Objective Viral encephalitis is an infectious disease severely affecting human health.It is caused by a wide variety of viral pathogens,including herpes viruses,flaviviruses,enteroviruses,and other viruses.The laborat...Objective Viral encephalitis is an infectious disease severely affecting human health.It is caused by a wide variety of viral pathogens,including herpes viruses,flaviviruses,enteroviruses,and other viruses.The laboratory diagnosis of viral encephalitis is a worldwide challenge.Recently,high-throughput sequencing technology has provided new tools for diagnosing central nervous system infections.Thus,In this study,we established a multipathogen detection platform for viral encephalitis based on amplicon sequencing.Methods We designed nine pairs of specific polymerase chain reaction(PCR)primers for the 12 viruses by reviewing the relevant literature.The detection ability of the primers was verified by software simulation and the detection of known positive samples.Amplicon sequencing was used to validate the samples,and consistency was compared with Sanger sequencing.Results The results showed that the target sequences of various pathogens were obtained at a coverage depth level greater than 20×,and the sequence lengths were consistent with the sizes of the predicted amplicons.The sequences were verified using the National Center for Biotechnology Information BLAST,and all results were consistent with the results of Sanger sequencing.Conclusion Amplicon-based high-throughput sequencing technology is feasible as a supplementary method for the pathogenic detection of viral encephalitis.It is also a useful tool for the high-volume screening of clinical samples.展开更多
Fish, which are vital for both aquatic ecosystem functionality and global food supply, rely heavily on theirgastrointestinal tract (GIT) microbiota for the digestion that underpins their growth and health. Takifugu pu...Fish, which are vital for both aquatic ecosystem functionality and global food supply, rely heavily on theirgastrointestinal tract (GIT) microbiota for the digestion that underpins their growth and health. Takifugu puf-ferfish, which are an example of species evolved through adaptive radiation, possess a GIT that is specialized forantipredator defense and gluttonous feeding behaviors, offering a unique model to explore the effects of GrTcompartmentalization and host genetics on gut microbial communities. Here we compiled 78 full and partial-length 16 S rRNA amplicon datasets across three anteroposteriorly distinct intestinal sites in a cohort of cohab-itating artificial hybrid and purebred Takifugu pufferfishes. Our findings reveal a compositional and functionalbiogeography of pufferfish gut microbiota along the GIT and between host genetics. Additionally, the differentialabundance of specific amplicon sequence variants and their correlation with host genetic backgrounds and in-testinal sections highlight the role of environmental filtering in shaping microbial communities,with certainbacterial taxa exhibiting strong preferences for particular intestinal sites or genetic backgrounds,suggestingpotential localized adaptation or functional specialization. This study enhances our understanding of the intricateinterplay between host genetics, gut anatomy, and microbiota in fish, underscoring the importance of detailedmicrobial profiling in conservation efforts and aquaculture practices, and emphasizing the necessity of integratingfull-length 16 S rRNA sequencing with partial-length datasets to comprehensively understand microbial diversityand function, paving the way for improved fish health management and sustainable aquaculture strategies.展开更多
The microbiome associated with brown planthopper(BPH)plays an important role in mediating host health and fitness.Characterization of the microbial community and its structure is prerequisite for understanding the int...The microbiome associated with brown planthopper(BPH)plays an important role in mediating host health and fitness.Characterization of the microbial community and its structure is prerequisite for understanding the intricate symbiotic relationships between microbes and host insect.Here,we investigated the bacterial and fungal communities of BPH at different developmental stages using high-throughput amplicon sequencing.Our results revealed that both the bacterial and fungal communities were diverse and dynamic during BPH development.The bacterial communities were generally richer than fungi in each developmental stage.At 97%similarly,19 phyla and 278 genera of bacteria were an-notated,while five fungal phyla comprising 80 genera were assigned.The highest species richness for the bacterial communities was detected in the nymphal stage.The taxonomic diversity of the fungal communities in female adults was generally at a relatively higher level when compared to other developmental stages.The most dominant phylum of bacteria and fungi at each developmental stage all belonged to Proteobacteria and Ascomycota,re-spectively.A significantly lower abundance of bacterial genus Acinetobacter was recorded in the egg stage when compared to other developmental stages,while the dominant fun-gal genus Wallemia was more abundant in the nymph and adult stages than in the egg stage.Additionally,the microbial composition differed between male and female adults,suggesting that the microbial communties In BPH were gender-dependent.Uverall,our study enriches our knowledge on the microbial communities associated with BPH and will provide clues to develop potential biocontrol techniques against this rice pest.展开更多
Wet-salted skin,as a special artificial high-salt environment,is rich in protein,fat,collagen and other nutrient substrates,and is a rich resource of halotolerant and halophilic microorganisms.However,knowledge gaps r...Wet-salted skin,as a special artificial high-salt environment,is rich in protein,fat,collagen and other nutrient substrates,and is a rich resource of halotolerant and halophilic microorganisms.However,knowledge gaps regarding the microbial community structure and inter taxa associations of wet-salted skin are large.In this study,the spatiotemporal dynamics and community structure of microorganisms present on wet-salted goatskins were investigated using 16S rRNA gene amplicon sequencing and culturable technique.Alpha diversity analysis based on Sobs,Chao,Ace and Shannon indices revealed that microbial diversity on the wet-salted goatskins exhibited a trend of‘down→up→down→flat’with time.During preservation,genera belonging to the bacteria domain such as Aci-netobacter,Weissella and Streptococcus were slowly dying out,whereas those belonging to halophilic archaea such as Natrialba and Haloterrigena were gradually flourishing.Moreover,to resist high-salt stress,microorganisms on the wet-salted goatskin gradually migrated from the outside to the inside,eventually leading to the microbial diversity inside the skin being the same as or even higher than that on the skin surface.Venn diagram analysis revealed that the strains of some genera,including Psychrobacter,Salimicrobium,Salinicola,Ornithinibacillus,Halomonas,Bacillus and Chromohalobacter,were distributed throughout the interior and exterior of the wet-salted goatskin and existed during various periods.Accordingly,45 protease-producing halophilic or halotolerant microorganisms were isolated and screened from the wet-salted goatskin using the gradient dilution plate method.Importantly,16S rRNA genes of some bacteria exhibited less than 99.5%similarity to valid published species,indicating that they likely are novel spe-cies and have a good potential for application.展开更多
China has a rich history of cultivating medicinal plants,whose root microbial communities closely interact with the medicinal plants,thereby influencing their growth,health,and medicinal properties.Currently,researche...China has a rich history of cultivating medicinal plants,whose root microbial communities closely interact with the medicinal plants,thereby influencing their growth,health,and medicinal properties.Currently,researchers widely use 16S rRNA gene amplicon sequencing to study these root microbial communities.However,publicly available sequence datasets often lack essential sample information or contain errors,impeding the reuse of the datasets in the future.In this study,we aimed to create a united,reliable,and readily usable source of 16S rRNA gene sequences for medicinal plant root microbiomes.We compiled a catalog of 1392 microbiome samples for 58 medicinal plants from 58 studies,and manually provided essential sample information based on the experimental setup described in the associated papers.We then processed the sequences using a custom pipeline,generating a united catalog of operational taxonomic units(OTUs)and conducting taxonomic classification.We also pre-dicted the ecological functions of the communities for each sample.Finally,we used this dataset,to compare the rhizosphere bacterial communities of Pseudostellaria heterophylla from Fujian and Guizhou Provinces,revealing significant differences in the community composition of the same plant from different geographic locations.By providing a comprehensive and united catalog of amplicon sequences and OTUs for medicinal plant root bacterial communities,this study offers an invaluable resource for future comparative studies and data mining.展开更多
Previously, we showed that prophylactic addition of glucose to Harsha Lake water samples could inhibit cyanobacteria growth, at least for a short period of time. The current study tested cyanobacterial control with gl...Previously, we showed that prophylactic addition of glucose to Harsha Lake water samples could inhibit cyanobacteria growth, at least for a short period of time. The current study tested cyanobacterial control with glucose for the entire Harsha Lake bloom season. Water samples (1000 ml) were collected weekly from Harsha Lake during the algal-bloom season starting June 9 and lasting until August 24, 2022. To each of two 7-liter polypropylene containers, 500 ml of Harsha Lake water was added, and the containers were placed in a controlled environment chamber. To one container labeled “Treated,” 0.15 g of glucose was added, and nothing was added to the container labeled “Control.” After that, three 25 ml samples from each container were collected and used for 16S rRNA gene sequencing each week. Then 1000 ml of Harsha Lake water was newly collected each week, with 500 ml added to each container, along with the addition of 0.15 g glucose to the “Treated” container. Sequencing data were used to examine differences in the composition of bacterial communities between Treated and Control containers. Treatment with glucose altered the microbial communities by 1) reducing taxonomic diversity, 2) largely eliminating cyanobacterial taxa, and 3) increasing the relative abundance of subsets of non-cyanobacterial taxa (such as Proteobacteria and Actinobacteriota). These effects were observed across time despite weekly inputs derived directly from Lake water. The addition of glucose to a container receiving weekly additions of Lake water suppressed the cyanobacterial populations during the entire summer bloom season. The glucose appears to stimulate the diversity of certain bacterial taxa at the expense of the cyanobacteria.展开更多
Studies have shown that gut microbiota metabolites can enter the central nervous system via the blood-spinal cord barrier and cause neuroinflammation, thus constituting secondary injury after spinal cord injury. To in...Studies have shown that gut microbiota metabolites can enter the central nervous system via the blood-spinal cord barrier and cause neuroinflammation, thus constituting secondary injury after spinal cord injury. To investigate the correlation between gut microbiota and metabolites and the possible mechanism underlying the effects of gut microbiota on secondary injury after spinal cord injury, in this study, we established mouse models of T8–T10 traumatic spinal cord injury. We used 16 S rRNA gene amplicon sequencing and metabolomics to reveal the changes in gut microbiota and metabolites in fecal samples from the mouse model. Results showed a severe gut microbiota disturbance after spinal cord injury, which included marked increases in pro-inflammatory bacteria, such as Shigella, Bacteroides, Rikenella, Staphylococcus, and Mucispirillum and decreases in anti-inflammatory bacteria, such as Lactobacillus, Allobaculum, and Sutterella. Meanwhile, we identified 27 metabolites that decreased and 320 metabolites that increased in the injured spinal cord. Combined with pathway enrichment analysis, five markedly differential amino acids(L-leucine, L-methionine, L-phenylalanine, L-isoleucine and L-valine) were screened out, which play a pivotal role in activating oxidative stress and inflammatory responses following spinal cord injury. Integrated correlation analysis indicated that the alteration of gut microbiota was related to the differences in amino acids, which suggests that disturbances in gut microbiota might participate in the secondary injury through the accumulation of partial metabolites that activate oxidative stress and inflammatory responses. Findings from this study provide a new theoretical basis for improving the secondary injury after spinal cord injury through fecal microbial transplantation.展开更多
A bstract Gut microbiota impacts the health of crustaceans. V ibrio alginolyticus is a main causative pathogen that induces the vibriosis in farmed swimming crabs, Portunus trituberculatus. However, it remains unknown...A bstract Gut microbiota impacts the health of crustaceans. V ibrio alginolyticus is a main causative pathogen that induces the vibriosis in farmed swimming crabs, Portunus trituberculatus. However, it remains unknown whether gut bacteria perform functions during the progression of vibriosis. In this study, 16 SrRNA gene amplicon sequencing was used to investigate temporal alteration of gut bacterial community in swimming crabs in response to 72-h V. alginolyticus challenge. Our results show that V. alginolyticus infection resulted in dynamic changes of bacterial community composition in swimming crabs. Such changes were highlighted by the overwhelming overabundance of V ibrio and a significant fluctuation in the gut bacteria including the bacteria with high relative abundance and especially those with low relative abundance. These findings reveal that crab vibriosis gradually develops with the infection time of V. alginolyticus and tightly relates to the dysbiosis of gut bacterial community structure. This work contributes to our appreciation of the importance of the balance of gut bacterial community structure in maintaining the health of crustaceans.展开更多
Meromictic soda and saline lakes are unique ecosystems characterized by the stability of physical,chemical and biological parameters,and they are distributed all over the world.Lakes located in regions with average an...Meromictic soda and saline lakes are unique ecosystems characterized by the stability of physical,chemical and biological parameters,and they are distributed all over the world.Lakes located in regions with average annual negative air temperature are of particular interest because of the presence of two periods with intensive and dynamic processes:the so-called biological summer and the long ice season with the biological spring.Soda Lake Doroninskoe is located in Eastern Transbaikalia(51°14′N,112°14′E) in the permafrost zone in an extreme continental climate,and is covered by ice for seven months per year.The structure and diversity of the microbial communities throughout the water column of the lake was studied by 16 S r RNA gene amplicon metasequencing.Different species with specific functions were found to dominate at different depths.Metabolically flexible bacteria with a capacity to switch between anoxygenic photosynthesis and aerobic chemotrophic metabolism dominate in soda Lake Doroninskoe.展开更多
Background:The direct use of medical zinc oxide in feed will be abandoned after 2022 in Europe,leaving an urgent need for substitutes to prevent post-weaning disorders.Results:This study investigated the effect of usi...Background:The direct use of medical zinc oxide in feed will be abandoned after 2022 in Europe,leaving an urgent need for substitutes to prevent post-weaning disorders.Results:This study investigated the effect of using rapeseed-seaweed blend(rapeseed meal added two brown macroalgae species Ascophylum nodosum and Saccharina latissima)fermented by lactobacilli(FRS)as feed ingredients in piglet weaning.From d 28 of life to d 85,the piglets were fed one of three different feeding regimens(n=230 each)with inclusion of 0%,2.5% and 5% FRS.In this period,no significant difference of piglet performance was found among the three groups.From a subset of piglets(n=10 from each treatment),blood samples for hematology,biochemistry and immunoglobulin analysis,colon digesta for microbiome analysis,and jejunum and colon tissues for histopathological analyses were collected.The piglets fed with 2.5% FRS manifested alleviated intraepithelial and stromal lymphocytes infiltration in the gut,enhanced colon mucosa barrier relative to the 0% FRS group.The colon microbiota composition was determined using V3 and V1-V8 region 16S rRNA gene amplicon sequencing by Illumina NextSeq and Oxford Nanopore MinION,respectively.The two amplicon sequencing strategies showed high consistency between the detected bacteria.Both sequencing strategies indicated that inclusion of FRS reshaped the colon microbiome of weaned piglets with increased Shannon diversity.Prevotella stercorea was verified by both methods to be more abundant in the piglets supplied with FRS feed,and its abundance was positively correlated with colonic mucosa thickness but negatively correlated with blood concentrations of leucocytes and IgG.Conclusions:FRS supplementation relieved the gut lymphocyte infiltration of the weaned piglets,improved the colon mucosa barrier with altered microbiota composition.Increasing the dietary inclusion of FRS from 2.5% to 5% did not lead to further improvements.展开更多
BACKGROUND The vaginal microbiome plays a critical role in the health of pregnant women and their newborns.Group B Streptococcus(GBS)and vaginal cleanliness significantly affect the vaginal microecosystem and are clos...BACKGROUND The vaginal microbiome plays a critical role in the health of pregnant women and their newborns.Group B Streptococcus(GBS)and vaginal cleanliness significantly affect the vaginal microecosystem and are closely associated with vaginal diseases.AIM To explore the effects of GBS status and vaginal cleanliness on vaginal microecosystems.METHODS We collected 160 vaginal swabs from pregnant women and divided them into the following four groups based on GBS status and vaginal cleanliness:GBS-positive+vaginal cleanliness I–II degree,GBS-negative+vaginal cleanliness I–II degree,GBS-positive+vaginal cleanliness III–IV degree,and GBS-negative+vaginal cleanliness III–IV degree.Samples were subjected to 16S rRNA gene amplicon sequencing.RESULTS Alpha diversity analysis showed that the Shannon index did not significantly differ between the four groups.We identified significant variation in taxa abundance between the GBS-positive and GBS-negative groups and between the vaginal cleanliness I–II degree and III–IV degree groups.Principal coordinate analysis and non-metric multidimensional scaling analysis further confirmed the microbial diversity of the four groups.Moreover,the linear discriminant analysis demonstrated that Lactobacillus jensenii and Actinobacteria were strongly associated with GBS-positive status,and Lactobacillus iners,Lactobacillaceae,Lactobacillus,Lactobacillales,Bacilli and Firmicutes were closely correlated with GBS-negative status.CONCLUSION GBS status and vaginal cleanliness significantly affect vaginal microbiome differences in pregnant women.Our findings provide instructional information for clinical antibiotic treatment in pregnant women with different GBS statuses and vaginal cleanliness degrees.展开更多
Multi-generational planting of Eucalyptus species degrades soil quality but the introduction of legumes can improve soil fertility and microbial diversity.However,the effects of introducing non-legume native tree spec...Multi-generational planting of Eucalyptus species degrades soil quality but the introduction of legumes can improve soil fertility and microbial diversity.However,the effects of introducing non-legume native tree species on soil nutrients and bacterial community structure remain poorly understood.This study investigated the impacts of the conversion of third generation monoculture Eucalyptus plantations to mixed systems including Eucalyptus urograndis with Cinnamomum camphora(EC)and E.urograndis with Castanopsis hystrix(EH),on soil chemical and biochemical properties and bacterial community structure,diversity and functions.First generation E.urophylla plantations were the control.Results show that planting the third generation Eucalyptus led to a significant decrease in p H,organic matter,nutrient content,enzyme activities(invertin,acid phosphataes,and urease),and bacterialα-diversity compare to the controls.However,the mixed planting showed significant improvement in soil chemical and biochemical attributes and bacterialα-diversity,although the E.urograndis and C.hystrix planting had no improvement.Chloroflexi(oligotrophic bacteria)were significantly enriched in third generation Eucalyptus and Eucalyptus+C.hystrix,while proteobacteria increased significantly in the E.urograndis with C.camphora plantings.The relative abundance of multiple metabolic pathways increased significantly in the third generation Eucalyptus plantations whereas membrane transportrelated genes were enriched in soils of the mixed systems.The changes in bacterial community structures in the two mixed systems were driven by diversity,organic matter and acid phosphatase,while bacterial functions were affected by invertase,NO_(3)^(-)-N,diversity and urease.These results suggest that the transformation of successive monoculture Eucalyptus plantations into mixed plantations reduces the depletion of soil nutrients and enhances the ecological function of soil microorganisms.展开更多
Application of nanotechnology in agriculture has been expanded to improve crop production.The impact of nanomaterials(NMs)on factors that influence the survival and function of beneficial microorganisms is a less stud...Application of nanotechnology in agriculture has been expanded to improve crop production.The impact of nanomaterials(NMs)on factors that influence the survival and function of beneficial microorganisms is a less studied aspect that needs to be better understood.Only a few studies have assessed the effects of NMs on beneficial soil microorganisms.This study was conducted to assess the effects of nanofertilizer FertiGroe?N(FG-N)and nano-plant hormone HormoGroe?auxin(HG-A)on the chemical properties and microbial communities of two contrasting soils,Lipa clay loam(CL)and Sariaya sandy loam(SL),over a 35-d incubation period in the laboratory.Bacterial and fungal communities were evaluated using amplicon sequencing analysis within the 16S and internal transcribed spacer regions,respectively.The application of FG-N significantly decreased soil pH,but did not affect total N and available P for both soil types.A significant increase in exchangeable K was observed only in Lipa CL.The application of HG-A had no significant effect on soil chemical properties.Regarding the bacterial community after incubation,the relative abundances of Acidobacteriia,Chthonomonadetes,and Saccharimonadia decreased,whereas Acidimicrobiia,Chloroflexia,and Gemmatimonadetes increased with FG-N application in Lipa CL.The application of HG-A increased the relative abundance of Rubrobacteria,Chthonomonadetes,and Chloroflexia in Lipa CL.For the fungal community,FG-N application increased the relative abundance of Sordariomycetes,Agaricomycetes,and Eurotiomycetes,whereas Dothideomycetes and Mortierellomycetes decreased in Lipa CL after incubation.In Sariaya SL,FG-N application increased the relative abundance of Dothideomycetes,Eurotiomycetes,and Mortierellomycetes,but decreased that of Sordariomycetes and Agaricomycetes.Fungal classes observed in the control samples were not detected in the HG-A treatment,but were recovered after incubation in Lipa CL.The microbial diversity in both soil types showed slight changes with FG-N and HG-A application.Principal coordinate analysis illustrated the clustering of bacterial and fungal taxa between Lipa CL and Sariaya SL.Pearson correlation analysis showed that several bacterial and fungal communities were positively or negatively correlated with soil pH.The results suggest that FG-N can be safely used in crop production and HG-A may be used mainly for vegetative propagation.展开更多
Despite coastal mudflats serving as essential ecological zones interconnecting terrestrial/freshwater and marine systems,little is known about the profiles of antibiotic resistance genes(ARGs)in this area.In this stud...Despite coastal mudflats serving as essential ecological zones interconnecting terrestrial/freshwater and marine systems,little is known about the profiles of antibiotic resistance genes(ARGs)in this area.In this study,characteristics of typical ARGs,involving both intracellular(iARGs)and extracellular ARGs(eARGs)at different physical states,were explored in over 1000 km of coastal mudflats in Eastern China.Results indicated the presence of iARGs and eARGs at states of both freely present or attached by particles.The abundance of eARGs was significantly higher than that of iARGs(87.3%vs 12.7%),and their dominance was more significant than those in other habitats(52.7%-76.3%).ARG abundance,especially for eARGs,showed an increasing trend(p<0.05)from southern(Nantong)to northern(Lianyungang)coastalmudflats.Higher salinity facilitated the transformation from iARGs to eARGs,and smaller soil particle size was conducive to the persistence of eARGs in northern coastal mudflats.This study addresses the neglected function of coastal mudflats as eARGs reservoirs.展开更多
Climate change and human activity have led to the degradation of desert wetlands.Free-living diazotrophs are vital for soil nitrogen input.However,a comprehensive understanding of how soil free-living diazotrophic com...Climate change and human activity have led to the degradation of desert wetlands.Free-living diazotrophs are vital for soil nitrogen input.However,a comprehensive understanding of how soil free-living diazotrophic communities and their co-occurrence patterns respond to desert wetland degradation is lacking.Here,quantitative polymerase chain reaction(qPCR),amplicon sequencing targeting nitrogenase gene(nifH),and network analysis were used to investigate the abundance,diversity,community composition,and co-occurrence patterns of soil free-living diazotrophs along the wetland degradation gradient,i.e.,non-degraded(ND),lightly degraded(LD),moderately degraded(MD),and severely degraded(SD),in the southeastern Mu Us Desert,northern China.The abundance and Shannon,Simpson,Chao 1,and ACE indexes decreased(P<0.05)by 14.6%,20.7%,2.1%,46.5%,and 45.0%,respectively,in SD wetland,whereas no significant difference(P>0.05)was observed between ND and LD wetlands.The relative abundance of Proteobacteria generally decreased(by 53.5%–19.7%)across the different degradation levels,while the relative abundance of Cyanobacteria increased(by 6.2%–40.1%)from ND to MD levels.The abundance,diversity,and community composition of diazotrophs were most strongly related to soil organic carbon,followed by total nitrogen,moisture,and pH.The least number of network nodes and edges and the lowest density were observed for MD and SD wetlands,indicating that the complexity of free-living diazotrophic networks was reduced by continued degeneration.Overall,severe desert wetland degradation affected the abundance,diversity,and network complexity of soil free-living diazotrophs more negatively than light degradation.This degradation promoted the growth of autotrophic diazotrophs and inhibited the growth of heterotrophic diazotrophs.These changes were mostly related to the loss of soil organic carbon.展开更多
Background： The purpose of this study was to investigate how inclusion of chicory forage or ribwort forage in a cereal-based diet influenced the fecal microbial community（microbiome） in newly weaned（35 days of age...Background： The purpose of this study was to investigate how inclusion of chicory forage or ribwort forage in a cereal-based diet influenced the fecal microbial community（microbiome） in newly weaned（35 days of age） piglets.The piglets were fed a cereal-based diet without（B） and with inclusion（80 and 160 g/kg air-dry forage） of vegetative shoots of chicory（C） and leaves of ribwort（R） forage in a 35-day growth trial. Fecal samples were collected at the start（D0）, 17（D17） and 35（D35） days after weaning and profiles of the microbial consortia were generated using terminal restriction fragment length polymorphism（T-RFLP）. 454-FLX pyrosequencing of 16 S r RNA gene amplicons was used to analyze the microbial composition in a subset of the samples already analyzed with T-RFLP.Results： The microbial clustering pattern was primarily dependent on age of the pigs, but diet effects could also be observed. Lactobacilli and enterobacteria were more abundant at D0, whereas the genera Streptococcus, Treponema,Clostridium, Clostridiaceae1 and Coprococcus were present in higher abundances at D35. Pigs fed ribwort had an increased abundance of sequences classified as Treponema and a reduction in lactobacilli. However, the abundance of Prevotellaceae increased with age in on both the chicory and the ribwort diet. Moreover, there were significant correlations between the abundance of Bacteroides and the digested amount of galactose, uronic acids and total non-starch polysaccharides, and between the abundance of Bacteroidales and the digested amount of xylose.Conclusion： This study demonstrated that both chicory and ribwort inclusion in the diet of newly weaned pigs influenced the composition of the fecal microbiota and that digestion of specific dietary components was correlated with species composition of the microbiota. Moreover, this study showed that the gut will be exposed to a dramatic shift in the microbial community structure several weeks after weaning.展开更多
Aeolian dust particles arising from arid and semiarid zones are known to carry microbes by air currents. The effect of wind-borne bacteria on atmospheric bacterial population at various downwind distances from the dus...Aeolian dust particles arising from arid and semiarid zones are known to carry microbes by air currents. The effect of wind-borne bacteria on atmospheric bacterial population at various downwind distances from the dust source regions must be clarified, but has not yet been reported. This study monitored the bacterial abundance and community composition in outdoor aerosol samples in Beijing, China, which is close to the Asian dust source regions, and compared them with the results obtained in a distant region（Osaka, Japan）.The Asian dust collected in Beijing contained（4 ± 3） × 10^4 bacterial cells/m^3, approximately 4 times higher than in Osaka. On 15 April 2015, Beijing experienced severe Asian dust events with a 1000-fold increase in bacterial abundance, relative to non-Asian dust days. Dominant bacterial phyla and classes in Asian dust collected in Beijing were Actinobacteria, Bacilli and Acidobacteria, and the bacterial community composition varied more widely than in Osaka.The bacterial community compositions differed between the Beijing and Osaka dusts, even for the same Asian dust events. These results indicated that aerosol bacterial communities nearer the dust source are more affected by eolian dust than their distant counterparts.展开更多
基金supported by the National Key Research and Development Program(grant number:2022YFC2305304).
文摘Objective Viral encephalitis is an infectious disease severely affecting human health.It is caused by a wide variety of viral pathogens,including herpes viruses,flaviviruses,enteroviruses,and other viruses.The laboratory diagnosis of viral encephalitis is a worldwide challenge.Recently,high-throughput sequencing technology has provided new tools for diagnosing central nervous system infections.Thus,In this study,we established a multipathogen detection platform for viral encephalitis based on amplicon sequencing.Methods We designed nine pairs of specific polymerase chain reaction(PCR)primers for the 12 viruses by reviewing the relevant literature.The detection ability of the primers was verified by software simulation and the detection of known positive samples.Amplicon sequencing was used to validate the samples,and consistency was compared with Sanger sequencing.Results The results showed that the target sequences of various pathogens were obtained at a coverage depth level greater than 20×,and the sequence lengths were consistent with the sizes of the predicted amplicons.The sequences were verified using the National Center for Biotechnology Information BLAST,and all results were consistent with the results of Sanger sequencing.Conclusion Amplicon-based high-throughput sequencing technology is feasible as a supplementary method for the pathogenic detection of viral encephalitis.It is also a useful tool for the high-volume screening of clinical samples.
基金supported by the National Natural Science Foundation of China(42376119 to X.J.)the Project for Seed Industry Vitalization of Jiangsu Province(JBGS[2021]133 to Z.Z.)the Natural Science Foundation of Jiangsu Province(BK20210362 to X.J.).
文摘Fish, which are vital for both aquatic ecosystem functionality and global food supply, rely heavily on theirgastrointestinal tract (GIT) microbiota for the digestion that underpins their growth and health. Takifugu puf-ferfish, which are an example of species evolved through adaptive radiation, possess a GIT that is specialized forantipredator defense and gluttonous feeding behaviors, offering a unique model to explore the effects of GrTcompartmentalization and host genetics on gut microbial communities. Here we compiled 78 full and partial-length 16 S rRNA amplicon datasets across three anteroposteriorly distinct intestinal sites in a cohort of cohab-itating artificial hybrid and purebred Takifugu pufferfishes. Our findings reveal a compositional and functionalbiogeography of pufferfish gut microbiota along the GIT and between host genetics. Additionally, the differentialabundance of specific amplicon sequence variants and their correlation with host genetic backgrounds and in-testinal sections highlight the role of environmental filtering in shaping microbial communities,with certainbacterial taxa exhibiting strong preferences for particular intestinal sites or genetic backgrounds,suggestingpotential localized adaptation or functional specialization. This study enhances our understanding of the intricateinterplay between host genetics, gut anatomy, and microbiota in fish, underscoring the importance of detailedmicrobial profiling in conservation efforts and aquaculture practices, and emphasizing the necessity of integratingfull-length 16 S rRNA sequencing with partial-length datasets to comprehensively understand microbial diversityand function, paving the way for improved fish health management and sustainable aquaculture strategies.
基金This work was.financially supported by the Na-tional Natural Science Foundation of China(Grant No.31601698)the Natural Science Foundation of Zhejiang Province(Grant No.LR 19C140001)+1 种基金the Young Elite Scientist Sponsorship Program by CAST(Grant No.2016QNRC001)the Key Research and Development Program of Zhejiang Province(Grant No.2019C02015).
文摘The microbiome associated with brown planthopper(BPH)plays an important role in mediating host health and fitness.Characterization of the microbial community and its structure is prerequisite for understanding the intricate symbiotic relationships between microbes and host insect.Here,we investigated the bacterial and fungal communities of BPH at different developmental stages using high-throughput amplicon sequencing.Our results revealed that both the bacterial and fungal communities were diverse and dynamic during BPH development.The bacterial communities were generally richer than fungi in each developmental stage.At 97%similarly,19 phyla and 278 genera of bacteria were an-notated,while five fungal phyla comprising 80 genera were assigned.The highest species richness for the bacterial communities was detected in the nymphal stage.The taxonomic diversity of the fungal communities in female adults was generally at a relatively higher level when compared to other developmental stages.The most dominant phylum of bacteria and fungi at each developmental stage all belonged to Proteobacteria and Ascomycota,re-spectively.A significantly lower abundance of bacterial genus Acinetobacter was recorded in the egg stage when compared to other developmental stages,while the dominant fun-gal genus Wallemia was more abundant in the nymph and adult stages than in the egg stage.Additionally,the microbial composition differed between male and female adults,suggesting that the microbial communties In BPH were gender-dependent.Uverall,our study enriches our knowledge on the microbial communities associated with BPH and will provide clues to develop potential biocontrol techniques against this rice pest.
基金National Key Research and Development Program of China(2017YFB0308401).
文摘Wet-salted skin,as a special artificial high-salt environment,is rich in protein,fat,collagen and other nutrient substrates,and is a rich resource of halotolerant and halophilic microorganisms.However,knowledge gaps regarding the microbial community structure and inter taxa associations of wet-salted skin are large.In this study,the spatiotemporal dynamics and community structure of microorganisms present on wet-salted goatskins were investigated using 16S rRNA gene amplicon sequencing and culturable technique.Alpha diversity analysis based on Sobs,Chao,Ace and Shannon indices revealed that microbial diversity on the wet-salted goatskins exhibited a trend of‘down→up→down→flat’with time.During preservation,genera belonging to the bacteria domain such as Aci-netobacter,Weissella and Streptococcus were slowly dying out,whereas those belonging to halophilic archaea such as Natrialba and Haloterrigena were gradually flourishing.Moreover,to resist high-salt stress,microorganisms on the wet-salted goatskin gradually migrated from the outside to the inside,eventually leading to the microbial diversity inside the skin being the same as or even higher than that on the skin surface.Venn diagram analysis revealed that the strains of some genera,including Psychrobacter,Salimicrobium,Salinicola,Ornithinibacillus,Halomonas,Bacillus and Chromohalobacter,were distributed throughout the interior and exterior of the wet-salted goatskin and existed during various periods.Accordingly,45 protease-producing halophilic or halotolerant microorganisms were isolated and screened from the wet-salted goatskin using the gradient dilution plate method.Importantly,16S rRNA genes of some bacteria exhibited less than 99.5%similarity to valid published species,indicating that they likely are novel spe-cies and have a good potential for application.
基金supported by the National Natural Science Foundation of China(31900038 and 31500048)the Natural Science Foundation of Hunan Province,China(2021JJ30029)+3 种基金Research Fund of The State Key Laboratory of Coal Resources and safe Mining(SKLCRSM22KF020)The Independent Exploration and Innovation project for Postgradu-ates of Hunan Province(CX20220357)the Independent Exploration and Innovation project for Postgraduates of Central South University(2022ZZTS0996)the Open Sharing Fund for the Large-scale Instruments and Equipments of Central South University(CSUZC202244).
文摘China has a rich history of cultivating medicinal plants,whose root microbial communities closely interact with the medicinal plants,thereby influencing their growth,health,and medicinal properties.Currently,researchers widely use 16S rRNA gene amplicon sequencing to study these root microbial communities.However,publicly available sequence datasets often lack essential sample information or contain errors,impeding the reuse of the datasets in the future.In this study,we aimed to create a united,reliable,and readily usable source of 16S rRNA gene sequences for medicinal plant root microbiomes.We compiled a catalog of 1392 microbiome samples for 58 medicinal plants from 58 studies,and manually provided essential sample information based on the experimental setup described in the associated papers.We then processed the sequences using a custom pipeline,generating a united catalog of operational taxonomic units(OTUs)and conducting taxonomic classification.We also pre-dicted the ecological functions of the communities for each sample.Finally,we used this dataset,to compare the rhizosphere bacterial communities of Pseudostellaria heterophylla from Fujian and Guizhou Provinces,revealing significant differences in the community composition of the same plant from different geographic locations.By providing a comprehensive and united catalog of amplicon sequences and OTUs for medicinal plant root bacterial communities,this study offers an invaluable resource for future comparative studies and data mining.
文摘Previously, we showed that prophylactic addition of glucose to Harsha Lake water samples could inhibit cyanobacteria growth, at least for a short period of time. The current study tested cyanobacterial control with glucose for the entire Harsha Lake bloom season. Water samples (1000 ml) were collected weekly from Harsha Lake during the algal-bloom season starting June 9 and lasting until August 24, 2022. To each of two 7-liter polypropylene containers, 500 ml of Harsha Lake water was added, and the containers were placed in a controlled environment chamber. To one container labeled “Treated,” 0.15 g of glucose was added, and nothing was added to the container labeled “Control.” After that, three 25 ml samples from each container were collected and used for 16S rRNA gene sequencing each week. Then 1000 ml of Harsha Lake water was newly collected each week, with 500 ml added to each container, along with the addition of 0.15 g glucose to the “Treated” container. Sequencing data were used to examine differences in the composition of bacterial communities between Treated and Control containers. Treatment with glucose altered the microbial communities by 1) reducing taxonomic diversity, 2) largely eliminating cyanobacterial taxa, and 3) increasing the relative abundance of subsets of non-cyanobacterial taxa (such as Proteobacteria and Actinobacteriota). These effects were observed across time despite weekly inputs derived directly from Lake water. The addition of glucose to a container receiving weekly additions of Lake water suppressed the cyanobacterial populations during the entire summer bloom season. The glucose appears to stimulate the diversity of certain bacterial taxa at the expense of the cyanobacteria.
基金supported by the National Natural Science Foundation of China,Nos. 81771346, 82071383the Natural Science Foundation of Shandong Province (Key Project),No. ZR2020KH007+3 种基金the Taishan Scholar Youth Program of Shandong Province,No. tsqn201812156Academic Promotion Program of Shandong First Medical University,Nos. 2019QL025, 2019RC021Spring Industry Leader Talent Support Plan,No. 201984Rongxiang Regenerative Medicine Fund,No. 2019SDRX-23 (all to BN)。
文摘Studies have shown that gut microbiota metabolites can enter the central nervous system via the blood-spinal cord barrier and cause neuroinflammation, thus constituting secondary injury after spinal cord injury. To investigate the correlation between gut microbiota and metabolites and the possible mechanism underlying the effects of gut microbiota on secondary injury after spinal cord injury, in this study, we established mouse models of T8–T10 traumatic spinal cord injury. We used 16 S rRNA gene amplicon sequencing and metabolomics to reveal the changes in gut microbiota and metabolites in fecal samples from the mouse model. Results showed a severe gut microbiota disturbance after spinal cord injury, which included marked increases in pro-inflammatory bacteria, such as Shigella, Bacteroides, Rikenella, Staphylococcus, and Mucispirillum and decreases in anti-inflammatory bacteria, such as Lactobacillus, Allobaculum, and Sutterella. Meanwhile, we identified 27 metabolites that decreased and 320 metabolites that increased in the injured spinal cord. Combined with pathway enrichment analysis, five markedly differential amino acids(L-leucine, L-methionine, L-phenylalanine, L-isoleucine and L-valine) were screened out, which play a pivotal role in activating oxidative stress and inflammatory responses following spinal cord injury. Integrated correlation analysis indicated that the alteration of gut microbiota was related to the differences in amino acids, which suggests that disturbances in gut microbiota might participate in the secondary injury through the accumulation of partial metabolites that activate oxidative stress and inflammatory responses. Findings from this study provide a new theoretical basis for improving the secondary injury after spinal cord injury through fecal microbial transplantation.
基金Supported by the National Natural Science Foundation of China(No.41673076)the Major Agriculture Program of Ningbo(No.2017C110007)the K.C.Wong Magna Fund in Ningbo University
文摘A bstract Gut microbiota impacts the health of crustaceans. V ibrio alginolyticus is a main causative pathogen that induces the vibriosis in farmed swimming crabs, Portunus trituberculatus. However, it remains unknown whether gut bacteria perform functions during the progression of vibriosis. In this study, 16 SrRNA gene amplicon sequencing was used to investigate temporal alteration of gut bacterial community in swimming crabs in response to 72-h V. alginolyticus challenge. Our results show that V. alginolyticus infection resulted in dynamic changes of bacterial community composition in swimming crabs. Such changes were highlighted by the overwhelming overabundance of V ibrio and a significant fluctuation in the gut bacteria including the bacteria with high relative abundance and especially those with low relative abundance. These findings reveal that crab vibriosis gradually develops with the infection time of V. alginolyticus and tightly relates to the dysbiosis of gut bacterial community structure. This work contributes to our appreciation of the importance of the balance of gut bacterial community structure in maintaining the health of crustaceans.
文摘Meromictic soda and saline lakes are unique ecosystems characterized by the stability of physical,chemical and biological parameters,and they are distributed all over the world.Lakes located in regions with average annual negative air temperature are of particular interest because of the presence of two periods with intensive and dynamic processes:the so-called biological summer and the long ice season with the biological spring.Soda Lake Doroninskoe is located in Eastern Transbaikalia(51°14′N,112°14′E) in the permafrost zone in an extreme continental climate,and is covered by ice for seven months per year.The structure and diversity of the microbial communities throughout the water column of the lake was studied by 16 S r RNA gene amplicon metasequencing.Different species with specific functions were found to dominate at different depths.Metabolically flexible bacteria with a capacity to switch between anoxygenic photosynthesis and aerobic chemotrophic metabolism dominate in soda Lake Doroninskoe.
基金financed by Bio-Based Industries Joint Undertaking under the European Union Horizon 2020 research and innovation program under grant agreement No 720755(Macro Cascade project)co-financed by the Innovation Fund Denmark and the University of Copenhagen under a PhD grant(file no.5157-00003B)for PhD studyfinanced by China Scholarship Council under a PhD scholarship(No.201706350028).
文摘Background:The direct use of medical zinc oxide in feed will be abandoned after 2022 in Europe,leaving an urgent need for substitutes to prevent post-weaning disorders.Results:This study investigated the effect of using rapeseed-seaweed blend(rapeseed meal added two brown macroalgae species Ascophylum nodosum and Saccharina latissima)fermented by lactobacilli(FRS)as feed ingredients in piglet weaning.From d 28 of life to d 85,the piglets were fed one of three different feeding regimens(n=230 each)with inclusion of 0%,2.5% and 5% FRS.In this period,no significant difference of piglet performance was found among the three groups.From a subset of piglets(n=10 from each treatment),blood samples for hematology,biochemistry and immunoglobulin analysis,colon digesta for microbiome analysis,and jejunum and colon tissues for histopathological analyses were collected.The piglets fed with 2.5% FRS manifested alleviated intraepithelial and stromal lymphocytes infiltration in the gut,enhanced colon mucosa barrier relative to the 0% FRS group.The colon microbiota composition was determined using V3 and V1-V8 region 16S rRNA gene amplicon sequencing by Illumina NextSeq and Oxford Nanopore MinION,respectively.The two amplicon sequencing strategies showed high consistency between the detected bacteria.Both sequencing strategies indicated that inclusion of FRS reshaped the colon microbiome of weaned piglets with increased Shannon diversity.Prevotella stercorea was verified by both methods to be more abundant in the piglets supplied with FRS feed,and its abundance was positively correlated with colonic mucosa thickness but negatively correlated with blood concentrations of leucocytes and IgG.Conclusions:FRS supplementation relieved the gut lymphocyte infiltration of the weaned piglets,improved the colon mucosa barrier with altered microbiota composition.Increasing the dietary inclusion of FRS from 2.5% to 5% did not lead to further improvements.
文摘BACKGROUND The vaginal microbiome plays a critical role in the health of pregnant women and their newborns.Group B Streptococcus(GBS)and vaginal cleanliness significantly affect the vaginal microecosystem and are closely associated with vaginal diseases.AIM To explore the effects of GBS status and vaginal cleanliness on vaginal microecosystems.METHODS We collected 160 vaginal swabs from pregnant women and divided them into the following four groups based on GBS status and vaginal cleanliness:GBS-positive+vaginal cleanliness I–II degree,GBS-negative+vaginal cleanliness I–II degree,GBS-positive+vaginal cleanliness III–IV degree,and GBS-negative+vaginal cleanliness III–IV degree.Samples were subjected to 16S rRNA gene amplicon sequencing.RESULTS Alpha diversity analysis showed that the Shannon index did not significantly differ between the four groups.We identified significant variation in taxa abundance between the GBS-positive and GBS-negative groups and between the vaginal cleanliness I–II degree and III–IV degree groups.Principal coordinate analysis and non-metric multidimensional scaling analysis further confirmed the microbial diversity of the four groups.Moreover,the linear discriminant analysis demonstrated that Lactobacillus jensenii and Actinobacteria were strongly associated with GBS-positive status,and Lactobacillus iners,Lactobacillaceae,Lactobacillus,Lactobacillales,Bacilli and Firmicutes were closely correlated with GBS-negative status.CONCLUSION GBS status and vaginal cleanliness significantly affect vaginal microbiome differences in pregnant women.Our findings provide instructional information for clinical antibiotic treatment in pregnant women with different GBS statuses and vaginal cleanliness degrees.
基金fully funded by the Natural Science Foundation of Guangdong Province(Grant No.2020A1515011404)Guangxi Major Science and Technology Project(Grant No.AA17204087-9)+2 种基金Guangdong Forestry SciTech Innovation Platform Project(Grant No.2020-KYXM-09)China National Key R&D Program during the 13th Five-year Plan Period(Grant No.2016YFD0600504)the Operation Project for Guangdong Zhanjiang Eucalyptus Forest Ecosystem National Positioning Observation and Research Station(Grant No.2019132141)。
文摘Multi-generational planting of Eucalyptus species degrades soil quality but the introduction of legumes can improve soil fertility and microbial diversity.However,the effects of introducing non-legume native tree species on soil nutrients and bacterial community structure remain poorly understood.This study investigated the impacts of the conversion of third generation monoculture Eucalyptus plantations to mixed systems including Eucalyptus urograndis with Cinnamomum camphora(EC)and E.urograndis with Castanopsis hystrix(EH),on soil chemical and biochemical properties and bacterial community structure,diversity and functions.First generation E.urophylla plantations were the control.Results show that planting the third generation Eucalyptus led to a significant decrease in p H,organic matter,nutrient content,enzyme activities(invertin,acid phosphataes,and urease),and bacterialα-diversity compare to the controls.However,the mixed planting showed significant improvement in soil chemical and biochemical attributes and bacterialα-diversity,although the E.urograndis and C.hystrix planting had no improvement.Chloroflexi(oligotrophic bacteria)were significantly enriched in third generation Eucalyptus and Eucalyptus+C.hystrix,while proteobacteria increased significantly in the E.urograndis with C.camphora plantings.The relative abundance of multiple metabolic pathways increased significantly in the third generation Eucalyptus plantations whereas membrane transportrelated genes were enriched in soils of the mixed systems.The changes in bacterial community structures in the two mixed systems were driven by diversity,organic matter and acid phosphatase,while bacterial functions were affected by invertase,NO_(3)^(-)-N,diversity and urease.These results suggest that the transformation of successive monoculture Eucalyptus plantations into mixed plantations reduces the depletion of soil nutrients and enhances the ecological function of soil microorganisms.
基金funded by the Department of Science and Technology(DOST),Philippine Council for Agriculture,Aquatic and Natural Resources Research and Development(No.N9-102-2A)the DOST,Accelerated Science and Technology Human Resource Development Program of Philippines。
文摘Application of nanotechnology in agriculture has been expanded to improve crop production.The impact of nanomaterials(NMs)on factors that influence the survival and function of beneficial microorganisms is a less studied aspect that needs to be better understood.Only a few studies have assessed the effects of NMs on beneficial soil microorganisms.This study was conducted to assess the effects of nanofertilizer FertiGroe?N(FG-N)and nano-plant hormone HormoGroe?auxin(HG-A)on the chemical properties and microbial communities of two contrasting soils,Lipa clay loam(CL)and Sariaya sandy loam(SL),over a 35-d incubation period in the laboratory.Bacterial and fungal communities were evaluated using amplicon sequencing analysis within the 16S and internal transcribed spacer regions,respectively.The application of FG-N significantly decreased soil pH,but did not affect total N and available P for both soil types.A significant increase in exchangeable K was observed only in Lipa CL.The application of HG-A had no significant effect on soil chemical properties.Regarding the bacterial community after incubation,the relative abundances of Acidobacteriia,Chthonomonadetes,and Saccharimonadia decreased,whereas Acidimicrobiia,Chloroflexia,and Gemmatimonadetes increased with FG-N application in Lipa CL.The application of HG-A increased the relative abundance of Rubrobacteria,Chthonomonadetes,and Chloroflexia in Lipa CL.For the fungal community,FG-N application increased the relative abundance of Sordariomycetes,Agaricomycetes,and Eurotiomycetes,whereas Dothideomycetes and Mortierellomycetes decreased in Lipa CL after incubation.In Sariaya SL,FG-N application increased the relative abundance of Dothideomycetes,Eurotiomycetes,and Mortierellomycetes,but decreased that of Sordariomycetes and Agaricomycetes.Fungal classes observed in the control samples were not detected in the HG-A treatment,but were recovered after incubation in Lipa CL.The microbial diversity in both soil types showed slight changes with FG-N and HG-A application.Principal coordinate analysis illustrated the clustering of bacterial and fungal taxa between Lipa CL and Sariaya SL.Pearson correlation analysis showed that several bacterial and fungal communities were positively or negatively correlated with soil pH.The results suggest that FG-N can be safely used in crop production and HG-A may be used mainly for vegetative propagation.
基金This study was supported by the National Natural Science Foundation of China(No.42177348)the Natural Science Foundation of Jiangsu Province(No.BK20201367)China Postdoctoral Science Foundation(No.2021M701663).
文摘Despite coastal mudflats serving as essential ecological zones interconnecting terrestrial/freshwater and marine systems,little is known about the profiles of antibiotic resistance genes(ARGs)in this area.In this study,characteristics of typical ARGs,involving both intracellular(iARGs)and extracellular ARGs(eARGs)at different physical states,were explored in over 1000 km of coastal mudflats in Eastern China.Results indicated the presence of iARGs and eARGs at states of both freely present or attached by particles.The abundance of eARGs was significantly higher than that of iARGs(87.3%vs 12.7%),and their dominance was more significant than those in other habitats(52.7%-76.3%).ARG abundance,especially for eARGs,showed an increasing trend(p<0.05)from southern(Nantong)to northern(Lianyungang)coastalmudflats.Higher salinity facilitated the transformation from iARGs to eARGs,and smaller soil particle size was conducive to the persistence of eARGs in northern coastal mudflats.This study addresses the neglected function of coastal mudflats as eARGs reservoirs.
基金supported by the National Natural Science Foundation of China(No.41471437)the National Key R&D Program of China(Nos.2016YFA0600801,2017YFC0504504)the West Light Foundation of the Chinese Academy of Sciences(No.XAB2016A04).
文摘Climate change and human activity have led to the degradation of desert wetlands.Free-living diazotrophs are vital for soil nitrogen input.However,a comprehensive understanding of how soil free-living diazotrophic communities and their co-occurrence patterns respond to desert wetland degradation is lacking.Here,quantitative polymerase chain reaction(qPCR),amplicon sequencing targeting nitrogenase gene(nifH),and network analysis were used to investigate the abundance,diversity,community composition,and co-occurrence patterns of soil free-living diazotrophs along the wetland degradation gradient,i.e.,non-degraded(ND),lightly degraded(LD),moderately degraded(MD),and severely degraded(SD),in the southeastern Mu Us Desert,northern China.The abundance and Shannon,Simpson,Chao 1,and ACE indexes decreased(P<0.05)by 14.6%,20.7%,2.1%,46.5%,and 45.0%,respectively,in SD wetland,whereas no significant difference(P>0.05)was observed between ND and LD wetlands.The relative abundance of Proteobacteria generally decreased(by 53.5%–19.7%)across the different degradation levels,while the relative abundance of Cyanobacteria increased(by 6.2%–40.1%)from ND to MD levels.The abundance,diversity,and community composition of diazotrophs were most strongly related to soil organic carbon,followed by total nitrogen,moisture,and pH.The least number of network nodes and edges and the lowest density were observed for MD and SD wetlands,indicating that the complexity of free-living diazotrophic networks was reduced by continued degeneration.Overall,severe desert wetland degradation affected the abundance,diversity,and network complexity of soil free-living diazotrophs more negatively than light degradation.This degradation promoted the growth of autotrophic diazotrophs and inhibited the growth of heterotrophic diazotrophs.These changes were mostly related to the loss of soil organic carbon.
文摘Background： The purpose of this study was to investigate how inclusion of chicory forage or ribwort forage in a cereal-based diet influenced the fecal microbial community（microbiome） in newly weaned（35 days of age） piglets.The piglets were fed a cereal-based diet without（B） and with inclusion（80 and 160 g/kg air-dry forage） of vegetative shoots of chicory（C） and leaves of ribwort（R） forage in a 35-day growth trial. Fecal samples were collected at the start（D0）, 17（D17） and 35（D35） days after weaning and profiles of the microbial consortia were generated using terminal restriction fragment length polymorphism（T-RFLP）. 454-FLX pyrosequencing of 16 S r RNA gene amplicons was used to analyze the microbial composition in a subset of the samples already analyzed with T-RFLP.Results： The microbial clustering pattern was primarily dependent on age of the pigs, but diet effects could also be observed. Lactobacilli and enterobacteria were more abundant at D0, whereas the genera Streptococcus, Treponema,Clostridium, Clostridiaceae1 and Coprococcus were present in higher abundances at D35. Pigs fed ribwort had an increased abundance of sequences classified as Treponema and a reduction in lactobacilli. However, the abundance of Prevotellaceae increased with age in on both the chicory and the ribwort diet. Moreover, there were significant correlations between the abundance of Bacteroides and the digested amount of galactose, uronic acids and total non-starch polysaccharides, and between the abundance of Bacteroidales and the digested amount of xylose.Conclusion： This study demonstrated that both chicory and ribwort inclusion in the diet of newly weaned pigs influenced the composition of the fecal microbiota and that digestion of specific dietary components was correlated with species composition of the microbiota. Moreover, this study showed that the gut will be exposed to a dramatic shift in the microbial community structure several weeks after weaning.
文摘Aeolian dust particles arising from arid and semiarid zones are known to carry microbes by air currents. The effect of wind-borne bacteria on atmospheric bacterial population at various downwind distances from the dust source regions must be clarified, but has not yet been reported. This study monitored the bacterial abundance and community composition in outdoor aerosol samples in Beijing, China, which is close to the Asian dust source regions, and compared them with the results obtained in a distant region（Osaka, Japan）.The Asian dust collected in Beijing contained（4 ± 3） × 10^4 bacterial cells/m^3, approximately 4 times higher than in Osaka. On 15 April 2015, Beijing experienced severe Asian dust events with a 1000-fold increase in bacterial abundance, relative to non-Asian dust days. Dominant bacterial phyla and classes in Asian dust collected in Beijing were Actinobacteria, Bacilli and Acidobacteria, and the bacterial community composition varied more widely than in Osaka.The bacterial community compositions differed between the Beijing and Osaka dusts, even for the same Asian dust events. These results indicated that aerosol bacterial communities nearer the dust source are more affected by eolian dust than their distant counterparts.
