There is an urgent necessity to shift our diets toward those rich in fruits and vegetables and at reduce postharvest losses of perishables.Approximately 20%-50%of fruits and vegetables are lost due to poor postharvest...There is an urgent necessity to shift our diets toward those rich in fruits and vegetables and at reduce postharvest losses of perishables.Approximately 20%-50%of fruits and vegetables are lost due to poor postharvest handling and pathogen infections in developing countries while it was estimated as 5%-35%in developed countries. Fresh fruits have evolved with a plethora of microorganisms having important roles in maintaining fruit health. However, little information is available on the dynamics, structure, and functional capacities of underpinning fruit microbiomes. The present review discussed environmental conditions favoring fruit-harbored antagonists and their different modes of action for suppressing postharvest pathogens in fruits. It also provides information on omics technologies such as next-generation sequencing (NGS),metaproteomics, metatranscriptomic, and metabolomics studies to characterize fruit microbiomes. With the advent of NGS and meta-omics technologies, microbiome research could bring remarkable development and understanding in succeeding biological treatments. In addition, they may provide us with a fundamental understanding of microclimate requirements for fruit microbiome establishment and microbiome shifts during post-harvest storage, which would be advantageous in developing composite biocontrol treatments for post-harvest decay management.展开更多
Regulation of gut microbiota and its impact on human health is the theme of intensive research.The incidence and prevalence of atrial fibrillation(AF)are continuously escalating as the global population ages and chron...Regulation of gut microbiota and its impact on human health is the theme of intensive research.The incidence and prevalence of atrial fibrillation(AF)are continuously escalating as the global population ages and chronic disease survival rates increase;however,the mechanisms are not entirely clarified.It is gaining awareness that alterations in the assembly,structure,and dynamics of gut microbiota are intimately engaged in the AF progression.Owing to advancements in next-generation sequencing technologies and computational strategies,researchers can explore novel linkages with the genomes,transcriptomes,proteomes,and metabolomes through parallel meta-omics approaches,rendering a panoramic view of the culture-independent microbial investigation.In this review,we summarized the evidence for a bidirectional correlation between AF and the gut microbiome.Furthermore,we proposed the concept of“gut-immune-heart”axis and addressed the direct and indirect causal roots between the gut microbiome and AF.The intricate relationship was unveiled to generate innovative microbiota-based preventive and therapeutic interventions,which shed light on a definite direction for future experiments.展开更多
Detection and monitoring of pathogens is a central aspect of maintaining public health.Rare and neglected zoonotic viruses have the potential to evolve and expand exponentially,leading to unforeseen outbreaks,epidemic...Detection and monitoring of pathogens is a central aspect of maintaining public health.Rare and neglected zoonotic viruses have the potential to evolve and expand exponentially,leading to unforeseen outbreaks,epidemics,and pandemics.The emerging multiomics and meta-omics techniques and workflows,such as proteogenomics and meta-genomics,offer the potential for the detection of harmful pathogens,as well as opportunities for the discovery of previously unknown bacterial,parasitic,or viral pathogens.Multiomics and meta-omics workflows provide molecular information for tracking pathogens and understanding the effectiveness of spread mitigation strategies.In addition to environmental monitoring,multiomics and meta-omics approaches have the potential for clinical applications and in-depth characterization of novel pathogens.In this review,we discuss recent applications of multiomics and meta-omics techniques,their advantages over traditional methods,and their potential implementations in biomedical research,environmental studies,and healthcare.We critically assess the benefits and challenges of multiomics and meta-omics studies and discuss their future perspectives.展开更多
Soil contamination with organic pollutants is a growing environmental concern,with the FAO reporting that 80%of agricultural soils contain such residues.Industrial chemical production has doubled to 2.3 billion tonnes...Soil contamination with organic pollutants is a growing environmental concern,with the FAO reporting that 80%of agricultural soils contain such residues.Industrial chemical production has doubled to 2.3 billion tonnes and is projected to increase by 85%by 2030,exacerbating the issue.Key pollutants include pesticides,pharmaceuticals,antimicrobials,and plastic residues,contributing to a 15–20%loss in agricultural productivity.In this context,rhizosphere-mediated remediation has gained significant attention for its potential to degrade organic contaminants.Rhizoremediation,when integrated with biochar application,not only enhances contaminant degradation but also supports plant and microbial growth due to biochar’s nutritive properties and its role in improving contaminant bioavailability.This review explores the synergistic interactions between plant–microbe systems and the role of biochar in accelerating the degradation of major organic contaminants,including crude oil,pesticides,polycyclic aromatic hydrocarbons(PAHs),antibiotics,and organic dyes,aligning with circular bioeconomy principles.Additionally,meta-omics approaches such as metagenomics,transcriptomics,and metabolomics provide insights into active microbial communities involved in the rhizoremediation-biochar process.The efficiency of pollutant sorption and desorption is influenced by biochar’s chemical structure,composition,porosity,surface area,pH,elemental ratios,and functional groups.Therefore,this review also highlights the potential of engineered biochar for enhanced rhizoremediation while addressing challenges associated with its application,emphasizing the need for optimization strategies to mitigate any negative impacts.Furthermore,the exponential growth of the biochar market,valued at USD 2.05 billion in 2023,presents a promising opportunity for both global economic expansion and ecosystem restoration,underscoring the significance of biochar in sustainable environmental management.展开更多
Rumen microbiota has a close and intensive interaction with the ruminants.Microbiota residing in the rumen digests and ferments plant organic matters into nutrients that are subsequently utilized by the host,making ru...Rumen microbiota has a close and intensive interaction with the ruminants.Microbiota residing in the rumen digests and ferments plant organic matters into nutrients that are subsequently utilized by the host,making ruminants a unique group of animals that can convert plant materials indigestible by humans into high-quality animal protein as meat and milk.Many studies using meta-omics technologies have demonstrated the relationships between rumen microbiome and animal phenotypes associated with nutrient metabolism.Recently,the causality and physiological mechanisms underpinning the host-microbiota interactions have attracted tremendous research interest among researchers.This review discusses the host-microbiota interactions and the factors affecting these interactions in ruminants and provides a summary of the advances in research on animal husbandry.Understanding the microbiota composition,the functions of key bacteria,and the host-microbiota interaction is crucial for the development of knowledge-based strategies to enhance animal productivity and host health.展开更多
Nitrous oxide(N_(2)O)is a potent greenhouse gas that can be emitted during the biological treatment of wastewater.In this study,a comparison of the long-term performance characteristics and N_(2)O production of sequen...Nitrous oxide(N_(2)O)is a potent greenhouse gas that can be emitted during the biological treatment of wastewater.In this study,a comparison of the long-term performance characteristics and N_(2)O production of sequencing batch reactors(SBR)and continuous stirred tank reactors(CSTR)during nitrite-based denitrification was undertaken.It was found that both reactors had NO_(2)^(-)-N removal efficiencies over 99.9%,but the N_(2)O-N emissions from the SBR reached~2.3%of the removal nitrite-N load,while in the CSTR it never exceeded 0.1%.High frequency sampling during one operation cycle of the SBR demonstrated that the N_(2)O accumulation ratio was~0.1%during the feast period,increased to~1.9%in the first five hours of the famine period,and then gradually reached~2.3%at the end of famine.Batch experiments showed that limiting extracellular electron donor is required for N_(2)O accumulation in cells from the SBR-famine period and that cells from the CSTR do not accumulate N_(2)O when either nitrite or carbon is limiting.Another notable difference in the two reactor communities was the high level of accumulation of intracellular granules,most likely polyhydroxybutyrate(PHB),in cells during the feast period in the SBR.Metagenome assembly and binning found that one genome(PRO1),which is a Thauera,accounted for over half the metagenomic reads in both reactors.Neither shifts in gene regulation nor community composition explained the observed differences in reactor performance suggesting some post-transcriptional regulation obligatorily linked to antecedent conditions underly increased N_(2)O production in the SBR.展开更多
基金the Deanship of Scientific Research,King Faisal University,Saudi Arabia(Grant No.5067).
文摘There is an urgent necessity to shift our diets toward those rich in fruits and vegetables and at reduce postharvest losses of perishables.Approximately 20%-50%of fruits and vegetables are lost due to poor postharvest handling and pathogen infections in developing countries while it was estimated as 5%-35%in developed countries. Fresh fruits have evolved with a plethora of microorganisms having important roles in maintaining fruit health. However, little information is available on the dynamics, structure, and functional capacities of underpinning fruit microbiomes. The present review discussed environmental conditions favoring fruit-harbored antagonists and their different modes of action for suppressing postharvest pathogens in fruits. It also provides information on omics technologies such as next-generation sequencing (NGS),metaproteomics, metatranscriptomic, and metabolomics studies to characterize fruit microbiomes. With the advent of NGS and meta-omics technologies, microbiome research could bring remarkable development and understanding in succeeding biological treatments. In addition, they may provide us with a fundamental understanding of microclimate requirements for fruit microbiome establishment and microbiome shifts during post-harvest storage, which would be advantageous in developing composite biocontrol treatments for post-harvest decay management.
基金National Key Research and Development Program of China(2022YFC2303100)Central Plains Talent Program-Central Plains Youth Top Talents,the Young and Middle-aged Academic Leaders of Henan Provincial Health Commission(HNSWJW-2022013)+1 种基金Funding for Scientific Research and Innovation Team of the First Affiliated Hospital of Zhengzhou University(QNCXTD2023002 and ZYCXTD2023002)Research Project of Jinan Microecological Biomedicine Shandong Laboratory(JNL-2022001A and JNL-2022015B).
文摘Regulation of gut microbiota and its impact on human health is the theme of intensive research.The incidence and prevalence of atrial fibrillation(AF)are continuously escalating as the global population ages and chronic disease survival rates increase;however,the mechanisms are not entirely clarified.It is gaining awareness that alterations in the assembly,structure,and dynamics of gut microbiota are intimately engaged in the AF progression.Owing to advancements in next-generation sequencing technologies and computational strategies,researchers can explore novel linkages with the genomes,transcriptomes,proteomes,and metabolomes through parallel meta-omics approaches,rendering a panoramic view of the culture-independent microbial investigation.In this review,we summarized the evidence for a bidirectional correlation between AF and the gut microbiome.Furthermore,we proposed the concept of“gut-immune-heart”axis and addressed the direct and indirect causal roots between the gut microbiome and AF.The intricate relationship was unveiled to generate innovative microbiota-based preventive and therapeutic interventions,which shed light on a definite direction for future experiments.
文摘Detection and monitoring of pathogens is a central aspect of maintaining public health.Rare and neglected zoonotic viruses have the potential to evolve and expand exponentially,leading to unforeseen outbreaks,epidemics,and pandemics.The emerging multiomics and meta-omics techniques and workflows,such as proteogenomics and meta-genomics,offer the potential for the detection of harmful pathogens,as well as opportunities for the discovery of previously unknown bacterial,parasitic,or viral pathogens.Multiomics and meta-omics workflows provide molecular information for tracking pathogens and understanding the effectiveness of spread mitigation strategies.In addition to environmental monitoring,multiomics and meta-omics approaches have the potential for clinical applications and in-depth characterization of novel pathogens.In this review,we discuss recent applications of multiomics and meta-omics techniques,their advantages over traditional methods,and their potential implementations in biomedical research,environmental studies,and healthcare.We critically assess the benefits and challenges of multiomics and meta-omics studies and discuss their future perspectives.
基金the financial support received from the Department of Biotechnology,Ministry of Science and Technology,Government of Indiaand Govind Ballabh Pant‘National Institute of Himalayan Environment’(NIHE),Ministry of Environment,Forest and Climate Change,Government of India.
文摘Soil contamination with organic pollutants is a growing environmental concern,with the FAO reporting that 80%of agricultural soils contain such residues.Industrial chemical production has doubled to 2.3 billion tonnes and is projected to increase by 85%by 2030,exacerbating the issue.Key pollutants include pesticides,pharmaceuticals,antimicrobials,and plastic residues,contributing to a 15–20%loss in agricultural productivity.In this context,rhizosphere-mediated remediation has gained significant attention for its potential to degrade organic contaminants.Rhizoremediation,when integrated with biochar application,not only enhances contaminant degradation but also supports plant and microbial growth due to biochar’s nutritive properties and its role in improving contaminant bioavailability.This review explores the synergistic interactions between plant–microbe systems and the role of biochar in accelerating the degradation of major organic contaminants,including crude oil,pesticides,polycyclic aromatic hydrocarbons(PAHs),antibiotics,and organic dyes,aligning with circular bioeconomy principles.Additionally,meta-omics approaches such as metagenomics,transcriptomics,and metabolomics provide insights into active microbial communities involved in the rhizoremediation-biochar process.The efficiency of pollutant sorption and desorption is influenced by biochar’s chemical structure,composition,porosity,surface area,pH,elemental ratios,and functional groups.Therefore,this review also highlights the potential of engineered biochar for enhanced rhizoremediation while addressing challenges associated with its application,emphasizing the need for optimization strategies to mitigate any negative impacts.Furthermore,the exponential growth of the biochar market,valued at USD 2.05 billion in 2023,presents a promising opportunity for both global economic expansion and ecosystem restoration,underscoring the significance of biochar in sustainable environmental management.
基金the National Natural Science Foundation of China(grant number:31601963)the Agricultural Science and Technology Innovation Program and Modern Agro-Industry Technology Research System of the PR China(CARS-36)the Scientific Research Project for Major Achievements of the Agricultural Science and Technology Innovation Program(CAAS-ZDXT2019004)for the financial support to the research in our laboratory.
文摘Rumen microbiota has a close and intensive interaction with the ruminants.Microbiota residing in the rumen digests and ferments plant organic matters into nutrients that are subsequently utilized by the host,making ruminants a unique group of animals that can convert plant materials indigestible by humans into high-quality animal protein as meat and milk.Many studies using meta-omics technologies have demonstrated the relationships between rumen microbiome and animal phenotypes associated with nutrient metabolism.Recently,the causality and physiological mechanisms underpinning the host-microbiota interactions have attracted tremendous research interest among researchers.This review discusses the host-microbiota interactions and the factors affecting these interactions in ruminants and provides a summary of the advances in research on animal husbandry.Understanding the microbiota composition,the functions of key bacteria,and the host-microbiota interaction is crucial for the development of knowledge-based strategies to enhance animal productivity and host health.
基金This work was supported by the National Natural Science Foundation of China(No.52170076)the Shanghai Rising-Star Program(China)(No.20QC1400500)the State Key Laboratory of Pollution Control and Resource Reuse(China)(No.PCRRF20024).
文摘Nitrous oxide(N_(2)O)is a potent greenhouse gas that can be emitted during the biological treatment of wastewater.In this study,a comparison of the long-term performance characteristics and N_(2)O production of sequencing batch reactors(SBR)and continuous stirred tank reactors(CSTR)during nitrite-based denitrification was undertaken.It was found that both reactors had NO_(2)^(-)-N removal efficiencies over 99.9%,but the N_(2)O-N emissions from the SBR reached~2.3%of the removal nitrite-N load,while in the CSTR it never exceeded 0.1%.High frequency sampling during one operation cycle of the SBR demonstrated that the N_(2)O accumulation ratio was~0.1%during the feast period,increased to~1.9%in the first five hours of the famine period,and then gradually reached~2.3%at the end of famine.Batch experiments showed that limiting extracellular electron donor is required for N_(2)O accumulation in cells from the SBR-famine period and that cells from the CSTR do not accumulate N_(2)O when either nitrite or carbon is limiting.Another notable difference in the two reactor communities was the high level of accumulation of intracellular granules,most likely polyhydroxybutyrate(PHB),in cells during the feast period in the SBR.Metagenome assembly and binning found that one genome(PRO1),which is a Thauera,accounted for over half the metagenomic reads in both reactors.Neither shifts in gene regulation nor community composition explained the observed differences in reactor performance suggesting some post-transcriptional regulation obligatorily linked to antecedent conditions underly increased N_(2)O production in the SBR.
