{"title":"Warming-driven migration of enterotypes mediates host health and disease statuses in ectotherm Litopenaeus vannamei.","authors":"Shenzheng Zeng, Zhijian Huang, Satapornvanit Kriengkrai, Renjun Zhou, Derun Yuan, Nguyễn Văn Tuấn, Zhiming Zhu, Luwei Zheng, Qilu Hou, Xuanting Li, Qi Chen, Lingyu Zhang, Dongwei Hou, Zhixuan Deng, Shicheng Bao, Wenjun Wang, Sukontorn Khoruamkid, Soo Loon Goh, Shaoping Weng, Jianguo He","doi":"10.1038/s42003-025-07558-2","DOIUrl":"10.1038/s42003-025-07558-2","url":null,"abstract":"<p><p>Global warming has threatened all-rounded hierarchical biosphere by reconstructing eco-structure and bringing biodiversity variations. Pacific white shrimp, a successful model of worldwide utilizing marine ectothermic resources, is facing huge losses due to multiple diseases relevant to intestinal microbiota (IM) dysbiosis during temperature fluctuation. However, how warming mediates shrimp health remains poorly understood. Herein, a global shrimp IM catalogue was conducted via 1,369 shrimp IM data from nine countries, including 918 samples from previously published data and 451 generated in the study. Shrimp IMs were stratified into three enterotypes with distinctive compositions and functions, dominated by Vibrio, Shewanella and Candidatus Bacilloplasma, which showed an obvious distribution bias between enterotypes and diseases. The ratio of Vibrio and Candidatus Bacilloplasma was a crucial indicator for shrimp health. Moreover, temperature was the most driving factor for microbial composition, which potentially led to the migration of enterotypes, and high probability of white feces syndrome and low risk of hepatopancreas necrosis syndrome. Collectively, the warming-driven enterotypes mediated shrimp health, which exemplified the causal relationship between temperature rising and ectothermic animals' health. These findings enlarged the cognition of shrimp health culture management from a microecological perspective, and alerted the inevitable challenge of global warming to ectothermic animals.</p>","PeriodicalId":10552,"journal":{"name":"Communications Biology","volume":"8 1","pages":"126"},"PeriodicalIF":5.2,"publicationDate":"2025-01-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11770195/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143045877","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}
Zhongliang Chen, Liangxia Jiang, Min Su, Qibing Zeng, Peng Luo, Liangzhao Chu
{"title":"NLRP7 maintains the genomic stability during early human embryogenesis via mediating alternative splicing.","authors":"Zhongliang Chen, Liangxia Jiang, Min Su, Qibing Zeng, Peng Luo, Liangzhao Chu","doi":"10.1038/s42003-025-07571-5","DOIUrl":"10.1038/s42003-025-07571-5","url":null,"abstract":"<p><p>Genomic instability is the main cause of abnormal embryo development and abortion. NLRP7 dysfunctions affect embryonic development and lead to Hydatidiform Moles, but the underlying mechanisms remain largely elusive. Here, we show that NLRP7 knockout affects the genetic stability, resulting in increased DNA damage in both human embryonic stem cells and blastoids, making embryonic cells in blastoids more susceptible to apoptosis. Mechanistically, NLRP7 can interact with factors related to alternative splicing and DNA damage response, including DDX39B, PRPF8, THRAP3 and PARP1. Moreover, NLRP7 dysfunction leads to abnormal alternative splicing of genes involved in homologous recombination in human embryonic stem cells, Such as Brca1 and Rad51. These results indicate that NLRP7-mediated Alternative splicing is potentially required for the maintenance of genome integrity during early human embryogenesis. Together, this study uncovers that NLRP7 plays an essential role in the maintenance of genetic stability during early human embryonic development by regulating alternative splicing of homologous recombination-related genes.</p>","PeriodicalId":10552,"journal":{"name":"Communications Biology","volume":"8 1","pages":"125"},"PeriodicalIF":5.2,"publicationDate":"2025-01-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11770114/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143045871","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 difference of oropharyngeal microbiome during acute respiratory viral infections in infants and children.","authors":"Zeni Wu, Mingyue Jiang, Mengmeng Jia, Jian Sang, Qing Wang, Yunshao Xu, Li Qi, Weizhong Yang, Luzhao Feng","doi":"10.1038/s42003-025-07559-1","DOIUrl":"10.1038/s42003-025-07559-1","url":null,"abstract":"<p><p>Acute respiratory infections (ARI) with multiple types of viruses are common in infants and children. This study was conducted to assess the difference of oropharyngeal microbiome during acute respiratory viral infection using whole-genome shotgun metagenomic sequencing. The overall taxonomic alpha diversity did not differ by the types of infected virus. The beta diversity differed by disease severity, disease-related symptoms, and types of infected virus. Nine species had significantly higher abundance in outpatients than in inpatients, with five of them in the genus Achromobacter. Three microbial community types were identified. The prevalence of community type (CT) 1 was higher among patients with influenza virus, enterovirus, and human adenvirus; CT2 was higher among patients with human metapneumovirus; and CT3 was higher among patients with respiratory syncytial virus and human adenvirus infections. Our results suggest that the oropharyngeal microbiome is associated with ARI disease severity, disease-related symptoms, and the types of infected virus.</p>","PeriodicalId":10552,"journal":{"name":"Communications Biology","volume":"8 1","pages":"127"},"PeriodicalIF":5.2,"publicationDate":"2025-01-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11770077/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143045874","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}
Ying Zheng, Benjamin Moorlach, Desiree Jakobs-Schönwandt, Anant Patel, Chiara Pastacaldi, Stefan Jacob, Ana R Sede, Manfred Heinlein, Minna M Poranen, Karl-Heinz Kogel, Maria Ladera Carmona
{"title":"Exogenous dsRNA triggers sequence-specific RNAi and fungal stress responses to control Magnaporthe oryzae in Brachypodium distachyon.","authors":"Ying Zheng, Benjamin Moorlach, Desiree Jakobs-Schönwandt, Anant Patel, Chiara Pastacaldi, Stefan Jacob, Ana R Sede, Manfred Heinlein, Minna M Poranen, Karl-Heinz Kogel, Maria Ladera Carmona","doi":"10.1038/s42003-025-07554-6","DOIUrl":"10.1038/s42003-025-07554-6","url":null,"abstract":"<p><p>In vertebrates and plants, dsRNA plays crucial roles as PAMP and as a mediator of RNAi. How higher fungi respond to dsRNA is not known. We demonstrate that Magnaporthe oryzae (Mo), a globally significant crop pathogen, internalizes dsRNA across a broad size range of 21 to about 3000 bp. Incubation of fungal conidia with 10 ng/µL dsRNA, regardless of size or sequence, induced aberrant germ tube elongation, revealing a strong sequence-unspecific effect of dsRNA in this fungus. Accordingly, the synthetic dsRNA analogue poly(I:C) and dsRNA of various sizes and sequences elicited canonical fungal stress pathways, including nuclear accumulation of the stress marker mitogen-activated protein kinase Hog1p and production of ROS. Leaf application of dsRNA to the cereal model species Brachypodium distachyon suppressed the progression of leaf blast disease. Notably, the sequence-unspecific effect of dsRNA depends on higher doses, while pure sequence-specific effects were observed at low concentrations of dsRNA ( < 0.03 ng/µL). The protective effects of dsRNA were further enhanced by maintaining a gap of at least seven days between dsRNA application and inoculation, and by stabilising the dsRNA in alginate-chitosan nanoparticles. Overall, our study opens up additional possibilities for the development and use of dsRNA pesticides in agriculture.</p>","PeriodicalId":10552,"journal":{"name":"Communications Biology","volume":"8 1","pages":"121"},"PeriodicalIF":5.2,"publicationDate":"2025-01-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11762700/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143037353","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}
Kangzhi Li, Xia Ling, Jing Zhao, Zhiqun Wang, Xu Yang
{"title":"Abnormal neural circuits and altered brain network topological properties in patients with persistent postural-perceptual dizziness.","authors":"Kangzhi Li, Xia Ling, Jing Zhao, Zhiqun Wang, Xu Yang","doi":"10.1038/s42003-024-07375-z","DOIUrl":"10.1038/s42003-024-07375-z","url":null,"abstract":"<p><p>Persistent Postural-Perceptual Dizziness (PPPD) is a common cause of chronic vestibular syndrome. Although previous studies have identified central abnormalities in PPPD, the specific neural circuits and the alterations in brain network topological properties, and their association with dizziness and postural instability in PPPD remain unclear. This study includes 30 PPPD patients and 30 healthy controls. Resting-state functional magnetic resonance imaging is used to construct whole-brain functional connectivity matrices, followed by network-based statistic and graph theoretical analysis. Network-based statistic results reveal an abnormal neural network in PPPD patients with key nodes in the occipital visual cortex, precuneus, sensorimotor cortex, multisensory vestibular cortex and cerebellum. The graph theoretical analysis shows less efficient information transmission at both local and global levels, indicating a state of disconnection between regions of the brain network. Decreased connections between the visual cortex, sensorimotor cortex, and multisensory vestibular cortex, and changes in brain network topological properties are correlated with the Dizziness Handicap Inventory score. Our study unveils the potential abnormal neural circuits, with the presence of multisensory and sensorimotor integration abnormalities and reveals altered brain network topological properties in PPPD patients. Our findings provide new insights for understanding the neural mechanisms of PPPD.</p>","PeriodicalId":10552,"journal":{"name":"Communications Biology","volume":"8 1","pages":"122"},"PeriodicalIF":5.2,"publicationDate":"2025-01-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11762978/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143037431","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}
Niepukolie Nipu, Lai Wei, Lauren Hamilton, Hyojin Lee, Jith Thomas, Jan A Mennigen
{"title":"Methylene blue at recommended concentrations alters metabolism in early zebrafish development.","authors":"Niepukolie Nipu, Lai Wei, Lauren Hamilton, Hyojin Lee, Jith Thomas, Jan A Mennigen","doi":"10.1038/s42003-025-07471-8","DOIUrl":"10.1038/s42003-025-07471-8","url":null,"abstract":"<p><p>Methylene blue (MB) is an antifungal agent widely used during critical stages of zebrafish development. Most guidelines recommend 0.00005% or 0.0001% of MB for embryo/larval rearing. The Organisation for Economic Co-operation and Development zebrafish embryo toxicity test guideline omits MB recommendations, leading to inconsistent MB use in zebrafish research. Because MB affects oxidative energy metabolism in vitro and in vivo, we investigate possible metabolic effects of recommended MB concentrations in developing zebrafish (1-5 days post-fertilization (dpf)). MB increases O<sub>2</sub> consumption rate at 1 dpf, followed by an overall reduction in oxidative energy metabolism in post-hatch eleutheroembryos (4-5 dpf). Concomitantly, mitochondrial transcripts decrease in 1 and 4 dpf zebrafish. Our findings show that MB, at recommended husbandry concentrations, affects oxidative metabolism and can thus confound experiments. Since the zebrafish embryo/larval model is gaining traction as a high-throughput New Approach Methodology (NAM) for toxicity assessment, researchers should reconsider MB use.</p>","PeriodicalId":10552,"journal":{"name":"Communications Biology","volume":"8 1","pages":"120"},"PeriodicalIF":5.2,"publicationDate":"2025-01-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11760885/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143037375","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}
Jieqiong Qu, Michelle Schinkel, Lisa Chiggiato, Samara Rosendo Machado, Gijs J Overheul, Pascal Miesen, Ronald P van Rij
{"title":"The Hsf1-sHsp cascade has pan-antiviral activity in mosquito cells.","authors":"Jieqiong Qu, Michelle Schinkel, Lisa Chiggiato, Samara Rosendo Machado, Gijs J Overheul, Pascal Miesen, Ronald P van Rij","doi":"10.1038/s42003-024-07435-4","DOIUrl":"10.1038/s42003-024-07435-4","url":null,"abstract":"<p><p>Aedes mosquitoes transmit pathogenic arthropod-borne (arbo) viruses, putting nearly half the world's population at risk. Blocking virus replication in mosquitoes is a promising approach to prevent arbovirus transmission, the development of which requires in-depth knowledge of virus-host interactions and mosquito immunity. By integrating multi-omics data, we find that heat shock factor 1 (Hsf1) regulates eight small heat shock protein (sHsp) genes within one topologically associated domain in the genome of the Aedes aegypti mosquito. This Hsf1-sHsp cascade acts as an early response against chikungunya virus infection and shows pan-antiviral activity against chikungunya, Sindbis, and dengue virus as well as the insect-specific Agua Salud alphavirus in Ae. aegypti cells and against chikungunya virus and O'nyong-nyong virus in Aedes albopictus and Anopheles gambiae cells, respectively. Our comprehensive in vitro data suggest that Hsf1 could serve as a promising target for the development of novel intervention strategies to limit arbovirus transmission by mosquitoes.</p>","PeriodicalId":10552,"journal":{"name":"Communications Biology","volume":"8 1","pages":"123"},"PeriodicalIF":5.2,"publicationDate":"2025-01-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11762766/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143037460","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}
L Zonca, F C Bellier, G Milior, P Aymard, J Visser, A Rancillac, N Rouach, D Holcman
{"title":"Unveiling the functional connectivity of astrocytic networks with AstroNet, a graph reconstruction algorithm coupled to image processing.","authors":"L Zonca, F C Bellier, G Milior, P Aymard, J Visser, A Rancillac, N Rouach, D Holcman","doi":"10.1038/s42003-024-07390-0","DOIUrl":"10.1038/s42003-024-07390-0","url":null,"abstract":"<p><p>Astrocytes form extensive networks with diverse calcium activity, yet the organization and connectivity of these networks across brain regions remain largely unknown. To address this, we developed AstroNet, a data-driven algorithm that uses two-photon calcium imaging to map temporal correlations in astrocyte activation. By organizing individual astrocyte activation events chronologically, our method reconstructs functional networks and extracts local astrocyte correlations. We create a graph of the astrocyte network by tallying direct co-activations between pairs of cells along these activation pathways. Applied to the CA1 hippocampus and motor cortex, AstroNet reveals notable differences: astrocytes in the hippocampus display stronger connectivity, while cortical astrocytes form sparser networks. In both regions, smaller, tightly connected sub-networks are embedded within a larger, loosely connected structure. This method not only identifies astrocyte activation paths and connectivity but also reveals distinct, region-specific network patterns, providing new insights into the functional organization of astrocytic networks in the brain.</p>","PeriodicalId":10552,"journal":{"name":"Communications Biology","volume":"8 1","pages":"114"},"PeriodicalIF":5.2,"publicationDate":"2025-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11759710/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143037461","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":"Structural model of a bacterial focal adhesion complex.","authors":"Christian Cambillau, Tâm Mignot","doi":"10.1038/s42003-025-07550-w","DOIUrl":"10.1038/s42003-025-07550-w","url":null,"abstract":"<p><p>Cell movement on surfaces relies on focal adhesion complexes (FAs), which connect cytoskeletal motors to the extracellular matrix to produce traction forces. The soil bacterium Myxococcus xanthus uses a bacterial FA (bFA), for surface movement and predation. The bFA system, known as Agl-Glt, is a complex network of at least 17 proteins spanning the cell envelope. Despite understanding the system dynamics, its molecular structure and protein interactions remain unclear. In this study, we utilize AlphaFold to generate models based on the known interactions and dynamics of gliding motility proteins. This approach provides us with a comprehensive view of the interactions across the entire complex. Our structural insights show the connection of essential functional modules throughout the cell envelope and offer an inspiring view of the force transduction mechanism from the inner molecular motor to the exterior of the cell.</p>","PeriodicalId":10552,"journal":{"name":"Communications Biology","volume":"8 1","pages":"119"},"PeriodicalIF":5.2,"publicationDate":"2025-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11761067/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143037459","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}
Matthew O Goodman, Tariq Faquih, Valentina Paz, Pavithra Nagarajan, Jacqueline M Lane, Brian Spitzer, Matthew Maher, Joon Chung, Brian E Cade, Shaun M Purcell, Xiaofeng Zhu, Raymond Noordam, Andrew J K Phillips, Simon D Kyle, Kai Spiegelhalder, Michael N Weedon, Deborah A Lawlor, Jerome I Rotter, Kent D Taylor, Carmen R Isasi, Tamar Sofer, Hassan S Dashti, Martin K Rutter, Susan Redline, Richa Saxena, Heming Wang
{"title":"Genome-wide association analysis of composite sleep health scores in 413,904 individuals.","authors":"Matthew O Goodman, Tariq Faquih, Valentina Paz, Pavithra Nagarajan, Jacqueline M Lane, Brian Spitzer, Matthew Maher, Joon Chung, Brian E Cade, Shaun M Purcell, Xiaofeng Zhu, Raymond Noordam, Andrew J K Phillips, Simon D Kyle, Kai Spiegelhalder, Michael N Weedon, Deborah A Lawlor, Jerome I Rotter, Kent D Taylor, Carmen R Isasi, Tamar Sofer, Hassan S Dashti, Martin K Rutter, Susan Redline, Richa Saxena, Heming Wang","doi":"10.1038/s42003-025-07514-0","DOIUrl":"10.1038/s42003-025-07514-0","url":null,"abstract":"<p><p>Recent genome-wide association studies (GWASs) of several individual sleep traits have identified hundreds of genetic loci, suggesting diverse mechanisms. Moreover, sleep traits are moderately correlated, so together may provide a more complete picture of sleep health, while illuminating distinct domains. Here we construct novel sleep health scores (SHSs) incorporating five core self-report measures: sleep duration, insomnia symptoms, chronotype, snoring, and daytime sleepiness, using additive (SHS-ADD) and five principal components-based (SHS-PCs) approaches. GWASs of these six SHSs identify 28 significant novel loci adjusting for multiple testing on six traits (p < 8.3e-9), along with 341 previously reported loci (p < 5e-08). The heritability of the first three SHS-PCs equals or exceeds that of SHS-ADD (SNP-h<sup>2</sup> = 0.094), while revealing sleep-domain-specific genetic discoveries. Significant loci enrich in multiple brain tissues and in metabolic and neuronal pathways. Post-GWAS analyses uncover novel genetic mechanisms underlying sleep health and reveal connections (including potential causal links) to behavioral, psychological, and cardiometabolic traits.</p>","PeriodicalId":10552,"journal":{"name":"Communications Biology","volume":"8 1","pages":"115"},"PeriodicalIF":5.2,"publicationDate":"2025-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11760956/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143037440","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}