Method development has always been and will continue to be a core driving force of microbiome science, In this perspective, we argue that in the next decade, method development in microbiome analysis will be driven by...Method development has always been and will continue to be a core driving force of microbiome science, In this perspective, we argue that in the next decade, method development in microbiome analysis will be driven by three key changes in both ways of thinking and technological platforms： ① a shift from dissecting microbiota structure by sequencing to tracking microbiota state, function, and intercellular interaction via imaging; ② a shift from interrogating a consortium or population of cells to probing individual cells; and ③a shift from microbiome data analysis to microbiome data science. Some of the recent methoddevelopment efforts by Chinese microbiome scientists and their international collaborators that underlie these technological trends are highlighted here. It is our belief that the China Microbiome Initiative has the opportunity to deliver outstanding ＂Made-in-China＂ tools to the international research community, by building an ambitious, competitive, and collaborative program at the forefront of method development for microbiome science.展开更多
Nitrogen pollution is an increasingly severe worldwide problem because of drainage of nitrogen-containing wastewater and intensive application of nitrogen-containing fertilizers. Denitrification, a key process in nitr...Nitrogen pollution is an increasingly severe worldwide problem because of drainage of nitrogen-containing wastewater and intensive application of nitrogen-containing fertilizers. Denitrification, a key process in nitrogen cycles, is commonly employed for nitrogen removal in engineered wastewater treatment systems. Biological denitrification is performed by denitrifying microbes(bacteria) that use nitrate as terminal electron acceptor. Better understanding the functions of diverse microbial populations in denitrification-based wastewater treatment systems, and the interactions of these populations with operating environments, is essential for improving both treatment performance and system stability. Recent advances in "meta-omics"(e.g., genomics, transcriptomics, proteomics, metabolomics), other molecular biology tools, and microbiome analysis have greatly enhanced such understanding. This minireview summarizes recent findings regarding microbial community structure and composition, key functional microbes and their physiology, functional genes involved in nitrogen cycle, and responses of microbes and their genes to changes of environmental factors or operating parameters, in denitrification processes in wastewater treatment systems. Of particular interest are heterotrophic denitrification systems(which require alternative organic carbon sources) and the autotrophic denitrification systems(which do not require an external carbon source). Integrated microbiome and-omics approaches have great future potential for determination of optimal environmental and biotechnological parameters,novel process development, and improvement of nitrogen removal efficiency and system stability.展开更多
The kitchen-oil wastewater is characterized by a high concentration of organicmatter,complex composition and refractory pollutants,which make wastewater treatment more difficult.Based on the study of using micro-elect...The kitchen-oil wastewater is characterized by a high concentration of organicmatter,complex composition and refractory pollutants,which make wastewater treatment more difficult.Based on the study of using micro-electric field characteristic catalyst HCLL-S8-M to enhance the electron transfer between microorganisms in kitchen-oil wastewater which further improved the COD removal rate,we focus on themicrobial community,intracellular metabolism and extracellular respiration,and make an in-depth analysis of the molecular biological mechanisms to microbial treatment in wastewater.It is found that electroactive microorganisms are enriched on the material surface,and the expression levels of cytochrome c and riboflavin genes related to electron transfer are up-regulated,confirming that the surface micro-electric field structure could enhance the electron transfer between microbial species and improve the efficiency ofwastewater degradation.This study provides a new idea for the treatment of refractory organic wastewater.展开更多
The microbiome in the gastrointestinal tract(GIT)of fish influences host health in both beneficial and detrimental ways and understanding the gut microbiota requires 16S amplicon sequencing.Although,Cirrhinus reba(Ham...The microbiome in the gastrointestinal tract(GIT)of fish influences host health in both beneficial and detrimental ways and understanding the gut microbiota requires 16S amplicon sequencing.Although,Cirrhinus reba(Hamilton,1822)has achieved widespread recognition for its nutritional and commercial value,the carp are currently confronting production lim-its.Probiotic-based carp captive breeding may be an effective method for enhancing the production and health condition of the carp and it requires conventional culture-based analysis.Hence,a comprehensive study was performed on the intestinal microbiota of C.reba by both 16S amplicon sequencing and culture-based approaches.At the phylum level,Proteobacteria,Firmicutes,Actinobacteria,Bacteroidetes,and Fusobacteria were dominating the GIT of the fish.Importantly,Gram-negative pathogenic genera like Pseudomonas,Serratia,Aeromonas,and Unclassified Clostridiales are found to be most abundant.Only Bacillus and Lactobacillus are found as the Gram positive bacterial genera among the top ten dominating bacteria in the GIT of the fish.The total load of culturable bacteria in the gut of the carp was 1.12±0.26×10^(8)cfu/g comprising twenty-four different types of colonies.The Gram negative bacterial load in the GIT of the carp is 6.9×10^(7)cfu/g.Only 37.5%(4.2×10^(7)cfu/g)of the isolates were Gram-positive and rod-shaped.Among them,one intestinal isolate(PKS9A)had shown significant antagonism against four common fish pathogens.The isolate was positive for the production of extracel-lular digestive enzymes like Protease,Amylase,Cellulase,Xylanase,Lipase,Phytase.The isolate PKS9A exhibited sufficient probiotic properties like bile salt hydrolase activity,cell surface hydrophobicity,antibiotic sensitivity,and is non-hemolytic in nature.16S rDNA sequencing and phylogeny analysis identified the isolate as Bacillus paramycoides PKS9A(Accession no.-OR003914).Hence,the isolate may be utilized as a potential autochthonous probiotic for the cultivation of C.reba to enhance the nutritional and health status of the carp and to protect it from further deterioration.展开更多
基金We are grateful to the support from the National Natural Science Foundation of China （NSFC） （31425002, 91231205, 81430011, 61303161, 31470220, and 31327001）, and the Frontier Science Research Program, the Soil-Microbe System Function and Regulation Program, and the Science and Technology Service Network Initiative （STS） from the Chinese Academy of Sciences （CAS）.
文摘Method development has always been and will continue to be a core driving force of microbiome science, In this perspective, we argue that in the next decade, method development in microbiome analysis will be driven by three key changes in both ways of thinking and technological platforms： ① a shift from dissecting microbiota structure by sequencing to tracking microbiota state, function, and intercellular interaction via imaging; ② a shift from interrogating a consortium or population of cells to probing individual cells; and ③a shift from microbiome data analysis to microbiome data science. Some of the recent methoddevelopment efforts by Chinese microbiome scientists and their international collaborators that underlie these technological trends are highlighted here. It is our belief that the China Microbiome Initiative has the opportunity to deliver outstanding ＂Made-in-China＂ tools to the international research community, by building an ambitious, competitive, and collaborative program at the forefront of method development for microbiome science.
基金supported by the projects of National Key Research and Development Program of China (2016YFD0501409)
文摘Nitrogen pollution is an increasingly severe worldwide problem because of drainage of nitrogen-containing wastewater and intensive application of nitrogen-containing fertilizers. Denitrification, a key process in nitrogen cycles, is commonly employed for nitrogen removal in engineered wastewater treatment systems. Biological denitrification is performed by denitrifying microbes(bacteria) that use nitrate as terminal electron acceptor. Better understanding the functions of diverse microbial populations in denitrification-based wastewater treatment systems, and the interactions of these populations with operating environments, is essential for improving both treatment performance and system stability. Recent advances in "meta-omics"(e.g., genomics, transcriptomics, proteomics, metabolomics), other molecular biology tools, and microbiome analysis have greatly enhanced such understanding. This minireview summarizes recent findings regarding microbial community structure and composition, key functional microbes and their physiology, functional genes involved in nitrogen cycle, and responses of microbes and their genes to changes of environmental factors or operating parameters, in denitrification processes in wastewater treatment systems. Of particular interest are heterotrophic denitrification systems(which require alternative organic carbon sources) and the autotrophic denitrification systems(which do not require an external carbon source). Integrated microbiome and-omics approaches have great future potential for determination of optimal environmental and biotechnological parameters,novel process development, and improvement of nitrogen removal efficiency and system stability.
基金supported by the National Natural Science Foundation of China(Nos.52150056 and 51838005)the Basic and Applied Basic Research Foundation of Guangdong Province(No.2023A1515111061).
文摘The kitchen-oil wastewater is characterized by a high concentration of organicmatter,complex composition and refractory pollutants,which make wastewater treatment more difficult.Based on the study of using micro-electric field characteristic catalyst HCLL-S8-M to enhance the electron transfer between microorganisms in kitchen-oil wastewater which further improved the COD removal rate,we focus on themicrobial community,intracellular metabolism and extracellular respiration,and make an in-depth analysis of the molecular biological mechanisms to microbial treatment in wastewater.It is found that electroactive microorganisms are enriched on the material surface,and the expression levels of cytochrome c and riboflavin genes related to electron transfer are up-regulated,confirming that the surface micro-electric field structure could enhance the electron transfer between microbial species and improve the efficiency ofwastewater degradation.This study provides a new idea for the treatment of refractory organic wastewater.
文摘The microbiome in the gastrointestinal tract(GIT)of fish influences host health in both beneficial and detrimental ways and understanding the gut microbiota requires 16S amplicon sequencing.Although,Cirrhinus reba(Hamilton,1822)has achieved widespread recognition for its nutritional and commercial value,the carp are currently confronting production lim-its.Probiotic-based carp captive breeding may be an effective method for enhancing the production and health condition of the carp and it requires conventional culture-based analysis.Hence,a comprehensive study was performed on the intestinal microbiota of C.reba by both 16S amplicon sequencing and culture-based approaches.At the phylum level,Proteobacteria,Firmicutes,Actinobacteria,Bacteroidetes,and Fusobacteria were dominating the GIT of the fish.Importantly,Gram-negative pathogenic genera like Pseudomonas,Serratia,Aeromonas,and Unclassified Clostridiales are found to be most abundant.Only Bacillus and Lactobacillus are found as the Gram positive bacterial genera among the top ten dominating bacteria in the GIT of the fish.The total load of culturable bacteria in the gut of the carp was 1.12±0.26×10^(8)cfu/g comprising twenty-four different types of colonies.The Gram negative bacterial load in the GIT of the carp is 6.9×10^(7)cfu/g.Only 37.5%(4.2×10^(7)cfu/g)of the isolates were Gram-positive and rod-shaped.Among them,one intestinal isolate(PKS9A)had shown significant antagonism against four common fish pathogens.The isolate was positive for the production of extracel-lular digestive enzymes like Protease,Amylase,Cellulase,Xylanase,Lipase,Phytase.The isolate PKS9A exhibited sufficient probiotic properties like bile salt hydrolase activity,cell surface hydrophobicity,antibiotic sensitivity,and is non-hemolytic in nature.16S rDNA sequencing and phylogeny analysis identified the isolate as Bacillus paramycoides PKS9A(Accession no.-OR003914).Hence,the isolate may be utilized as a potential autochthonous probiotic for the cultivation of C.reba to enhance the nutritional and health status of the carp and to protect it from further deterioration.
