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Genetic diversity of RNA viruses infecting invertebrate pests of rice

Science China(Life Sciences) 2024年第1期67卷 175-187页

作者： Haoran Wang Shufen Chao Qing Yan Shu Zhang Guoqing Chen Chonghui Mao Yang Hu Fengquan Yu Shuo Wang Liang Lv Baojun Yang Jiachun He Songbai Zhang Liangsheng Zhang Peter Simmonds Guozhong Feng State Key Laboratory of Rice Biology and Breeding China National Rice Research InstituteChinese Academy of Agricultural SciencesHangzhou 311400China State Key Laboratory of Agricultural Microbiology College of Life Science and TechnologyHuazhong Agricultural UniversityWuhan 430070China Institute of Plant Protection&Soil Fertilizer Hubei Academy of Agricultural SciencesWuhan 430064China Institute of Plant Protection Guizhou Academy of Agricultural SciencesGuiyang 550000China Institute of Plant Protection Liaoning Academy of Agricultural SciencesShenyang 110161China Sanya Agricultural Technology Extension and Service Centre Sanya 572000China College of Agriculture Yangtze UniversityJingzhou 434000China Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology Fujian Agriculture and Forestry UniversityFuzhou 350002China Genomics and Genetic Engineering Laboratory of Ornamental Plants College of Agriculture and BiotechnologyZhejiang UniversityHangzhou 310012China Nuffield Department of Medicine Peter Medawar Building for Pathogen ResearchUniversity of OxfordOxford OX13SYUnited Kingdom

Invertebrate species are a natural reservoir of viral genetic diversity,and invertebrate pests are widely distributed in crop fields.However,information on viruses infecting invertebrate pests of crops is limited.In this report,we describe the deep metatranscriptomic sequencing of 88 invertebrate samples covering all major invertebrate pests in rice fields.We identified 296 new RNA viruses and 13 known RNA viruses.These viruses clustered within 31 families,with many highly divergent viruses constituting potentially new families and genera.Of the identified viruses,13 RNA viruses clustered within the Fiersviridae family of bacteriophages,and 48 RNA viruses clustered within families and genera of mycoviruses.We detected known rice viruses in novel invertebrate hosts at high abundances.Furthermore,some novel RNA viruses have genome structures closely matching to known plant viruses and clustered within genera of several plant virus species.Fortyfive potential insect pathogenic RNA viruses were detected in invertebrate species.Our analysis revealed that host taxonomy plays a major role and geographical location plays an important role in structuring viral diversity.Cross-species transmission of RNA viruses was detected between invertebrate hosts.Newly identified viral genomes showed extensive variation for invertebrate viral families or genera.Together,the large-scale metatranscriptomic analysis greatly expands our understanding of RNA viruses in rice invertebrate species,the results provide valuable information for developing efficient strategies to manage insect pests and virus-mediated crop diseases.

关键词： invertebrate species metatranscriptome viral diversity viral transmission viral genomes

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Washed microbiota transplantation for Crohn’s disease:A metagenomic,metatranscriptomic,and metabolomic-based study

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World Journal of Gastroenterology 2024年第11期30卷 1572-1587页

作者： Shi-Ju Chen Da-Ya Zhang Xia Wu Fa-Ming Zhang Bo-Ta Cui Yi-Hao Huang Zu-Lun Zhang Rui Wang Fei-Hu Bai Graduate School Hainan Medical UniversityHaikou 571199Hainan ProvinceChina Department of Microbiota Medicine&Medical Center for Digestive Diseases The Second Affiliated Hospital of Nanjing Medical UniversityNanjing 210011Jiangsu ProvinceChina Department of Gastroenterology The Second Affiliated Hospital of Hainan Medical UniversityHaikou 570216Hainan ProvinceChina

BACKGROUND Fecal microbiota transplantation(FMT)is a promising therapeutic approach for treating Crohn’s disease(CD).The new method of FMT,based on the automatic washing process,was named as washed microbiota transplantation(WMT).Most existing studies have focused on observing the clinical phenomena.However,the mechanism of action of FMT for the effective management of CD-particularly in-depth multi-omics analysis involving the metagenome,metatranscriptome,and metabolome-has not yet been reported.AIM To assess the efficacy of WMT for CD and explore alterations in the microbiome and metabolome in response to WMT.METHODS We conducted a prospective,open-label,single-center clinical study.Eleven CD patients underwent WMT.Their clinical responses(defined as a decrease in their CD Activity Index score of>100 points)and their microbiome(metagenome,metatranscriptome)and metabolome profiles were evaluated three months after the procedure.RESULTS Seven of the 11 patients(63.6%)showed an optimal clinical response three months post-WMT.Gut microbiome diversity significantly increased after WMT,consistent with improved clinical symptoms.Comparison of the metagenome and metatranscriptome analyses revealed consistent alterations in certain strains,such as Faecalibac-terium prausnitzii,Roseburia intestinalis,and Escherichia coli.In addition,metabolomics analyses demonstrated that CD patients had elevated levels of various amino acids before treatment compared to the donors.However,levels of vital amino acids that may be associated with disease progression(e.g.,L-glutamic acid,gamma-glutamyl-leucine,and prolyl-glutamine)were reduced after WMT.CONCLUSION WMT demonstrated therapeutic efficacy in CD treatment,likely due to the effective reconstruction of the patient’s microbiome.Multi-omics techniques can effectively help decipher the potential mechanisms of WMT in treating CD.

关键词： Crohn’s disease Clinical trials Fecal microbiota transplant Metagenome metatranscriptome Metabolome

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Exploration of the metabolic flexibility of glycogen accumulating organisms through metatranscriptome analysis and metabolic characterization

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Journal of Environmental Sciences 2023年第4期126卷 234-248页

作者： Bin Zhao Yanping Yang Chen Zhao Chunchun Zhang Zhaohui Zhang Liang Wang Shang Wang Jingfeng Wang School of Environmental Science Engineering Tiangong UniversityTianjin 300387China Department of Hygienic Toxicology and Environmental Hygiene Tianjin Institute of Environmental and Operational MedicineTianjin 300201China

Glycogen accumulating organisms(GAOs) are closely related to the deterioration of enhanced biological phosphorus removal systems. However, the metabolic mechanisms that drive GAOs remain unclear. Here, the two-thirds supernatant of a reactor were decanted following the anaerobic period to enrich GAOs. Long-term monitoring demonstrated that the system was stable and exhibited typical characteristics of GAOs metabolism. Acetate was completely consumed after 60 min of the anaerobic phase. The level of glycogen decreased from 0.20 to 0.14 g/gSS during the anaerobic phase, whereas the level of glycogen significantly increased to 0.21g/gSS at the end of the aerobic period. Moreover, there was almost no phosphate release and absorption in the complete periods, thus confirming the successful construction of a GAOs enrichment system. Microbial community analysis demonstrated that Ca. Contendobacter was among the core functional genera and showed the highest activity among all of the communities. Furthermore, our study is the first to identify the involvement of the ethyl-malonyl-CoA pathway in the synthesis of polyhydroxyvalerate via croR, ccr, ecm, mcd, mch and mcl genes. The Embden-Meyerhof-Parnas(EMP) pathway was preferentially used via glgP. Furthermore, the glyoxylate cycle was the main source of ATP under anaerobic conditions, whereas the tricarboxylic acid cycle provided ATP under aerobic conditions. aceA and mdh appeared to be major modulators of the glyoxylate pathway for controlling energy flow. Collectively, our findings not only revealed the crucial metabolic mechanisms in a GAOs enrichment system but also provided insights into the potential application of Ca. Contendobacter for wastewater treatment.

关键词： Glycogen accumulating organisms Intracellular storage metatranscriptome Bacterial community Glyoxylate pathway

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metatranscriptome of the protistan community in Reticufitermes flaviceps

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Insect Science 2016年第4期23卷 543-547页

作者： Xiao-Jing Liu Min Che Lei Xie Shuai Zhan Zhi-Hua Zhou Yong-Ping Huang Qian Wang Institute of Plant Physiology and Ecology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences Shanghai College of Science Air Force Engineering University Xi'an Institute Pasteur of Shanghai Chinese Academy of Sciences Shanghai China

The hindgut of lower termites harbors various symbiotic protists, which per- form varied functions in lignocellulose decomposition. As termites are social insects, the species and numbers of these flagellated protists in the termite gut vary among the different castes. Juvenile hormones （JHs） can regulate caste differentiation in termites. In this study, we used the juvenile hormone analog fenoxycarh to induce termite workers （Reticulitermesflaviceps） to differentiate into pre-soldiers. A metatranscriptomic investigation of the protistan community was then performed by 454 pyrosequencing. From a thorough analysis based on 597 312 generated reads, we found that the starch and sucrose metabolism pathway was the most abundant pathway across the metatranscriptome. The current study demonstrates that the metatranscriptome of the protistan community in termites contains an abundance of lignocellulase, which plays a vital role in termite nutrition.

关键词： juvenile hormone analogues metatranscriptome protest Reticulitermes flaviceps lignocellulase

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Genomic and transcriptomic dissection of Theionarchaea in marine ecosystem

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Science China(Life Sciences) 2022年第6期65卷 1222-1234页

作者： Mingwei Cai Changhai Duan Xinxu Zhang Jie Pan Yang Liu Cuijing Zhang Meng Li Archaeal Biology Center Shenzhen Key Laboratory of Marine Microbiome EngineeringInstitute for Advanced StudyShenzhen UniversityShenzhen 518060China SZU-HKUST Joint PhD Program in Marine Environmental Science Shenzhen UniversityShenzhen 518060China

Theionarchaea is a recently described archaeal class within the Euryarchaeota.While it is widely distributed in sediment ecosystems,little is known about its metabolic potential and ecological features.Here,we used metagenomics and metatranscriptomics to characterize 12 theionarchaeal metagenome-assembled genomes,which were further divided into two subgroups,from coastal mangrove sediments of China and seawater columns of the Yap Trench.Genomic analysis revealed that apart from the canonical sulfhydrogenase,Theionarchaea harbor genes encoding heliorhodopsin,group 4[NiFe]-hydrogenase,and flagellin,in which genes for heliorhodopsin and group 4[NiFe]-hydrogenase were transcribed in mangrove sediment.Further,the theionarchaeal substrate spectrum may be broader than previously reported as revealed by metagenomics and metatranscriptomics,and the potential carbon substrates include detrital proteins,hemicellulose,ethanol,and CO_(2).The genes for organic substrate metabolism(mainly detrital protein and amino acid metabolism genes)have relatively higher transcripts in the top sediment layers in mangrove wetlands.In addition,co-occurrence analysis suggested that the degradation of these organic compounds by Theionarchaea might be processed in syntrophy with fermenters(e.g.,Chloroflexi)and methanogens.Collectively,these observations expand the current knowledge of the metabolic potential of Theionarchaea,and shed light on the metabolic strategies and roles of these archaea in the marine ecosystems.

关键词： Theionarchaea metagenome metatranscriptome metabolic potentials ecological roles

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Reconstruction and Dynamics of the Human Intestinal Microbiome Observed In Situ

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Engineering 2022年第8期8卷 89-101页

作者： Xiaolin Liu Min Dai Yue Ma Na Zhao Ziyu Wang Ying Yu Yakun Xu Huijie Zhang Liyuan Xiang He Tian Guanghou Shui Faming Zhang Jun Wang CAS Key Laboratory of Pathogenic Microbiology and Immunology Institute of MicrobiologyChinese Academy of SciencesBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China Medical Center for Digestive Diseases the Second Affiliated Hospital of Nanjing Medical UniversityNanjing 210011China Clinical Trial Center Office the Second Affiliated Hospital of Nanjing Medical UniversityNanjing 210011China State Key Laboratory of Molecular Developmental Biology Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijing 100101China Key Lab of Holistic Integrative Enterology Nanjing Medical UniversityNanjing 210011China

The human gut microbiome has primarily been studied through the use of fecal samples,a practice that has generated vital knowledge on the composition and functional capacities of gastrointestinal microbial communities.However,this reliance on fecal materials limits the investigation of microbial dynamics in other locations along the gastrointestinal tract(in situ),and the infrequent availability of fecal samples prevents analysis at finer temporal scales(e.g.,hours).In our study,we utilized colonic transendoscopic enteral tubing,a technology originally developed for fecal microbiota transplantation,to sample the ileocecal microbiome twice daily;metagenomic and metatranscriptomic analyses were then conducted on these samples.A total of 43 ileocecal and 28 urine and fecal samples were collected from five healthy volunteers.The ileocecal and fecal microbiomes,as profiled in the five volunteers,were found to be similar in metagenomic profiling,yet their active genes(metatranscriptome)were found to be highly distinct.Both microbiomes were perturbed after laxative exposure;over time,they exhibited reduced dissimilarity to their pre-treatment state,thereby demonstrating resilience as an innate property of the gut microbiome,although they did not fully recover within our observation time window.Sampling of the ileocecal microbiome during the day and at night revealed the existence of diurnal rhythms in a series of bacterial species and functional pathways,particularly those related to short-chain fatty acid production,such as Propionibacterium acnes and coenzyme A biosynthesis Ⅱ.Autocorrelation analysis and fluctuations decomposition further indicated the significant periodicity of the diurnal oscillations.Metabolomic profiling in the fecal and urine samples mirrored the perturbance and recovery in the gut microbiome,indicating the crucial contribution of the gut microbiome to many key metabolites involved in host health.This study provides novel insights into the human gut microbiome and its inner resilience and diurnal

关键词： Diurnal rhythm Reconstruction Metagenome metatranscriptome Metabolome Transendoscopic enteral tubing

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Diverse Asgard archaea including the novel phylum Gerdarchaeota participate in organic matter degradation

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Science China(Life Sciences) 2020年第6期63卷 886-897页

作者： Mingwei Cai Yang Liu Xiuran Yin Zhichao Zhou Michael WFriedrich Tim Richter Heitmann Rolf Nimzyk Ajinkya Kulkarni Xiaowen Wang Wenjin Li Jie Pan Yuchun Yang Ji-Dong Gu Meng Li Shenzhen Key Laboratory of Marine Microbiome Engineering Institute for Advanced StudyShenzhen UniversityShenzhen 518060China Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province College of Optoelectronic EngineeringShenzhen UniversityShenzhen 518060China Microbial Ecophysiology Group Faculty of Biology/ChemistryUniversity of BremenBremen D-28359Germany MARUM Center for Marine Environmental SciencesUniversity of BremenBremen D-28359Germany Laboratory of Environmental Microbiology and Toxicology School of Biological SciencesThe University of Hong KongHong Kong 99077 China Department of Microbe-Plant Interactions Faculty of Biology/ChemistryUniversity of BremenBremen D-28359Giermany

Asgard is an archaeal superphylum that might hold the key to understand the origin of eukaryotes, but its diversity and ecological roles remain poorly understood. Here, we reconstructed 15 metagenomic-assembled genomes from coastal sediments covering most known Asgard archaea and a novel group, which is proposed as a new Asgard phylum named as the "Gerdarchaeota".Genomic analyses predict that Gerdarchaeota are facultative anaerobes in utilizing both organic and inorganic carbon. Unlike their closest relatives Heimdallarchaeota, Gerdarchaeota have genes encoding for cellulase and enzymes involved in the tetrahydromethanopterin-based Wood–Ljungdahl pathway. Transcriptomics showed that most of our identified Asgard archaea are capable of degrading organic matter, including peptides, amino acids and fatty acids, occupying ecological niches in different depths of layers of the sediments. Overall, this study broadens the diversity of the mysterious Asgard archaea and provides evidence for their ecological roles in coastal sediments.

关键词： Asgard archaea Gerdarchaeota coastal sediment metagenome metatranscriptome

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Identification of Diverse Mycoviruses Through Metatranscriptomics Characterization of the Viromes of Wheat Fusarium Head Blight pathogens

Identification of Diverse Mycoviruses Through Metatranscript...

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中国植物病理学会2016年学术年会

作者： ZHANG Zhong-mei PENG Yun-liang JIANG Dao-hong Institute of Plant Protection Sichuan Academy of Agricultural Sciences/Key Laboratory of Integrated Pest Management on Crops in Southwest ChinaMinistry of Agriculture College of Plant Sciences & Technology of Huazhong Agricultural University

To characterize the viromes of wheat Fusarium Head Blight pathogens,a high-throughput sequencing-based metatranscriptomic approach was used to detect viral sequences.Total RNA from mycelia of 150 Fusarium spp.strains isolated from diseased wheat grain from Sichuan province in 2015 was sequenced.Sequence data were assembled de novo,and contigs with predicted amino acid sequence similarities to viruses in the non-redundant protein database were selected.The analysis identified 55 genome segments representing at least 14 mycoviruses,and 11 of them were previously undescribed.The novel mycovirus genomes showed similarity to 5 distinct lineages including Mononegavirales,ourmiavirus,Narnaviridae,Gamaflexiviridae and Partitiviridae,respectively.

关键词： Fusarium spp. metatranscriptome mycovirus

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