ISME communicationsPub Date : 2026-03-25eCollection Date: 2026-01-01DOI: 10.1093/ismeco/ycag065
Pranav Mukund Pande, Julien Tremblay, Marc St-Arnaud, Etienne Yergeau
{"title":"The metatranscriptomic response of the wheat rhizosphere to drought varies with growth stages.","authors":"Pranav Mukund Pande, Julien Tremblay, Marc St-Arnaud, Etienne Yergeau","doi":"10.1093/ismeco/ycag065","DOIUrl":"https://doi.org/10.1093/ismeco/ycag065","url":null,"abstract":"<p><p>Microbes can help plant sustain abiotic stresses, such as drought. Plant-microbe interactions are, however, dynamic and the timing of the stress will affect both partners, directly and indirectly. Here, we hypothesize that the effect of drought stress on the wheat rhizosphere microbiome would change between key growth stages. We grew wheat in pots and reduced soil water content for two weeks at stem elongation, booting, or heading. We then sampled the rhizosphere soil and sequenced its metatranscriptome. The timing of the drought strongly affected the transcriptional response of the microbes, but few differentially abundant transcripts were shared across all stages. Some common patterns were, however, observed at higher taxonomical or functional levels. Drought also affected the normal succession across wheat growth stages. Many of the differentially abundant transcripts, taxa, and functions between growth stages of the control plants were not significant anymore for plants that experienced drought. Our results suggest that the timing of the drought event is paramount to the microbial rhizosphere communities and that it could explain the heightened sensitivity of younger plants to stresses.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"6 1","pages":"ycag065"},"PeriodicalIF":6.1,"publicationDate":"2026-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13082227/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147700919","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
ISME communicationsPub Date : 2026-03-24eCollection Date: 2026-01-01DOI: 10.1093/ismeco/ycag073
Xiao-Lan Yue, Yue-Hong Wu, Dao-Qiong Zheng, Cong Sun, Lin Xu, Li Cui, Xue-Wei Xu
{"title":"<sup>13</sup>C-labeled single-cell Raman sorting reveals sulfur-driven dark carbon fixation in coastal sediments.","authors":"Xiao-Lan Yue, Yue-Hong Wu, Dao-Qiong Zheng, Cong Sun, Lin Xu, Li Cui, Xue-Wei Xu","doi":"10.1093/ismeco/ycag073","DOIUrl":"https://doi.org/10.1093/ismeco/ycag073","url":null,"abstract":"<p><p>Chemoautotrophs drive carbon fixation in coastal sediments, but most of them remain uncultured with poorly characterized <i>in situ</i> activities. In this study, a cultivation-independent single-cell approach combining Raman spectroscopy with <sup>13</sup>C-stable isotope probing was developed to enable direct identification of active chemoautotrophs in coastal sediments using function-specific spectral biomarkers, targeted metagenomic sequencing and pure culture verification. <sup>13</sup>C-induced shifts in cytochrome <i>c</i> (749, 1129, 1312, 1589 cm<sup>-1</sup>) and phenylalanine (1002 cm<sup>-1</sup>) Raman bands were systematically evaluated and applied as functional biomarkers through investigations of both representative chemoautotrophic strains and environmental samples. The combined analysis of targeted sorting of active chemoautotrophic cells and metagenomic sequencing revealed dominant species and a complete Calvin-Benson-Bassham (CBB) cycle pathway in sulfur-oxidizing guilds. Remarkably, a novel sulfur-oxidizing chemoautotroph, <i>Guyparkeria</i> sp. TX1, which showed ≥99% gene sequence similarity to contigs recovered from sorted-cell metagenomes, was isolated from enrichment cultures. Its significant carbon fixation capacity provided experimental validation for the effectiveness of Raman-based <i>in situ</i> functional screening. This study establishes Raman-based functional biomarkers applicable to chemoautotrophic carbon fixation, enabling <i>in situ</i> mapping of microbial carbon fluxes. By integrating single-cell phenotypic activity with genomic potential, this work advances the mechanistic understanding of sulfur-driven dark carbon fixation, which sustains coastal blue carbon ecosystems as a keystone process.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"6 1","pages":"ycag073"},"PeriodicalIF":6.1,"publicationDate":"2026-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13082230/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147700874","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
ISME communicationsPub Date : 2026-03-23eCollection Date: 2026-01-01DOI: 10.1093/ismeco/ycag071
Brittany A Baker, Romain B Leroy, Purificación López-García, Laura Eme, David Moreira
{"title":"<i>Methanonatronarchaeia</i> are deep-branching ancestrally methanogenic archaea distant from <i>Halobacteria</i>.","authors":"Brittany A Baker, Romain B Leroy, Purificación López-García, Laura Eme, David Moreira","doi":"10.1093/ismeco/ycag071","DOIUrl":"https://doi.org/10.1093/ismeco/ycag071","url":null,"abstract":"<p><p>Since their discovery, the phylogenetic placement of the extremely halophilic, methanogenic <i>Methanonatronarchaeia</i> has remained controversial. Different studies have variably placed this lineage as sister to the archaeal class <i>Halobacteria</i> (haloarchaea) or as a deep-branching euryarchaeal group. These conflicting results may reflect methodological artefacts linked to the strong amino acid compositional bias characteristic of halophilic archaea and evolutionary model misspecification. Here, we reanalyse published phylogenomic datasets using site-heterogeneous mixture models that mitigate such biases. Our analyses consistently recover <i>Methanonatronarchaeia</i> as a deep-branching lineage basal to the <i>Methanotecta</i>, independent of the inclusion of the recently described <i>Ordosarchaeia</i>. We further show that <i>Ordosarchaeia</i> do not constitute a distinct lineage but fall within the previously described <i>Halorutilales</i> and <i>Afararchaeaceae</i>. Re-examination of the methyl-coenzyme M reductase phylogeny indicates that the placement of <i>Methanonatronarchaeia mcr</i> genes is best explained by vertical inheritance, without invoking horizontal gene transfer from unknown donors. Together, our results support ancestral methanogenesis within this lineage and its independent adaptation to extreme halophily.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"6 1","pages":"ycag071"},"PeriodicalIF":6.1,"publicationDate":"2026-03-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13082222/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147700937","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
ISME communicationsPub Date : 2026-03-23eCollection Date: 2026-01-01DOI: 10.1093/ismeco/ycag072
Cleopatra Collado, Pedro Romero-Tena, Gunter Wegener, Marcus Elvert, Walter Menapace, Rafael Laso-Pérez
{"title":"Anaerobic oxidation of methane supports a minimal microbial community in a subsurface biofilm at Ginsburg mud volcano.","authors":"Cleopatra Collado, Pedro Romero-Tena, Gunter Wegener, Marcus Elvert, Walter Menapace, Rafael Laso-Pérez","doi":"10.1093/ismeco/ycag072","DOIUrl":"https://doi.org/10.1093/ismeco/ycag072","url":null,"abstract":"<p><p>Deep marine sediments generate large amounts of methane, but most of this gas is consumed by the anaerobic oxidation of methane (AOM) mediated by microscopic consortia of anaerobic methane-oxidizing archaea (ANME) and sulfate-reducing bacteria (SRB). In this study, we investigated the AOM within a sulfate-methane transition zone (SMTZ) at a depth of ~9.6 m at the rim of the Ginsburg mud volcano in the Gulf of Cádiz. The SMTZ is supplied with sulfate from both overlying seawater and an underlying evaporitic deposit, and it coincides with a fracture zone that hosts a visible biofilm. Here, carbon dioxide shows the strongest <sup>13</sup>C-depletion, indicating intense methane consumption. Metagenomic and lipid biomarker analysis of the biofilm revealed an exceptionally simple microbial community dominated by ANME-1b archaea (63%), which predominantly produce strongly <sup>13</sup>C-depleted glycerol dialkyl glycerol tetraethers and, to a lesser extent, the less common macrocyclic archaeols. The putative partner bacterium Seep-SRB1c (<i>Desulfobacterota</i>) is less abundant (9%). Additionally, the biofilm contained five low-abundance heterotrophs that likely rely on biomass or metabolites released from the ANME-SRB consortium. Our study highlights the presence of active methanotrophic biofilms in subsurface sediments and suggests that these communities may play an overlooked role in mitigating seafloor methane emissions.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"6 1","pages":"ycag072"},"PeriodicalIF":6.1,"publicationDate":"2026-03-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13109099/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147791061","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
ISME communicationsPub Date : 2026-03-23eCollection Date: 2026-01-01DOI: 10.1093/ismeco/ycag074
Reid G Griggs, David A Mills, Nicholas A Bokulich
{"title":"Spatial heterogeneity and microbial terroir: balancing dispersal limitation and cultivar as drivers of microbial diversity in viticulture.","authors":"Reid G Griggs, David A Mills, Nicholas A Bokulich","doi":"10.1093/ismeco/ycag074","DOIUrl":"https://doi.org/10.1093/ismeco/ycag074","url":null,"abstract":"<p><p>The microbial communities inhabiting grapevines and wines exhibit spatiotemporal patterns linked to region, climate, and cultivar. However, the degree of spatial heterogeneity within and between vineyards and its relationship to cultivar-associated biodiversity selection has not been studied previously. We combined high-density sampling of grapevine microbiota (<i>N</i> = 230) with spatial modeling and satellite imagery in two experiments: (i) two monoclonal Chardonnay vineyards to examine spatial heterogeneity in a genetically homogenous population and (ii) three old-vine vineyards interplanted with mixed cultivars to investigate the relative effects of spatial distance and cultivar on the microbiota. Contrary to expectations based on monoclonal vineyards, cultivar effects were not apparent in mixed-cultivar vineyards. Instead, we demonstrate extensive spatial variation in the bacterial and fungal communities inhabiting individual grapevines and vineyards, and that community similarity is correlated with spatial distance within and between vineyards. This suggests that dispersal limitation may play an important role in shaping grapevine microbiota, as well as cumulative diversity within the vineyard ecosystem (gamma diversity), with implications for both plant health and wine quality. Spatial models may identify abnormalities in microbial communities, such as contaminant sources within vineyards, and future studies examining microbiota in agricultural settings should account for spatial variation within the study design, e.g. by sufficiently dense spatial sampling or collection of aggregate samples (e.g. grape musts) to avoid undersampling bias. Overall, this study adds to the complicated story of microbial biogeography associated with winegrowing and wine quality (microbial 'terroir'), highlighting the roles of dispersal and potential microclimate effects in agricultural settings.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"6 1","pages":"ycag074"},"PeriodicalIF":6.1,"publicationDate":"2026-03-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13134041/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147824338","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
ISME communicationsPub Date : 2026-03-23eCollection Date: 2026-01-01DOI: 10.1093/ismeco/ycag069
María Del Mar Quiñonero-Coronel, M Pilar Garcillán-Barcia
{"title":"Plasmids serve as vehicles and reservoirs of type VI secretion systems.","authors":"María Del Mar Quiñonero-Coronel, M Pilar Garcillán-Barcia","doi":"10.1093/ismeco/ycag069","DOIUrl":"https://doi.org/10.1093/ismeco/ycag069","url":null,"abstract":"<p><p>The Type VI secretion system (T6SS) is a major determinant of bacterial competition, yet its dissemination across lineages remains unclear. By analyzing 43 213 plasmids and 29 161 chromosomes, we reveal plasmids as an underestimated reservoir and vehicle for T6SS diversification. We identified 405 complete plasmid-encoded T6SSs and 929 orphan islands containing <i>hcp, vgrG</i>, and/or <i>PAAR</i> genes, often independent of full systems. Plasmid-encoded T6SSs are biased toward large replicons, frequently megaplasmids, with distinct stability and mobility traits: orphan island plasmids are enriched in conjugation modules, whereas complete systems are associated with partition and toxin-antitoxin maintenance systems. Phylogenomic analyses show that some plasmid lineages stably integrate T6SSs as core traits, while others undergo recurrent acquisition and diversification. Comparative and ancestral analyses indicate pervasive bidirectional transfers between plasmids and chromosomes, with insertion sequences frequently detected in their vicinity. The presence of near-identical homologs across compartments underscores the capacity of plasmids to transcend phylogenetic barriers and propagate these nanoweapons. Together, our results identify plasmids as dual evolutionary actors in T6SS ecology, functioning as short-term vectors for rapid horizontal spread and as long-term reservoirs that foster stabilization and adaptive diversification.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"6 1","pages":"ycag069"},"PeriodicalIF":6.1,"publicationDate":"2026-03-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13098142/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147791088","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Unique characteristics of acid-tolerant comammox bacteria revealed by multi-omics analyses.","authors":"Tingting Zhang, Junhao Pan, Alejandro Palomo, Zilu Ouyang, Xianghua Wen, Jiyun Li, Chengwen Wang, Min Zheng","doi":"10.1093/ismeco/ycag070","DOIUrl":"https://doi.org/10.1093/ismeco/ycag070","url":null,"abstract":"<p><p>Complete ammonia oxidation (comammox) is a critical biogeochemical process in the nitrogen cycle. In this study, we utilized comammox <i>Nitrospira</i> to convert urine wastewater into ammonium nitrate by operating a laboratory-scale membrane bioreactor at pH 3 ~ 4. During the process, the acid-tolerant comammox <i>Nitrospira</i> was highly enriched. The metagenomic and metatranscriptomic analyses were applied to reveal its unique characteristics. Comparative genomic analysis among previously reported comammox <i>Nitrospira</i> demonstrated that this species was phylogenetically novel, named <i>Candidatus</i> Nitrospira aciditolerans. Key mechanisms were further identified to enable this species to thrive in acidic environments. These include active proton efflux, regulation of proton consumption, inhibition of proton influx, and cellular strategies for acid stress management and repair. Remarkably, different from other comammox <i>Nitrospira</i> and acid-tolerant ammonia-oxidizing bacteria (AOB), <i>Candidatus</i> Nitrospira aciditolerans possesses highly expressed V-type ATPases that are typically associated with acidophilic ammonia-oxidizing archaea (AOA). This may indicate an ecologically significant role for comammox bacteria and AOA in co-maintaining ammonia oxidation activity in low pH environments. Kinetic characterization revealed an apparent ammonium half-saturation coefficient <i>K</i> <sub>m</sub> of 0.50 ± 0.05 <i>μ</i>M NH<sub>3</sub> and an apparent ammonium inhibition constant <i>K</i> <sub>i</sub> of 241.43 ± 45.64 <i>μ</i>M NH<sub>3</sub>. The enrichment culture demonstrated optimal ammonia oxidation activity at neutral pH but maintained functionality across a broader pH range between 4 and 8. Like other nitrifying bacteria, this comammox culture was sensitive to temperature and salinity changes. The findings enhance our understanding of the nitrogen cycle under acidic conditions and also present opportunities for engineering applications of acid-tolerant ammonia oxidizers.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"6 1","pages":"ycag070"},"PeriodicalIF":6.1,"publicationDate":"2026-03-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13109103/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147791150","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
ISME communicationsPub Date : 2026-03-21eCollection Date: 2026-01-01DOI: 10.1093/ismeco/ycag067
Silvia Talavera-Marcos, Daniel Aguirre de Cárcer
{"title":"Ecological drift simulations reveal key factors influencing minimal microbiome engineering and community assembly.","authors":"Silvia Talavera-Marcos, Daniel Aguirre de Cárcer","doi":"10.1093/ismeco/ycag067","DOIUrl":"https://doi.org/10.1093/ismeco/ycag067","url":null,"abstract":"<p><p>In this work, we describe an engineering approach that leverages ecological drift to generate minimal microbiomes; microbial consortia that are relatively simple, cohesive, and functionally complete. This process can be applied to any microbial ecosystem, provided that the target microbiome can be experimentally mimicked. Empirical support for this approach has emerged from multiple independent studies. We use simulations across diverse scenarios, significantly varying niche structures and biotic interactions, to explore the experimental conditions and source microbiome characteristics that favor successful outcomes, within a computational framework that also enables the study of microbial community assembly. Our results indicate that the effectiveness of this approach is constrained by several factors, and that perfect outcomes should not be routinely expected. Nevertheless, despite its drawbacks, this strategy remains a powerful tool for simplifying microbiomes and isolating key co-adapted populations, enabling the construction of low-diversity consortia that retain community function and present ecological cohesion.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"6 1","pages":"ycag067"},"PeriodicalIF":6.1,"publicationDate":"2026-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13098171/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147791139","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
ISME communicationsPub Date : 2026-03-21eCollection Date: 2026-01-01DOI: 10.1093/ismeco/ycag068
Roth E Conrad, Luis M Rodriguez-R, Blake G Lindner, Kenji Gerhardt, Konstantinos T Konstantinidis
{"title":"An ANIr-based methodology to determine if two sequence-discrete populations are identical and identify cosmopolitan prokaryotic populations.","authors":"Roth E Conrad, Luis M Rodriguez-R, Blake G Lindner, Kenji Gerhardt, Konstantinos T Konstantinidis","doi":"10.1093/ismeco/ycag068","DOIUrl":"https://doi.org/10.1093/ismeco/ycag068","url":null,"abstract":"<p><p>Although sequence-discrete species appear to dominate microbial communities, readily distinguishing between distinct populations of a species recovered from different short-read metagenomic samples is challenging due to technical limitations associated with read length. To close this gap, we developed a novel algorithm to evaluate which reads in a metagenome belong to a target population based on the distribution of sequence identities of reads aligned to a reference sequence, which are filtered using a Kernel density estimation (KDE) as a flexible alternative to the commonly used static 95% nucleotide identity cutoff. Subsequently, we employed the average nucleotide identity of reads (ANIr) aligning above the KDE threshold, and resampling techniques for estimating the confidence intervals of ANIr values, to quantify intrapopulation sequence diversity and compare populations across globally representative marine samples. Most populations showed high ANIr in only a few samples at similar depths and decreased ANIr and increased gene-content difference between samples where a closely related population is detected (e.g. same 95% ANI-based species). Accordingly, ANIr correlated with the physical distance between the samples, and only a few truly cosmopolitan populations were identified. Among the latter, <i>Alteromonas macleodii</i> [97% average amino-acid identity (AAI) to the type genome] and <i>Prochlorococcus marinus</i> (79% AAI) showed high relative abundance in both surface (0-200 m) and deep (>1000 m) samples. These results suggest that microbial communities under different environmental conditions share very few identical and abundant populations and provide a highly needed methodology to track such populations over space and time, in marine or other habitats.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"6 1","pages":"ycag068"},"PeriodicalIF":6.1,"publicationDate":"2026-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13098170/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147791074","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
ISME communicationsPub Date : 2026-03-21eCollection Date: 2026-01-01DOI: 10.1093/ismeco/ycag066
Jack Jansma, Pietro Landi, Cang Hui
{"title":"Bayesian inference captures metabolite-bacteria interactions in a microbial community.","authors":"Jack Jansma, Pietro Landi, Cang Hui","doi":"10.1093/ismeco/ycag066","DOIUrl":"https://doi.org/10.1093/ismeco/ycag066","url":null,"abstract":"<p><p>Macro-ecosystems, including the human gut, host a vast and diverse set of microbes that indirectly interact with each other through consuming and producing metabolites. Disruptions in this microbial network can affect macro-ecosystem functioning and, in the human gut, contribute to the onset and progression of various disorders, including diabetes, rheumatoid arthritis, and Parkinson's disease. A theoretical foundation for understanding the intricate and dynamic interactions between microbes and metabolites is essential for developing microbiota-targeted interventions to improve macro-ecosystem functioning and health. To this end, a precise mathematical framework is crucial to capture and quantify the complex dynamics of the microbial system. Here, we develop a dynamic network model of coupled ordinary differential equations and present a computational workflow that integrates a generative model with Bayesian inference for model identification. Our approach infers interaction rates, quantifying metabolite consumption and production from simulated time-series data within a Bayesian framework, incorporating prior knowledge and uncertainty quantification. We show that our approach is accurate and reliable in communities of various sizes, sparsity, and with different levels of observational noise. This workflow enables <i>in silico</i> predictions of system behaviour under perturbations and offers a robust method to integrate high-dimensional biological data with dynamic network models. By refining our understanding of microbial dynamics, this framework is capable of assessing microbiota-targeted interventions and their potential to improve the health of the macro-ecosystem.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"6 1","pages":"ycag066"},"PeriodicalIF":6.1,"publicationDate":"2026-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13082234/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147700921","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}