Microbiome最新文献

{"title":"MicrobeRX: a tool for enzymatic-reaction-based metabolite prediction in the gut microbiome.","authors":"Angel J Ruiz-Moreno, Ángela Del Castillo-Izquierdo, Isabel Tamargo-Rubio, Jingyuan Fu","doi":"10.1186/s40168-025-02070-5","DOIUrl":"10.1186/s40168-025-02070-5","url":null,"abstract":"<p><strong>Background: </strong>The gut microbiome functions as a metabolic organ, producing numerous enzymes that influence host health; however, their substrates and metabolites remain largely unknown.</p><p><strong>Results: </strong>We present MicrobeRX, an enzyme-based metabolite prediction tool that employs 5487 human reactions and 4030 unique microbial reactions from 6286 genome-scale models, as well as 3650 drug metabolic reactions from the DrugBank database (v.5.1.12). MicrobeRX includes additional analysis modules for metabolite visualization and enzymatic and taxonomic analyses. When we applied MicrobeRX to 1083 orally administered drugs that have been approved in at least one jurisdiction at some point in time (DrugBank), it predicted metabolites with physicochemical properties and structures similar to metabolites found in biosamples (from MiMeDB). It also outperformed another existing metabolite prediction tool (BioTransformer 3.0) in terms of predictive potential, molecular diversity, reduction of redundant predictions, and enzyme annotation.</p><p><strong>Conclusions: </strong>Our analysis revealed both unique and overlapping metabolic capabilities in human and microbial metabolism and chemo- and taxa-specific microbial biotransformations. MicrobeRX bridges the genomic and chemical spaces of the gut microbiome, making it a valuable tool for unlocking the chemical potential of the gut microbiome in human health, the food and pharmaceutical industries, and environmental safety. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"78"},"PeriodicalIF":13.8,"publicationDate":"2025-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11921629/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143663999","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Global analysis of the metaplasmidome: ecological drivers and spread of antibiotic resistance genes across ecosystems.","authors":"Didier Debroas","doi":"10.1186/s40168-025-02062-5","DOIUrl":"10.1186/s40168-025-02062-5","url":null,"abstract":"<p><strong>Background: </strong>Plasmids act as vehicles for the rapid spread of antibiotic resistance genes (ARGs). However, few studies of the resistome at the community level distinguish between ARGs carried by mobile genetic elements and those carried by chromosomes, and these studies have been limited to a few ecosystems. This is the first study to focus on ARGs carried by the metaplasmidome on a global scale.</p><p><strong>Results: </strong>This study shows that only a small fraction of the plasmids reconstructed from 27 ecosystems representing 9 biomes are catalogued in public databases. The abundance of ARGs harboured by the metaplasmidome was significantly explained by bacterial richness. Few plasmids with or without ARGs were shared between ecosystems or biomes, suggesting that plasmid distribution on a global scale is mainly driven by ecology rather than geography. The network linking plasmids to their hosts shows that these mobile elements have thus been shared between bacteria across geographically distant environmental niches. However, certain plasmids carrying ARGs involved in human health were identified as being shared between multiple ecosystems and hosted by a wide variety of hosts. Some of these mobile elements, identified as keystone plasmids, were characterised by an enrichment in antibiotic resistance genes (ARGs) and CAS-CRISPR components which may explain their ecological success. The ARGs accounted for 9.2% of the recent horizontal transfers between bacteria and plasmids.</p><p><strong>Conclusions: </strong>By comprehensively analysing the plasmidome content of ecosystems, some key habitats have emerged as particularly important for monitoring the spread of ARGs in relation to human health. Of particular note is the potential for air to act as a vector for long-distance transport of ARGs and accessory genes across ecosystems and continents. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"77"},"PeriodicalIF":13.8,"publicationDate":"2025-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11921664/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143663997","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Short-term and long-term high-fat diet promote metabolic disorder through reprogramming mRNA m⁶A in white adipose tissue by gut microbiota.","authors":"Youhua Liu, Jiaqi Liu, Ruiti Ren, Zimeng Xin, Yaojun Luo, Yushi Chen, Chaoqun Huang, Yuxi Liu, Tongyudan Yang, Xinxia Wang","doi":"10.1186/s40168-025-02047-4","DOIUrl":"10.1186/s40168-025-02047-4","url":null,"abstract":"<p><strong>Background: </strong>Although short-term high-fat diet (S-HFD) and long-term high-fat diet (L-HFD) induce metabolic disorder, the underlying epigenetic mechanism is still unclear.</p><p><strong>Results: </strong>Here, we found that both 4 days of S-HFD and 10 weeks of L-HFD increased mRNA m⁶A level in epididymal white adipose tissue (eWAT) and impaired metabolic health. Interestingly, S-HFD activated transposable elements (TEs), especially endogenous retroviruses (ERVs) in eWAT, while L-HFD activated long interspersed elements (LINEs). Subsequently, we demonstrated that both S-HFD and L-HFD increased m⁶A level of Ehmt2 and decreased EHMT2 protein expression and H3K9me2 level, accounting for activation of ERVs and LINEs. Overexpression of EHMT2 in eWAT or inhibition of ERVs and LINEs by antiviral therapy improved metabolic health under HFD feeding. Notably, we found that both short-term and long-term HFD feeding increased Fimicutes/Bacteroidota ratio and decreased the gut microbiome health index. Fecal microbiota transplantation (FMT) experiments demonstrated that gut microbiota from S-HFD and L-HFD was responsible for increased m⁶A level in eWAT, resulting in glucose intolerance and insulin insensitivity. Furthermore, we identified that both S-HFD and L-HFD increased the abundance of the gut microbial metabolite homogentisic acid (HGA), and HGA level was positively correlated with unclassified_f__Lachnospiraceae which was both increased in S-HFD and L-HFD feeding mice. Administration of HGA increased the m⁶A level of Ehmt2 and decreased the EHMT2 protein expression and H3K9me2 level in eWAT, leading to metabolic disorder in mice.</p><p><strong>Conclusions: </strong>Together, this study reveals a novel mechanism that S-HFD and L-HFD induce metabolism disorder through gut microbiota-HGA-m⁶A-Ehmt2-ERV/LINE signaling. These findings may provide a novel insight for prevention and treatment of metabolism disorder upon short-term or long-term dietary fat intake. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"75"},"PeriodicalIF":13.8,"publicationDate":"2025-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11912683/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143649363","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Correction: The intestinal microbiome and metabolome discern disease severity in cytotoxic T-lymphocyte-associated protein 4 deficiency.","authors":"Prabha Chandrasekaran, Máté Krausz, Yu Han, Noriko Mitsuiki, Annemarie Gabrysch, Christina Nöltner, Michele Proietti, Theo Heller, Caroline Grou, Virginie Calderon, Poorani Subramanian, Drew R Jones, Yik Siu, Clayton Deming, Sean Conlan, Steven M Holland, Julia A Segre, Gulbu Uzel, Bodo Grimbacher, Emilia Liana Falcone","doi":"10.1186/s40168-025-02069-y","DOIUrl":"10.1186/s40168-025-02069-y","url":null,"abstract":"","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"74"},"PeriodicalIF":13.8,"publicationDate":"2025-03-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11909905/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143634265","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Disruption and adaptation: infant gut microbiota's dynamic response to SARS-CoV-2 infection.","authors":"Li-Ting Zhu, Lei Zhao, Yue Zhu, Xue-Li Xu, Jing-Jing Lin, Yi-Fang Duan, Lu Long, Yang-Yu Wu, Wen-Juan Xu, Jing-Yu Chen, Yu-Han Yin, Alex Ujong Obeten, Qiansheng Huang","doi":"10.1186/s40168-025-02029-6","DOIUrl":"10.1186/s40168-025-02029-6","url":null,"abstract":"<p><strong>Background: </strong>The responses of the infant gut microbiota to infection significantly disrupt the natural intrahost evolutionary processes of the microbiome. Here, we collected a 16-month longitudinal cohort of infant gut microbiomes affected by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Then, we developed a multicriteria approach to identify core interaction network driving community dynamics under environmental disturbances, which we termed the Conserved Variated Interaction Group (CVIgroup).</p><p><strong>Results: </strong>The CVIgroup showed significant advantages on pinpointing a sparse set associated with the disturbances, as validated both our own and publicly available datasets. Leveraging the Oxford Nanopore Technology, we found this group facilitates the ecosystem's adaptation to environmental disruptions by enhancing the mobility of mobile genetic elements, including the reinforcement of the twin-arginine translocation pathway in response to increased virulence factors. Furthermore, the CVIgroup serves as an effective indicator of ecosystem health. The timescale for the gut microbiota's adaptation extends beyond 10 months. Members of the CVIgroup, such as Bacteroides thetaiotaomicron and Faecalibacterium, exhibit varying degrees of genomic structural variants, which contribute to guiding the community toward a new stable state rather than returning to its original configuration.</p><p><strong>Conclusions: </strong>Collectively, the CVIgroup offers a snapshot of the gut microbiota's adaptive response to environmental disturbances. The disruption and subsequent adaptation of the gut microbiota in infants after COVID-19 infection underscores the necessity of re-evaluating reference standards in the context of the post-pandemic era. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"72"},"PeriodicalIF":13.8,"publicationDate":"2025-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11895207/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143604889","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comprehensive profiling of genomic invertons in defined gut microbial community reveals associations with intestinal colonization and surface adhesion.","authors":"Xiaofan Jin, Alice G Cheng, Rachael B Chanin, Feiqiao B Yu, Alejandra Dimas, Marissa Jasper, Allison Weakley, Jia Yan, Ami S Bhatt, Katherine S Pollard","doi":"10.1186/s40168-025-02052-7","DOIUrl":"10.1186/s40168-025-02052-7","url":null,"abstract":"<p><strong>Background: </strong>Bacteria use invertible genetic elements known as invertons to generate heterogeneity among a population and adapt to new and changing environments. In human gut bacteria, invertons are often found near genes associated with cell surface modifications, suggesting key roles in modulating dynamic processes such as surface adhesion and intestinal colonization. However, comprehensive testing of this hypothesis across complex bacterial communities like the human gut microbiome remains challenging. Metagenomic sequencing holds promise for detecting inversions without isolation and culturing, but ambiguity in read alignment limits the accuracy of the resulting inverton predictions.</p><p><strong>Results: </strong>Here, we developed a customized bioinformatic workflow-PhaseFinderDC-to identify and track invertons in metagenomic data. Applying this method to a defined yet complex gut community (hCom2) across different growth environments over time using both in vitro and in vivo metagenomic samples, we detected invertons in most hCom2 strains. These include invertons whose orientation probabilities change over time and are statistically associated with environmental conditions. We used motif enrichment to identify putative inverton promoters and predict genes regulated by inverton flipping during intestinal colonization and surface adhesion. Analysis of inverton-proximal genes also revealed candidate invertases that may regulate flipping of specific invertons.</p><p><strong>Conclusions: </strong>Collectively, these findings suggest that surface adhesion and intestinal colonization in complex gut communities directly modulate inverton dynamics, offering new insights into the genetic mechanisms underlying these processes. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"71"},"PeriodicalIF":13.8,"publicationDate":"2025-03-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11892184/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143586269","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Correction: Seed microbiomes promote Astragalus mongholicus seed germination through pathogen suppression and cellulose degradation.","authors":"Da Li, Weimin Chen, Wen Luo, Haofei Zhang, Yang Liu, Duntao Shu, Gehong Wei","doi":"10.1186/s40168-025-02057-2","DOIUrl":"10.1186/s40168-025-02057-2","url":null,"abstract":"","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"70"},"PeriodicalIF":13.8,"publicationDate":"2025-03-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11889854/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143586270","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Rumen microbiome associates with postpartum ketosis development in dairy cows: a prospective nested case-control study.","authors":"Fanlin Kong, Shuo Wang, Yijia Zhang, Chen Li, Dongwen Dai, Cheng Guo, Yajing Wang, Zhijun Cao, Hongjian Yang, Yanliang Bi, Wei Wang, Shengli Li","doi":"10.1186/s40168-025-02072-3","DOIUrl":"10.1186/s40168-025-02072-3","url":null,"abstract":"<p><strong>Background: </strong>Approximately, one-third of dairy cows suffer from postpartum diseases. Ketosis is considered an important inducer of other postpartum diseases by disrupting energy metabolism. Although the rumen microbiome may be involved in the etiology of ketosis by supplying volatile fatty acids, the rumen environmental dynamics of ketosis cows are unclear. Using multi-omics, this study aimed to elucidate changes in the rumen microbiome during parturition of ketosis cows and the association between the rumen microbiome and host energy metabolism. The study included 810 rumen content samples and 789 serum samples from day - 21 and 21 relative to calving day from 61 ketosis cows and 84 healthy cows.</p><p><strong>Results: </strong>In ketosis cows, the rumen bacterial composition after parturition changed dramatically and needed a longer time to restore. The molar proportions of propionate were lower in ketosis cows than those in healthy cows on days 3 and 7 and negatively correlated with the serum β-hydroxybutyrate (BHBA) levels. The fermentation sub-pathway of propionate metabolism and partial glucogenic amino acid pathways were downregulated on day 3. Prevotella, UBA1066, and microbiota diversity indices regulate serum BHBA and glucose (GLU) levels via arginine, alanine, glycine, or propionate. Propionate administration to ketosis cows potentially decreased the serum BHBA concentration.</p><p><strong>Conclusions: </strong>Collectively, we found rumen disruption happened after calving among ketosis cows, and insufficient glycogenic substrates, such as propionate, may be related to ketosis development. The study findings have implications for the relationship between rumen microbiome dynamics and host energy metabolism, which lays the foundation for the future rumen microbiome investigation for improving postpartum management in cows. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"69"},"PeriodicalIF":13.8,"publicationDate":"2025-03-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11889851/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143586276","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The universal accumulation of p-aminophenol during the microbial degradation of analgesic and antipyretic acetaminophen in WWTPs: a novel metagenomic perspective.","authors":"Chao-Fan Yin, Piaopiao Pan, Tao Li, Xin Song, Ying Xu, Ning-Yi Zhou","doi":"10.1186/s40168-025-02065-2","DOIUrl":"10.1186/s40168-025-02065-2","url":null,"abstract":"<p><strong>Background: </strong>Acetaminophen, a widely used analgesic and antipyretic drug, has become a significant aquatic micro-pollutant due to its extensive global production and increased consumption, particularly during the COVID-19 pandemic. Its high-water solubility leads to its pervasive presence in wastewater treatment plants (WWTPs), posing substantial risks to the environment and human health. Biological treatment is one of the promising approaches to remove such pollutants. Although previous studies have isolated acetaminophen-degrading pure cultures and proposed catabolic pathways, the interactions between microbiotas and acetaminophen, the distribution feature of acetaminophen degradation genes, and the gene-driven fate of acetaminophen in the real-world environment remain largely unexplored.</p><p><strong>Results: </strong>Among the water samples from 20 WWTPs across China, acetaminophen was detected from 19 samples at concentrations ranging from 0.06 to 29.20 nM. However, p-aminophenol, a more toxic metabolite, was detected in all samples at significantly higher concentrations (23.93 to 108.68 nM), indicating the presence of a catabolic bottleneck in WWTPs. Metagenomic analysis from both the above 20 samples and global datasets revealed a consistently higher abundance of initial acetaminophen amidases compared to downstream enzymes, potentially having explained the reason for the bottleneck. Meanwhile, a close correlation between initial amidases and Actinomycetota revealed by genome-based taxonomy suggests a species-dependent degradation pattern. Additionally, a distinct amidase ApaA was characterized by newly isolated Rhodococcus sp. NyZ502 (Actinomycetota), represents a predominant category of amidase in WWTPs. Significant phylogenetic and structural diversity observed among putative amidases suggest versatile acetaminophen hydrolysis potential in WWTPs.</p><p><strong>Conclusions: </strong>This study enhances our understanding of acetaminophen's environmental fate and highlights the possible occurrence of ecological risks driven by imbalanced genes in the process of acetaminophen degradation in global WWTPs. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"68"},"PeriodicalIF":13.8,"publicationDate":"2025-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11887370/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143586279","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Challenges in capturing the mycobiome from shotgun metagenome data: lack of software and databases.","authors":"Ekaterina Avershina, Arfa Irej Qureshi, Hanne C Winther-Larsen, Trine B Rounge","doi":"10.1186/s40168-025-02048-3","DOIUrl":"10.1186/s40168-025-02048-3","url":null,"abstract":"<p><strong>Background: </strong>The mycobiome, representing the fungal component of microbial communities, is increasingly acknowledged as an integral part of the gut microbiome. However, research in this area remains relatively limited. The characterization of mycobiome taxa from metagenomic data is heavily reliant on the quality of the software and databases. In this study, we evaluated the feasibility of mycobiome profiling using existing bioinformatics tools on simulated fungal metagenomic data.</p><p><strong>Results: </strong>We identified seven tools claiming to perform taxonomic assignment of fungal shotgun metagenomic sequences. One of these was outdated and required substantial modifications of the code to be functional and was thus excluded. To evaluate the accuracy of identification and relative abundance of the remaining tools (Kraken2, MetaPhlAn4, EukDetect, FunOMIC, MiCoP, and HumanMycobiomeScan), we constructed 18 mock communities of varying species richness and abundance levels. The mock communities comprised up to 165 fungal species belonging to the phyla Ascomycota and Basidiomycota, commonly found in gut microbiomes. Of the tools, FunOMIC and HumanMycobiomeScan needed source code modifications to run. Notably, only one species, Candida orthopsilosis, was consistently identified by all tools across all communities where it was included. Increasing community richness improved precision of Kraken2 and the relative abundance accuracy of all tools on species, genus, and family levels. MetaPhlAn4 accurately identified all genera present in the communities and FunOMIC identified most species. The top three tools for overall accuracy in both identification and relative abundance estimation were EukDetect, MiCoP, and FunOMIC, respectively. Adding 90% and 99% bacterial background did not significantly impact these tools' performance. Among the whole genome reference tools (Kraken2, HMS, and MiCoP), MiCoP exhibited the highest accuracy when the same reference database was used.</p><p><strong>Conclusion: </strong>Our survey of mycobiome-specific software revealed a very limited selection of such tools and their poor robustness due to error-prone software, along with a significant lack of comprehensive databases enabling characterization of the mycobiome. None of the implemented tools fully agreed on the mock community profiles. FunOMIC recognized most of the species, but EukDetect and MiCoP provided predictions that were closest to the correct compositions. The bacterial background did not impact these tools' performance. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"66"},"PeriodicalIF":13.8,"publicationDate":"2025-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11887097/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143586267","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}