Zhanjiang Bay is a major aquaculture area in China with many types of mariculture products(such as oysters,fish,and shrimp).The culture area and shrimp output in Zhanjiang Bay are ranked first in China.We investigated...Zhanjiang Bay is a major aquaculture area in China with many types of mariculture products(such as oysters,fish,and shrimp).The culture area and shrimp output in Zhanjiang Bay are ranked first in China.We investigated the total organic carbon(TOC),total nitrogen(TN),TOC/TN ratio,and stable isotopes(δ^(13)C and δ^(15)N) of the fish and shrimp feed,fish and shrimp feces,and sedimentary organic matter(SOM) in and around different aquaculture areas of northeastern Zhanjiang B ay to study the impact of aquaculture activities on SOM.The average TOC contents of fish and shrimp feed were 39.20%±0.91% and 39.29%±0.21%,respectively.The average TOC content in the surface sediments of the oyster culture area,the mixed(fish and shrimp) culture area,and the cage fish farm area were 0.66%,0.88%±0.10%,and 0.58%±0.19%,respectively,which may indicate that mixed culture had a greater impact on SOM.The relatively high TOC and TN contents and relatively low TOC/TN ratios,and δ^(15)N values in the upper layer of the core sediment in the mixed culture area could also support the significant influence of mixed culture.The average δ^(13)C and δ^(15)N values of fish and shrimp feed were -20.6‰±2.2‰ and 1.8‰±1.2‰,respectively,which were different from the isotopic values of SOM in the study area.δ^(13)C and δ^(15)N values for SOM in different aquaculture areas were different from those of nearby reference stations,probably reflecting the influence of aquaculture.The δ^(13)C and δ^(15)N values in the oyster culture area(-25.9‰ and6.0‰,respectively) seemed to have reduced δ^(13)C and enriched δ^(15)N relative to those of the reference station(-24.6‰ and 5.8‰,respectively).This may reflect the influence of organic matter on oyster culture.The δ^(15)N value of the station in the mixed culture area(7.1‰±0.4‰) seemed to be relatively enriched in δ^(15)N relative to that of the reference station(6.6‰).Sedimentation and the subsequent degradation of organic matter from mixed cultures may have contributed to this phenomenon.The surface sediment at the cage fish farm area seemed to be affected by fish feces and primary production based on the indication of δ^(13)C and δ^(15)N values.The sediment core at the mixed culture region(NS6) had lower TOC/TN ratios and more positive δ^(13)C and δ^(15)N values than the sediment core at the oyster culture area,suggesting a higher proportionate contribution of marine organic matter in the mixed culture area.In summary,oyster culture,mixed culture,and cage fish culture in northeastern Zhanjiang Bay had a certain degree of impact on SOM,and mixed culture had more significant influences on SOM based on the high TOC contents and the significant vertical variations of TOC/TN ratio and δ^(15)N value in the sediment of this area.This study provides new insights into the impact of aquaculture activities on SOM content.展开更多
The global Coronavirus disease 2019(COVID-19)pandemic caused by SARS-CoV-2 has affected more than eight million people.There is an urgent need to investigate how the adaptive immunity is established in COVID-19 patien...The global Coronavirus disease 2019(COVID-19)pandemic caused by SARS-CoV-2 has affected more than eight million people.There is an urgent need to investigate how the adaptive immunity is established in COVID-19 patients.In this study,we proled adaptive immune cells of PBMCs from recovered COVID-19 patients with varying disease severity using single-cell RNA and TCR/BCR V(D)J sequencing.The sequencing data revealed SARS-CoV-2-specic shufing of adaptive immune repertories and COVID-19-induced remodeling of peripheral lymphocytes.Characterization of variations in the peripheral T and B cells from the COVID-19 patients revealed a positive correlation of humoral immune response and T-cell immune memory with disease severity.Sequencing and functional data revealed SARS-CoV-2-specic T-cell immune memory in the convalescent COVID-19 patients.Furthermore,we also identied novel antigens that are responsive in the convalescent patients.Altogether,our study reveals adaptive immune repertories underlying pathogenesis and recovery in severe versus mild COVID-19 patients,providing valuable information for potential vaccine and therapeutic development against SARS-CoV-2 infection.展开更多
COVID-19 remains a serious emerging global health problem,and little is known about the role of oropharynx commensal microbes in infection susceptibility and severity.Here,we present the oropharyngeal microbiota chara...COVID-19 remains a serious emerging global health problem,and little is known about the role of oropharynx commensal microbes in infection susceptibility and severity.Here,we present the oropharyngeal microbiota characteristics identified by shotgun metagenomic sequencing analyses of oropharynx swab specimens from 31 COVID-19 patients,29 influenza B patients,and 28 healthy controls.Our results revealed a distinct oropharyngeal microbiota composition in the COVID-19 patients,characterized by enrichment of opportunistic pathogens such as Veillonella and Megasphaera and depletion of Pseudopropionibacterium,Rothia,and Streptococcus.Based on the relative abundance of the oropharyngeal microbiome,we built a microbial classifier to distinguish COVID-19 patients from flu patients and healthy controls with an AUC of 0.889,in which Veillonella was identified as the most prominent biomarker for COVID-19 group.Several members of the genus Veillonella,especially Veillonella parvula which was highly enriched in the oropharynx of our COVID-19 patients,were also overrepresented in the BALF of COVID-19 patients,indicating that the oral cavity acts as a natural reservoir for pathogens to induce co-infections in the lungs of COVID-19 patients.We also found the increased ratios of Klebsiella sp.,Acinetobacter sp.,and Serratia sp.were correlated with both disease severity and elevated systemic inflammation markers(neutrophil-lymphocyte ratio,NLR),suggesting that these oropharynx microbiota alterations may impact COVID-19 severity by influencing the inflammatory response.Moreover,the oropharyngeal microbiome of COVID-19 patients exhibited a significant enrichment in amino acid metabolism and xenobiotic biodegradation and metabolism.In addition,all 26 drug classes of antimicrobial resistance genes were detected in the COVID-19 group,and were significantly enriched in critical cases.In conclusion,we found that oropharyngeal microbiota alterations and functional differences were associated with COVID-19 severity.展开更多
Phage-microbe interactions are appealing systems to study coevolution,and have also been increasingly emphasized due to their roles in human health,disease,and the development of novel therapeutics.Phage-microbe inter...Phage-microbe interactions are appealing systems to study coevolution,and have also been increasingly emphasized due to their roles in human health,disease,and the development of novel therapeutics.Phage-microbe interactions leave diverse signals in bacterial and phage genomic sequences,defined as phage-host interaction signals(PHISs),which include clustered regularly interspaced short palindromic repeats(CRISPR)targeting,prophage,and protein-protein interaction signals.In the present study,we developed a novel tool phage-host interaction signal detector(PHISDetector)to predict phage-host interactions by detecting and integrating diverse in silico PHISs,and scoring the probability of phage-host interactions using machine learning models based on PHIS features.We evaluated the performance of PHISDetector on multiple benchmark datasets and application cases.When tested on a dataset of 758 annotated phage-host pairs,PHISDetector yields the prediction accuracies of 0.51 and 0.73 at the species and genus levels,respectively,outperforming other phage-host prediction tools.When applied to 125,842 metagenomic viral contigs(mVCs)derived from 3042 geographically diverse samples,a detection rate of 54.54% could be achieved.Furthermore,PHISDetector could predict infecting phages for 85.6% of 368 multidrug-resistant(MDR)bacteria and 30% of 454 human gut bacteria obtained from the National Institutes of Health(NIH)Human Microbiome Project(HMP).The PHISDetector can be run either as a web server(http://www.microbiome-bigdata.com/PHISDetector/)for general users to study individual inputs or as a stand-alone version(https://github.com/HITImmunologyLab/PHISDetector)to process massive phage contigs from virome studies.展开更多
基金The National Natural Science Foundation of China under contract No.42276047the Guangdong Basic and Applied Basic Research Foundation under contract Nos 2023A1515110473 and 2021A1515110172+1 种基金the Program for Scientific Research Start-up Funds of Guangdong Ocean University under contract No.R17058the National College Student Innovation and Entrepreneurship Training Program Project under contract No.202310566007。
文摘Zhanjiang Bay is a major aquaculture area in China with many types of mariculture products(such as oysters,fish,and shrimp).The culture area and shrimp output in Zhanjiang Bay are ranked first in China.We investigated the total organic carbon(TOC),total nitrogen(TN),TOC/TN ratio,and stable isotopes(δ^(13)C and δ^(15)N) of the fish and shrimp feed,fish and shrimp feces,and sedimentary organic matter(SOM) in and around different aquaculture areas of northeastern Zhanjiang B ay to study the impact of aquaculture activities on SOM.The average TOC contents of fish and shrimp feed were 39.20%±0.91% and 39.29%±0.21%,respectively.The average TOC content in the surface sediments of the oyster culture area,the mixed(fish and shrimp) culture area,and the cage fish farm area were 0.66%,0.88%±0.10%,and 0.58%±0.19%,respectively,which may indicate that mixed culture had a greater impact on SOM.The relatively high TOC and TN contents and relatively low TOC/TN ratios,and δ^(15)N values in the upper layer of the core sediment in the mixed culture area could also support the significant influence of mixed culture.The average δ^(13)C and δ^(15)N values of fish and shrimp feed were -20.6‰±2.2‰ and 1.8‰±1.2‰,respectively,which were different from the isotopic values of SOM in the study area.δ^(13)C and δ^(15)N values for SOM in different aquaculture areas were different from those of nearby reference stations,probably reflecting the influence of aquaculture.The δ^(13)C and δ^(15)N values in the oyster culture area(-25.9‰ and6.0‰,respectively) seemed to have reduced δ^(13)C and enriched δ^(15)N relative to those of the reference station(-24.6‰ and 5.8‰,respectively).This may reflect the influence of organic matter on oyster culture.The δ^(15)N value of the station in the mixed culture area(7.1‰±0.4‰) seemed to be relatively enriched in δ^(15)N relative to that of the reference station(6.6‰).Sedimentation and the subsequent degradation of organic matter from mixed cultures may have contributed to this phenomenon.The surface sediment at the cage fish farm area seemed to be affected by fish feces and primary production based on the indication of δ^(13)C and δ^(15)N values.The sediment core at the mixed culture region(NS6) had lower TOC/TN ratios and more positive δ^(13)C and δ^(15)N values than the sediment core at the oyster culture area,suggesting a higher proportionate contribution of marine organic matter in the mixed culture area.In summary,oyster culture,mixed culture,and cage fish culture in northeastern Zhanjiang Bay had a certain degree of impact on SOM,and mixed culture had more significant influences on SOM based on the high TOC contents and the significant vertical variations of TOC/TN ratio and δ^(15)N value in the sediment of this area.This study provides new insights into the impact of aquaculture activities on SOM content.
基金funded by the National Natural Science Foundation of China grant no.31825008 and 31422014 to Z.H.and grant no.61872117 to F.Z.
文摘The global Coronavirus disease 2019(COVID-19)pandemic caused by SARS-CoV-2 has affected more than eight million people.There is an urgent need to investigate how the adaptive immunity is established in COVID-19 patients.In this study,we proled adaptive immune cells of PBMCs from recovered COVID-19 patients with varying disease severity using single-cell RNA and TCR/BCR V(D)J sequencing.The sequencing data revealed SARS-CoV-2-specic shufing of adaptive immune repertories and COVID-19-induced remodeling of peripheral lymphocytes.Characterization of variations in the peripheral T and B cells from the COVID-19 patients revealed a positive correlation of humoral immune response and T-cell immune memory with disease severity.Sequencing and functional data revealed SARS-CoV-2-specic T-cell immune memory in the convalescent COVID-19 patients.Furthermore,we also identied novel antigens that are responsive in the convalescent patients.Altogether,our study reveals adaptive immune repertories underlying pathogenesis and recovery in severe versus mild COVID-19 patients,providing valuable information for potential vaccine and therapeutic development against SARS-CoV-2 infection.
基金The authors thank the Heilongjiang Province Oral Microecological Technology Innovation Center for providing technical support,and the funding of Heilongjiang Province Applied Technology Research and Development Program(GA20C003,GA20C006)the Medical Science Research Fund of Beijing Medical and Health Foundation(YWJKJJHKYJJ-B20284EN)the Program for Innovation Research of Heilongjiang Provincial Hospital and the National Natural Science Foundation of China(31825008 and 31422014 to Z.H.and 61872117 to F.Zha).
文摘COVID-19 remains a serious emerging global health problem,and little is known about the role of oropharynx commensal microbes in infection susceptibility and severity.Here,we present the oropharyngeal microbiota characteristics identified by shotgun metagenomic sequencing analyses of oropharynx swab specimens from 31 COVID-19 patients,29 influenza B patients,and 28 healthy controls.Our results revealed a distinct oropharyngeal microbiota composition in the COVID-19 patients,characterized by enrichment of opportunistic pathogens such as Veillonella and Megasphaera and depletion of Pseudopropionibacterium,Rothia,and Streptococcus.Based on the relative abundance of the oropharyngeal microbiome,we built a microbial classifier to distinguish COVID-19 patients from flu patients and healthy controls with an AUC of 0.889,in which Veillonella was identified as the most prominent biomarker for COVID-19 group.Several members of the genus Veillonella,especially Veillonella parvula which was highly enriched in the oropharynx of our COVID-19 patients,were also overrepresented in the BALF of COVID-19 patients,indicating that the oral cavity acts as a natural reservoir for pathogens to induce co-infections in the lungs of COVID-19 patients.We also found the increased ratios of Klebsiella sp.,Acinetobacter sp.,and Serratia sp.were correlated with both disease severity and elevated systemic inflammation markers(neutrophil-lymphocyte ratio,NLR),suggesting that these oropharynx microbiota alterations may impact COVID-19 severity by influencing the inflammatory response.Moreover,the oropharyngeal microbiome of COVID-19 patients exhibited a significant enrichment in amino acid metabolism and xenobiotic biodegradation and metabolism.In addition,all 26 drug classes of antimicrobial resistance genes were detected in the COVID-19 group,and were significantly enriched in critical cases.In conclusion,we found that oropharyngeal microbiota alterations and functional differences were associated with COVID-19 severity.
基金supported by the National Natural Science Foundation of China(Grant Nos.31825008,31422014,and 61872117).
文摘Phage-microbe interactions are appealing systems to study coevolution,and have also been increasingly emphasized due to their roles in human health,disease,and the development of novel therapeutics.Phage-microbe interactions leave diverse signals in bacterial and phage genomic sequences,defined as phage-host interaction signals(PHISs),which include clustered regularly interspaced short palindromic repeats(CRISPR)targeting,prophage,and protein-protein interaction signals.In the present study,we developed a novel tool phage-host interaction signal detector(PHISDetector)to predict phage-host interactions by detecting and integrating diverse in silico PHISs,and scoring the probability of phage-host interactions using machine learning models based on PHIS features.We evaluated the performance of PHISDetector on multiple benchmark datasets and application cases.When tested on a dataset of 758 annotated phage-host pairs,PHISDetector yields the prediction accuracies of 0.51 and 0.73 at the species and genus levels,respectively,outperforming other phage-host prediction tools.When applied to 125,842 metagenomic viral contigs(mVCs)derived from 3042 geographically diverse samples,a detection rate of 54.54% could be achieved.Furthermore,PHISDetector could predict infecting phages for 85.6% of 368 multidrug-resistant(MDR)bacteria and 30% of 454 human gut bacteria obtained from the National Institutes of Health(NIH)Human Microbiome Project(HMP).The PHISDetector can be run either as a web server(http://www.microbiome-bigdata.com/PHISDetector/)for general users to study individual inputs or as a stand-alone version(https://github.com/HITImmunologyLab/PHISDetector)to process massive phage contigs from virome studies.
