iMetaOmics最新文献

{"title":"Artificial intelligence driven diet-intestinal microbiota-host health integration: A four-dimensional paradigm for advancing host wellness research.","authors":"Tianle He, Shuobo Zhang, Jiaxin Chen, Xiaoling Zheng, Jixin Zhao, Huifeng Li, Jiani Mao, Ju Luo, Jundan Zheng, Dengjun Ma, Lihong Wang, Junhui Liu, Wen Tian, Shuangming Yang, Chengli Liu, Ke Tian, Zhenguo Yang","doi":"10.1002/imo2.70133","DOIUrl":"10.1002/imo2.70133","url":null,"abstract":"<p><p>The artificial intelligence (AI)-driven diet-intestinal microbiota-host health integration paradigm has emerged as a novel framework for advancing host health research. Intestinal microbiota serves as a key mediator linking dietary signals to host homeostasis, while AI enables efficient integration of multi-omics data to construct microbial metabolic models, identify interaction patterns across biological scales, and support prediction-informed modulation of diet-microbiota interactions. This paradigm synergizes dietary intervention design, AI technology, intestinal microbiota modulation, and host health enhancement, offering innovative solutions for chronic disease management, animal health breeding, and food safety monitoring. In this review, we summarize the core mechanisms of the four-dimensional interaction and the application value of AI-driven informed optimization. This review also discusses the major challenges currently facing the field, including model interpretability, multi-source data heterogeneity, and cross-species translation, and further highlights that future research should focus on establishing interpretable and iterative AI-driven closed-loop systems. This integrated approach holds immense potential to revolutionize host wellness research and promote the development of nutritional health and related industries. Unlike existing diet-microbiota-host frameworks and AI-assisted precision nutrition approaches that mainly focus on association analysis or outcome prediction, our proposed paradigm positions AI as an active coordination layer linking dietary inputs, microbial responses, and host outcomes. By integrating mechanism-informed modeling with iterative feedback, this framework enables dynamic optimization of diet-microbiota interactions and supports more precise host health regulation.</p>","PeriodicalId":521007,"journal":{"name":"iMetaOmics","volume":"3 3","pages":"e70133"},"PeriodicalIF":0.0,"publicationDate":"2026-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13674463/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149217733","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":"Bacterial indole-3-butyric acid promotes fish PUFA synthesis.","authors":"Ruojing Li, Biao Yuan, Xin Yi, Jieyan Lin, Bi Huang, Ermei Yin, Jiayu Zhou, Qianwen Min, Meiqi Lv, Bo Zhang, Na Zhao","doi":"10.1002/imo2.70136","DOIUrl":"10.1002/imo2.70136","url":null,"abstract":"<p><p>Marine fish are paradoxically rich in polyunsaturated fatty acids (PUFAs) despite limited endogenous biosynthetic capacity, suggesting a critical contribution from the gut microbiota. Here, we first characterized the gut microbiota of <i>Seriola dumerili</i>, a PUFA-rich marine fish, functionally enriched in the biosynthesis of unsaturated fatty acids. Further functional validation was performed using zebrafish as a model. Strain screening revealed the <i>Bacillus thuringiensis</i> strain Sd_h10 exhibited potent lipid utilization capacity <i>in vitro</i> and in zebrafish on a high-fat diet, and remodeled transcription of lipid-related pathways to promote lipid accumulation and PUFA biosynthesis. Notably, indole-3-butyric acid (IBA), a major metabolite of Sd_h10, was found in the intestinal tissue of <i>S. dumerili</i> and regulated peroxisome proliferator-activated receptor gamma (PPARγ), mimicking the effects of the PPARγ agonist rosiglitazone in zebrafish. Long-term IBA administration in conventional zebrafish increased body weight gain, hepatic lipid accumulation, and muscle docosahexaenoate (DHA) content, accompanied by upregulation of PPARγ downstream target genes, including <i>dgat2</i>, <i>fads6</i>, and <i>elovl6l</i>. Simultaneously, IBA reshaped the intestinal microbiota, depleting <i>Burkholderiaceae</i> while enriching <i>Acidovorax</i> abundance, accompanied by enrichment of functions related to fatty acid uptake, lipid utilization, and unsaturated fatty acid modification. These findings support a potential role for the microbiota-derived metabolite IBA in modulating PPARγ-associated signaling pathways linked to host DHA biosynthesis and accumulation. Our study provides additional evidence supporting microbiota-host lipid metabolic interactions and highlights the potential application of probiotic-associated microbial metabolites for improving lipid nutritional quality in marine fish.</p>","PeriodicalId":521007,"journal":{"name":"iMetaOmics","volume":"3 3","pages":"e70136"},"PeriodicalIF":0.0,"publicationDate":"2026-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13674406/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149217696","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":"Evidence tiers for strain-resolved long-read metagenomics.","authors":"Yanhua Han, Yunjuan Peng, Minghui Li, Xiaoyuan Wei, Jianmin Chai, Jiangchao Zhao, Ying Li, Feilong Deng","doi":"10.1002/imo2.70130","DOIUrl":"10.1002/imo2.70130","url":null,"abstract":"<p><p>Long-read metagenomics links variants, repeats, and mobile elements across individual molecules and can reveal lineage turnover that is obscured at the species level. The strength of the resulting inference, however, depends on the type and genomic span of the recovered linkage. We distinguish four evidence units-strain profiles, local haplotype blocks, genome-scale strain candidates, and host-linkage evidence-and describe the diagnostics appropriate to each. Confidence is reported separately as candidate, supported, or high confidence in context, based on read assignment, allele coherence, coverage continuity, boundary support, and independent confirmation. Ambiguous placement, contamination, consensus collapse, coverage breaks, reference bias, or unresolved linkage should prompt more conservative terminology. Aligning terms with the available evidence reduces overstatement in claims of strain reconstruction, host assignment, persistence, replacement, and engraftment, while making analyses easier to compare and review.</p>","PeriodicalId":521007,"journal":{"name":"iMetaOmics","volume":"3 3","pages":"e70130"},"PeriodicalIF":0.0,"publicationDate":"2026-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13674440/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149217756","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":"Climate change amplifies global mycotoxin exposure: Emerging risks and sustainable solutions.","authors":"Mengyao Xue, Zheng Qu, Tingting Jiang, Antonio F Logrieco, Antonio Moretti, Ke Dong, Yanpo Yao, Qi Zhang, Peiwu Li","doi":"10.1002/imo2.70131","DOIUrl":"10.1002/imo2.70131","url":null,"abstract":"<p><p>Climate change intensifies mycotoxin contamination through rising temperatures, elevated CO₂, and altered precipitation. Global surveys reveal a high and widespread prevalence of major mycotoxins in staple cereals, with low-income countries bearing the greatest burden. This escalating contamination poses a growing threat to global food security, compromising both food availability and safety. To mitigate these risks, we propose four actions: establish a predictive global surveillance system integrating climate-crop-fungal models, deploy field-ready biosensors, scale up climate-resilient agriculture and resistant varieties, and implement a multi-stakeholder governance protocol focused on developing regions. These measures offer feasible solutions to protect global food security in a changing climate.</p>","PeriodicalId":521007,"journal":{"name":"iMetaOmics","volume":"3 3","pages":"e70131"},"PeriodicalIF":0.0,"publicationDate":"2026-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13674422/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149217775","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":"Chromosome-level genome and methylome of vine tea suggest roles for tandem duplication and CHH hypomethylation in high dihydromyricetin accumulation.","authors":"Yingmei Wu, Hanrui Hu, Qing Ye, Xueqing Chen, Miyuan Tian, Jing Li, Li Lu, Yifei Liu, Yi Shang, Yanling Li, Xingyao Xiong, Junbo Gou","doi":"10.1002/imo2.70129","DOIUrl":"10.1002/imo2.70129","url":null,"abstract":"<p><p>A chromosome-level genome assembly and single-base resolution methylome of vine tea (<i>Nekemias grossedentata</i>) reveal that lineage-specific tandem duplications of dihydromyricetin (DHM) biosynthetic genes (<i>NgCHS</i> and <i>NgF3'5' H</i>) have expanded their copy numbers, providing the genetic basis for high DHM flux. Tissue-specific CHH hypomethylation in young leaves, associated with downregulation of RNA-directed DNA methylation (RdDM)-related methyltransferases and upregulation of the demethylase NgDML1, correlates with the selective high expression of these duplicated genes, while competing pathway branches (e.g., STS for stilbene synthase, HCT for shikimate hydroxycinnamoyl transferase, DFR for dihydroflavonol 4-reductase) maintain hypermethylation and low expression. Candidate v-myb avian myeloblastosis viral oncogene homolog (MYB) and basic helix-loop-helix (bHLH) transcription factors co-expressed with DHM pathway genes are identified. These findings suggest a \"duplication-associated activation\" model integrating genomic, epigenomic, and transcriptomic layers for high DHM accumulation.</p>","PeriodicalId":521007,"journal":{"name":"iMetaOmics","volume":"3 3","pages":"e70129"},"PeriodicalIF":0.0,"publicationDate":"2026-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13674461/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149217772","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":"A uterine-centric view of reproductive senescence: Genetic insights into late-life performance in laying hens.","authors":"Junnan Zhang, Mingyue Gao, Ronglang Cai, Xinwei Jiang, Boxuan Zhang, Zhaojie Li, Ning Yang, Congjiao Sun","doi":"10.1002/imo2.70128","DOIUrl":"10.1002/imo2.70128","url":null,"abstract":"<p><p>This study identifies uterus weight as a heritable (<i>h</i> ² = 0.45) intermediate phenotype that independently associates with late-life egg production and eggshell quality in aged laying hens. Genome-wide association study (GWAS) reveals a genome-wide significant locus on chromosome 3 and suggestive loci on chromosome 11 for uterus weight, mediation analysis statistically decomposed genetic effects into indirect and direct components, with uterus weight serving as a statistically supported intermediate phenotype, thereby uncovering associations missed by conventional GWAS. Integrative multi-omics: transcriptome-wide association study (TWAS), summary-data-based mendelian randomization (SMR) and weighted gene co-expression network analysis (WGCNA) prioritize 11 candidate genes spanning endocrine signaling, lipid metabolism, ion transport, and tissue remodeling. Collectively, these findings establish uterus weight as a biologically central hub connecting genetic variation to reproductive aging, providing potential molecular markers for enhancing laying persistence in extended production cycles.</p>","PeriodicalId":521007,"journal":{"name":"iMetaOmics","volume":"3 3","pages":"e70128"},"PeriodicalIF":0.0,"publicationDate":"2026-07-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13674417/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149218085","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":"Biological age in the meta omics era: Integrating physical activity, sleep, and diet to reshape paths of healthy ageing.","authors":"Yanwei You, Yicong Cui, Yuquan Chen, Jiarong He, Dongmin Wang, Danijela Gasevic, Xifeng Wu, Steve Horvath, Mingming Zhang, Xindong Ma","doi":"10.1002/imo2.70127","DOIUrl":"10.1002/imo2.70127","url":null,"abstract":"<p><p>Biological age provides a translational endpoint linking modifiable lifestyle behaviors-physical activity, sleep, and diet-to multi-omics changes and downstream clinical outcomes. Integrating multiple ageing clocks with inflammatory, metabolic, and oxidative pathways supports reproducible, intervention-ready strategies to slow ageing and extend healthspan.</p>","PeriodicalId":521007,"journal":{"name":"iMetaOmics","volume":"3 3","pages":"e70127"},"PeriodicalIF":0.0,"publicationDate":"2026-07-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13674388/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149217800","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":"Microbiome-pancreatic cancer crosstalk: From tumor biology to therapeutic intervention.","authors":"Yuqin Xie, Jingyuan Ye, Sheng Wang, Maoyun Liu, Fengsheng Dai, Mingzhen Bai, Yi Wang, Athena Savoji, Yu Wang, Phillip B Hylemon, Huiping Zhou, Hui Li, Dewei Li","doi":"10.1002/imo2.70126","DOIUrl":"10.1002/imo2.70126","url":null,"abstract":"<p><p>Pancreatic cancer (PC) remains one of the most lethal malignancies worldwide, characterized by dense desmoplastic stroma, profound immunosuppression, and poor responsiveness to conventional therapies. Accumulating evidence positions the intratumoral microbiome, encompassing bacteria as well as understudied fungal and viral components, as a critical regulator of PC pathogenesis, tumor microenvironment (TME) remodeling, and therapeutic efficacy. In this review, we synthesize the current understanding of the pancreatic intratumoral microbiome, including its distinct composition relative to normal pancreatic tissue, gut microbiota, and oral microbiota. The PC intratumoral microbiome is characterized by enrichment of validated pro-tumorigenic drivers (e.g., <i>Pseudomonas</i>, <i>Bacteroides</i> species) alongside protective taxa (e.g., <i>Lactobacillus</i> species). These taxonomic profiles vary significantly based on disease stage, patient demographics, and treatment history. We dissected the mechanisms by which microbes and their derivatives drive PC initiation and progression, including immune suppression through modulation of myeloid-derived suppressor cells and regulatory T cells, metabolic reprogramming involving short-chain fatty acids and the tryptophan metabolite 3-indoleacetic acid (3-IAA), and stromal remodeling via activation of cancer-associated fibroblasts. The influence of the microbiome on therapeutic response is examined, with particular emphasis on microbial-mediated mechanisms that undermine treatment efficacy. We further summarize diagnostic and prognostic biomarkers, including salivary microbial signatures with moderate sensitivity and specificity, circulating microbial DNA, and composite microbial risk scores that integrate multiple bacterial species to predict survival. Therapeutic strategies targeting the microbiome are discussed, distinguishing clinically translatable approaches from experimental concepts requiring further validation. Finally, we outline challenges in standardizing profiling methods, validating microbial signatures across diverse populations, and translating preclinical insights to clinical practice, emphasizing the need for multi-omics integration and interdisciplinary collaboration to advance microbiome-driven PC management.</p>","PeriodicalId":521007,"journal":{"name":"iMetaOmics","volume":"3 3","pages":"e70126"},"PeriodicalIF":0.0,"publicationDate":"2026-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13674442/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149218067","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":"Strategies and mechanisms of precision genome engineering: From gene editing to genome writing.","authors":"Kerui Huang, Jianhong Tian, Wenyan Zhao, Siqin Zhang, Lixuan Xiang, Meiqing Yang, Lu Liu, Yazhou Huang, Ningyun Zhang, Lei Sun, Peng Xie, Nanyu Kuang, Hong Zhou, Chengfeng Qiu, Jun Yan, Xiaocheng Jiang, Qiang Tu, Yun Wang, Haoliang Hu, Youming Zhang","doi":"10.1002/imo2.70115","DOIUrl":"10.1002/imo2.70115","url":null,"abstract":"<p><p>Genomic manipulation has advanced from stochastic nuclease-mediated disruption toward programmable, deterministic precision. Early clustered regularly interspaced short palindromic repeats (CRISPR) strategies enabled targeted mutagenesis through double-strand breaks; however, their therapeutic application is limited by genotoxicity, chromosomal instability, and dependence on endogenous repair pathways that are difficult to predict. In this review, we examined the transition from gene editing to genome writing, an approach that decouples genomic modification from host repair pathways to better balance efficiency, precision, and payload delivery. We also discussed the principles of precision technologies, including base and prime editors, and described emerging large-scale writers, such as CRISPR-associated transposases and recombinase-based bridge RNAs, which enable the integration of multi-kilobase synthetic modules. Beyond enzymatic mechanisms, we further considered the combined use of generative artificial intelligence, structural biology, and novel delivery architectures as potential strategies to overcome current biological limitations. Taken together, these developments point toward Generative Biology, in which computational design and high-throughput screening transform the genome from a static substrate into a more dynamic model for complex, synthetic functional design.</p>","PeriodicalId":521007,"journal":{"name":"iMetaOmics","volume":"3 3","pages":"e70115"},"PeriodicalIF":0.0,"publicationDate":"2026-07-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13674456/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149218074","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":"Viruses in the sediments around the trenches harbor diverse survival mechanisms.","authors":"Yue Su, Hao Yu, Shujuan Sun, Kaiyang Zheng, Ziyue Wang, Chen Gao, Guangxue Li, Xiaoshou Liu, Hongbing Shao, David Paez-Espino, Andrew McMinn, Yantao Liang, Min Wang","doi":"10.1002/imo2.70124","DOIUrl":"10.1002/imo2.70124","url":null,"abstract":"<p><p>Deep-sea trenches are the deepest and most isolated environments in the global ocean but the diversity and adaptation of the viral communities remain poorly characterized. In this study, 5563 viral operational taxonomic units (vOTUs) were identified from sediments of the Yap Trench and Western Caroline Basin. More than 99% of these vOTUs could not be assigned to known viral families and showed limited similarity to sequences in current global viral databases, indicating substantial novelty. Viral community composition and diversity were found to significantly vary with water depth. The vOTUs also encoded a diverse range of functional genes possibly related to their ability to survive in extreme deep-sea sediments, including genes involved in lipid metabolism, DNA modification, and immune evasion. The results show that deep-sea trench sediments contain highly distinct viral communities structured by depth-associated environmental variations.</p>","PeriodicalId":521007,"journal":{"name":"iMetaOmics","volume":"3 3","pages":"e70124"},"PeriodicalIF":0.0,"publicationDate":"2026-07-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13674397/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149218087","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}