Background:There is growing evidence indicating that the microbial communities that dwell on the human ocular surface are crucially important for ocular surface health and disease.Little is known about interspecies in...Background:There is growing evidence indicating that the microbial communities that dwell on the human ocular surface are crucially important for ocular surface health and disease.Little is known about interspecies interactions,functional profiles,and strain heterogeneity across individuals in healthy ocular surface microbiomes.Methods:To comprehensively characterize the strain heterogeneity,cooccurrence network,taxonomic composition and functional profile of the healthy ocular surface microbiome,we performed shotgun metagenomics sequencing on ocular surface mucosal membrane swabs of 17 healthy volunteers.Results:The healthy ocular surface microbiome was classified into 12 phyla,70 genera,and 140 species.The number of species in each healthy ocular surface microbiome ranged from 6 to 47,indicating differences in microbial diversity among individuals.The species with high relative abundances and high positivity rates were Streptococcus pyogenes,Staphylococcus epidermidis,Propionibacterium acnes,Corynebacterium accolens,and Enhydrobacter aerosaccus.A correlation network analysis revealed a competitive interaction of Staphylococcus epidermidis with Streptococcus pyogenes in ocular surface microbial ecosystems.Staphylococcus epidermidis and Streptococcus pyogenes revealed phylogenetic diversity among different individuals.At the functional level,the pathways related to transcription were the most abundant.We also found that there were abundant lipid and amino acid metabolism pathways in the healthy ocular surface microbiome.Conclusion:This study explored the strain heterogeneity,cooccurrence network,taxonomic composition,and functional profile of the healthy ocular surface microbiome.These findings have important significance for the future development of probiotic-based eye therapeutic drugs.展开更多
Alfalfa is a perennial herbaceous forage legume that is remarkably and negatively affected by monocropping.However,the contribution of the changes in bacterial communities to soil sickness in alfalfa have not been elu...Alfalfa is a perennial herbaceous forage legume that is remarkably and negatively affected by monocropping.However,the contribution of the changes in bacterial communities to soil sickness in alfalfa have not been elucidated.Therefore,we investigated bacterial community structures in response to monocropped alfalfa along the chronosequence.Continuous cropping remarkably reduced bacterial alpha diversity and altered community structures,and soil pH,total P and available P were strongly associated with the changes of bacterial diversity and community structures.Intriguingly,10 years of monocropped alfalfa might be a demarcation point separating soil bacterial community structures into two obvious groups that containing soil samples collected in less and more than 10 years.The relative abundances of copiotrophic bacteria of Actinobacteria and Gammaproteobacteria significantly increased with the extension of continuous cropping years,while the oligotrophic bacteria of Armatimonadetes,Chloroflexi,Firmicutes and Gemmatimonadetes showed the opposite changing patterns.Among those altered phyla,Actinobacteria,Chloroflexi,Alphaproteobacteria and Acidobacteria were the most important bacteria which contributed 50.86%of the community variations. Additionally, the relative abundances of nitrogen fixation bacteria ofBradyrhizobium and Mesorhizobium obviously increased with continuous cropping years, while theabundances of Arthrobacter, Bacillus, Burkholderiaceae and Microbacterium with potential functionsof solubilizing phosphorus and potassium remarkably decreased after long-term continuouscropping. Furthermore, bacterial cooccurrence patterns were significantly influenced by continuouscropping years, with long-term monocropped alfalfa simplifying the complexity of the cooccurrencenetworks. These findings enhanced our understandings and provided references for forecasting howsoil bacterial communities responds to monocropped alfalfa.展开更多
基金supported by the National Science and Technology Major Project(Grant No.2018ZX10201001).
文摘Background:There is growing evidence indicating that the microbial communities that dwell on the human ocular surface are crucially important for ocular surface health and disease.Little is known about interspecies interactions,functional profiles,and strain heterogeneity across individuals in healthy ocular surface microbiomes.Methods:To comprehensively characterize the strain heterogeneity,cooccurrence network,taxonomic composition and functional profile of the healthy ocular surface microbiome,we performed shotgun metagenomics sequencing on ocular surface mucosal membrane swabs of 17 healthy volunteers.Results:The healthy ocular surface microbiome was classified into 12 phyla,70 genera,and 140 species.The number of species in each healthy ocular surface microbiome ranged from 6 to 47,indicating differences in microbial diversity among individuals.The species with high relative abundances and high positivity rates were Streptococcus pyogenes,Staphylococcus epidermidis,Propionibacterium acnes,Corynebacterium accolens,and Enhydrobacter aerosaccus.A correlation network analysis revealed a competitive interaction of Staphylococcus epidermidis with Streptococcus pyogenes in ocular surface microbial ecosystems.Staphylococcus epidermidis and Streptococcus pyogenes revealed phylogenetic diversity among different individuals.At the functional level,the pathways related to transcription were the most abundant.We also found that there were abundant lipid and amino acid metabolism pathways in the healthy ocular surface microbiome.Conclusion:This study explored the strain heterogeneity,cooccurrence network,taxonomic composition,and functional profile of the healthy ocular surface microbiome.These findings have important significance for the future development of probiotic-based eye therapeutic drugs.
基金This work was supported by grants from National Key Research and Development Program of China(2017YFD0200604)Key Research Program of Frontier Sciences,CAS(ZDBS-LYDQC017)+5 种基金the National Natural Science Foundation of China(41671251)Earmarked Fund for China Agriculture Research System(CR34)Heilongjiang Provincial Natural Science Foundation of China(D2018009)the Grass-field Rotation Scientist Studio of Heilongjiang Province(202004)Outstanding Youth Fund of Heilongjiang Academy of Agricultural Sciences(2020JCQN003)Youth Innovation Promotion Association,CAS(2017276).
文摘Alfalfa is a perennial herbaceous forage legume that is remarkably and negatively affected by monocropping.However,the contribution of the changes in bacterial communities to soil sickness in alfalfa have not been elucidated.Therefore,we investigated bacterial community structures in response to monocropped alfalfa along the chronosequence.Continuous cropping remarkably reduced bacterial alpha diversity and altered community structures,and soil pH,total P and available P were strongly associated with the changes of bacterial diversity and community structures.Intriguingly,10 years of monocropped alfalfa might be a demarcation point separating soil bacterial community structures into two obvious groups that containing soil samples collected in less and more than 10 years.The relative abundances of copiotrophic bacteria of Actinobacteria and Gammaproteobacteria significantly increased with the extension of continuous cropping years,while the oligotrophic bacteria of Armatimonadetes,Chloroflexi,Firmicutes and Gemmatimonadetes showed the opposite changing patterns.Among those altered phyla,Actinobacteria,Chloroflexi,Alphaproteobacteria and Acidobacteria were the most important bacteria which contributed 50.86%of the community variations. Additionally, the relative abundances of nitrogen fixation bacteria ofBradyrhizobium and Mesorhizobium obviously increased with continuous cropping years, while theabundances of Arthrobacter, Bacillus, Burkholderiaceae and Microbacterium with potential functionsof solubilizing phosphorus and potassium remarkably decreased after long-term continuouscropping. Furthermore, bacterial cooccurrence patterns were significantly influenced by continuouscropping years, with long-term monocropped alfalfa simplifying the complexity of the cooccurrencenetworks. These findings enhanced our understandings and provided references for forecasting howsoil bacterial communities responds to monocropped alfalfa.
