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Advancements in prokaryotic systematics and the role of Bergey's International Society for Microbial Systematics in addressing challenges in the meta-data era

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National Science Review 2024年第7期11卷 292-304页

作者： Jian-Yu Jiao Rashidin Abdugheni Dao-Feng Zhang Iftikhar Ahmed Mukhtiar Ali Maria Chuvochina Svetlana N.Dedysh Xiuzhu Dong Markus G?ker Brian P.Hedlund Philip Hugenholtz Kamlesh Jangid Shuang-Jiang Liu Edward R.B.Moore Manik Prabhu Narsing Rao Aharon Oren Ramon Rossello-Mora Bhagwan Narayan Rekadwad Nimaichand Salam Wensheng Shu Iain C.Sutcliffe Wee Fei Aaron Teo Martha E.Trujillo Stephanus N.Venter William B.Whitman Guoping Zhao Wen-Jun Li State Key laboratory of Biocontrol Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory(Zhuhai) School of Life Sciences Sun Yat-Sen University State Key laboratory of Desert and Oasis Ecology Key Laboratory of Ecological Safety and Sustainable Development in Arid LandsXinjiang Institute of Ecology and Geography Chinese Academy of Sciences Jiangsu Province Engineering Research Center for Marine Bio-resources Sustainable Utilization&College of Oceanography Hohai University National Culture Collection of Pakistan(NCCP) Land Resources Research Institute(LRRI) National Agricultural Research Centre(NARC) The University of Queensland School of Chemistry and Molecular Biosciences Australian Centre for Ecogenomics Winogradsky Institute of Microbiology Research Center of BiotechnologyRussian Academy of Sciences State Key laboratory of Microbial Resources Institute of Microbiology Chinese Academy of Sciences Leibniz Institute DSMZ–German Collection of Microorganisms and Cell Cultures School of Life Sciences University of Nevada Nevada Institute of Personalized Medicine University of Nevada Bioenergy Group MACS Collection of Microorganisms Agharkar Research Institute State Key laboratory of Microbial Technology Shandong University Department of infectious Disease Institute for Biomedicine and Culture Collection University of Gothenburg(CCUG) Institute for BiomedicineSahlgrenska AcademyUniversity of Gothenburg Instituto de Ciencias Aplicadas Facultad de Ingeniería Universidad Autónoma de Chile The Alexander Silberman Institute of Life Sciences The Edmond J.Safra Campus The Hebrew University of Jerusalem Marine Microbiology Group Department of Animal and Microbial Biodiversity Mediterranean Institute for Advanced Studies(IMEDEA CSIC-UIB) MicrobeAI Lab Division of Microbiology and Biotechnology Yenepoya Research Centre Yenepoya(Deemed to be University) National Agri-Food Biotechnology Institute Institute of Ecological Science Sch

Prokaryotes are ubiquitous in the biosphere, important for human health and drive diverse biological and environmental processes. Systematics of prokaryotes, whose origins can be traced to the discovery of microorganisms in the 17th century, has transitioned from a phenotype-based classification to a more comprehensive polyphasic taxonomy and eventually to the current genome-based taxonomic *** transition aligns with a foundational shift from studies focused on phenotypic traits that have limited comparative value to those using genome sequences. In this context, Bergey's Manual of Systematics of Archaea and Bacteria(BMSAB) and Bergey's International Society for Microbial Systematics(BISMiS) play a pivotal role in guiding prokaryotic systematics. This review focuses on the historical development of prokaryotic systematics with a focus on the roles of BMSAB and BISMiS. We also explore significant contributions and achievements by microbiologists, highlight the latest progress in the field and anticipate challenges and opportunities within prokaryotic systematics. Additionally, we outline five focal points of BISMiS that are aimed at addressing these challenges. In conclusion, our collaborative effort seeks to enhance ongoing advancements in prokaryotic systematics, ensuring its continued relevance and innovative characters in the contemporary landscape of genomics and bioinformatics.

关键词： prokaryotic systematics Bergey's Manual of Systematics of Archaea and Bacteria (BMSAB) Bergey's International Society for Microbial Systematics (BISMiS) meta-data era

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ArcA Gene Expression Level of Actinobacillus pleuropneumoniae in Anaerobic Culture

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畜牧兽医学报 2009年第S1期40卷 34-38页

作者： DUAN Li-li WEN Xin-tian CAO San-jie HUANG Xiao-bo laboratory of animal infectious Disease and Microarray Key Laboratory of Animal Disease and Human Health of Sichuan ProvinceCollege of Animal MedicineSichuan Agricultural University

In the present study,mRNA levels of the ArcA gene of Actinobacillus pleuropneumoniae serotype1 were measured during response to stress by growing under anaerobic *** levels were measured by semi-quantitative RT-PCR using the housekeeping gene recF as an internal *** expression of ArcA was undetectable until about 3 hours under standard culture conditions,but it was promptly and highly expressed in anaerobic *** results are consistent with ArcA being a potential virulence gene of Actinobacillus pleuropneumoniae,and likely playing an important role in pathogenesis caused by this organism.

关键词： semi-quantitative RT-PCR Actinobacillus pleuropneumoniae ArcA gene anaerobic stress

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Parameter identifiability of a within-host SARS-CoV-2 epidemic model

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infectious Disease Modelling 2024年第3期9卷 975-994页

作者： Junyuan Yang Sijin Wu Xuezhi Li Xiaoyan Wang Xue-Song Zhang Lu Hou Complex Systems Research Center Shanxi UniversityTaiyuan030006China Shanxi Key laboratory of Mathematical Techniques and Big Data Analysis on Disease Control and Prevention Shanxi UniversityTaiyuan030006China School of Mathematics and Science Henan Normal UniversityXinxiang453000China School of Information Shanxi University of Finance and EconomicsTaiyuan030006China Agriculture and animal Husbandry Technology Promotion Center of Xingan League Xingan League137400China

Parameter identification involves the estimation of undisclosed parameters within a system based on observed data and mathematical *** this investigation,we employ DAISY to meticulously examine the structural identifiability of parameters of a within-host SARS-CoV-2 epidemic model,taking into account an array of observable ***,Monte Carlo simulations are performed to offer a comprehensive practical analysis of model ***,sensitivity analysis is employed to ascertain that decreasing the replication rate of the SARS-CoV-2 virus and curbing the infectious period are the most efficacious measures in alleviating the dissemination of COVID-19 amongst hosts.

关键词： Structural identifiability Practical identifiability Sensitivity analysis The basic reproduction number

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Evaluating the efficacy of an attenuated Streptococcus equi ssp. zooepidemicus vaccine produced by multi-gene deletion in pathogenicity island SeseCisland_4

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Journal of Integrative Agriculture 2019年第5期18卷 1093-1102页

作者： MA Fang WANG Guang-yu ZHOU Hong MA Zhe LIN Hui-xing FAN Hong-jie MOE joint International Research laboratory of animal Health and Food Safety College of Veterinary Medicine Nanjing Agricultural University National Center of Meat Quality and Safety Control Nanjing Agricultural University Jiangsu Co-Innovation Center for Prevention and Control of Important animal infectious Diseases and Zoonoses Yangzhou University

Streptococcus equi ssp. zooepidemicus(SEZ) is a pathogen associated with a wild range of animal species. Frequent outbreaks have occurred in recent years in pigs, horses, goats and dogs which is liable to infect humans. There is a lack of efficient vaccines against this disease and the occurrence of antibiotic resistance may render drug therapies ineffective. In this study, gene deletion mutant(ΔSEZ) in pathogenicity islands SeseCisland_4 was constructed. The mutant ΔSEZ had a 52-fold decrease in 50% lethal dose(LD_(50)) and had less capacity to adhere epithelial cells. Importantly, immunization of mice with attenuated vaccine ΔSEZ at the dose of 10~2 colony-forming units(CFU) mL^(–1) elicited a significant humoral antibody response, with an antibody titer of 1:12 800. Therefore, 10~2 CFU mL^(–1) might be used as the appropriate immune dose for the attenuated vaccine ΔSEZ, which provided mice with efficient protection against virulent SEZ. In addition, the hyperimmune sera against 10~2 CFU m L–1 attenuated vaccine ΔSEZ could confer significant protection against virulent SEZ infection in the passive immunization experiment and exhibited efficient bactericidal activity in the whole blood assay. Meanwhile, no viable bacteria was detected in blood when mice were immunized with ΔSEZ at the dose of 10~2 CFU mL^(–1) via hypodermic injection. Thereafter, the mutant ΔSEZ at the dose of 10~2 CFU mL^(–1) could confer significant protection in mice and had less negative effects on host, which could be an effective attenuated vaccine candidate for the prevention of SEZ.

关键词： Streptococcus equi ssp.zooepidemicus zoonosis attenuated vaccine immune dose

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Monocyte and macrophage function in respiratory viral infections

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animal Diseases 2024年第1期4卷 40-47页

作者： Mohd Arish Jie Sun Beirne B.Carter Center for Immunology Research University of VirginiaCharlottesvilleVA 22908USA Division of infectious Disease and International Health Department of MedicineUniversity of VirginiaCharlottesvilleVA 22908USA

Pulmonary macrophages,such as tissue-resident alveolar and interstitial macrophages and recruited monocyte-derived macrophages,are the major macrophages present in the lungs during homeostasis and diseased *** tissue-resident macrophages act as sentinels of the alveolar space and play an important role in maintaining homeostasis and immune regulation,recruited macrophages accumulate in the respiratory tract after acute viral *** sharing similar anatomical niches,these macrophages are distinct in terms of their origins,surface marker expression,and transcriptional profiles,which impart macrophages with distinguished characteristics in physi-ological and pathophysiological *** this review,we summarize the current view on these macrophage populations,their shared functions,and what makes them distinct from each other in the context of homeostasis andrespiratoryviral infections.

关键词： Alveolar macrophages Interstitial macrophages Monocytes derived macrophages Viral infection IAV RSV SARS-COV-2

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Genome characterization of the Caprine arthritis-encephalitis virus in China:A retrospective genomic analysis of the earliest Chinese isolates

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Journal of Integrative Agriculture 2023年第3期22卷 872-880页

作者： WANG Deng-feng YANG Xue-yun WEI Yu-rong LI Jian-jun BOLATI Hongduzi MENG Xiao-xiao TUERXUN Gunuer NUERDAN Nuerbaiheti WU Jian-yong Engineering laboratory of animal Pharmaceuticals College of Animal Science(College of Bee Science)Fujian Agriculture and Forestry UniversityFuzhou 350002P.R.China Xinjiang Key laboratory of animal infectious Diseases Institute of Veterinary MedicineXinjiang Academy of Animal SciencesUrumqi 830013P.R.China

Caprine arthritis-encephalitis virus(CAEV) is an under-studied virus infecting caprines and ovines worldwide. Over the last four decades, CAEV has spread in China, obtaining genomic data on CAEV strains circulating in China is of importance for developing diagnostic methods and eradicating associated diseases. However, there is limited information on the genome, including characterizations, and the probable origin. This work aimed to characterize Chinese CAEV genomes and population structures. Five CAEV strains isolated from infected dairy goats between 1989and 1994 in Gansu, Guizhou, Shaanxi, Shandong and Sichuan provinces were cloned and sequenced. The Chinese CAEV had a 58–93% genome similarities to strains outside of China, and they belonged to subgenotype B1. The highest similarity levels(98.3–99.3%) were with two other Chinese strains, and they shared a 91.8–92.3% similarity with the strain Clements(GenBank accession no. NC_001463.1) from outside of China. The Chinese CAEV strains isolated from different provinces over five years were still highly homologous and contained unique ancestral population components,indicating that these Chinese strains had a common origin that differed from other known strains. Our results provide genomic data on circulating Chinese CAEV strains and will be useful for future epidemiological investigations and CAEV eradication programs.

关键词： Caprine arthritis-encephalitis virus genotype phylogenetic analysis population structure similarity dairy goat

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Beneficial roles of nutrients as immunostimulants in aquaculture:A review

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Aquaculture and Fisheries 2024年第5期9卷 707-720页

作者： Seerengaraj Vijayaram Einar Ringø Antonio Zuorro Hien van Doan Yunzhang Sun Xiamen Key laboratory for Feed Quality Testing and Safety Evaluation Fisheries CollegeJimei UniversityXiamen361021China Norwegian College of Fishery Science Faculty of BioscienceFisheries and EconomicsUiT the Arctic University of NorwayTromsø9037Norway Department of Chemical Engineering Materials and EnvironmentSapienza UniversityVia Eudossiana 18Rome00184Italy Department of animal and Aquatic Sciences Faculty of AgricultureChiang Mai UniversityChiang Mai50200Thailand

Protein deficiency is a major difficulty for human needs in the past few decades,while different types of aquatic species are rich in high quality ***,aquaculture is considered as the main developing food production sector *** infections are the main problem for aquaculture,and their outbreaks have a great impact on productivity,and previously indiscriminate use of antibiotics to control ***,the emergence of multidrug-resistant pathogens might lead to sudden infectious disease outbreaks resulting in serious economic *** application is an effective technique to protect and enhance the immune system of aquatic animals and therefore improve aquaculture *** immunostimulants such as essential fatty acids,amino acids,vitamins,and minerals are the most important responsibility to improve aquaculture production,as well as the cost of this method,which is effective,non-toxic,and environment *** nutrient immunostimulants are supportive to increase the immune system,antioxidant,anti-inflammatory,and infection resistance of aquatic *** addition,nutritional feed additives improved feed palatability and the excellence of aquatic products and also enhance gut *** information is available on nutrient immunostimulants in aquaculture applications,and this review provides information on different kinds of nutritional administration used in aquaculture to enhance positive impacts on aquatic animals’health as well as feed quality *** review will provide theoretical references for the application of nutrient immunostimulants in aquatic feeds.

关键词： Immunostimulants Amino acids Vitamins Minerals Nucleotides Aquaculture

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Endemicity of H9N2 and H5N1 avian influenza viruses in poultry in China poses a serious threat to poultry industry and public health

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Frontiers of Agricultural Science and Engineering 2016年第1期3卷 11-24页

作者： Jiao HU Xiufan LIU animal infectious Disease laboratory School of Veterinary MedicineJiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis Yangzhou University

The H9N2 and H5N1 avian in fluenza viruses(AIVs) have been circulating in poultry in China and become endemic since 1998 and 2004, ***, they are prevalent in poultry throughout China. This endemicity makes them actively involved in the emergence of the novel lineages of other subtypes of in fluenza viruses, such as the well-known viruses of the highly pathogenic avian in fluenza(HPAI) H5N2 and the2013 novel H7N7, H7N9 and H10N8 subtypes, thereby threatening both the poultry industry and public ***, we will review brie fly the prevalence and evolution,pathogenicity, transmission, and disease control of these two subtypes and also discuss the possibility of emergence of potentially virulent and highly transmissible AIVs to humans.

关键词： avian influenza virus H9N2 H5N1 novel viruses public health

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Advances in pathogenesis of Streptococcus suis serotype 2

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Journal of Integrative Agriculture 2017年第12期16卷 2834-2847页

作者： FAN Hong-jie MOE joint International Research laboratory of animal Health and Food Safety College of Veterinary Medicine Nanjing Agricultural University Nanjing 210095 P.R.China Jiangsu Co-Innovation Center for Prevention and Control of Important animal infectious Diseases and Zoonoses Yangzhou 225009 P.R.China

Streptococcus suis is one of the major pathogens of swine streptococcosis. Among them, the strongest virulence and highest rate of clinical isolation serotype is S. suis serotype 2（SS2）. Moreover, SS2 is also an important zoonosis pathogen, which caused severe public health issues in China. It has been reported that SS2 has several virulence factors, including muramidase released protein, extracellular factors, capsule, fibronectin-binding protein, enolase, hemolysin, small RNA, biofilm, two-component regulatory systems, STK/STP, etc., whose functions involved in adhesion, anti-phagocytosis, inflammatory pathway activation, invasion, etc. Actually, SS2 has developed a variety of ways to escape from host immune system during evolution. In particularly, capsule could resist phagocytosis through inhibiting sphingosine dependent immune cell recognition, which plays an important role in escaping host inflammation response; moreover, superoxide dismutase encoding by sod A enables SS2 escaping reactive oxygen species（ROS） in host immune cells; besides, binding complement factor h with Fhb could suppress the activation of complement alternative pathway and bactericidal effect. And SS2 could also hinder the formation of neutrophil extracellular traps（NETs） to avoid trapping by swine neutrophils, while host immune globulin could be degraded by Ig A1 hydrolase and Ig M protease. In addition, SS2 could escape host immune defense with the help of multiple transcriptional factors and micro-RNA. So far, the pathogenesis of meningitis, arthritis caused by SS2 infection, is still unclear, and the virulence regulatory mechanism of phosphorylation, micro-RNA need to be further clarified. Importantly, the study of interaction mechanism of pathogen and host contribute to further demonstration the pathogenesis of SS2.

关键词： Advances in pathogenesis of Streptococcus suis serotype 2

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iTRAQ quantitative analysis of plasma proteome changes of cow from pregnancy to lactation

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Journal of Integrative Agriculture 2015年第7期14卷 1407-1413页

作者： MA Lu BU Deng-pan YANG Yong-xing YAN Su-mei WANG Jia-qi Inner Mongolia Agricultural University State Key laboratory of animal Nutrition/CAAS-ICRAF joint laboratory on Agroforestry and Sustainable animal Husbandry/Institute of animal Sciences Chinese Academy of Agricultural Sciences Synergetic Innovation Center of Food Safety and Nutrition Northeast Agricultural University

Dairy cows undergo tremendous changes in physiological, metabolism and the immune function from pregnancy to lac- tation that are associated with cows being susceptible to metabolic and infectious diseases. The objective of this study is to investigate the changes of plasma proteome on 21 d before expected calving and 1 d after calving from dairy cows using an integrated proteomic approach consisting of minor abundance protein enrichment by ProteoMiner beads, protein labeling by isobaric tags for relative and absolute quantification, and protein identification by liquid chromatography coupled with tandem mass spectrometry. Nineteen proteins were changed around the time of calving. These proteins were asso- ciated with response to stress, including acute-phase response and defense response, based on the proteins annotation. In particular, three up-regulated proteins after calving including factor V, a2-antiplasmin and prothrombin were assigned into the complement and coagulation pathway. These results may provide new information in elucidating host response to lactation and parturition stress, and inflammatory-like conditions at the protein level. Differential proteins may serve as potential markers to regulate the lactation and parturition stress in periparturient dairy cows.

关键词： dairy cow periparturient plasma proteomic quantitative analysis

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