Nitrogen removal from domestic sewage is usually limited by insufficient carbon source and electron donor.An economical solid carbon source was developed by composition of polyvinyl alcohol,sodium alginate,and corncob...Nitrogen removal from domestic sewage is usually limited by insufficient carbon source and electron donor.An economical solid carbon source was developed by composition of polyvinyl alcohol,sodium alginate,and corncob,which was utilized as external carbon source in the anaerobic anoxic oxic(AAO)-biofilter for the treatment of low carbon-to-nitrogen ratio domestic sewage,and the nitrogen removal was remarkably improved from 63.2%to 96.5%.Furthermore,the effluent chemical oxygen demand maintained at 35 mg/L or even lower,and the total nitrogenwas reduced to less than 2mg/L.Metagenomic analysis demonstrated that the microbial communities responsible for potential denitrification and organic matter degradation in both AAO and the biofilter reactors were mainly composed of Proteobacteria and Bacteroides,respectively.The solid carbon source addition resulted in relatively high abundance of functional enzymes responsible for NO_(3)^(−)-N to NO_(2)^(−)-N con-version in both AAO and the biofilter reactors,thus enabled stable reaction.The carbon source addition during glycolysis primarily led to the increase of genes associated with the metabolic conversion of fructose 1.6P2 to glycerol-3P The reactor maintained high abun-dance of genes related to the tricarboxylic acid cycle,and then guaranteed efficient carbon metabolism.The results indicate that the composite carbon source is feasible for denitri-fication enhancement of AAO-biofilter,which contribute to the theoretical foundation for practical nitrogen removal application.展开更多
Limitations regarding phosphorus(P)are widespread in ecosystems.Understanding the impacts of the wetland types on microbially mediated soil P availability and cycling is essential for the effective management of wetla...Limitations regarding phosphorus(P)are widespread in ecosystems.Understanding the impacts of the wetland types on microbially mediated soil P availability and cycling is essential for the effective management of wetlands.In this study,the Beidagang wetland,Baodi paddy field,and Dahuangpu wetland in Tianjin,China were chosen as representatives of the coastal wetland(B),constructed wetland(R),and swampy wetland(W),respectively.Sequential P extraction and metagenomics approaches were adopted to explore the soil P fraction and microbially regulated P cycle.Proteobacteria were the predominant microbes-related soil P cycle.IMPA,gph,rsbU_P,ugpQ,and glpK genes were dominant in organic P(Po)mineralization,while gcd,ppa,and ppx genes were dominant in inorganic P(Pi)solubilization.The salinity,NO_(3)^(-)-N concentration,the ratio of total carbon to total nitrogen(TC/TN),total carbon(TC),and the ratio of soil organic carbon to total P(SOC/TP)were the co-drivers of microbially mediated P cycle processes.Microbial network complexity-relate P cycle was the lowest in the coastal wetland.Salinity and NO_(3)^(-)-N exhibited a significant negative relation to the abundance of most genes-relate Pi solubilization and a remarkable positive correlation with the abundance of many genes-relate Po mineralization.These findings demonstrated that Po mineralization tended to occur in habitats with high salinity and nutrient imbalances,whereas the dissolution of Pi was prone to occur in low-salinity environments with relatively balanced soil nutrients.This study improves understanding of how salinity and soil nutrients jointly shape microbial-regulated soil P cycle in different types of wetlands.展开更多
There are limited biosecurity measures directed at preventing airborne transmission of viruses in swine.The effectiveness of dust mitigation strategies such as oil sprinkling,to decrease risk of airborne virus transmi...There are limited biosecurity measures directed at preventing airborne transmission of viruses in swine.The effectiveness of dust mitigation strategies such as oil sprinkling,to decrease risk of airborne virus transmission are unknown.Metagenomics and qPCR for common fecal viruses were used to hunt for a ubiquitous virus to serve as a proxy when evaluating the efficiency of mitigation strategies against airborne viral infectious agents.Air particles were collected from swine buildings using high-volume air samplers.Extracted DNA and RNA were used to perform specific RT-qPCR and qPCR and analyzed by highthroughput sequencing.Porcine astroviruses group 2 were common(from 102 to 105 genomic copies per cubic meter of air or gc/m^(3),93%positivity)while no norovirus genogroup II was recovered from air samples.Porcine torque teno sus virus were detected by qPCR in low concentrations(from 101 to 102 gc/m^(3),47%positivity).Among the identified viral families by metagenomics analysis,Herelleviridae,Microviridae,Myoviridae,Podoviridae,and Siphoviridae were dominant.The phage vB_AviM_AVP of Aerococcus was present in all air samples and a newly designed qPCR revealed between 101 and 105 gc/m^(3) among the samples taken for the present study(97%positivity)and banked samples from5-and 15-year old studies(89%positivity).According to the present study,both the porcine astrovirus group 2 and the phage vB_AviM_AVP of Aerococcus could be proxy for airborne viruses of swine buildings.展开更多
Erythromycin fermentation residue(EFR)represents a typical hazardous waste produced by the microbial pharmaceutical industry.Although electrolysis is promising for EFR disposal,its microbial threats remain unclear.Her...Erythromycin fermentation residue(EFR)represents a typical hazardous waste produced by the microbial pharmaceutical industry.Although electrolysis is promising for EFR disposal,its microbial threats remain unclear.Herein,metagenomics was coupled with the random forest technique to decipher the antibiotic resistance patterns of electrochemically treated EFR.Results showed that 95.75%of erythromycin could be removed in 2 hr.Electrolysis temporarily influenced EFRmicrobiota,where the relative abundances of Proteobacteria and Actinobacteria increased,while those of Fusobacteria,Firmicutes,and Bacteroidetes decreased.A total of 505 antibiotic resistance gene(ARG)subtypes encoding resistance to 21 antibiotic types and 150 mobile genetic elements(MGEs),mainly including plasmid(72)and transposase(52)were assembled in EFR.Significant linear regression models were identified among microbial richness,ARG subtypes,and MGE numbers(r^(2)=0.50-0.81,p<0.001).Physicochemical factors of EFR(Total nitrogen,total organic carbon,protein,and humus)regulated ARG and MGE assembly(%IncMSE value=5.14-14.85).The core ARG,MGE,and microbe sets(93.08%-99.85%)successfully explained 89.71%-92.92%of total ARG and MGE abundances.Specifically,gene aph(3 )-I,transposase tnpA,and Mycolicibacterium were the primary drivers of the resistance dissemination system.This study also proposes efficient resistance mitigation measures,and provides recommendations for future management of antibiotic fermentation residue.展开更多
With the rapid development of molecular biology technology,especially the application of metagenomics,many challenges in groundwater microbial research have been overcome.Metagenomics has enabled the exploration of th...With the rapid development of molecular biology technology,especially the application of metagenomics,many challenges in groundwater microbial research have been overcome.Metagenomics has enabled the exploration of the diversity of unculturable microorganisms in groundwater.This paper reviews macro genomics 16S rRNA and metagenomics sequencing data,highlighting recent applications of metagenomics in investigating groundwater microbial communities.It also examines the relationship between microbial diversity and environmental factors,the identification of functional microbial groups,the role of microorganisms in groundwater pollution remediation,and their contribution to the hydrogeochemi-cal cycle.Finally,it provide insights into future research directions in groundwater microbiology.展开更多
There are more than 1000 microbial species living in the complex human intestine.The gut microbial community plays an important role in protecting the host against pathogenic microbes,modulating immunity,regulating me...There are more than 1000 microbial species living in the complex human intestine.The gut microbial community plays an important role in protecting the host against pathogenic microbes,modulating immunity,regulating metabolic processes,and is even regarded as an endocrine organ.However,traditional culture methods are very limited for identifying microbes.With the application of molecular biologic technology in the field of the intestinal microbiome,especially metagenomic sequencing of the next-generation sequencing technology,progress has been made in the study of the human intestinal microbiome.Metagenomics can be used to study intestinal microbiome diversity and dysbiosis,as well as its relationship to health and disease.Moreover,functional metagenomics can identify novel functional genes,microbial pathways,antibiotic resistance genes,functional dysbiosis of the intestinal microbiome,and determine interactions and co-evolution between microbiota and host,though there are still some limitations.Metatranscriptomics,metaproteomics and metabolomics represent enormous complements to the understanding of the human gut microbiome.This review aims to demonstrate that metagenomics can be a powerful tool in studying the human gut microbiome with encouraging prospects.The limitations of metagenomics to be overcome are also discussed.Metatranscriptomics,metaproteomics and metabolomics in relation to the study of the human gut microbiome are also briefly discussed.展开更多
A growing body of evidence suggests that the gut microbiota contributes to the development of neurodegenerative diseases via the microbiota-gut-brain axis.As a contributing factor,microbiota dysbiosis always occurs in...A growing body of evidence suggests that the gut microbiota contributes to the development of neurodegenerative diseases via the microbiota-gut-brain axis.As a contributing factor,microbiota dysbiosis always occurs in pathological changes of neurodegenerative diseases,such as Alzheimer’s disease,Parkinson’s disease,and amyotrophic lateral sclerosis.High-throughput sequencing technology has helped to reveal that the bidirectional communication between the central nervous system and the enteric nervous system is facilitated by the microbiota’s diverse microorganisms,and for both neuroimmune and neuroendocrine systems.Here,we summarize the bioinformatics analysis and wet-biology validation for the gut metagenomics in neurodegenerative diseases,with an emphasis on multi-omics studies and the gut virome.The pathogen-associated signaling biomarkers for identifying brain disorders and potential therapeutic targets are also elucidated.Finally,we discuss the role of diet,prebiotics,probiotics,postbiotics and exercise interventions in remodeling the microbiome and reducing the symptoms of neurodegenerative diseases.展开更多
East Lake(Lake Donghu),located in Wuhan,China,is a typical city freshwater lake that has been experiencing eutrophic conditions and algal blooming during recent years.Marine and fresh water are considered to contain a...East Lake(Lake Donghu),located in Wuhan,China,is a typical city freshwater lake that has been experiencing eutrophic conditions and algal blooming during recent years.Marine and fresh water are considered to contain a large number of viruses.However,little is known about their genetic diversity because of the limited techniques for culturing viruses.In this study,we conducted a viral metagenomic analysis using a high-throughput sequencing technique with samples collected from East Lake in Spring,Summer,Autumn,and Winter.The libraries from four samples each generated 234,669,71,837,12,820,and 34,236 contigs(>90 bp each),respectively.The genetic structure of the viral community revealed a high genetic diversity covering 23 viral families,with the majority of contigs homologous to DNA viruses,including members of Myoviridae,Podoviridae,Siphoviridae,Phycodnaviridae,and Microviridae,which infect bacteria or algae,and members of Circoviridae,which infect invertebrates and vertebrates.The highest viral genetic diversity occurred in samples collected in August,then December and June,and the least diversity in March.Most contigs have low-sequence identities with known viruses.PCR detection targeting the conserved sequences of genes(g20,psbA,psbD,and DNApol)of cyanophages further confirmed that there are novel cyanophages in the East Lake.Our viral metagenomic data provide the first preliminary understanding of the virome in one freshwater lake in China and would be helpful for novel virus discovery and the control of algal blooming in the future.展开更多
Infectious diseases are a great threat to human health.Rapid and accurate detection of pathogens is important in the diagnosis and treatment of infectious diseases.Metagenomics next-generation sequencing(mNGS)is an un...Infectious diseases are a great threat to human health.Rapid and accurate detection of pathogens is important in the diagnosis and treatment of infectious diseases.Metagenomics next-generation sequencing(mNGS)is an unbiased and comprehensive approach for detecting all RNA and DNA in a sample.With the development of sequencing and bioinformatics technologies,mNGS is moving from research to clinical application,which opens a new avenue for pathogen detection.Numerous studies have revealed good potential for the clinical application of mNGS in infectious diseases,especially in difficult-to-detect,rare,and novel pathogens.However,there are several hurdles in the clinical application of mNGS,such as:(1)lack of universal workflow validation and quality assurance;(2)insensitivity to high-host background and low-biomass samples;and(3)lack of standardized instructions for mass data analysis and report interpretation.Therefore,a complete understanding of this new technology will help promote the clinical application of mNGS to infectious diseases.This review briefly introduces the history of next-generation sequencing,mainstream sequencing platforms,and mNGS workflow,and discusses the clinical applications of mNGS to infectious diseases and its advantages and disadvantages.展开更多
Mainstream partial nitritation-anammox(PNA)process easily suffers from performance instability and even reactor collapse in application.Thus,it is of great significance to unveil the characteristic of performance reco...Mainstream partial nitritation-anammox(PNA)process easily suffers from performance instability and even reactor collapse in application.Thus,it is of great significance to unveil the characteristic of performance recovery,understand the intrinsic mechanism and then propose operational strategy.In this study,we combined long-term reactor operation,batch tests,and metagenomics to reveal the succession of microbial community and functional metabolism variation from system collapse to recovery.Proper aeration control(0.10-0.25mg O_(2)/L)was critical for performance recovery.It was also found that Candidatus Brocadia became the dominant flora and its abundance increased from 3.5%to 11.0%.Significant enhancements in carbon metabolism and phospholipid biosynthesis were observed during system recovery,and the genes abundance related to signal transduction was dramatically increased.The up-regulation of sdh and suc genes showed the processes of succinate dehydrogenation and succinyl-CoA synthesis might stimulate the production of amino acids and the synthesis of proteins,thereby possibly improving the activity and abundance of AnAOB,which was conducive to the performance recovery.Moreover,the increase in abundance of hzs and hdh genes suggested the enhancement of the anammox process.Changes in the abundance of key genes involved in nitrogen metabolism indicated that nitrogen removal pathway was more diverse after system recovery.The achievement of performance recovery was driven by anammox,nitrification and denitrification coupled with dissimilatory nitrate reduction to ammonium.These results provide deeper insights into the recovery mechanism of PNA system and also provide a potential regulation strategy for the stable operation of the mainstream PNA process.展开更多
The symptoms of disseminated strongyloidiasis are not typical,and it is difficult for clinicians to identify strongyloidiasis in some non-endemic areas.We report a 70-year-old woman who was diagnosed with Guillain-Bar...The symptoms of disseminated strongyloidiasis are not typical,and it is difficult for clinicians to identify strongyloidiasis in some non-endemic areas.We report a 70-year-old woman who was diagnosed with Guillain-Barrésyndrome due to autonomic disturbance,symmetrical bulbar palsy,and lower-motor-nerve damage in the extremities;her symptoms continued to worsen after hormone and immunoglobulin therapy.Later,parasitic larvae were found in the patient’s gastric fluid,and metagenomic next generation sequencing(mNGS)detection of bronchoalveolar-lavage fluid also found a large number of Strongyloides roundworms.The patient was diagnosed with disseminated strongyloidiasis.The patient was given albendazole for anthelmintic treatment,but died two days after being transferred to the intensive care unit due to the excessive strongyloidiasis burden.In recent years,mNGS has been increasingly used in clinical practice,and is becoming the main means of detecting strongyloides stercoralis in non-endemic areas.Especially during the corona virus disease 2019 pandemic,mNGS technology has irreplaceable value in identifying the source of infection.展开更多
Diarrhea is the third leading cause of death in developing countries in children under the age of five.About half a million children die of diarrhea every year,most of which in developing countries.Viruses are the mai...Diarrhea is the third leading cause of death in developing countries in children under the age of five.About half a million children die of diarrhea every year,most of which in developing countries.Viruses are the main pathogen of diarrhea.In China,the fecal virome of children with diarrhea has been rarely studied.Using an unbiased viral metagenomics approach,we analyzed the fecal virome in children with diarrhea.Many DNA or RNA viruses associated with diarrhea identified in those fecal samples were mainly from six families of Adenoviridae,Astroviridae,Caliciviridae,Parvoviridae,Picornaviridae,and Reoviridae.Among them,the family of Caliciviridae accounts for the largest proportion of 78.42%,following with Adenoviridae(8.94%)and Picornaviridae(8.36%).In addition to those diarrhea-related viruses that have already been confirmed to cause human diarrhea,the viruses not associated with diarrhea were also identified including anellovirus and picobirnavirus.This study increased our understanding of diarrheic children fecal virome and provided valuable information for the prevention and treatment of viral diarrhea in this area.展开更多
Recent studies have declared that members of the ss DNA virus family Microviridae play an important role in multiple environments, as they have been found taking a dominant position in the human gut. The aim of this s...Recent studies have declared that members of the ss DNA virus family Microviridae play an important role in multiple environments, as they have been found taking a dominant position in the human gut. The aim of this study was to analyze the overall composition of the gut virome in coronary heart disease(CHD) patients, and try to discover the potential link between the human gut virome and CHD. Viral metagenomics methods were performed to detect the viral sequences in fecal samples collected from CHD inpatients and healthy persons as controls. We present the analysis of the virome composition in these CHD patients and controls. Our data shows that the virome composition may be linked to daily living habits and the medical therapy of CHD.Virgaviridae and Microviridae were the two dominant types of viruses found in the enteric virome of CHD patients. Fourteen divergent viruses belonging to the family Microviridae were found, twelve of which were grouped into the subfamily Gokushovirinae, while the remaining two strains might represent two new subfamilies within Microviridae, according to the phylogenetic analysis. In addition, the genomic organization of these viruses has been characterized.展开更多
The human microbiota is made up of trillions of bacteria that live in the human being,whereas the microbiome is made up of the microbiota's genes and gene products.Bacteria have long been thought of as pathogens t...The human microbiota is made up of trillions of bacteria that live in the human being,whereas the microbiome is made up of the microbiota's genes and gene products.Bacteria have long been thought of as pathogens that eventually lead to human illness.Bacteria are increasingly recognized as generally beneficial commensal organisms and hence crucial to proper and healthy human development,thanks to breakthroughs in both cultivation-based approaches and the advent of metagenomics.This relatively new field of medical study has given more information on illnesses such as inflammatory bowel disease,obesity,metabolic and atopic disorders.However,there is a lot we don't know about the complexities of microbe-microbe and microbe-host interactions.Future work targeted at resolving crucial concerns about the early formation of the microbiome,in addition,what determines its dysbiosis,will most likely lead to long-term mitigation of health.In this article,review the research on prenatal and newborn microbiome modulations,the role of maternal and environmental variables on forming the newborn microbiome,and future issues and directions in the exciting new field of metagenomic medicine.展开更多
Background:Camels,known as the enduring“ships of the desert,”host a complex gut microbiota that plays a crucial role in their survival in extreme environments.However,amidst the fascinating discoveries about the cam...Background:Camels,known as the enduring“ships of the desert,”host a complex gut microbiota that plays a crucial role in their survival in extreme environments.However,amidst the fascinating discoveries about the camel gut microbiota,concerns about antibiotic resistance have emerged as a significant global challenge affecting both human and animal populations.Indeed,the continued use of antibiotics in veterinary medicine has led to the widespread emergence of antibiotic-resistant bacteria,which has worsened through gene transfer.Methods:This study offers a deeper examination of this pressing issue by harnessing the potent tools of metagenomics to explore the intricate interplay between the camel(Camelus ferus)gut microbiota and antibiotic resistance.Results:Samples from wild camels yielded varying amounts of raw and clean data,generating scaftigs and open reading frames.The camel fecal microbiome was dominated by bacteria(mainly Bacillota and Bacteriodota),followed by viruses,archaea,and eukaryota.The most abundant genera were the Bacteroides,Ruminococcus,and Clostridium.Functional annotation revealed enriched pathways in metabolism,genetic information processing,and cellular processes,with key pathways involving carbohydrate transport and metabolism,replication,and amino acid transport.CAZy database analysis showed high abundances of glycoside hydrolases and glycosyl transferases.Antibiotic resistance gene(ARG)analysis identified Bacillota and Bacteroidota as the main reservoirs,with vancomycin resistance genes being the most prevalent.This study identified three major resistance mechanisms:antibiotic target alteration,antibiotic target protection,and antibiotic efflux.Conclusion:These findings contribute to a broader understanding of antibiotic resistance within animal microbiomes and provide a foundation for further investigations of strategies to manage and mitigate antibiotic resistance.展开更多
Probiotics exert beneficial effects on the host.This study aimed to investigate whether maternally ingested Lacticaseibacillus rhamnosus Probio-M9 during pregnancy could access and colonize the infant gut.This study r...Probiotics exert beneficial effects on the host.This study aimed to investigate whether maternally ingested Lacticaseibacillus rhamnosus Probio-M9 during pregnancy could access and colonize the infant gut.This study recruited one pregnant woman,who ingested Probio-M9 daily from 35 weeks of gestation to delivery.Feces of the mother-infant pair were regularly collected from one month before delivery to 6 months of infant's age for metagenomic sequencing.Probio-M9 genomes were mappable to all infant fecal samples,suggesting the ingested probiotics could be vertically transmitted from mother to infant.Infant-or mother-specific differential metabolic pathways were found between the maternal and infant's gut microbiome,implicating apparent differences in the intestinal metagenomic potential/function between the mother and the infant.In conclusion,maternal ingestion of Probio-M9 during the final weeks of gestation could deliver to the infant gut.The findings provided novel insights into shaping infant's gut microbiota.展开更多
With the improvement of transportation and the rise of tourism on the Qinghai-Xizang Plateau,the scope of human activities has continuously expanded,increasing opportunities for contact with wildlife,also exacerbating...With the improvement of transportation and the rise of tourism on the Qinghai-Xizang Plateau,the scope of human activities has continuously expanded,increasing opportunities for contact with wildlife,also exacerbating the outbreak rate of zoonotic emerging infectious diseases.Currently,research on the gut microbiota of wildlife,especially Marmota himalayana(M.himalayana),which are reservoir hosts for plague,is scarce.In this study,we investigated the composition,function,and regional variations of the gut microbiota in M.himalayana based on the metagenomic sequencing of 45 fecal samples from the Sanjiangyuan National Nature Reserve in Qinghai Province.The results indicated that at the phylum level,the dominant bacterial phyla in the gut microbiota of the M.himalayana were Firmicutes,Bacteroidota,and Proteobacteria,collectively accounting for 74.16% of the community.At the genus level,the top three most abundant genera were Alistipes(11.86%±1.56%),Bacteroides(6.68%±0.95%),and Clostridium(4.92%±1.04%).Kyoto encyclopedia of genes and genomes(KEGG)database annotation results showed that the most enriched functional categories of the marmot gut microbiota were metabolism,genetic information processing(GIP),and environmental information processing(EIP).These active functions played a crucial role in food digestion,nutrient absorption,metabolic balance maintenance,and pathogen defense,aiding the marmot in better adapting to the extreme environment of the Qinghai-Xizang Plateau.The study provided critical insights into host-microbe interactions,highlighting the role of microbiota in the survival and conservation of endangered species in unique habitats.展开更多
The rapid advancement of nanopore metagenomic sequencing has revolutionized microbiome research,enabling significant breakthroughs in the study of microbial communities,ecological dynamics,and genome-level functions[1...The rapid advancement of nanopore metagenomic sequencing has revolutionized microbiome research,enabling significant breakthroughs in the study of microbial communities,ecological dynamics,and genome-level functions[1–5].This innovative sequencing technology stands out due to its ability to generate long sequencing reads,which are pivotal in resolving complex microbial genomic structures that short-read sequencing often fails to address[2,6].展开更多
Microbial community studies have established enzymes’pivotal catalytic roles in ecosystem metabolism,yet cultivation-dependent methods fail to exploit uncultured microbial enzyme resources.Metagenomics overcomes this...Microbial community studies have established enzymes’pivotal catalytic roles in ecosystem metabolism,yet cultivation-dependent methods fail to exploit uncultured microbial enzyme resources.Metagenomics overcomes this by directly accessing microbial genetic information,but its massive data generation challenges precise enzyme identification:(1)Restricted applicability across varied sample types.(2)Narrow functional scope in target enzyme discovery.To address this,we developed Gene Surfing,a bioinformatics workflow platform based on Snakemake.It integrates modules for data quality control(Fastp),genome assembly(MEGAHIT),assembly evaluation(QUAST and MetaQUAST),functional annotation(Prokka),and homologous sequence retrieval(MMseqs2).Gene Surfing offers scalability,reproducibility,and efficiency,addressing key challenges in enzyme identification.Validation results include:Cellulose-degrading enzymes(GH5 family):1,311,316 potential lignocellulolytic enzyme se-quences were identified,with 127 sequences functionally validated(84.25%activity rate);Polyethylenedegrading enzymes:705 candidate sequences were found,38 of which were heterologously expressed,showing an 81.5%activity rate(31/38);Endonucleases(HNH superfamily):585 potential sequences were retrieved,with 4 out of 7 tested showing activity(57.1%success rate).展开更多
Metagenomics is the study of microbial communities sampled directly from their natural environment, without prior culturing. By enabling an analysis of populations including many （so-far） unculturable and often unkn...Metagenomics is the study of microbial communities sampled directly from their natural environment, without prior culturing. By enabling an analysis of populations including many （so-far） unculturable and often unknown microbes, metagenomics is revolutionizing the field of microbiology, and has excited researchers in many disciplines that could benefit from the study of environmental microbes, including those in ecology, environmental sciences, and biomedicine. Specific computational and statistical tools have been developed for metagenomic data analysis and comparison. New studies, however, have revealed various kinds of artifacts present in metagenomics data caused by limitations in the experimental protocols and/or inadequate data analysis procedures, which often lead to incorrect conclusions about a microbial community. Here, we review some of the artifacts, such as overestimation of species diversity and incorrect estimation of gene family frequencies, and discuss emerging computational approaches to address them. We also review potential challenges that metagenomics may encounter with the extensive application of next-generation sequencing （NGS） techniques.展开更多
基金supported by the Special Funds for Chengde national innovation demonstration area construction of science and technology special project sustainable development agenda(No.202104F001)the National Basic Research Program of China(No.2019YFC0408602).
文摘Nitrogen removal from domestic sewage is usually limited by insufficient carbon source and electron donor.An economical solid carbon source was developed by composition of polyvinyl alcohol,sodium alginate,and corncob,which was utilized as external carbon source in the anaerobic anoxic oxic(AAO)-biofilter for the treatment of low carbon-to-nitrogen ratio domestic sewage,and the nitrogen removal was remarkably improved from 63.2%to 96.5%.Furthermore,the effluent chemical oxygen demand maintained at 35 mg/L or even lower,and the total nitrogenwas reduced to less than 2mg/L.Metagenomic analysis demonstrated that the microbial communities responsible for potential denitrification and organic matter degradation in both AAO and the biofilter reactors were mainly composed of Proteobacteria and Bacteroides,respectively.The solid carbon source addition resulted in relatively high abundance of functional enzymes responsible for NO_(3)^(−)-N to NO_(2)^(−)-N con-version in both AAO and the biofilter reactors,thus enabled stable reaction.The carbon source addition during glycolysis primarily led to the increase of genes associated with the metabolic conversion of fructose 1.6P2 to glycerol-3P The reactor maintained high abun-dance of genes related to the tricarboxylic acid cycle,and then guaranteed efficient carbon metabolism.The results indicate that the composite carbon source is feasible for denitri-fication enhancement of AAO-biofilter,which contribute to the theoretical foundation for practical nitrogen removal application.
基金supported by the National Natural Science Foundation of China(Nos.32271777,31500365,31770499,and 42303014)Tianjin Natural Science Foundation(Nos.12JCYBJC19700 and 18JCYBJC96500)+1 种基金Tianjin Science and Technology Support Program(Nos.23YFZCSN00100,15ZCZDSF00410,and 23YFZCSN00210)the Special Investigation of Technological Basic Resources(No.2021FY101002)。
文摘Limitations regarding phosphorus(P)are widespread in ecosystems.Understanding the impacts of the wetland types on microbially mediated soil P availability and cycling is essential for the effective management of wetlands.In this study,the Beidagang wetland,Baodi paddy field,and Dahuangpu wetland in Tianjin,China were chosen as representatives of the coastal wetland(B),constructed wetland(R),and swampy wetland(W),respectively.Sequential P extraction and metagenomics approaches were adopted to explore the soil P fraction and microbially regulated P cycle.Proteobacteria were the predominant microbes-related soil P cycle.IMPA,gph,rsbU_P,ugpQ,and glpK genes were dominant in organic P(Po)mineralization,while gcd,ppa,and ppx genes were dominant in inorganic P(Pi)solubilization.The salinity,NO_(3)^(-)-N concentration,the ratio of total carbon to total nitrogen(TC/TN),total carbon(TC),and the ratio of soil organic carbon to total P(SOC/TP)were the co-drivers of microbially mediated P cycle processes.Microbial network complexity-relate P cycle was the lowest in the coastal wetland.Salinity and NO_(3)^(-)-N exhibited a significant negative relation to the abundance of most genes-relate Pi solubilization and a remarkable positive correlation with the abundance of many genes-relate Po mineralization.These findings demonstrated that Po mineralization tended to occur in habitats with high salinity and nutrient imbalances,whereas the dissolution of Pi was prone to occur in low-salinity environments with relatively balanced soil nutrients.This study improves understanding of how salinity and soil nutrients jointly shape microbial-regulated soil P cycle in different types of wetlands.
文摘There are limited biosecurity measures directed at preventing airborne transmission of viruses in swine.The effectiveness of dust mitigation strategies such as oil sprinkling,to decrease risk of airborne virus transmission are unknown.Metagenomics and qPCR for common fecal viruses were used to hunt for a ubiquitous virus to serve as a proxy when evaluating the efficiency of mitigation strategies against airborne viral infectious agents.Air particles were collected from swine buildings using high-volume air samplers.Extracted DNA and RNA were used to perform specific RT-qPCR and qPCR and analyzed by highthroughput sequencing.Porcine astroviruses group 2 were common(from 102 to 105 genomic copies per cubic meter of air or gc/m^(3),93%positivity)while no norovirus genogroup II was recovered from air samples.Porcine torque teno sus virus were detected by qPCR in low concentrations(from 101 to 102 gc/m^(3),47%positivity).Among the identified viral families by metagenomics analysis,Herelleviridae,Microviridae,Myoviridae,Podoviridae,and Siphoviridae were dominant.The phage vB_AviM_AVP of Aerococcus was present in all air samples and a newly designed qPCR revealed between 101 and 105 gc/m^(3) among the samples taken for the present study(97%positivity)and banked samples from5-and 15-year old studies(89%positivity).According to the present study,both the porcine astrovirus group 2 and the phage vB_AviM_AVP of Aerococcus could be proxy for airborne viruses of swine buildings.
基金supported by the Special Project of Basic Scientific Research Business of Central Public Welfare Scientific Research Institutes (No.2019YSKY-027).
文摘Erythromycin fermentation residue(EFR)represents a typical hazardous waste produced by the microbial pharmaceutical industry.Although electrolysis is promising for EFR disposal,its microbial threats remain unclear.Herein,metagenomics was coupled with the random forest technique to decipher the antibiotic resistance patterns of electrochemically treated EFR.Results showed that 95.75%of erythromycin could be removed in 2 hr.Electrolysis temporarily influenced EFRmicrobiota,where the relative abundances of Proteobacteria and Actinobacteria increased,while those of Fusobacteria,Firmicutes,and Bacteroidetes decreased.A total of 505 antibiotic resistance gene(ARG)subtypes encoding resistance to 21 antibiotic types and 150 mobile genetic elements(MGEs),mainly including plasmid(72)and transposase(52)were assembled in EFR.Significant linear regression models were identified among microbial richness,ARG subtypes,and MGE numbers(r^(2)=0.50-0.81,p<0.001).Physicochemical factors of EFR(Total nitrogen,total organic carbon,protein,and humus)regulated ARG and MGE assembly(%IncMSE value=5.14-14.85).The core ARG,MGE,and microbe sets(93.08%-99.85%)successfully explained 89.71%-92.92%of total ARG and MGE abundances.Specifically,gene aph(3 )-I,transposase tnpA,and Mycolicibacterium were the primary drivers of the resistance dissemination system.This study also proposes efficient resistance mitigation measures,and provides recommendations for future management of antibiotic fermentation residue.
基金funded by Basic Research Funds of Chinese Academy of Geological Sciences(CSJ-2021-10).
文摘With the rapid development of molecular biology technology,especially the application of metagenomics,many challenges in groundwater microbial research have been overcome.Metagenomics has enabled the exploration of the diversity of unculturable microorganisms in groundwater.This paper reviews macro genomics 16S rRNA and metagenomics sequencing data,highlighting recent applications of metagenomics in investigating groundwater microbial communities.It also examines the relationship between microbial diversity and environmental factors,the identification of functional microbial groups,the role of microorganisms in groundwater pollution remediation,and their contribution to the hydrogeochemi-cal cycle.Finally,it provide insights into future research directions in groundwater microbiology.
基金Supported by National Basic Research Program(973 Program)of China,No.2013CB531403
文摘There are more than 1000 microbial species living in the complex human intestine.The gut microbial community plays an important role in protecting the host against pathogenic microbes,modulating immunity,regulating metabolic processes,and is even regarded as an endocrine organ.However,traditional culture methods are very limited for identifying microbes.With the application of molecular biologic technology in the field of the intestinal microbiome,especially metagenomic sequencing of the next-generation sequencing technology,progress has been made in the study of the human intestinal microbiome.Metagenomics can be used to study intestinal microbiome diversity and dysbiosis,as well as its relationship to health and disease.Moreover,functional metagenomics can identify novel functional genes,microbial pathways,antibiotic resistance genes,functional dysbiosis of the intestinal microbiome,and determine interactions and co-evolution between microbiota and host,though there are still some limitations.Metatranscriptomics,metaproteomics and metabolomics represent enormous complements to the understanding of the human gut microbiome.This review aims to demonstrate that metagenomics can be a powerful tool in studying the human gut microbiome with encouraging prospects.The limitations of metagenomics to be overcome are also discussed.Metatranscriptomics,metaproteomics and metabolomics in relation to the study of the human gut microbiome are also briefly discussed.
基金financially supported by the National Natural Science Foundation of China,No.32002235(to MT)the Science and Technology Foundation of Taian of Shandong Province,No.2020NS216(to XL)。
文摘A growing body of evidence suggests that the gut microbiota contributes to the development of neurodegenerative diseases via the microbiota-gut-brain axis.As a contributing factor,microbiota dysbiosis always occurs in pathological changes of neurodegenerative diseases,such as Alzheimer’s disease,Parkinson’s disease,and amyotrophic lateral sclerosis.High-throughput sequencing technology has helped to reveal that the bidirectional communication between the central nervous system and the enteric nervous system is facilitated by the microbiota’s diverse microorganisms,and for both neuroimmune and neuroendocrine systems.Here,we summarize the bioinformatics analysis and wet-biology validation for the gut metagenomics in neurodegenerative diseases,with an emphasis on multi-omics studies and the gut virome.The pathogen-associated signaling biomarkers for identifying brain disorders and potential therapeutic targets are also elucidated.Finally,we discuss the role of diet,prebiotics,probiotics,postbiotics and exercise interventions in remodeling the microbiome and reducing the symptoms of neurodegenerative diseases.
文摘East Lake(Lake Donghu),located in Wuhan,China,is a typical city freshwater lake that has been experiencing eutrophic conditions and algal blooming during recent years.Marine and fresh water are considered to contain a large number of viruses.However,little is known about their genetic diversity because of the limited techniques for culturing viruses.In this study,we conducted a viral metagenomic analysis using a high-throughput sequencing technique with samples collected from East Lake in Spring,Summer,Autumn,and Winter.The libraries from four samples each generated 234,669,71,837,12,820,and 34,236 contigs(>90 bp each),respectively.The genetic structure of the viral community revealed a high genetic diversity covering 23 viral families,with the majority of contigs homologous to DNA viruses,including members of Myoviridae,Podoviridae,Siphoviridae,Phycodnaviridae,and Microviridae,which infect bacteria or algae,and members of Circoviridae,which infect invertebrates and vertebrates.The highest viral genetic diversity occurred in samples collected in August,then December and June,and the least diversity in March.Most contigs have low-sequence identities with known viruses.PCR detection targeting the conserved sequences of genes(g20,psbA,psbD,and DNApol)of cyanophages further confirmed that there are novel cyanophages in the East Lake.Our viral metagenomic data provide the first preliminary understanding of the virome in one freshwater lake in China and would be helpful for novel virus discovery and the control of algal blooming in the future.
基金supported by the Medicine and Health,Science and Technology Plan Project of Zhejiang(Nos.2020KY1009 and 2021KY387)the Jinhua Science and Technology Planning Project Social Development Key Project(No.2021-3-072),China.
文摘Infectious diseases are a great threat to human health.Rapid and accurate detection of pathogens is important in the diagnosis and treatment of infectious diseases.Metagenomics next-generation sequencing(mNGS)is an unbiased and comprehensive approach for detecting all RNA and DNA in a sample.With the development of sequencing and bioinformatics technologies,mNGS is moving from research to clinical application,which opens a new avenue for pathogen detection.Numerous studies have revealed good potential for the clinical application of mNGS in infectious diseases,especially in difficult-to-detect,rare,and novel pathogens.However,there are several hurdles in the clinical application of mNGS,such as:(1)lack of universal workflow validation and quality assurance;(2)insensitivity to high-host background and low-biomass samples;and(3)lack of standardized instructions for mass data analysis and report interpretation.Therefore,a complete understanding of this new technology will help promote the clinical application of mNGS to infectious diseases.This review briefly introduces the history of next-generation sequencing,mainstream sequencing platforms,and mNGS workflow,and discusses the clinical applications of mNGS to infectious diseases and its advantages and disadvantages.
基金supported by the National Key Research and Development Program of China (No.2021YFC3201504)the National Natural Science Foundations of China (No.52000140)the Social Development Program of Science and Technology Committee Foundations of Shanghai (No.22dz1209200)。
文摘Mainstream partial nitritation-anammox(PNA)process easily suffers from performance instability and even reactor collapse in application.Thus,it is of great significance to unveil the characteristic of performance recovery,understand the intrinsic mechanism and then propose operational strategy.In this study,we combined long-term reactor operation,batch tests,and metagenomics to reveal the succession of microbial community and functional metabolism variation from system collapse to recovery.Proper aeration control(0.10-0.25mg O_(2)/L)was critical for performance recovery.It was also found that Candidatus Brocadia became the dominant flora and its abundance increased from 3.5%to 11.0%.Significant enhancements in carbon metabolism and phospholipid biosynthesis were observed during system recovery,and the genes abundance related to signal transduction was dramatically increased.The up-regulation of sdh and suc genes showed the processes of succinate dehydrogenation and succinyl-CoA synthesis might stimulate the production of amino acids and the synthesis of proteins,thereby possibly improving the activity and abundance of AnAOB,which was conducive to the performance recovery.Moreover,the increase in abundance of hzs and hdh genes suggested the enhancement of the anammox process.Changes in the abundance of key genes involved in nitrogen metabolism indicated that nitrogen removal pathway was more diverse after system recovery.The achievement of performance recovery was driven by anammox,nitrification and denitrification coupled with dissimilatory nitrate reduction to ammonium.These results provide deeper insights into the recovery mechanism of PNA system and also provide a potential regulation strategy for the stable operation of the mainstream PNA process.
文摘The symptoms of disseminated strongyloidiasis are not typical,and it is difficult for clinicians to identify strongyloidiasis in some non-endemic areas.We report a 70-year-old woman who was diagnosed with Guillain-Barrésyndrome due to autonomic disturbance,symmetrical bulbar palsy,and lower-motor-nerve damage in the extremities;her symptoms continued to worsen after hormone and immunoglobulin therapy.Later,parasitic larvae were found in the patient’s gastric fluid,and metagenomic next generation sequencing(mNGS)detection of bronchoalveolar-lavage fluid also found a large number of Strongyloides roundworms.The patient was diagnosed with disseminated strongyloidiasis.The patient was given albendazole for anthelmintic treatment,but died two days after being transferred to the intensive care unit due to the excessive strongyloidiasis burden.In recent years,mNGS has been increasingly used in clinical practice,and is becoming the main means of detecting strongyloides stercoralis in non-endemic areas.Especially during the corona virus disease 2019 pandemic,mNGS technology has irreplaceable value in identifying the source of infection.
基金supported by Jiangsu Provincial Key Research and Development Projects No.BE2017693National Natural Science Foundation of China No.81741062
文摘Diarrhea is the third leading cause of death in developing countries in children under the age of five.About half a million children die of diarrhea every year,most of which in developing countries.Viruses are the main pathogen of diarrhea.In China,the fecal virome of children with diarrhea has been rarely studied.Using an unbiased viral metagenomics approach,we analyzed the fecal virome in children with diarrhea.Many DNA or RNA viruses associated with diarrhea identified in those fecal samples were mainly from six families of Adenoviridae,Astroviridae,Caliciviridae,Parvoviridae,Picornaviridae,and Reoviridae.Among them,the family of Caliciviridae accounts for the largest proportion of 78.42%,following with Adenoviridae(8.94%)and Picornaviridae(8.36%).In addition to those diarrhea-related viruses that have already been confirmed to cause human diarrhea,the viruses not associated with diarrhea were also identified including anellovirus and picobirnavirus.This study increased our understanding of diarrheic children fecal virome and provided valuable information for the prevention and treatment of viral diarrhea in this area.
基金financially supported by the "2014 AgriX" Project Found of Shanghai Jiao Tong University(No. AF1500028/001)
文摘Recent studies have declared that members of the ss DNA virus family Microviridae play an important role in multiple environments, as they have been found taking a dominant position in the human gut. The aim of this study was to analyze the overall composition of the gut virome in coronary heart disease(CHD) patients, and try to discover the potential link between the human gut virome and CHD. Viral metagenomics methods were performed to detect the viral sequences in fecal samples collected from CHD inpatients and healthy persons as controls. We present the analysis of the virome composition in these CHD patients and controls. Our data shows that the virome composition may be linked to daily living habits and the medical therapy of CHD.Virgaviridae and Microviridae were the two dominant types of viruses found in the enteric virome of CHD patients. Fourteen divergent viruses belonging to the family Microviridae were found, twelve of which were grouped into the subfamily Gokushovirinae, while the remaining two strains might represent two new subfamilies within Microviridae, according to the phylogenetic analysis. In addition, the genomic organization of these viruses has been characterized.
文摘The human microbiota is made up of trillions of bacteria that live in the human being,whereas the microbiome is made up of the microbiota's genes and gene products.Bacteria have long been thought of as pathogens that eventually lead to human illness.Bacteria are increasingly recognized as generally beneficial commensal organisms and hence crucial to proper and healthy human development,thanks to breakthroughs in both cultivation-based approaches and the advent of metagenomics.This relatively new field of medical study has given more information on illnesses such as inflammatory bowel disease,obesity,metabolic and atopic disorders.However,there is a lot we don't know about the complexities of microbe-microbe and microbe-host interactions.Future work targeted at resolving crucial concerns about the early formation of the microbiome,in addition,what determines its dysbiosis,will most likely lead to long-term mitigation of health.In this article,review the research on prenatal and newborn microbiome modulations,the role of maternal and environmental variables on forming the newborn microbiome,and future issues and directions in the exciting new field of metagenomic medicine.
基金supported by the Project of Fund for Stable Support to Agricultural Sci-Tech Renovation of XAAS(grant number:xjnkywdzc-2023005-6)Key Laboratory of Biological Resources and Ecology of the Pamir Plateau,Xinjiang(grant number:XJDX1714-2021-01)+1 种基金The Major Science and Technology Project of Xinjiang Uygur Autonomous Region(grant number:2022A02005-4-2)Xinjiang Uygur Autonomous Region Rural Revitalization Industry Development Science and Technology Action Project(grant number:2022NC073).
文摘Background:Camels,known as the enduring“ships of the desert,”host a complex gut microbiota that plays a crucial role in their survival in extreme environments.However,amidst the fascinating discoveries about the camel gut microbiota,concerns about antibiotic resistance have emerged as a significant global challenge affecting both human and animal populations.Indeed,the continued use of antibiotics in veterinary medicine has led to the widespread emergence of antibiotic-resistant bacteria,which has worsened through gene transfer.Methods:This study offers a deeper examination of this pressing issue by harnessing the potent tools of metagenomics to explore the intricate interplay between the camel(Camelus ferus)gut microbiota and antibiotic resistance.Results:Samples from wild camels yielded varying amounts of raw and clean data,generating scaftigs and open reading frames.The camel fecal microbiome was dominated by bacteria(mainly Bacillota and Bacteriodota),followed by viruses,archaea,and eukaryota.The most abundant genera were the Bacteroides,Ruminococcus,and Clostridium.Functional annotation revealed enriched pathways in metabolism,genetic information processing,and cellular processes,with key pathways involving carbohydrate transport and metabolism,replication,and amino acid transport.CAZy database analysis showed high abundances of glycoside hydrolases and glycosyl transferases.Antibiotic resistance gene(ARG)analysis identified Bacillota and Bacteroidota as the main reservoirs,with vancomycin resistance genes being the most prevalent.This study identified three major resistance mechanisms:antibiotic target alteration,antibiotic target protection,and antibiotic efflux.Conclusion:These findings contribute to a broader understanding of antibiotic resistance within animal microbiomes and provide a foundation for further investigations of strategies to manage and mitigate antibiotic resistance.
基金supported by Science and Technology Major Projects of Inner Mongolia Autonomous Region(2021ZD0014)。
文摘Probiotics exert beneficial effects on the host.This study aimed to investigate whether maternally ingested Lacticaseibacillus rhamnosus Probio-M9 during pregnancy could access and colonize the infant gut.This study recruited one pregnant woman,who ingested Probio-M9 daily from 35 weeks of gestation to delivery.Feces of the mother-infant pair were regularly collected from one month before delivery to 6 months of infant's age for metagenomic sequencing.Probio-M9 genomes were mappable to all infant fecal samples,suggesting the ingested probiotics could be vertically transmitted from mother to infant.Infant-or mother-specific differential metabolic pathways were found between the maternal and infant's gut microbiome,implicating apparent differences in the intestinal metagenomic potential/function between the mother and the infant.In conclusion,maternal ingestion of Probio-M9 during the final weeks of gestation could deliver to the infant gut.The findings provided novel insights into shaping infant's gut microbiota.
基金supported by the Key Research and Development and Transformation Plan of Qinghai Province,China(Grant No.2025-QY-208)National Natural Science Foundation of China,China(Grant No.82460660)Entrepreneurship and Innovation Team for Disease Vector Prevention and Control Research in Qinghai,China.
文摘With the improvement of transportation and the rise of tourism on the Qinghai-Xizang Plateau,the scope of human activities has continuously expanded,increasing opportunities for contact with wildlife,also exacerbating the outbreak rate of zoonotic emerging infectious diseases.Currently,research on the gut microbiota of wildlife,especially Marmota himalayana(M.himalayana),which are reservoir hosts for plague,is scarce.In this study,we investigated the composition,function,and regional variations of the gut microbiota in M.himalayana based on the metagenomic sequencing of 45 fecal samples from the Sanjiangyuan National Nature Reserve in Qinghai Province.The results indicated that at the phylum level,the dominant bacterial phyla in the gut microbiota of the M.himalayana were Firmicutes,Bacteroidota,and Proteobacteria,collectively accounting for 74.16% of the community.At the genus level,the top three most abundant genera were Alistipes(11.86%±1.56%),Bacteroides(6.68%±0.95%),and Clostridium(4.92%±1.04%).Kyoto encyclopedia of genes and genomes(KEGG)database annotation results showed that the most enriched functional categories of the marmot gut microbiota were metabolism,genetic information processing(GIP),and environmental information processing(EIP).These active functions played a crucial role in food digestion,nutrient absorption,metabolic balance maintenance,and pathogen defense,aiding the marmot in better adapting to the extreme environment of the Qinghai-Xizang Plateau.The study provided critical insights into host-microbe interactions,highlighting the role of microbiota in the survival and conservation of endangered species in unique habitats.
文摘The rapid advancement of nanopore metagenomic sequencing has revolutionized microbiome research,enabling significant breakthroughs in the study of microbial communities,ecological dynamics,and genome-level functions[1–5].This innovative sequencing technology stands out due to its ability to generate long sequencing reads,which are pivotal in resolving complex microbial genomic structures that short-read sequencing often fails to address[2,6].
基金supported by the Third Xinjiang Scientific Expedition Program,the National Key Research and Development Program of China(grant 2022xjkk020603)Key Research and Development Project of Xinjiang Uygur Autonomous Region of China(grant 2023B02034,2023B02034-2)+1 种基金the National Natural Science Foundation of China(grant U2003305,31860018)the Tianshan Young Top Talents-Basic Research Talents(2024TSYCJU0002).
文摘Microbial community studies have established enzymes’pivotal catalytic roles in ecosystem metabolism,yet cultivation-dependent methods fail to exploit uncultured microbial enzyme resources.Metagenomics overcomes this by directly accessing microbial genetic information,but its massive data generation challenges precise enzyme identification:(1)Restricted applicability across varied sample types.(2)Narrow functional scope in target enzyme discovery.To address this,we developed Gene Surfing,a bioinformatics workflow platform based on Snakemake.It integrates modules for data quality control(Fastp),genome assembly(MEGAHIT),assembly evaluation(QUAST and MetaQUAST),functional annotation(Prokka),and homologous sequence retrieval(MMseqs2).Gene Surfing offers scalability,reproducibility,and efficiency,addressing key challenges in enzyme identification.Validation results include:Cellulose-degrading enzymes(GH5 family):1,311,316 potential lignocellulolytic enzyme se-quences were identified,with 127 sequences functionally validated(84.25%activity rate);Polyethylenedegrading enzymes:705 candidate sequences were found,38 of which were heterologously expressed,showing an 81.5%activity rate(31/38);Endonucleases(HNH superfamily):585 potential sequences were retrieved,with 4 out of 7 tested showing activity(57.1%success rate).
基金supported by NIH under Grant No. 1R01HG004908-01NSF of USA under Grant No. DBI-0845685 (YY)the Gordon and Betty Moore Foundation for the Community Cyberinfrastructure for Marine Microbial Ecological Research and Analysis (CAMERA) Project (JW)
文摘Metagenomics is the study of microbial communities sampled directly from their natural environment, without prior culturing. By enabling an analysis of populations including many （so-far） unculturable and often unknown microbes, metagenomics is revolutionizing the field of microbiology, and has excited researchers in many disciplines that could benefit from the study of environmental microbes, including those in ecology, environmental sciences, and biomedicine. Specific computational and statistical tools have been developed for metagenomic data analysis and comparison. New studies, however, have revealed various kinds of artifacts present in metagenomics data caused by limitations in the experimental protocols and/or inadequate data analysis procedures, which often lead to incorrect conclusions about a microbial community. Here, we review some of the artifacts, such as overestimation of species diversity and incorrect estimation of gene family frequencies, and discuss emerging computational approaches to address them. We also review potential challenges that metagenomics may encounter with the extensive application of next-generation sequencing （NGS） techniques.
