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
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
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
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
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
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
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
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
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
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
Multifaceted approaches are required to monitor wildlife populations and improve conservation efforts. In the last decade,increasing evidence suggests that metagenomic analysis offers valuable perspectives and tools f...Multifaceted approaches are required to monitor wildlife populations and improve conservation efforts. In the last decade,increasing evidence suggests that metagenomic analysis offers valuable perspectives and tools for identifying microbial communities and functions. It has become clear that gut microbiome plays a critical role in health, nutrition, and physiology of wildlife, including numerous endangered animals in the wild and in captivity. In this review, we first introduce the human microbiome and metagenomics, highlighting the importance of microbiome for host fitness. Then, for the first time, we propose the concept of conservation metagenomics, an emerging subdiscipline of conservation biology, which aims to understand the roles of the microbiota in evolution and conservation of endangered animals. We define what conservation metagenomics is along with current approaches, main scientific issues and significant implications in the study of host evolution, physiology,nutrition, ecology and conservation. We also discuss future research directions of conservation metagenomics. Although there is still a long way to go, conservation metagenomics has already shown a significant potential for improving the conservation and management of wildlife.展开更多
With the development of high throughput sequencing and single-cell genomics technologies, many uncultured bacterial communities have been dissected by combining these two techniques. Especially, by simul- taneously le...With the development of high throughput sequencing and single-cell genomics technologies, many uncultured bacterial communities have been dissected by combining these two techniques. Especially, by simul- taneously leveraging of single-cell genomics and metagenomics, researchers can greatly improve the efficiency and accuracy of obtaining whole genome information from complex microbial communities, which not only allow us to identify microbes but also link function to species, identify subspecies variations, study host-virus interactions and etc. Here, we review recent developments and the challenges need to be addressed in single-cell metagenomics, including potential contamination, uneven sequence coverage, sequence chimera, genome assembly and annotation. With the development of sequencing and computational methods, single-cell metagenomics will undoubtedly broaden its application in various microbiome studies.展开更多
Pharmaceutical residues, mainly antibiotics, have been called "emerging contaminants" in the environment because of their increasing frequency of detection in aquatic and terrestrial systems and their sublet...Pharmaceutical residues, mainly antibiotics, have been called "emerging contaminants" in the environment because of their increasing frequency of detection in aquatic and terrestrial systems and their sublethal ecological effects. Most of them are undiscovered. Both human and veterinary pharmaceuticals, including antibiotics, are introduced into the environment via many different routes, including discharges from municipal wastewater treatment plants and land application of animal manure and biosolids to fertilize croplands. To gain a comprehensive understanding of the widespread problem of antibiotic resistance, modem and scientific approaches have been developed to gain knowledge of the entire antibiotic-resistant microbiota of various ecosystems, which is called the resistome. In this review, two omics methods, i.e. culturomics, a new approach, and metagenomics, used to study antibiotic resistance in environmental samples, are described. Moreover, we discuss how both omics methods have become core scientific tools to characterize microbiomes or resistomes, study natural communities and discover new microbes and new antibiotic resistance genes from environments. The combination of the method for get better outcome of both culturomics and metagenomics will significantly advance our understanding of the role of microbes and their specific properties in the environment.展开更多
Captive conditions can affect the symbiotic microbiome of animals.In this study,we compared the structural and functional differences of the gastrointestinal microbiomes of wild Bactrian camels(Camelus ferus)between w...Captive conditions can affect the symbiotic microbiome of animals.In this study,we compared the structural and functional differences of the gastrointestinal microbiomes of wild Bactrian camels(Camelus ferus)between wild and captive populations,as well as their different host energy utilization performances through metagenomics.The results showed that wild-living camels harbored more microbial taxa related to the production of volatile fatty acids,fewer methanogens,and fewer genes encoding enzymes involved in methanogenesis,leading to higher energy utilization efficiency compared to that of captive-living camels.These findings suggest that the wild-living camel fecal microbiome demonstrates a series of adaptive characteristics that enable the host to adjust to a relatively barren field environment.Our study provides novel insights into the mechanisms of wildlife adaptations to habitats from the perspective of the microbiome.展开更多
Many viruses can cause respiratory diseases in humans.Although great advances have been achieved in methods of diagnosis,it remains challenging to identify pathogens in unexplained pneumonia(UP) cases.In this study,we...Many viruses can cause respiratory diseases in humans.Although great advances have been achieved in methods of diagnosis,it remains challenging to identify pathogens in unexplained pneumonia(UP) cases.In this study,we applied next-generation sequencing(NGS) technology and a metagenomic approach to detect and characterize respiratory viruses in UP cases from Guizhou Province,China.A total of 33 oropharyngeal swabs were obtained from hospitalized UP patients and subjected to NGS.An unbiased metagenomic analysis pipeline identified 13 virus species in 16 samples.Human rhinovirus C was the virus most frequently detected and was identified in seven samples.Human measles virus,adenovirus B 55 and coxsackievirus A10 were also identified.Metagenomic sequencing also provided virus genomic sequences,which enabled genotype characterization and phylogenetic analysis.For cases of multiple infection,metagenomic sequencing afforded information regarding the quantity of each virus in the sample,which could be used to evaluate each viruses' role in the disease.Our study highlights the potential of metagenomic sequencing for pathogen identification in UP cases.展开更多
Droplet microfluidic techniques have shown promising outcome to study single cells at high throughput.However,their adoption in laboratories studying“-omics”sciences is still irrelevant due to the complex and multid...Droplet microfluidic techniques have shown promising outcome to study single cells at high throughput.However,their adoption in laboratories studying“-omics”sciences is still irrelevant due to the complex and multidisciplinary nature of the field.To facilitate their use,here we provide engineering details and organized protocols for integrating three droplet-based microfluidic technologies into the metagenomic pipeline to enable functional screening of bioproducts at high throughput.First,a device encapsulating single cells in droplets at a rate of~250 Hz is described considering droplet size and cell growth.Then,we expand on previously reported fluorescence-activated droplet sorting systems to integrate the use of 4 independent fluorescence-exciting lasers(i.e.,405,488,561,and 637 nm)in a single platform to make it compatible with different fluorescence-emitting biosensors.For this sorter,both hardware and software are provided and optimized for effortlessly sorting droplets at 60 Hz.Then,a passive droplet merger is also integrated into our pipeline to enable adding new reagents to already-made droplets at a rate of 200 Hz.Finally,we provide an optimized recipe for manufacturing these chips using silicon dry-etching tools.Because of the overall integration and the technical details presented here,our approach allows biologists to quickly use microfluidic technologies and achieve both single-cell resolution and high-throughput capability(>50,000 cells/day)for mining and bioprospecting metagenomic data.展开更多
The coronavirus disease 2019(COVID-19)pandemic represents an enormous challenge to all countries,regardless of their development status.The manipulation of its etiologic agent SARS-CoV-2 requires a biosafety containme...The coronavirus disease 2019(COVID-19)pandemic represents an enormous challenge to all countries,regardless of their development status.The manipulation of its etiologic agent SARS-CoV-2 requires a biosafety containment level 3 laboratories(BSL-3)to understand virus biology and in vivo pathogenesis as well as the translation of new knowledge into the preclinical development of vaccines and antivirals.As such,BSL-3 facilities should be considered an integral part of any public health response to emerging infectious disease prevention,control and management.Differently from BSL-2,BSL-3 units vary considerably along the range from industrialized to the least developed countries.Innovative Developing Countries(IDCs)such as Brazil,which excelled at controlling the 2015-2017 Zika epidemic,had to face a serious flaw in its disease control and prevention structure:the scarcity and uneven geographic distribution of its BSL-3 facilities,including those for preclinical animal experimentation.展开更多
Microbial oceanography is an emerging discipline resulted from the interaction,cross-fertilization and integration of life science and ocean science.Microbial oceanography integrates the principles of marine microbiol...Microbial oceanography is an emerging discipline resulted from the interaction,cross-fertilization and integration of life science and ocean science.Microbial oceanography integrates the principles of marine microbiology,microbial ecology and oceanography to study the role of microorganisms in the biogeochemical dynamics of natural marine ecosystems.The application of genomics tools to study marine microbes is resulting in rapid advancements in microbial oceanography that has important implications in global carbon cycle,climate change,and ecosystem function.Here we review the application of genomics and metagenomics in microbial oceanography and suggest future directions in microbial oceanography research.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
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.
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 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.
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.
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.
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 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.
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 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.
基金funded by the Strategic Priority Research Program of the Chinese Academy of Sciences (XDB31000000)the National Key Program of Research and Development, Ministry of Science and Technology of China (2016YFC0503200)the Creative Research Group Project of National Natural Science Foundation of China (31821001)
文摘Multifaceted approaches are required to monitor wildlife populations and improve conservation efforts. In the last decade,increasing evidence suggests that metagenomic analysis offers valuable perspectives and tools for identifying microbial communities and functions. It has become clear that gut microbiome plays a critical role in health, nutrition, and physiology of wildlife, including numerous endangered animals in the wild and in captivity. In this review, we first introduce the human microbiome and metagenomics, highlighting the importance of microbiome for host fitness. Then, for the first time, we propose the concept of conservation metagenomics, an emerging subdiscipline of conservation biology, which aims to understand the roles of the microbiota in evolution and conservation of endangered animals. We define what conservation metagenomics is along with current approaches, main scientific issues and significant implications in the study of host evolution, physiology,nutrition, ecology and conservation. We also discuss future research directions of conservation metagenomics. Although there is still a long way to go, conservation metagenomics has already shown a significant potential for improving the conservation and management of wildlife.
文摘With the development of high throughput sequencing and single-cell genomics technologies, many uncultured bacterial communities have been dissected by combining these two techniques. Especially, by simul- taneously leveraging of single-cell genomics and metagenomics, researchers can greatly improve the efficiency and accuracy of obtaining whole genome information from complex microbial communities, which not only allow us to identify microbes but also link function to species, identify subspecies variations, study host-virus interactions and etc. Here, we review recent developments and the challenges need to be addressed in single-cell metagenomics, including potential contamination, uneven sequence coverage, sequence chimera, genome assembly and annotation. With the development of sequencing and computational methods, single-cell metagenomics will undoubtedly broaden its application in various microbiome studies.
文摘Pharmaceutical residues, mainly antibiotics, have been called "emerging contaminants" in the environment because of their increasing frequency of detection in aquatic and terrestrial systems and their sublethal ecological effects. Most of them are undiscovered. Both human and veterinary pharmaceuticals, including antibiotics, are introduced into the environment via many different routes, including discharges from municipal wastewater treatment plants and land application of animal manure and biosolids to fertilize croplands. To gain a comprehensive understanding of the widespread problem of antibiotic resistance, modem and scientific approaches have been developed to gain knowledge of the entire antibiotic-resistant microbiota of various ecosystems, which is called the resistome. In this review, two omics methods, i.e. culturomics, a new approach, and metagenomics, used to study antibiotic resistance in environmental samples, are described. Moreover, we discuss how both omics methods have become core scientific tools to characterize microbiomes or resistomes, study natural communities and discover new microbes and new antibiotic resistance genes from environments. The combination of the method for get better outcome of both culturomics and metagenomics will significantly advance our understanding of the role of microbes and their specific properties in the environment.
基金This study was funded by the Beijing Forestry University Outstanding Young Talent Cultivation Project(No.2019JQ03018)Postdoctoral Innovative Talents Support Program(No.BX20190042)China Postdoctoral Science Foundation(2020M670177).
文摘Captive conditions can affect the symbiotic microbiome of animals.In this study,we compared the structural and functional differences of the gastrointestinal microbiomes of wild Bactrian camels(Camelus ferus)between wild and captive populations,as well as their different host energy utilization performances through metagenomics.The results showed that wild-living camels harbored more microbial taxa related to the production of volatile fatty acids,fewer methanogens,and fewer genes encoding enzymes involved in methanogenesis,leading to higher energy utilization efficiency compared to that of captive-living camels.These findings suggest that the wild-living camel fecal microbiome demonstrates a series of adaptive characteristics that enable the host to adjust to a relatively barren field environment.Our study provides novel insights into the mechanisms of wildlife adaptations to habitats from the perspective of the microbiome.
基金supported by the National Mega-projects for Infectious Diseases(2014ZX10004002)Beijing Municipal Science and Technology Commission grant(D151100002115003)
文摘Many viruses can cause respiratory diseases in humans.Although great advances have been achieved in methods of diagnosis,it remains challenging to identify pathogens in unexplained pneumonia(UP) cases.In this study,we applied next-generation sequencing(NGS) technology and a metagenomic approach to detect and characterize respiratory viruses in UP cases from Guizhou Province,China.A total of 33 oropharyngeal swabs were obtained from hospitalized UP patients and subjected to NGS.An unbiased metagenomic analysis pipeline identified 13 virus species in 16 samples.Human rhinovirus C was the virus most frequently detected and was identified in seven samples.Human measles virus,adenovirus B 55 and coxsackievirus A10 were also identified.Metagenomic sequencing also provided virus genomic sequences,which enabled genotype characterization and phylogenetic analysis.For cases of multiple infection,metagenomic sequencing afforded information regarding the quantity of each virus in the sample,which could be used to evaluate each viruses' role in the disease.Our study highlights the potential of metagenomic sequencing for pathogen identification in UP cases.
基金The work was supported by the grants from King Abdullah University of Science and Technology(KAUST),Saudi Arabia(Grant Nos.BAS/1/1059/01/01,URF/1/1976/03/01,URF/1/1976-17-01,URF/1/1976-20-01,and FCS/1/3326-01-01).
文摘Droplet microfluidic techniques have shown promising outcome to study single cells at high throughput.However,their adoption in laboratories studying“-omics”sciences is still irrelevant due to the complex and multidisciplinary nature of the field.To facilitate their use,here we provide engineering details and organized protocols for integrating three droplet-based microfluidic technologies into the metagenomic pipeline to enable functional screening of bioproducts at high throughput.First,a device encapsulating single cells in droplets at a rate of~250 Hz is described considering droplet size and cell growth.Then,we expand on previously reported fluorescence-activated droplet sorting systems to integrate the use of 4 independent fluorescence-exciting lasers(i.e.,405,488,561,and 637 nm)in a single platform to make it compatible with different fluorescence-emitting biosensors.For this sorter,both hardware and software are provided and optimized for effortlessly sorting droplets at 60 Hz.Then,a passive droplet merger is also integrated into our pipeline to enable adding new reagents to already-made droplets at a rate of 200 Hz.Finally,we provide an optimized recipe for manufacturing these chips using silicon dry-etching tools.Because of the overall integration and the technical details presented here,our approach allows biologists to quickly use microfluidic technologies and achieve both single-cell resolution and high-throughput capability(>50,000 cells/day)for mining and bioprospecting metagenomic data.
基金supported by CNPq(ConselhoNacional deDesenvolvimento Cientifico e Tecnologico),FAPERJ(Fundacao de Amparo a Pesquisa do Estado do Rio de Janeiro)through grants received by TMLSFunding was also provided by CNPq,CAPES(Coordenacao de Aperfeicoamento de Pessoal de Nivel Superior)and FAPERJ through the National Institutes of Science and Technology Program(INCT)to CMM(INCT-IDPN)Thanks are due to Oswaldo Cruz Foundation/FIOCRUZ under the auspicious of Inova program(B3-Bovespa funding).
文摘The coronavirus disease 2019(COVID-19)pandemic represents an enormous challenge to all countries,regardless of their development status.The manipulation of its etiologic agent SARS-CoV-2 requires a biosafety containment level 3 laboratories(BSL-3)to understand virus biology and in vivo pathogenesis as well as the translation of new knowledge into the preclinical development of vaccines and antivirals.As such,BSL-3 facilities should be considered an integral part of any public health response to emerging infectious disease prevention,control and management.Differently from BSL-2,BSL-3 units vary considerably along the range from industrialized to the least developed countries.Innovative Developing Countries(IDCs)such as Brazil,which excelled at controlling the 2015-2017 Zika epidemic,had to face a serious flaw in its disease control and prevention structure:the scarcity and uneven geographic distribution of its BSL-3 facilities,including those for preclinical animal experimentation.
文摘Microbial oceanography is an emerging discipline resulted from the interaction,cross-fertilization and integration of life science and ocean science.Microbial oceanography integrates the principles of marine microbiology,microbial ecology and oceanography to study the role of microorganisms in the biogeochemical dynamics of natural marine ecosystems.The application of genomics tools to study marine microbes is resulting in rapid advancements in microbial oceanography that has important implications in global carbon cycle,climate change,and ecosystem function.Here we review the application of genomics and metagenomics in microbial oceanography and suggest future directions in microbial oceanography research.
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.
