life history diversity of related aquatic microbial viruses in unprecedented detail. We measured nine life history traits in 34 strains belonging to the phytoplankton-infecting genus Chlorovirus. Chloroviral traits varied 5- to 77-fold across strains, in some cases rivaling the known trait range for all phytoplankton viruses. Contrary to expectations, only specific infectivity was predictive of viral growth and there was no evidence of life history trade-offs. Our results suggest that more detailed studies of viral diversity could change our understanding of their function in aquatic ecosystems. More broadly, we show that known virus strains may not be representative of their relatives.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"28 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144577950","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}