Genomics最新文献

{"title":"Identification of cross-talk pathways and PANoptosis-related genes in periodontitis and atherosclerosis by bioinformatics analysis and machine learning","authors":"Nan Yang ,&nbsp;Shiqun Sun ,&nbsp;Xiantao Chen ,&nbsp;Tongtong Yan ,&nbsp;Nan Gu ,&nbsp;Zhihui Liu","doi":"10.1016/j.ygeno.2025.111106","DOIUrl":"10.1016/j.ygeno.2025.111106","url":null,"abstract":"<div><h3>Background and objectives</h3><div>Periodontitis(PD) is a chronic inflammatory disease that poses a serious threat to oral health and is one of the risk factors for atherosclerosis(AS). A growing body of evidence suggests that the two diseases are closely related. However, current studies have yet to fully understand the common genes and common mechanisms between PD and AS. This study aimed to screen the tandem genes of PD and AS and the potential relationship between the tandem genes and pan-apoptosis-related genes. By analyzing the relationship between the core genes and immune cells, it will provide new targets for clinical treatment.</div></div><div><h3>Materials and methods</h3><div>The PD and AS datasets were downloaded from the GEO database and differential expression analysis was performed to obtain DEGs. AS-related genes were downloaded from the GeneCards database, and PANoptosis-related genes were obtained through literature review. AS-related genes were merged into AS DEGs, and overlapping DEGs were cross-talk genes for PD and AS. Protein-protein interaction (PPI) network was constructed using the STRING database and Cytoscape software. Pearson coefficients were used to calculate the correlation between cross-talk genes and PANoptosis-related genes in the PD and AS datasets. The intersection of cross-talk genes and PANoptosis-related genes was defined as cross-talk-PANoptosis genes. Core genes were screened using ROC analysis and XGBoost. PPI sub-network, gene-biological processes and gene-pathway networks were constructed based on the core genes. In addition, immune infiltration on the PD and AS datasets was analyzed using the CIBERSORT algorithm.</div></div><div><h3>Results</h3><div>285 cross-talk genes overlapped between PD DEGs and AS DEGs. The intersection of cross-talk genes with 109 PANoptosis-related genes was defined as cross-talk-PAoptosis genes. ROC and XGBoost showed that MLKL, ZBP1, CD14, and IL6 were more accurate than the other cross-talk-PAoptosis genes in predicting the diseases, and were better in terms of the overall characteristics. GO and KEGG analyses showed that these four core genes were involved in the immune and inflammatory response of the organism. The results of immune infiltration showed that Monocytes and Mast cells resting were altered to a greater extent in PD and AS patients. Finally, 24 drugs related to the core genes were retrieved from the DGIDB database.</div></div><div><h3>Conclusions</h3><div>This study reveals the joint mechanism between PD and AS associated with PANoptosis. Analyzing the four core genes and immune cells may provide new therapeutic directions for the pathogenesis of PD combined with AS.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 6","pages":"Article 111106"},"PeriodicalIF":3.0,"publicationDate":"2025-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145045581","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Regulation of alternative splicing of retinol metabolism in lipid abnormality of PCOS liver by Cyp4a32 and Hsd17b6","authors":"Guangyi Chen ,&nbsp;Junhui Zhang ,&nbsp;Jiayi Wang ,&nbsp;Wenxiu Chen ,&nbsp;Haoran Li ,&nbsp;Haoran Su ,&nbsp;Shaoyi Dai ,&nbsp;Yumei Tao ,&nbsp;Yunxia Cao ,&nbsp;Qiang Hong ,&nbsp;Fenfen Xie","doi":"10.1016/j.ygeno.2025.111136","DOIUrl":"10.1016/j.ygeno.2025.111136","url":null,"abstract":"<div><div>Liver lipid disorders are common in polycystic ovary syndrome (PCOS) patients. A DHEA-induced PCOS mouse model exhibited elevated liver triglyceride (TG) and total cholesterol (TC), reinforcing this association between liver lipids and PCOS. Liver transcriptomic sequencing revealed that 168 differentially expressed genes and 285 alternative splicing (AS) event genes, significantly enriching retinol metabolism. Further combined analyses showed the Cyp4a32 and Hsd17b6 genes were abnormally expressed in the livers of PCOS mice. AS analysis revealed that Cyp4a32 had upregulated exon skipping (SE), including SE and mutually exclusive exons (MXE), while among the modes of SE, MXE, and alternative 3′ splice site (A3SS), Hsd17b6 showed downregulated MXE. These findings suggest that Cyp4a32 and Hsd17b6 may change the retinol metabolism by modulating AS patterns, which then dysregulate hepatic lipid metabolism in PCOS. This study highlights potential therapeutic targets for PCOS-associated liver lipid disorders.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 6","pages":"Article 111136"},"PeriodicalIF":3.0,"publicationDate":"2025-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145285962","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"TIMP1: A novel immune-related signature associated with invasiveness and inhibition of pituitary adenoma","authors":"Hongyu Wu ,&nbsp;Yu Zhang ,&nbsp;Xin Ma ,&nbsp;Zenghua Mi ,&nbsp;Zhijun Yang","doi":"10.1016/j.ygeno.2025.111140","DOIUrl":"10.1016/j.ygeno.2025.111140","url":null,"abstract":"<div><div>The invasiveness of pituitary adenomas is closely related to the tumour immune microenvironment. This study aimed to identify immune-related genes associated with IPAs. Transcriptomic data from 32 patient-derived samples were analysed to screen immune-related differentially expressed genes between IPAs and non-invasive pituitary adenomas. Weighted gene co-expression network analysis of merged datasets (GSE26966 and GSE51618) was performed to identify hub genes, which were then intersected with immune-related DEGs. Least absolute shrinkage and selection operator regression and support vector machine algorithms consistently identified tissue inhibitor of metalloproteinases 1 (<em>TIMP1</em>) as a key immune-associated invasive gene. Multi-omics validation confirmed significant downregulation of <em>TIMP1</em> in IPAs. Functional enrichment, single-sample gene set enrichment analysis, CIBERSORT, and immune checkpoint profiling linked TIMP1 to macrophage infiltration and immune regulation. Immunohistochemistry and in vitro experiments further demonstrated that TIMP1 overexpression inhibited tumour-cell proliferation, invasion, and migration. Collectively, these findings suggest that TIMP1 downregulation may promote IPA progression through immune dysregulation.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 6","pages":"Article 111140"},"PeriodicalIF":3.0,"publicationDate":"2025-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145328733","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"High-fat diet promotes kidney lipid droplet deposition contributing to the pathogenesis of obesity-related glomerulopathy in mice through gut microbial metabolism","authors":"Kai-Wen Cai ,&nbsp;Ying-Ying Xie ,&nbsp;Zi-Yan Deng ,&nbsp;Zong-Chao Yu ,&nbsp;Hong-Wei Wu ,&nbsp;Zhuang-Feng Weng ,&nbsp;Zhen-Chuan Lin ,&nbsp;Bin Xia ,&nbsp;Xiao-Hua Wang ,&nbsp;Zhi-Hua Zheng ,&nbsp;Chun Tang ,&nbsp;Ting Zhu ,&nbsp;Yong-Ping Lu","doi":"10.1016/j.ygeno.2025.111151","DOIUrl":"10.1016/j.ygeno.2025.111151","url":null,"abstract":"<div><h3>Background</h3><div>Obesity-related glomerulopathy (ORG) is a kidney disorder associated with obesity, where dysbiosis of the gut microbiota and disturbances in lipid metabolism play crucial roles in its development. However, the exact mechanisms by which imbalances in gut microbiota influence lipid metabolism and contribute to the pathogenesis of ORG are still not fully understood.</div></div><div><h3>Methods</h3><div>A high-fat diet (HFD)-induced ORG model was established using 6-week-old male C57BL/6 J mice to investigate the role of gut microbiota and gut-derived metabolites in ORG progression. 16S rRNA sequencing was employed to profile the gut microbiota, while liquid chromatography-tandem mass spectrometry (LC-MS/MS) was applied for metabolite analysis in fecal, serum, and kidney samples.</div></div><div><h3>Results</h3><div>Compared to age-matched normal diet (ND) mice, ORG mice exhibited significant increases in triglycerides (TG), cholesterol (CHO), and urinary albumin-to-creatinine ratio (UACR), alongside enhanced lipid droplet accumulation in renal tubules and glomerular hypertrophy. Metabolomic analysis revealed altered metabolic profiles in ORG mice, particularly the reprogramming of glycerophospholipid metabolism. Additionally, 16S rRNA sequencing demonstrated reduced gut microbiota diversity in ORG mice relative to the ND group. Further investigation revealed that the shift in renal glycerophospholipid metabolism and elevated blood lipid levels in ORG mice were closely linked to gut microbiota dysbiosis, specifically increased abundance of <em>Lachnospiraceae</em> and decreased abundance of <em>Muribaculaceae</em>.</div></div><div><h3>Conclusion</h3><div>The dysbiosis of gut microbiota induced by a HFD leads to glycerophospholipid metabolic reprogramming, promoting lipid droplet deposition in the kidneys and contributing to ORG progression. Our study highlights the contribution of gut microbial metabolism to the development of ORG, offering new perspectives for potential therapeutic strategies targeting the gut in ORG treatment.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 6","pages":"Article 111151"},"PeriodicalIF":3.0,"publicationDate":"2025-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145451456","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Construction of a genome-wide linkage map and QTL mapping for growth and hypoxia tolerance traits in Chinese longsnout catfish (Leiocassis longirostris)","authors":"Fenfei Liang ,&nbsp;Zhiru Yang ,&nbsp;Wei Liu ,&nbsp;Faling Zhang ,&nbsp;Xia Liang ,&nbsp;Cheng Zhao ,&nbsp;Guosong Zhang","doi":"10.1016/j.ygeno.2025.111157","DOIUrl":"10.1016/j.ygeno.2025.111157","url":null,"abstract":"<div><div>The Chinese longsnout catfish (<em>Leiocassis longirostris</em>) is an important freshwater aquaculture species, and the selective breeding of fast-growth and hypoxia tolerance population will have a positive impact on its industry. In order to promote the breeding process of Chinese longsnout catfish, construction of the genetic linkage map and identification of molecular markers associated with fast-growth and hypoxia tolerance is critical for the marker-assisted selection (MAS) of Chinese longsnout catfish. In the present study, whole-genome resequencing was used to construct a high-density genetic linkage map of the Chinese longsnout catfish. The map containing 2946 bin markers was distributed over 26 linkage groups (LGs) with a total genetic coverage of 1980.76 cM and an average density of 0.67 cM. Based on the genetic map, quantitative trait locus (QTL) mapping results suggested that 17 QTLs associated with growth traits and 1 QTL associated with hypoxia tolerance were identified in eight LGs with the phenotypic variability explained (PVE) ranged from 5.1 % to 9.3 %. Four SNP loci from these QTLs were associated with the phenotypic traits validated by Kompetitive Allele Specific PCR or Sanger sequencing. In addition, the expression of three candidate genes for growth traits and five candidate genes for hypoxia tolerance was examined in different growth speed populations and the process of hypoxia exposure and reoxygenation, respectively. The high-density genetic linkage map and QTLs for growth traits and hypoxia tolerance obtained in the present study could further provide the basis for genetic breeding and molecular marker-assisted breeding of Chinese longsnout catfish.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 6","pages":"Article 111157"},"PeriodicalIF":3.0,"publicationDate":"2025-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145568304","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Organelle genomes of progeny of Tripidium arundinaceum × Saccharum spontaneum and sugarcane cultivar revealed their inheritance and characterization after hybridization","authors":"Sicheng Li ,&nbsp;Shan Zhou ,&nbsp;Fengzhen Wu ,&nbsp;Yuxin Huang ,&nbsp;Yang Zhao ,&nbsp;Baoqing Zhang ,&nbsp;Gemin Zhang ,&nbsp;Weixing Duan ,&nbsp;Xiping Yang","doi":"10.1016/j.ygeno.2025.111107","DOIUrl":"10.1016/j.ygeno.2025.111107","url":null,"abstract":"<div><div>Sugarcane (<em>Saccharum</em> spp.) breeding often involves hybridization with distantly related wild species (such as <em>Tripidium arundinaceum</em>) to improve stress resistance, but mitochondrial and chloroplast inheritance across multiple backcross generations remains poorly understood. In this study, we employed PacBio and Illumina sequencing to assemble and compare the mitochondrial genomes (mitogenomes) and chloroplast genome of four genotypes: an distant hybrid F₁ GXAS 07–6-1 (<em>Tripidium arundinaceum</em> × <em>Saccharum spontaneum</em>), a subsequent hybrid F₁ GXASF₁ 08–2-28, a first-generation backcross GXASBC₁ 12-A6–3, and a second-generation backcross GXASBC₂ 15–114. Maternal inheritance preserves key co-linear gene clusters, whereas MTPT content varies, indicating post-hybridization structural adjustments. Our study confirms strict maternal inheritance of mitochondrial and chloroplast genomes across hybrid and backcross generations and validates mitochondrial transmission using organelle-specific markers, providing insights into organellar inheritance and references for sugarcane breeding.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 6","pages":"Article 111107"},"PeriodicalIF":3.0,"publicationDate":"2025-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145091662","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comparative transcriptome analysis revealed the molecular response mechanism of sugar beet (Beta vulgaris L.) against Cercospora Leaf Spot disease","authors":"Hongyong Lou ,&nbsp;Guangzhou Ding ,&nbsp;Fangpu Cai ,&nbsp;Chunlei Zhao ,&nbsp;Yanli Li","doi":"10.1016/j.ygeno.2025.111109","DOIUrl":"10.1016/j.ygeno.2025.111109","url":null,"abstract":"<div><div><em>Cercospora leaf spot</em> (CLS), caused by the hemibiotrophic fungus <em>Cercospora beticola</em> (<em>C. beticola</em>), critically threatens global sugar beet production through defoliation and chlorosis, reducing root yields by ≤50 % and impairing sucrose crystallization. As fungicide resistance escalates in <em>C. beticola</em> populations, developing genetically resistant sugar beet becomes imperative. We dissected CLS resistance mechanisms via comparative transcriptomics of resistant (81GM241) and susceptible (KWS6661) genotypes across four infection stages (0–30 dpi). Resistant plants deployed a triphasic defense strategy: During early infection (10 dpi), rapid activation of phenylpropanoid biosynthesis, fatty acid elongation, and glutathione metabolism established dual barriers of lignin-mediated cell wall fortification and ROS scavenging. By mid-infection (20 dpi), pathogen recognition receptors triggered MAPK-WRKY cascades that amplified jasmonate-mediated defenses while mobilizing flavonoid antimicrobials. In late infection (30 dpi), systemic downregulation of photosynthetic antenna proteins redirected resources to tryptophan-derived phytoalexins, sustaining defense without growth penalties. Crucially, resistant plants proactively anticipated stress through coordinated calcium signaling (CDPK), pectin methylesterase-driven cell wall remodeling, and antioxidant activation before pathogen proliferation. In contrast, susceptible plants exhibited delayed ROS detoxification and impaired signal transduction. This phased defense architecture—initiating with pathogen recognition and transient oxidative bursts, progressing through sustained immune activation, and culminating in metabolic optimization—provides a molecular framework for breeding resistant varieties by stacking phase-specific defense regulators.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 6","pages":"Article 111109"},"PeriodicalIF":3.0,"publicationDate":"2025-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145045580","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Computational methods for the analysis of long-read RNA-seq data","authors":"Kristina Santucci,&nbsp;Yuning Cheng,&nbsp;Si-Mei Xu,&nbsp;Michael Janitz","doi":"10.1016/j.ygeno.2025.111144","DOIUrl":"10.1016/j.ygeno.2025.111144","url":null,"abstract":"<div><div>Advancements in the accuracy of long-read sequencing technologies and bioinformatic approaches have broadened the applications of RNA sequencing (RNA-seq). This review covers such developments across various aspects of genomics, transcriptomics, and proteomics, focussing on the discovery and characterisation of new genes, transcriptional isoforms, and proteins. This review also explores the different approaches to characterise transcript isoforms that transcribed from both annotated and unannotated novel genes, such as determining protein-coding potential, functional domains, and conserved regions. Finally, the long-read RNA-seq (lrRNA-seq) based approaches for analysing co-transcriptional and post-transcriptional events, such as alternative splicing, polyadenylation, and RNA modifications, are elaborated. Conflicting recommendations, limitations, and priorities for future research for such methods reported by previous studies are also addressed. Overall, this review intends to demonstrate how integrated analyses can be achieved with lrRNA-seq in various areas of molecular biology.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 6","pages":"Article 111144"},"PeriodicalIF":3.0,"publicationDate":"2025-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145321326","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Integrated genomic and transcriptomic analysis identifies novel candidate genes affecting carcass backfat thickness in pigs","authors":"Qian Liu ,&nbsp;Jianghui Yu ,&nbsp;Xinjie Ai ,&nbsp;Huiying Xu ,&nbsp;Zijian Qiu ,&nbsp;Liming Xu ,&nbsp;Jinfeng Ma ,&nbsp;Jin Zhou ,&nbsp;Chenxi Liu ,&nbsp;Qingbo Zhao ,&nbsp;Pinghua Li ,&nbsp;Ruihua Huang","doi":"10.1016/j.ygeno.2025.111117","DOIUrl":"10.1016/j.ygeno.2025.111117","url":null,"abstract":"<div><div>The carcass backfat thickness (BFT) provides a valuable indication of fat deposition and carcass leanness, which are essential for the determination of carcass grading and pricing. Identifying genetic loci and crucial genes related to BFT using integrated multi-omics methods offers significant contributions to the genetic advancement of pig. In the present study, 418 Chinese Suhuai pigs were slaughtered, and carcass BFT were subsequently measure. We conducted a genome-wide association study (GWAS) based on SNP chip data and imputed whole-genome sequencing data (iWGS), respectively. Significant quantitative trait loci (QTL) correlated with carcass BFT were identified on <em>Sus scrofa</em> chromosome (SSC) 2, SSC4, and SSC14, with the most significant single-nucleotide polymorphisms (SNPs) explaining 6.58 %–9.91 % of the phenotypic variance. Bayesian fine mapping validated two previously reported quantitative trait loci (QTLs), narrowing the most refined confidence interval to 3 kb (SSC2, 37.337–37.340 Mb and SSC4, 75.407–77.006 Mb), while identifying two novel QTLs (SSC14, 137.086–138.863 Mb and SSC4, 95.237–96.894 Mb) associated with carcass BFT. Furthermore, transcriptome analysis identified 322 differentially expressed genes (DEGs) and several critical regulatory pathways related to lipid and energy metabolism, including fatty acid and pyruvate metabolism. The integration of genomic and transcriptomic data identified three pivotal candidate genes, <em>S100A12</em>, <em>XKR4</em> and <em>PENK</em>, which are typically associated with BFT. Transcriptome-wide association study (TWAS) and Phenome-wide association study (PheWAS) provided further evidence that these three genes were significantly associated with BFT and fatty acid composition. This study uncovers novel insights into the important genes and molecular markers related to carcass BFT in pig.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 6","pages":"Article 111117"},"PeriodicalIF":3.0,"publicationDate":"2025-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145212461","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genomic and physiological characterization of beer spoiling Megasphaera spp.","authors":"Manuel J. Arnold ,&nbsp;Matthias A. Ehrmann ,&nbsp;Yohanes N. Kurniawan ,&nbsp;Koji Suzuki ,&nbsp;Wolfgang Liebl","doi":"10.1016/j.ygeno.2025.111139","DOIUrl":"10.1016/j.ygeno.2025.111139","url":null,"abstract":"<div><div>Beer spoiling bacteria represent a major concern for the brewing industry. Anaerobic spoilers of the genus Megasphaera are especially dreadful. Until now, the genome analysis of Megasphaera spp. was limited to mammal-associated species, yet beer borne Megasphaera species and their abilities to tolerate the multiple high stress factors in their niche were broadly overlooked. This study is the first to carry out an in silico genome comparison of ten strains from three different beer spoiling Megasphaera species (<em>M. cerevisiae</em>, <em>M. paucivorans</em> and <em>M. sueciensis</em>). We experimentally show a hitherto unseen resilience of beer spoiling Megasphaera strains, which can grow in lager beer with an isoα-acids content of up to 120 IBU, an ethanol concentration of up to 7.0 % (<em>v</em>/v) and at pH 4.0. The genomes revealed genes appearing to aid survival in the harsh brewing environment mainly comprised of hop, ethanol and acid stress.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 6","pages":"Article 111139"},"PeriodicalIF":3.0,"publicationDate":"2025-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145400499","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}