Antimicrobial resistance(AMR)is a public health problem of global concern.The presence of antibiotic resistance genes(ARGs)in food may aggravate the spread of AMR.Understanding the distribution and transfer of drug-re...Antimicrobial resistance(AMR)is a public health problem of global concern.The presence of antibiotic resistance genes(ARGs)in food may aggravate the spread of AMR.Understanding the distribution and transfer of drug-resistant bacteria and ARGs in pickled vegetable foods was critical for food quality and safety.Therefore,this study used metagenomic sequencing,binning technology,and antibiotic susceptibility tests to explore the distribution and transfer of drug-resistant bacteria and ARGs in pickled vegetable foods.The results showed that Bacillota,Lactobacillus,and Salmonella were the dominant bacteria in all samples.A total of 12 ARG types and 52 ARG subtypes were identified.The abundance of bacitracin ARGs in high-salt samples(<2%)was higher,and multidrug ARGs in low-salt samples(7%-10%)was higher.The most abundant ARG subtypes,baca and acrb,were associated with Salmonella.Furthermore,a total of 34 metagenome assembly genomes(MAGs)were obtained by metagenomic binning.MAG8 and MAG25,which carried the largest number of ARGs,virulence factors(VFs),and MGEs,were all derived from Vibrio.More importantly,horizontal gene transfer(HGT)could occur between microorganisms in pickled vegetable samples.In addition,most of the 25 isolates were resistant to bacitracin and multidrug antibiotics.Levilactobacillus brevis PNS3 carried a large number of multidrug ARG genes(patA,macB)and transposable MGE genes(recT,SadA).The results of the drug resistance phenotype were consistent with the results of the drug resistance genotype.These findings suggested that there was a risk of ARGs being carrying and spreading in pickled vegetable foods.展开更多
Previous investigations into gut microbiota dysbiosis in patients with Parkinson’s disease have relied on 16S rRNA amplicon sequencing and assembly-free metagenomic approaches.However,there is an urgent need to study...Previous investigations into gut microbiota dysbiosis in patients with Parkinson’s disease have relied on 16S rRNA amplicon sequencing and assembly-free metagenomic approaches.However,there is an urgent need to study the function of the gut microbiome at the genome level using metagenome-assembled genomes.Here,we conducted single-sample metagenomic binning analysis using shotgun metagenomic sequencing data and retrieved 2837 metagenome-assembled genomes to explore the gut microbiota profile at the genome level.Reconstructing microbial genomes from metagenomic sequences greatly enriched the diversity and number of microbial genomes,especially those of uncultivable strains.By integrating the analysis of metagenome-assembled genomes with clinical parameters,we observed higherα-diversity indexes and a very different composition of microbial communities in patients with Parkinson’s disease.We also identified microbial species and metagenome-assembled genomes that were significantly associated with clinical characteristics,including disease severity,medication,motor complications,and non-motor symptoms.The genes of Parkinson’s disease severity-associated metagenome-assembled genomes were distributed across multiple pathways,such as carbon metabolism,phosphonate metabolism,carbohydrate metabolism,amino acid metabolism,fatty acid metabolism,bile acid metabolism,metabolism of cofactors and vitamins,neuroprotective molecules,immunogenic components,toxic metabolites,translation,and bacterial secretion.Our work provides a comprehensive resource for investigating the gut microbiota-Parkinson’s disease relationship at the genome level,which may enhance our comprehension of the underlying mechanisms of this disease.展开更多
A method was developed to restore degraded images to some extent after the pixel binning pro- cess in image sensors to improve the resolution. A pixel binning model was used to approximate the original un-binned image...A method was developed to restore degraded images to some extent after the pixel binning pro- cess in image sensors to improve the resolution. A pixel binning model was used to approximate the original un-binned image. Then, the least squares error criterion was used as a constraint to reconstruct the re- stored pixel values from the binning model. The technique achieves about a one-decibel increase in the peak signal-to-noise ratio compared with the original estimated image. The technique has good detail pre- servation performance as well as low computation load. Thus, this restoration technique provides valuable improvements in practical, real time image processing.展开更多
Temperature plays a crucial role in shaping microbial ecosystems during anaerobic digestion.However,the specific microbial communities and their functions across a wide temperature range still remain elusive.This stud...Temperature plays a crucial role in shaping microbial ecosystems during anaerobic digestion.However,the specific microbial communities and their functions across a wide temperature range still remain elusive.This study employed a genome-centric metagenomic approach to explore microbial metabolic pathways and synergistic networks at temperatures of 35,44,53,55,and 65℃.A total of 84 metagenome assembled genomes(MAGs)were assembled,with over 65%of these MAGs corresponding to novel bacterial and archaeal species(including Firmicutes,Chloroflexota,Bacteroidia and Methanobacteriota),greatly enhancing our current comprehension anaerobic digestion process.Notably,functional annotation identified that 44_bin.2(Methanothrix_A sp.001602645)harbors enzymes associated with hydrogenotrophic metabolism.Additionally,this microorganism exhibited diverse metabolic capabilities at 44℃,a temperature commonly employed in industrial practice yet less explored in bench studies.Consequently,it implies a promising potential for conducting anaerobic digestion at a moderate thermophilic temperature,as opposed to the conventional mesophilic range.The microorganism exhibited a variety of metabolic capabilities at 44℃,a temperature frequently employed in industrial applications but underexplored in laboratory investigations.The findings suggest that anaerobic digestion carried out at moderate thermophilic temperatures may have a higher potential for methane production.展开更多
文摘Antimicrobial resistance(AMR)is a public health problem of global concern.The presence of antibiotic resistance genes(ARGs)in food may aggravate the spread of AMR.Understanding the distribution and transfer of drug-resistant bacteria and ARGs in pickled vegetable foods was critical for food quality and safety.Therefore,this study used metagenomic sequencing,binning technology,and antibiotic susceptibility tests to explore the distribution and transfer of drug-resistant bacteria and ARGs in pickled vegetable foods.The results showed that Bacillota,Lactobacillus,and Salmonella were the dominant bacteria in all samples.A total of 12 ARG types and 52 ARG subtypes were identified.The abundance of bacitracin ARGs in high-salt samples(<2%)was higher,and multidrug ARGs in low-salt samples(7%-10%)was higher.The most abundant ARG subtypes,baca and acrb,were associated with Salmonella.Furthermore,a total of 34 metagenome assembly genomes(MAGs)were obtained by metagenomic binning.MAG8 and MAG25,which carried the largest number of ARGs,virulence factors(VFs),and MGEs,were all derived from Vibrio.More importantly,horizontal gene transfer(HGT)could occur between microorganisms in pickled vegetable samples.In addition,most of the 25 isolates were resistant to bacitracin and multidrug antibiotics.Levilactobacillus brevis PNS3 carried a large number of multidrug ARG genes(patA,macB)and transposable MGE genes(recT,SadA).The results of the drug resistance phenotype were consistent with the results of the drug resistance genotype.These findings suggested that there was a risk of ARGs being carrying and spreading in pickled vegetable foods.
基金supported by the National Key R&D Program of China,No.2022YFE0210100(to XY)the Shanghai Rising-Star Program,No.22QA1405700(to XY)the National Natural Science Foundation of China,Nos.82301418(to YZ),82171246(to QX),and 82371251(to QX).
文摘Previous investigations into gut microbiota dysbiosis in patients with Parkinson’s disease have relied on 16S rRNA amplicon sequencing and assembly-free metagenomic approaches.However,there is an urgent need to study the function of the gut microbiome at the genome level using metagenome-assembled genomes.Here,we conducted single-sample metagenomic binning analysis using shotgun metagenomic sequencing data and retrieved 2837 metagenome-assembled genomes to explore the gut microbiota profile at the genome level.Reconstructing microbial genomes from metagenomic sequences greatly enriched the diversity and number of microbial genomes,especially those of uncultivable strains.By integrating the analysis of metagenome-assembled genomes with clinical parameters,we observed higherα-diversity indexes and a very different composition of microbial communities in patients with Parkinson’s disease.We also identified microbial species and metagenome-assembled genomes that were significantly associated with clinical characteristics,including disease severity,medication,motor complications,and non-motor symptoms.The genes of Parkinson’s disease severity-associated metagenome-assembled genomes were distributed across multiple pathways,such as carbon metabolism,phosphonate metabolism,carbohydrate metabolism,amino acid metabolism,fatty acid metabolism,bile acid metabolism,metabolism of cofactors and vitamins,neuroprotective molecules,immunogenic components,toxic metabolites,translation,and bacterial secretion.Our work provides a comprehensive resource for investigating the gut microbiota-Parkinson’s disease relationship at the genome level,which may enhance our comprehension of the underlying mechanisms of this disease.
基金Supported by the National Key Basic Research and Development(973) Program of China (No. 2006CB705700)
文摘A method was developed to restore degraded images to some extent after the pixel binning pro- cess in image sensors to improve the resolution. A pixel binning model was used to approximate the original un-binned image. Then, the least squares error criterion was used as a constraint to reconstruct the re- stored pixel values from the binning model. The technique achieves about a one-decibel increase in the peak signal-to-noise ratio compared with the original estimated image. The technique has good detail pre- servation performance as well as low computation load. Thus, this restoration technique provides valuable improvements in practical, real time image processing.
基金supported by the National Natural Science Foundation of China(No.52270138)。
文摘Temperature plays a crucial role in shaping microbial ecosystems during anaerobic digestion.However,the specific microbial communities and their functions across a wide temperature range still remain elusive.This study employed a genome-centric metagenomic approach to explore microbial metabolic pathways and synergistic networks at temperatures of 35,44,53,55,and 65℃.A total of 84 metagenome assembled genomes(MAGs)were assembled,with over 65%of these MAGs corresponding to novel bacterial and archaeal species(including Firmicutes,Chloroflexota,Bacteroidia and Methanobacteriota),greatly enhancing our current comprehension anaerobic digestion process.Notably,functional annotation identified that 44_bin.2(Methanothrix_A sp.001602645)harbors enzymes associated with hydrogenotrophic metabolism.Additionally,this microorganism exhibited diverse metabolic capabilities at 44℃,a temperature commonly employed in industrial practice yet less explored in bench studies.Consequently,it implies a promising potential for conducting anaerobic digestion at a moderate thermophilic temperature,as opposed to the conventional mesophilic range.The microorganism exhibited a variety of metabolic capabilities at 44℃,a temperature frequently employed in industrial applications but underexplored in laboratory investigations.The findings suggest that anaerobic digestion carried out at moderate thermophilic temperatures may have a higher potential for methane production.
