ISME communications最新文献

{"title":"Unexpected diversity and ecological significance of uncultivable large virus-like particles in aquatic environments.","authors":"Hermine Billard, Maxime Fuster, François Enault, Jean-François Carrias, Léa Fargette, Margot Carrouée, Perrine Desmares, Tom O Delmont, Pauline Nogaret, Estelle Bigeard, Gwenn Tanguy, Anne-Claire Baudoux, Urania Christaki, Télesphore Sime-Ngando, Jonathan Colombet","doi":"10.1093/ismeco/ycaf098","DOIUrl":"10.1093/ismeco/ycaf098","url":null,"abstract":"<p><p>The discovery of jumbo phages and giant viruses of microeukaryotes has transformed our perception of the virosphere. Metagenomic and metatranscriptomic data further highlight their diversity and ecological impact. Nevertheless, sequence-based approaches fail to take into account the morphological diversity of non-cultivated viruses, resulting in our fragmented understanding of their nature and role in the environment. Here, we combined flow cytometry and electron microscopy to uncover both previously unsuspected morphological diversity and significant abundances of large virus-like particles in aquatic environments. We discovered new viral morphotypes, all likely to be associated with microeukaryotes. We also obtained insights into the multi-year dynamics of the abundances of both giant microeukaryotic virus-like particles and jumbo phage-like particles. This work deepens our understanding of large virus and reveals their key role as regulators of microbial communities.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf098"},"PeriodicalIF":5.1,"publicationDate":"2025-06-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12204322/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144531471","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":"Host-level biodiversity shapes the dynamics and networks within the coral reef microbiome.","authors":"Fabienne Wiederkehr, Kara Elena Engelhardt, Jana Vetter, Hans-Joachim Ruscheweyh, Guillem Salazar, James O'Brien, Taylor Priest, Maren Ziegler, Shinichi Sunagawa","doi":"10.1093/ismeco/ycaf097","DOIUrl":"10.1093/ismeco/ycaf097","url":null,"abstract":"<p><p>Coral reefs face severe threats from human activity, resulting in drastic biodiversity loss. Despite the urgency of safeguarding these ecosystems, we know little about the ecological impacts of losing coral reef host-associated microbial communities (microbiomes). Here, we experimentally studied the microbiomes attached to or released from seven benthic reef hosts belonging to the functional groups of stony corals, soft corals, macroalgae, and sponges while manipulating the coral reef metacommunity to mimic biodiverse or degraded reef habitats. Developing an ecological framework, we found host species and functional groups to show distinct patterns of interacting with the environment (i.e. by exuding, maintaining, acquiring, or exchanging microbiome members), with habitat biodiversity primarily influencing microbial acquisition. In a degraded compared to a biodiverse habitat, the microbiomes of stony corals were less connected to soft corals and sponges, while those of soft corals, macroalgae, and sponges became more tightly linked. Our study demonstrates that a decline in metacommunity biodiversity is not merely associated with a proportional loss in microbial diversity; rather, it triggers complex changes in the microbial interactions among the persisting hosts with each other and the environment. These results emphasize the importance of conserving coral reef host biodiversity to preserve the intricately linked microbiomes-and with them the ecosystem functions and services coral reefs provide.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf097"},"PeriodicalIF":5.1,"publicationDate":"2025-06-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12192423/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144499741","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":"Response of marine microbes to iron contained in colloids of glacial origin: a Kerguelen Island case study.","authors":"Rhea Thoppil, Stéphane Blain, Rui Zhang, Audrey Guéneuguès, Olivier Crispi, Philippe Catala, Barbara Marie, Ingrid Obernosterer","doi":"10.1093/ismeco/ycaf093","DOIUrl":"10.1093/ismeco/ycaf093","url":null,"abstract":"<p><p>The trace element iron (Fe) is a major constraint for microbially mediated processes in the Southern Ocean. The accelerated melting of glaciers could present a novel source of Fe, but whether glacial Fe is bioavailable to marine microbes is not known. We investigated the response of marine heterotrophic prokaryotes to Fe contained in colloids (20-200 nm) of glacial origin collected on Kerguelen Island (Southern Ocean). We followed prokaryotic growth in incubation experiments amended with colloids of either glacial or nonglacial origin and determined community composition and the abundance of genes involved in Fe-related processes in metagenomes and metagenome-assembled genomes (MAGs) at the final time point. Prokaryotic taxa belonging to <i>Vibrionaceae</i> and <i>Pseudomonadaceae</i> accounted together for 32% to 67% of the relative abundances in the glacial colloid-amended treatments, while <i>Rhodobacteraceae</i>, <i>Flavobacteriaceae</i>, and <i>Alteromonadaceae</i> were the dominant contributors to the communities in the incubations amended with nonglacial colloids. Metagenomic analysis revealed a higher abundance of genes involved in the biosynthesis of the siderophores pyoverdine and vibrioferrin as well as their respective transporters in the presence of glacial colloids compared to nonglacial colloids. Genes for the transport of both siderophores were present in diverse MAGs, while biosynthesis genes were detected in fewer MAGs. Our results suggest that the utilization of siderophores facilitates access to Fe from glacial colloids and points to the key role of specific prokaryotes in rendering this source of Fe available to Southern Ocean microbial communities.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf093"},"PeriodicalIF":6.1,"publicationDate":"2025-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12445661/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145115135","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":"KSGP 3.1: improved taxonomic annotation of Archaea communities using LotuS2, the genome taxonomy database and RNAseq data.","authors":"Alastair Grant, Abdullah Aleidan, Charli S Davies, Solomon C Udochi, Joachim Fritscher, Mohammad Bahram, Falk Hildebrand","doi":"10.1093/ismeco/ycaf094","DOIUrl":"10.1093/ismeco/ycaf094","url":null,"abstract":"<p><p>Taxonomic annotation is a substantial challenge for Archaea metabarcoding. A limited number of reference sequences are available; a substantial fraction of phylogenetic diversity is not fully characterized; widely used databases do not reflect current archaeal taxonomy and contain mislabelled sequences. We address these gaps with a systematic and tractable approach based around the Genome Taxonomy Database (GTDB) combined with the eukaryote PR2 and MIDORI mitochondrial databases. After removing incongruent, chimeric and duplicate SSU sequences, this combination (<i>GTDB+</i>) provides a small improvement in annotation of a set of estuarine Archaea Operational Taxonomic Units (OTUs) compared to SILVA. We add to this a collection of near full length rRNA sequences and the prokaryote SSU sequences in SILVA, creating a new reference database, KSGP ( <b><i>K</i></b> arst, <b><i>S</i></b> ilva, <b><i>G</i></b> TDB, and <b>P</b>R2). The additional sequences are (re-)annotated using three different approaches. The most conservative, using lowest common ancestor, gives a further small improvement. Annotation using SINTAX increases Class and Order assignments by 2.7 and 4.2 times over SILVA, although this may include some \"lumping\" of un-named and named clades. Still further improvement can be made using similarity based clustering to group database sequences into putative taxa at all taxonomic levels, assigning 60% and 41% of Archaea OTUs to putative family and genus level taxa respectively. GTDB without cleaning and GreenGenes2 both perform poorly and cannot be recommended for use with Archaea. We make the GTDB+ and KSGP databases available at ksgp.earlham.ac.uk; integrate them into a metabarcoding pipeline, LotuS2 and outline their use to annotate Archaea OTUs and metatranscriptomic data.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf094"},"PeriodicalIF":5.1,"publicationDate":"2025-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12203549/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144531467","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":"Dark ocean archaeal and bacterial chemoautotrophs drive vitamin B1 production in oxygen minimum zones.","authors":"Kristin Bergauer, Christopher P Suffridge, Fabian Wittmers, Sebastian Sudek, Stephen J Giovannoni, Alexandra Z Worden","doi":"10.1093/ismeco/ycaf077","DOIUrl":"10.1093/ismeco/ycaf077","url":null,"abstract":"<p><p>Vitamin B1 (thiamine) is essential for all cells, yet many marine microbes cannot synthesize B1 <i>de novo.</i> Dissolved thiamine and its related chemical congeners (TRCs) concentrations are not well characterized beyond the surface ocean, where they are typically low. Here, we observed unexpected enrichment of TRCs in regions of low dissolved oxygen levels (9.4 < O₂ < 12.5 μmol kg^-1) across vertical profiles in Monterey Bay and Pacific waters 145 km offshore (Station 67-70). TRC concentrations ranged from fM to pM, with 1.1 to 4.5 fold increases from near-surface waters to the mesopelagic Oxygen Minimum Zone (OMZ). Notably, at 67-70, dissolved B1 increased 3.5-fold within the mesopelagic OMZ. Paired metagenomic analysis suggests that chemoautotrophic ammonia-oxidizing Archaea (AOA) and Thioglobaceae, alongside nitrite-oxidizing <i>Nitrospina</i>, are important B1 producers in OMZs. Metagenome-assembled genomes indicate that <i>Nitrospina</i> may alternate between B1 biosynthesis and energy-preserving salvage pathways in synergy with co-occurring AOA. Re-analysis of metatranscriptomic reads from a previous study established Thioglobaceae can be dominant expressors of key <i>de novo</i> B1 biosynthesis genes in Monterey Bay. These findings suggest that deep ocean chemoautotrophs are B1 prototrophs in OMZs, analogous to photoautotrophs in the epipelagic ocean, and provide the foundation for B1 trafficking.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf077"},"PeriodicalIF":5.1,"publicationDate":"2025-05-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12236431/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144593067","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":"Deciphering community assembly processes of the microbial community in subtropical coastal-estuarine seawater over a 6-year exploration.","authors":"Yu Wang, Qiongqiong Yang, Qi Chen, Shengwei Hou, Nianzhi Jiao, Qiang Zheng","doi":"10.1093/ismeco/ycaf091","DOIUrl":"10.1093/ismeco/ycaf091","url":null,"abstract":"<p><p>Understanding community assembly in ecosystems is crucial for ecology, yet the interplay between selection and dispersal remains unclear. We examined bacterial and microeukaryotic communities in a dynamic estuarine-coastal ecosystem over six years to investigate the roles of dispersal and environmental selection. Our approach combined species-time relationships (STRs) analysis, a temporal approach focusing on colonization and extinction dynamics, and a process model for community dynamics, revealing insights into the interplay between selection and dispersal along environmental gradients. Both communities showed significant STRs, but their responses varied by taxon and environmental conditions. For bacteria, salinity increased STR exponents, indicating faster richness growth over time, whereas microeukaryotic STR exponents decreased, suggesting distinct assembly mechanisms. Higher salinity reduced bacterial community determinism but heightened it for microeukaryotes, affecting community turnover: microeukaryote turnover decreased with rising salinity due to changes in colonization and extinction, while bacterial turnover increased due to slower dynamics. This study highlights the complex interaction between selection and dispersal, shaped by environmental factors and unique microbial traits, emphasizing the need for tailored conservation strategies in fluctuating coastal ecosystems.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf091"},"PeriodicalIF":5.1,"publicationDate":"2025-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12203064/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144531451","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":"Methanol chemoreceptor MtpA- and flagellin protein FliC-dependent methylotaxis contributes to the spatial colonization of PPFM in the phyllosphere.","authors":"Shiori Katayama, Kosuke Shiraishi, Kanae Kaji, Kazuya Kawabata, Naoki Tamura, Akio Tani, Hiroya Yurimoto, Yasuyoshi Sakai","doi":"10.1093/ismeco/ycaf092","DOIUrl":"10.1093/ismeco/ycaf092","url":null,"abstract":"<p><p>Pink-pigmented facultative methylotrophs (PPFMs) capable of growth on methanol are dominant and versatile phyllosphere bacteria that provide positive effects on plant growth through symbiosis. However, the spatial behavior of PPFMs on plant surfaces and its molecular basis are unknown. Here, we show that <i>Methylobacterium</i> sp. strain OR01 inoculated onto red perilla seeds colonized across the entire plant surface in the phyllosphere concomitant with the plant growth. During its transmission, strain OR01 was found to be present on the entire leaf surface with a preference to sites around the periphery, vein, trichome, and stomata. We found that methanol-sensing chemoreceptor MtpA-dependent chemotaxis (methylotaxis; chemotaxis toward methanol) and flagellin protein FliC-dependent motility facilitated the bacterial entry into the stomatal cavity and their colonization in the phyllosphere.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf092"},"PeriodicalIF":5.1,"publicationDate":"2025-05-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12202990/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144531468","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":"Upcycling human excrement: the gut microbiome to soil microbiome axis.","authors":"Jeff Meilander, Chloe Herman, Andrew Manley, Georgia Augustine, Dawn Birdsell, Evan Bolyen, Kimberly R Celona, Hayden Coffey, Jill Cocking, Teddy Donoghue, Alexis Draves, Daryn Erickson, Marissa Foley, Liz Gehret, Johannah Hagen, Crystal Hepp, Parker Ingram, David John, Katarina Kadar, Paul Keim, Victoria Lloyd, Christina Osterink, Victoria Monsaint-Queeney, Diego Ramirez, Antonio Romero, Megan C Ruby, Jason W Sahl, Sydni Soloway, Nathan E Stone, Shannon Trottier, Kaleb Van Orden, Alexis Painter, Sam Wallace, Larissa Wilcox, Colin V Wood, Jaiden Yancey, J Gregory Caporaso","doi":"10.1093/ismeco/ycaf089","DOIUrl":"10.1093/ismeco/ycaf089","url":null,"abstract":"<p><p>Human excrement composting (HEC) is a sustainable strategy for human excrement (HE) management that recycles nutrients and mitigates health risks while reducing reliance on freshwater, fossil fuels, and fertilizers. A mixture of HE and bulking material was collected from 15 composting toilets and composted as 15 biological replicates in modified 19-liter buckets under mesophilic conditions with weekly sampling for one year. We hypothesized that (i) the microbiome of 1 year old compost would resemble that of a soil and/or food and landscape waste compost microbiome more closely than the original HE; and (ii) the human fecal indicators, <i>Escherichia coli</i> and <i>Clostridium perfringens</i>, would be undetectable after 52 weeks using qPCR and culturing. This investigation identified unique successional trajectories within buckets (i.e. biological replicates) and significant shifts in microbial communities around 25 weeks across buckets, with reductions in fecal-associated taxa and increases in environmental taxa indicating effective composting. We present a comprehensive microbial time series analysis of HEC and show that the initial gut-like microbiome of HEC systems transitions to a microbiome similar to soil and traditional compost but that pathogen risk assessment is important if thermophilic temperatures are not achieved. This study also produced the highest resolution composting microbiome data to date, establishing a baseline for HEC optimization and thermophilic composting studies while serving as a resource for bioprospecting for enzymes and organisms relevant to upcycling waste.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf089"},"PeriodicalIF":6.1,"publicationDate":"2025-05-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12393218/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144981536","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":"Improved methane mitigation potential and modulated methane cycling microbial communities in arable soil by compost addition.","authors":"Stijn G van den Bergh, Iris Chardon, Marion Meima-Franke, Germán Pérez, Gabriel S Rocha, Kristof Brenzinger, Gerard W Korthals, Jochen Mayer, Mathias Cougnon, Dirk Reheul, Wietse de Boer, Paul L E Bodelier","doi":"10.1093/ismeco/ycaf139","DOIUrl":"10.1093/ismeco/ycaf139","url":null,"abstract":"<p><p>The global atmospheric concentration of the potent greenhouse gas methane (CH₄) is rising rapidly, and agriculture is responsible for 30%-50% of the yearly CH₄ emissions. To limit its global warming effects, strong and sustained reductions are needed. Sustainable agricultural management strategies, as the use of organic amendments like compost, have previously proven to have a potent CH₄ mitigation effect in laboratory experiments. Here we investigated, using an extensive field study, the effect of organic amendments on the CH₄ mitigation potential and CH₄ cycling microbial communities of arable soils. Organic-amended soils had higher potential CH₄ uptake rates and an improved potential to oxidize CH₄ to sub-atmospheric concentrations. Also, we showed for the first time that the methanotrophic and methanogenic microbial communities of arable soils were unequivocally altered after organic amendment application by increasing in size while getting less diverse. Compost-amended soils became dominated by the compost-originating methanotroph <i>Methylocaldum szegediense</i> and methanogen <i>Methanosarcina horonobensis</i>, replacing the indigenous methane cycling community members. However, multivariate analyses didn't point out type Ib methanotrophs like <i>M. szegediense</i> as significant driving factors for the observed improved soil CH₄ uptake potential. Conventional type IIa methanotrophs like <i>Methylocystis</i> sp. also had higher differential abundances in organic-amended soils and are speculated to contribute to the improved CH₄ uptake potential. Altogether, the results showed that compost serves as a vector for the introduction of CH₄ cycling microbes and improves the soil's CH₄ uptake potential, which emphasizes the potential of organic fertilization with compost to contribute to CH₄ mitigation in agricultural soils.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf139"},"PeriodicalIF":6.1,"publicationDate":"2025-05-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12395338/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144981507","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":"Benchmarking and optimizing qualitative and quantitative pipelines in environmental metatranscriptomics using mixture controlling experiments.","authors":"Weiyi Li, Qilian Fan, Yi Yang, Xiang Xiao, Jing Li, Yu Zhang","doi":"10.1093/ismeco/ycaf090","DOIUrl":"10.1093/ismeco/ycaf090","url":null,"abstract":"<p><p>Metatranscriptomic analysis is increasingly performed in environments to provide dynamic gene expression information on ecosystems, responding to their changing conditions. Many computational methods have undergone remarkable development in the past years, but a comprehensive benchmark study is still lacking. There are concerns regarding the accuracies of the qualitative and quantitative profilers obtained from metatranscriptomic analysis, especially for the microbiota in extreme environments, most of them are unculturable and lack well-annotated reference genomes. Here, we presented a benchmark experiment that included 10 single-species and their cell or RNA-admixtures with the predefined species compositions and varying evenness, simulating the low annotation rate and high heterogeneity. In total, 1 metagenome sample and 24 metatranscriptome were sequenced for the comparisons of 36 combination of analysis methods for tasks ranging from sample preparation, quality control, rRNA removal, alignment strategies, taxonomic profiling, and transcript quantification. For each part of the workflow mentioned above, corresponding metrics have been established to serve as standards for assessment and comparison. Evaluation revealed the performances and proposed an optimized pipeline named MT-Enviro (MetaTranscriptomic analysis for ENVIROnmental microbiome). Our data and analysis provide a comprehensive framework for benchmarking computational methods with metatranscriptomic analysis. MT-Enviro is implemented in Nextflow and is freely available from https://github.com/Li-Lab-SJTU/MT-Enviro.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf090"},"PeriodicalIF":5.1,"publicationDate":"2025-05-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12202999/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144531449","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}