iMeta最新文献

{"title":"Bacterial social interactions in synthetic Bacillus consortia enhance plant growth","authors":"Yan Liu,&nbsp;Baolei Jia,&nbsp;Yi Ren,&nbsp;Weibing Xun,&nbsp;Polonca Stefanic,&nbsp;Tianjie Yang,&nbsp;Youzhi Miao,&nbsp;Nan Zhang,&nbsp;Yanlai Yao,&nbsp;Ruifu Zhang,&nbsp;Zhihui Xu,&nbsp;Qirong Shen,&nbsp;Ines Mandic-Mulec","doi":"10.1002/imt2.70053","DOIUrl":"https://doi.org/10.1002/imt2.70053","url":null,"abstract":"<p>Plant growth-promoting rhizobacteria (PGPR) represent a sustainable method to improve crop productivity. Synthetic microbial consortia have emerged as a powerful tool for engineering rhizosphere microbiomes. However, designing functionally stable consortia remains challenging due to an insufficient understanding of bacterial social interactions. In this study, we investigated the effects of <i>Bacillus velezensis</i> SQR9 (i.e., a commercially important PGPR) on social interactions within the rhizosphere community, particularly among <i>Bacillus</i> species. SQR9 inoculation significantly enhanced cucumber plant growth and altered the structure of rhizosphere <i>Bacillus</i> and its related bacterial communities. The results of swarm boundary and carbon utilization assays, revealed that phylogenetically closer <i>Bacillus</i> strains exhibited increased social cooperation and increased metabolic niche overlap. Building on these social interactions, we designed 30 consortia comprising both highly related (HR) and moderately related (MR) types across four richness levels (1, 2, 3, and 4 strains), with MR consortia demonstrating superior PGP effects through enhanced plant growth, root colonization, indole-3-acetic acid production, and siderophore production, than the HR consortia. Expanding these findings to 300 consortia across four richness levels (1, 2, 4, and 8 strains) confirmed enhanced PGP effects in MR consortia with increasing richness. These findings highlight the importance of bacterial interactions and phylogenetic relationships in shaping rhizosphere communities and designing synthetic microbial consortia. Specifically, this study provides a framework for assembling <i>Bacillus</i> consortia that enhance cooperation, which would aid in improving their stability and effectiveness in agricultural applications.</p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":"4 4","pages":""},"PeriodicalIF":23.7,"publicationDate":"2025-06-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/imt2.70053","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144888298","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":"Single-cell sequencing reveals the role of IL-33+ endothelial subsets in promoting early gastric cancer progression","authors":"Li Zhou,&nbsp;Mei Yang,&nbsp;Chao Deng,&nbsp;Manqiu Hu,&nbsp;Suhua Wu,&nbsp;Kewen Lai,&nbsp;Lili Zhang,&nbsp;Zhiji Chen,&nbsp;Qin Tang,&nbsp;Qingliang Wang,&nbsp;Lu Chen,&nbsp;Runmin Zha,&nbsp;Yuanyuan Chen,&nbsp;Yibo Tan,&nbsp;Song He,&nbsp;Zhihang Zhou","doi":"10.1002/imt2.70050","DOIUrl":"https://doi.org/10.1002/imt2.70050","url":null,"abstract":"<p>Early gastric cancer (EGC) represents a critical stage in preventing and controlling the progression from gastritis to advanced gastric cancer (AGC). Therefore, identifying the single-cell characteristics of EGC, particularly the cellular composition of the tumor microenvironment (TME), as well as identifying potential predictive markers and therapeutic targets, could significantly enhance the monitoring of gastric cancer and improve clinical cure rates. We constructed a comprehensive single-cell RNA sequencing atlas for 184,426 high-quality gastric cancer cells from various stages, utilizing clinical biopsies and surgical samples. Our single-cell atlas highlights the cellular and molecular characteristics of EGC. Eight distinct cell lineage states were identified, and it was observed that the number of epithelial cell meta-clusters gradually decreased, while the number of T&amp;NK, B, plasma, fibroblast, myeloid, and endothelial cells increased with disease progression. Certain epithelial subclusters (metaplastic stem-like cells (MSCs), pit mucous-like cells (PMC-like), proliferating cells), T-cell subclusters (T_reg, <i>CCR7</i>⁺ naive, <i>CH25H</i>⁺ CD4⁺, T_EM CD8⁺, and <i>GFPT2</i>⁺ CD8⁺ T cells), and endothelial subclusters (<i>IL-33</i>⁺ Venous-1 and <i>AMAMTSL2</i>⁺ Artery-2) were found to be increased in EGC. The Venous-1 subcluster was found to express high levels of <i>IL-33</i>. Mechanistically, it was revealed that IL-33 enhances the survival and angiogenesis of endothelial cells by upregulating the expression of adhesion proteins CD34 and PECAM1. Patient-derived EGC and AGC organoids were subsequently generated, and it was demonstrated that endothelial-derived IL-33 promoted the growth of both EGC and AGC organoids <i>ex vitro</i> and <i>in vivo</i>. Furthermore, IL-33 was found to increase the expression of KRT17 in EGC organoids. Notably, we also found that high expression of IL-33 was positively correlated with the depth of invasion and malignancy of EGC. This study provides novel insights into the single-cell components involved in EGC and reveals the role of the <i>IL-33</i>⁺ endothelial subcluster in EGC progression.</p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":"4 4","pages":""},"PeriodicalIF":23.7,"publicationDate":"2025-06-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/imt2.70050","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144888165","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":"Age-specific reference intervals for plasma amino acids and their associations with nutrient intake in the Chinese pediatric population","authors":"Yang Wen,&nbsp;Qing Liu,&nbsp;Hongbo Zeng,&nbsp;Lina Lyu,&nbsp;Xuezhen He,&nbsp;Xin Zhang,&nbsp;Wentao Lyu,&nbsp;Weijun Chen,&nbsp;Yingping Xiao","doi":"10.1002/imt2.70051","DOIUrl":"https://doi.org/10.1002/imt2.70051","url":null,"abstract":"<p>A total of 2901 healthy Chinese children aged 0–12 years were enrolled in the reference group; 102 confirmed Phenylketonuria cases were included as validation individuals. Establishing the age-specific reference intervals of 42 plasma amino acids in Chinese pediatric populations. Profiling dynamic interactions between multiple nutrient intake and amino acid change patterns.\u0000 <figure>\u0000 <div><picture>\u0000 <source></source></picture><p></p>\u0000 </div>\u0000 </figure></p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":"4 3","pages":""},"PeriodicalIF":23.7,"publicationDate":"2025-05-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/imt2.70051","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144197595","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":"RepliChrom: Interpretable machine learning predicts cancer-associated enhancer-promoter interactions using DNA replication timing","authors":"Fuying Dao,&nbsp;Benjamin Lebeau,&nbsp;Crystal Chia Yin Ling,&nbsp;Mi Yang,&nbsp;Xueqin Xie,&nbsp;Melissa Jane Fullwood,&nbsp;Hao Lin,&nbsp;Hao Lyu","doi":"10.1002/imt2.70052","DOIUrl":"https://doi.org/10.1002/imt2.70052","url":null,"abstract":"<p>RepliChrom is an interpretable machine learning model that predicts enhancer-promoter interactions using DNA replication timing across multiple cell types. By integrating replication timing with chromatin interaction data from multiple experimental platforms, it accurately distinguishes true interactions and reveals promoter-region signals as key regulatory drivers. Importantly, the RepliChrom uncovers cancer-specific chromatin patterns in leukemia, offering mechanistic insights into how replication timing shapes long-range gene regulation in both normal and diseased genomes.\u0000 <figure>\u0000 <div><picture>\u0000 <source></source></picture><p></p>\u0000 </div>\u0000 </figure></p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":"4 4","pages":""},"PeriodicalIF":23.7,"publicationDate":"2025-05-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/imt2.70052","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144888464","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 multi-centered prospective birth cohort study in Western China","authors":"Xiangyu Li,&nbsp;Ying Wu,&nbsp;Bin Yi,&nbsp;Mengjie Chen,&nbsp;Gang Zhang,&nbsp;Xiaoshan Shao,&nbsp;Xiulian Jiang,&nbsp;Yuxia Cui,&nbsp;Li Chen,&nbsp;Xiaojing Dong,&nbsp;Shu Zhang,&nbsp;Yao Zhao,&nbsp;Yuebi Deng,&nbsp;Xueqi Li,&nbsp;Yang Wang,&nbsp;Lei Wu,&nbsp;Yu Fu,&nbsp;Dan Ran,&nbsp;Chen Peng,&nbsp;Xiao Yang,&nbsp;Lan Zhang,&nbsp;Yanxia Wang,&nbsp;Yi Zhu,&nbsp;Dina Sun,&nbsp;Yuchen Ran,&nbsp;Dan Zheng,&nbsp;Xuan Yin,&nbsp;Yufen Chen,&nbsp;Yu Long,&nbsp;Wenjing Wang,&nbsp;Xiaodong Zhao,&nbsp;Enmei Liu,&nbsp;Tao Xu,&nbsp;Qiu Li,&nbsp;Wen Zhong","doi":"10.1002/imt2.70049","DOIUrl":"https://doi.org/10.1002/imt2.70049","url":null,"abstract":"<p>The Western China Birth Cohort (WCBC) is a large-scale, multi-centered, prospective birth cohort study designed to address critical gaps in maternal and child health research in Western China, a region with diverse altitudes, ethnic groups, and unique environmental exposures. WCBC had enrolled 15,093 pregnant women across eight clinical centers in five provinces (Qinghai, Gansu, Guizhou, Chongqing, and Sichuan), spanning from the high-altitude Qinghai-Tibet Plateau to lowland regions. WCBC has collected over 220,000 medical records, 80,000 questionnaires, and 12 different types of biological samples, including peripheral blood, cord blood, dried blood spots, placenta, umbilical cord, decidua, saliva, feces, throat and nasal swabs, vaginal swabs, and breast milk. By integrating advanced multi-omics measurement, including genomics, proteomics, exosome profiling, metabolomics, spatial transcriptomics, single-cell RNA sequencing, culturome, metagenomics, and virosome analysis, WCBC provides a valuable platform to explore gene-environment interplay, early-life determinants of health, and long-term disease risks in diverse populations in Western China.\u0000 <figure>\u0000 <div><picture>\u0000 <source></source></picture><p></p>\u0000 </div>\u0000 </figure></p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":"4 3","pages":""},"PeriodicalIF":23.7,"publicationDate":"2025-05-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/imt2.70049","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144197003","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 Hiplot-based web service for cold atmospheric plasma high-throughput data integration and analysis on breast cancer","authors":"Xiaofeng Dai,&nbsp;Mingjie Wang,&nbsp;Yang Liu","doi":"10.1002/imt2.70045","DOIUrl":"https://doi.org/10.1002/imt2.70045","url":null,"abstract":"<p>Incremental evidence on the effect of cold atmospheric plasma (CAP) in specifically killing transformed cells and advances in sequencing technologies at multiple omics have led to the demand of in-depth exploration on the mechanisms of action driving the potency of CAP against cancer cells at the molecular level. However, high-throughput data detailing the effect of CAP on cancer cells is lacking, let alone the corresponding database and analytical tool. Here, we sequenced the whole transcriptome, proteome, phosphorylome, acetylome, and lactylome of transformed cells in response to CAP using breast cancer cells as the disease model; and advanced our previously developed Hiplot platform by establishing a focus-driven tumor-specific module, namely CAP medicine in breast cancer (CAPmed-BC) (https://capbc.hiplot.com.cn). CAPmed-BC is the first multi-omics data resource in plasma medicine for analyzing the treatment response of breast cancer cells to CAP. It can analyze each type of omics data regarding differentially expressed biomarkers, expression landscape, gene ontology analysis, pathway interpretation, gene set enrichment analysis, and protein-protein interaction network. It can also interrogate the dynamic fluctuation, functional activity, and metabolic vulnerability of cancer cells in response to CAP by combinatorially analyzing omics at multiple carefully defined dimensions. We also built in a visualization module to support users for producing personalized graphs via adjusting parameters. We believe that CAPmed-BC will become a valuable resource for characterizing the outcome of CAP on breast cancers at the omics and molecular levels, and make considerable contributions to both plasma medicine and oncology.</p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":"4 4","pages":""},"PeriodicalIF":23.7,"publicationDate":"2025-05-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/imt2.70045","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144888504","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":"Soyasaponin and vertical microbial transmission: Maternal effect on the intestinal development and health of early chicks","authors":"Mingkun Gao,&nbsp;Shu Chen,&nbsp;Hao Fan,&nbsp;Peng Li,&nbsp;Aiqiao Liu,&nbsp;Dongli Li,&nbsp;Xiaomin Li,&nbsp;Yongfei Hu,&nbsp;Guofeng Han,&nbsp;Yuming Guo,&nbsp;Zengpeng Lv","doi":"10.1002/imt2.70044","DOIUrl":"https://doi.org/10.1002/imt2.70044","url":null,"abstract":"<p>Multiple factors, including genetics, nutrition, and health, influence the vertical transmission of microbiota from mothers to their offspring. Recent studies have shown that avian microbiota can be passed to the next generation via the eggshell and egg albumen. However, it remains unclear whether these microbial communities are regulated by nutrition and how they are associated with the host genotype. Chickens, with their controlled rearing conditions and stable genotypes, provide a promising model for investigating microbiome transmission in birds. This study aims to determine whether host genotype-associated bacteria are vertically transmitted between generations, and how maternal nutritional intervention with soyasaponin modulates this microbial transfer, thereby shaping chick intestinal development and informing effective nutritional strategies. We established a microbial vertical transmission model across various anatomical sites in breeder hens, chicken embryos, and chicks. Avian gut microbiota and reproductive tract microbiota can both be found in chicks at various developmental stages. Supplementing breeder hen diets with soyasaponin interacts with vertically transmitted <i>Bifidobacterium adolescentis</i> to produce γ-aminobutyric acid. This compound modulates offspring intestinal development through distinct mechanisms in chick epithelial cells, including the inhibition of LC3 and caspase3-associated autophagy and apoptosis pathways, as well as the promotion of proliferation and differentiation pathways mediated by LGR5 and Olfm4. Our study highlights that avian gut and reproductive tract microbiota are transmitted to chicks through the cloaca, with the yolk sac also being instrumental in this vertical transfer. The incorporation of soyasaponin in avian diets affects microbial transfer, providing a theoretical basis for studying maternal effects in poultry and formulating corresponding dietary strategies.</p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":"4 4","pages":""},"PeriodicalIF":23.7,"publicationDate":"2025-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/imt2.70044","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144888310","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":"Phage-mediated horizontal transfer of Salmonella enterica virulence genes with regulatory feedback from the host","authors":"Tianjing She,&nbsp;Demeng Tan,&nbsp;Jose Luis Balcazar,&nbsp;Ville-Petri Friman,&nbsp;Danrui Wang,&nbsp;Dong Zhu,&nbsp;Mao Ye,&nbsp;Mingming Sun,&nbsp;Shujian Yuan,&nbsp;Feng Hu","doi":"10.1002/imt2.70042","DOIUrl":"https://doi.org/10.1002/imt2.70042","url":null,"abstract":"<p>Phage-mediated horizontal transfer of virulence genes can enhance the transmission and pathogenicity of <i>Salmonella enterica</i> (<i>S. enterica</i>), a process potentially regulated by its regulatory mechanisms. In this study, we explored the global dynamics of phage-mediated horizontal transfer in <i>S. enterica</i> and investigated the role of its regulatory mechanisms in transduction. A total of 5178 viral sequences encoding 12 <i>S. enterica</i> virulence genes were retrieved from the Integrated Microbial Genomes and Virome (IMG/VR) database, alongside 466,136 <i>S. enterica</i> genomes from EnteroBase. Virulence genes, including <i>iacP</i> (acyl carrier protein), <i>mgtB</i> (P-type Mg²⁺ transporter), <i>misL</i> (autotransporter porin), and <i>fliC</i> (flagellar filament protein), were widely distributed in phages and <i>S. enterica</i> across North America, Europe, and Asia. Phylogenetic analysis revealed close genetic affinity between phage- and bacterial-encoded virulence genes, suggesting shared ancestry and historical horizontal gene transfer events. The global regulator carbon storage regulator A (<i>csrA</i>) was highly conserved and ubiquitous in <i>S. enterica</i>. Overexpression of <i>csrA</i> inhibited prophage cyclization and release by upregulating the prophage <i>cI</i> repressor during horizontal gene transfer. Overall, these findings enhance our understanding of phage-mediated horizontal transfer of virulence genes, explore new areas of bacterial regulators that inhibit gene exchange and evolution by affecting phage life cycles, and offer a novel approach to controlling the transmission of phage-mediated <i>S. enterica</i> virulence genes.</p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":"4 4","pages":""},"PeriodicalIF":23.7,"publicationDate":"2025-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/imt2.70042","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144888286","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":"Gut microbiota-derived butyric acid regulates calcific aortic valve disease pathogenesis by modulating GAPDH lactylation and butyrylation","authors":"Chunli Wang,&nbsp;Zongtao Liu,&nbsp;Tingwen Zhou,&nbsp;Jiaqin Wu,&nbsp;Fan Feng,&nbsp;Shunshun Wang,&nbsp;Qingjia Chi,&nbsp;Yongqiang Sha,&nbsp;Shuai Zha,&nbsp;Songren Shu,&nbsp;Linghang Qu,&nbsp;Qianqian Du,&nbsp;Huiming Yu,&nbsp;Li Yang,&nbsp;Anna Malashicheva,&nbsp;Nianguo Dong,&nbsp;Fei Xie,&nbsp;Guixue Wang,&nbsp;Kang Xu","doi":"10.1002/imt2.70048","DOIUrl":"https://doi.org/10.1002/imt2.70048","url":null,"abstract":"<p>The involvement of gut microbiota in calcific aortic valve disease (CAVD) pathogenesis remains underexplored. Here, we provide evidence for a strong association between the gut microbiota and CAVD development. ApoE^−/− mice were stratified into easy- and difficult- to calcify groups using neural network and cluster analyses, and subsequent faecal transplantation and dirty cage sharing experiments demonstrated that the microbiota from difficult-to-calcify mice significantly ameliorated CAVD. 16S rRNA sequencing revealed that reduced abundance of <i>Faecalibacterium prausnitzii</i> (<i>F. prausnitzii</i>) was significantly associated with increased calcification severity. Association analysis identified <i>F. prausnitzii</i>-derived butyric acid as a key anti-calcific metabolite. These findings were validated in a clinical cohort (25 CAVD patients vs. 25 controls), where serum butyric acid levels inversely correlated with disease severity. Functional experiments showed that butyric acid effectively hindered osteogenic differentiation in human aortic valve interstitial cells (hVICs) and attenuated CAVD progression in mice. Isotope labeling and ¹³C flux analyses confirmed that butyric acid produced in the intestine can reach heart tissue, where it reshapes glycolysis by specifically modifying GAPDH. Mechanistically, butyric acid-induced butyrylation (Kbu) at lysine 263 of GAPDH competitively inhibited lactylation (Kla) at the same site, thereby counteracting glycolysis-driven calcification. These findings uncover a novel mechanism through which <i>F. prausnitzii</i> and its metabolite butyric acid contribute to the preservation of valve function in CAVD, highlighting the gut microbiota-metabolite-glycolysis axis as a promising therapeutic target.</p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":"4 4","pages":""},"PeriodicalIF":23.7,"publicationDate":"2025-05-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/imt2.70048","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144885076","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":"Spatio-temporal characteristics of the gastrointestinal resistome in a cow-to-calf model and its environmental dissemination in a dairy production system","authors":"Shuai Liu,&nbsp;Yimin Zhuang,&nbsp;Tianyu Chen,&nbsp;Duo Gao,&nbsp;Jianxin Xiao,&nbsp;Jinfeng Wang,&nbsp;Jinghui Li,&nbsp;Xinjie Zhao,&nbsp;Rong Peng,&nbsp;Wenli Guo,&nbsp;Jialin Wei,&nbsp;Mo Sha,&nbsp;Jingjun Wang,&nbsp;Jiaying Ma,&nbsp;Mei Ma,&nbsp;Mengmeng Li,&nbsp;Wei Wang,&nbsp;Ya-Jing Wang,&nbsp;Shengli Li,&nbsp;Zhijun Cao","doi":"10.1002/imt2.70047","DOIUrl":"https://doi.org/10.1002/imt2.70047","url":null,"abstract":"<p>Microbiome and resistome transmission from mother to child, as well as from animal to environment, has been widely discussed in recent years. Dairy cows mainly provide milk and meat. However, in the dairy production system, the characteristics and transmission trends of resistome assembly and the microbiome in the gastrointestinal tract (GIT) remain unclear. In this study, we sequenced the GIT (rumen fluid and feces) microbiome of dairy cow populations from two provinces in China (136 cows and 36 calves), determined the characteristics of their resistome profiles and the distribution of antibiotics resistance genes (ARGs) across bacteria and further tracked the temporal dynamics of the resistome in offspring during early life using multi-omics technologies (16S ribosomal RNA [rRNA] sequencing, metagenome, and metatranscriptome). We characterized the GIT resistome in cows, distinguished by gut sites and regions. The abundance of ARGs in calves peaked within the first 3 days after birth, with <i>Enterobacteriaceae</i> as the dominant microbial host. As calves aged, resistome composition stabilized, and overall ARG abundance gradually decreased. Both diet and age influenced carbohydrate-active enzymes and ARG profiles. Resistance profiles in ecological niches (meconium, colostrum, soil, and wastewater) were unique, resembling maternal sources. Mobile genetic elements (MGEs), mainly found in soil and wastewater, played an important role in mediating these interactions. Multidrug resistance consistently emerged as the most significant form of resistance at the both the metagenome and metatranscriptome levels. Several antibiotic classes showed higher proportions at the RNA level than at the DNA level, indicating that even low-abundance gene groups can have a considerable influence through high expression. This study broadens our understanding of ARG dissemination in livestock production systems, providing a foundation for developing future preventive and control strategies.</p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":"4 4","pages":""},"PeriodicalIF":23.7,"publicationDate":"2025-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/imt2.70047","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144888158","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}