The anaerobic/anoxic/oxic（A2O） process is globally one of the widely used biological sewage treatment processes. This is the first report of a metagenomic analysis using Illumina sequencing of full-scale A2O sludge ...The anaerobic/anoxic/oxic（A2O） process is globally one of the widely used biological sewage treatment processes. This is the first report of a metagenomic analysis using Illumina sequencing of full-scale A2O sludge from a municipal sewage treatment plant.With more than 530,000 clean reads from different taxa and metabolic categories, the metagenome results allow us to gain insight into the functioning of the biological community of the A2O sludge. There are 51 phyla and nearly 900 genera identified from the A2O activated sludge ecosystem. Proteobacteria, Bacteroidetes, Nitrospirae and Chloroflexi are predominant phyla in the activated sludge, suggesting that these organisms play key roles in the biodegradation processes in the A2O sewage treatment system.Nitrospira, Thauera, Dechloromonas and Ignavibacterium, which have abilities to metabolize nitrogen and aromatic compounds, are most prevalent genera. The percent of nitrogen and phosphorus metabolism in the A2O sludge is 2.72% and 1.48%, respectively. In the current A2O sludge, the proportion of Candidatus Accumulibacter is 1.37%, which is several times more than that reported in a recent study of A2O sludge. Among the four processes of nitrogen metabolism, denitrification related genes had the highest number of sequences（76.74%）, followed by ammonification（15.77%）, nitrogen fixation（3.88%） and nitrification（3.61%）. In phylum Planctomycetes, four genera（Planctomyces, Pirellula, Gemmata and Singulisphaera） are included in the top 30 abundant genera, suggesting the key role of ANAMMOX in nitrogen metabolism in the A2O sludge.展开更多
In this study, the 454 pyrosequencing technology was used to analyze the DNA of the Microcystis aeruginosa symbiosis system from cyanobacterial algal blooms in Taihu Lake, China. We generated 183 228 reads with an ave...In this study, the 454 pyrosequencing technology was used to analyze the DNA of the Microcystis aeruginosa symbiosis system from cyanobacterial algal blooms in Taihu Lake, China. We generated 183 228 reads with an average length of 248 bp. Running the 454 assembly algorithm over our sequences yielded 22 239 significant contigs. After excluding the M. aeruginosa sequences, we obtained 1 322 assembled contigs longer than 1 000 bp. Taxonomic analysis indicated that four kingdoms were represented in the community: Archaea (n = 9; 0.01%), Bacteria (n = 98 921; 99.6%), Eukaryota (n = 373; 3.7%), and Viruses (n = 18; 0.02%). The bacterial sequences were predominantly Alphaproteobacteria (n = 41 805; 83.3%), Betaproteobacteria (n = 5 254; 10.5%) and Gammaproteobacteria (n = 1 180; 2.4%). Gene annotations and assignment of COG (clusters of orthologous groups) functional categories indicate that a large number of the predicted genes are involved in metabolic, genetic, and environmental information processes. Our results demonstrate the extraordinary diversity of a microbial community in an ectosymbiotic system and further establish the tremendous utility of pyrosequencing.展开更多
Lipolytic enzymes, including esterases and lipases, represent a group of hydrolases that catalyze the cleavage and formation of ester bonds. A novel esterase gene, scsEst01, was cloned from a South China Sea sediment ...Lipolytic enzymes, including esterases and lipases, represent a group of hydrolases that catalyze the cleavage and formation of ester bonds. A novel esterase gene, scsEst01, was cloned from a South China Sea sediment metagenome. The scsEst01 gene consisted of 921 bp encoding 307 amino acid residues. The predicted amino acid sequence shared less than 90% identity with other lipolytic enzymes in the NCBI nonredundant protein database. Scs Est01 was successfully co-expressed in E scherichia coli BL21(DE3) with chaperones(dnaK-dna J-grp E) to prevent the formation of inclusion bodies. The recombinant protein was purified on an immobilized metal ion affinity column containing chelating Sepharose charged with Ni2 +. The enzyme was characterized using p-nitrophenol butyrate as a substrate. Scs Est01 had the highest lipolytic activity at 35℃ and p H 8.0, indicative of a meso-thermophilic alkaline esterase. Scs Est01 was thermostable at 20℃. The lipolytic activity of scs Est01 was strongly increased by Fe2 +, Mn 2+ and 1% Tween 80 or Tween 20.展开更多
With the aim of identifying novel thermostable esterases, comprehensive sequence databases and cloned fosmid libraries of metagenomes derived from an offshore oil reservoir on the Norwegian Continental Shelf were scre...With the aim of identifying novel thermostable esterases, comprehensive sequence databases and cloned fosmid libraries of metagenomes derived from an offshore oil reservoir on the Norwegian Continental Shelf were screened for enzyme candidates using both sequence-and function-based screening. From several candidates identified in both approaches, one enzyme discovered by the functional approach was verified as a novel esterase and subjected to a deeper characterization. The enzyme was successfully over-produced in Escherichia coli and was shown to be thermostable up to 90°C, with the highest esterase activity on short-chain ester substrates and with tolerance to solvents and metal ions. The fact that the thermostable enzyme was solely found by functional screening of the oil reservoir metagenomes illustrates the importance of this approach as a complement to purely sequence-based screening, in which the enzyme candidate was not detected. In addition, this example indicates the large potential of deep-sub-surface oil reservoir metagenomes as a source of novel, thermostable enzymes of potential relevance for industrial applications.展开更多
Antimicrobial resistance has become a global problem that poses great threats to human health. Antimicrobials are widely used in broiler chicken production and consequently affect their gut microbiota and resistome. T...Antimicrobial resistance has become a global problem that poses great threats to human health. Antimicrobials are widely used in broiler chicken production and consequently affect their gut microbiota and resistome. To better understand how continuous antimicrobial use in farm animals alters their microbial ecology, we used a metagenomic approach to investigate the effects of pulsed antimicrobial administration on the bacterial community, antibiotic resistance genes(ARGs) and ARG bacterial hosts in the feces of broiler chickens. Chickens received three 5-day courses of individual or combined antimicrobials, including amoxicillin, chlortetracycline and florfenicol. The florfenicol administration significantly increased the abundance of mcr-1 gene accompanied by floR gene, while amoxicillin significantly increased the abundance of genes encoding the AcrAB-tolC multidrug efflux pump(marA, soxS, sdiA, rob, evgS and phoP).These three antimicrobials all led to an increase in Proteobacteria. The increase in ARG host, Escherichia, was mainly attributed to the β-lactam, chloramphenicol and tetracycline resistance genes harbored by Escherichia under the pulsed antimicrobial treatments. These results indicated that pulsed antimicrobial administration with amoxicillin,chlortetracycline, florfenicol or their combinations significantly increased the abundance of Proteobacteria and enhanced the abundance of particular ARGs. The ARG types were occupied by the multidrug resistance genes and had significant correlations with the total ARGs in the antimicrobial-treated groups. The results of this study provide comprehensive insight into pulsed antimicrobial-mediated alteration of chicken fecal microbiota and resistome.展开更多
White sand heath forests(WS) or kerangas, an unusual variant of tropical forests in Borneo, characterized by open scrubby vegetation, low productivity, and distinctive plant species composition and soil microbial comm...White sand heath forests(WS) or kerangas, an unusual variant of tropical forests in Borneo, characterized by open scrubby vegetation, low productivity, and distinctive plant species composition and soil microbial community, are regarded as a stressful lowpH and/or nutrient environment. We investigated whether the functional soil metagenome also shows a predicted set of indicators of stressful conditions in WS. Based on stress-tolerant strategies exhibited by larger organisms, we hypothesized that genes for stress tolerance, dormancy, sporulation, and nutrient processing are more abundant in the soil microbiota of WS. We also hypothesized that there is less evidence of biotic interaction in white sand soils, with lower connectivity and fewer genes related to organismic interactions. In Brunei, we sampled soils from a WS and a normal primary dipterocarp forest, together with an inland heath, an intermediate forest type. Soil DNA was extracted, and shotgun sequencing was performed using Illumina HiSeq platform, with classification by the Metagenomics Rapid Annotation using Subsystem Technology(MG-RAST). The results, on one hand, supported our hypothesis(on greater abundance of dormancy, virulence, and sporulation-related genes). However, some aspects of our results showed no significant difference(specifically in stress tolerance, antibiotic resistance, viruses, and clustered regularly interspaced short palindrome repeats(CRISPRs)). It appears that in certain respects, the extreme white sand environment produces the predicted strategy of less biotic interaction, but exhibits high soil microbiota connectivity and functional diversity.展开更多
Wild bees are ecologically vital but increasingly threatened by anthropogenic activities,leading to uncertain survival and health outcomes in urban environments.The gut microbiome contains features indicating host hea...Wild bees are ecologically vital but increasingly threatened by anthropogenic activities,leading to uncertain survival and health outcomes in urban environments.The gut microbiome contains features indicating host health and reflecting long-term evolutionary adaptation and acute reactions to real-time stressors.Moving beyond bacteria,we propose a comprehensive analysis integrating diet,bacteriome,virome,resistome,and their association to understand the survival status of urban lives better.We conducted a study on mason bees(Osmia excavata)across 10 urban agricultural sites in Suzhou,China,using shotgun gut metagenome sequencing for data derived from total gut DNA.Our findings revealed that most ingested pollen originated from Brassica crops and the unexpected garden tree Plantanus,indicating that floral resources at the 10 sites supported Osmia but with limited plant diversity.Varied city landscapes revealed site-specific flowers that all contributed to Osmia sustenance.The gut bacterial community,dominated by Gammaproteobacteria,showed remarkable structural stability across 8 sites but suggested perturbations at 2 sites.Antibiotic resistance gene profiles highly varied across 10 sites with prevalent unclassified drug classes,highlighting environmental threats to both bees and humans.The virome analysis identified honeybee pathogens,suggesting potential virus spillover.Many unknown bacteriophages were detected,some of which targeted the core gut bacteria,underscoring their role in maintaining gut homeostasis.These multifaceted metagenomic insights hold the potential to predict bee health and identify environmental threats,thereby guiding probiotic development and city management for effective bee conservation.展开更多
The plankton community plays an especially important role in the functioning of aquatic ecosystems and also in biogeochemical cycles. Since the beginning of marine research expeditions in the 1870s, an enormous number...The plankton community plays an especially important role in the functioning of aquatic ecosystems and also in biogeochemical cycles. Since the beginning of marine research expeditions in the 1870s, an enormous number of planktonic organisms have been described and studied. Plankton investigation has become one of the most important areas of aquatic ecological study, as well as a crucial component of aquatic environmental evaluation. Nonetheless, traditional investigations have mainly focused on morphospecies composition, abundances and dynamics, which primarily depend on morphological identification and counting under microscopes. However, for many species/groups, with few readily observable characteristics, morphological identification and counting have historically been a difficult task. Over the past decades, microbiologists have endeavored to apply and extend molecular techniques to address questions in microbial ecology. These culture-independent studies have generated new insights into microbial ecology. One such strategy, metagenome-based analysis, has also proved to be a powerful tool for plankton research. This mini-review presents a brief history of plankton research using morphological and metagenome-based approaches and the potential applications and further directions of metagenomic analyses in plankton ecological studies are discussed. The use of metagenome-based approaches for plankton ecological study in aquatic ecosystems is encouraged.展开更多
Using high-throughput sequencing on metagenome to analyze marine microbial community, it is one of current main issues in the field of environmental microbe research. In this paper, we conducted the functional analysi...Using high-throughput sequencing on metagenome to analyze marine microbial community, it is one of current main issues in the field of environmental microbe research. In this paper, we conducted the functional analysis on seven samples of metagenomic data from different depth seawater in Hawaii. The results of gene prediction and function annotation indicate that there are large amounts of potential novel genes of which functions remain unknown at present. Based on the gene annotation, codon usage bias is studied on ribosomal protein-related genes and shows an evident influence by the marine extreme environment. Furthermore, focusing on the marine environmental differences such as light intensity, dissolved oxygen, temperature and pressure among various depths, comparative analysis is carried out on related genes and metabolic pathways. Thus, the understanding as well as new insights into the correlation between marine environment and microbes are proposed at molecular level. Therefore, the studies herein afford a clue to reveal the special living strategies of microbial community from sea surface to deep sea.展开更多
Estimating taxonomic content constitutes a key problem in metagenomic sequencing data analysis.However,extracting such content from high-throughput data of next-generation sequencing is very time-consuming with the cu...Estimating taxonomic content constitutes a key problem in metagenomic sequencing data analysis.However,extracting such content from high-throughput data of next-generation sequencing is very time-consuming with the currently available software.Here,we present CloudLCA,a parallel LCA algorithm that significantly improves the efficiency of determining taxonomic composition in metagenomic data analysis.Results show that CloudLCA(1)has a running time nearly linear with the increase of dataset magnitude,(2)displays linear speedup as the number of processors grows,especially for large datasets,and(3)reaches a speed of nearly 215 million reads each minute on a cluster with ten thin nodes.In comparison with MEGAN,a well-known metagenome analyzer,the speed of CloudLCA is up to 5 more times faster,and its peak memory usage is approximately 18.5%that of MEGAN,running on a fat node.CloudLCA can be run on one multiprocessor node or a cluster.It is expected to be part of MEGAN to accelerate analyzing reads,with the same output generated as MEGAN,which can be import into MEGAN in a direct way to finish the following analysis.Moreover,CloudLCA is a universal solution for finding the lowest common ancestor,and it can be applied in other fields requiring an LCA algorithm.展开更多
In this study,we introduce a novel bioinformatics program,Spore-associated Symbiotic Microbes Position-specific Function(SeSaMe PS Function),for position-specific functional analysis of short sequences derived from me...In this study,we introduce a novel bioinformatics program,Spore-associated Symbiotic Microbes Position-specific Function(SeSaMe PS Function),for position-specific functional analysis of short sequences derived from metagenome sequencing data of the arbuscular mycorrhizal fungi.The unique advantage of the program lies in databases created based on genus-specific sequence properties derived from protein secondary structure,namely amino acid usages,codon usages,and codon contexts of 3-codon DNA 9-mers.SeSaMe PS Function searches a query sequence against reference sequence database,identifies 3-codon DNA 9-mers with structural roles,and creates a comparative dataset containing the codon usage biases of the 3-codon DNA 9-mers from 54 bacterial and fungal genera.The program applies correlation principal component analysis in conjunction with K-means clustering method to the comparative dataset.3-codon DNA 9-mers clustered as a sole member or with only a few members are often structurally and functionally distinctive sites that provide useful insights into important molecular interactions.The program provides a versatile means for studying functions of short sequences from metagenome sequencing and has a wide spectrum of applications.SeSaMe PS Function is freely accessible at www.fungalsesame.org.展开更多
Analysis of environmental samples for bacterial antibiotic resistance genes may have different objectives and analysis strategies. In some cases, the purpose was to study diversity and evolution of genes that could be...Analysis of environmental samples for bacterial antibiotic resistance genes may have different objectives and analysis strategies. In some cases, the purpose was to study diversity and evolution of genes that could be grouped within a mechanism of antibiotic resistance. Different protocols have been designed for detection and confirmation that a functional gene was found. In this study, we present a sequence-based screening of candidate genes encoding beta-lactamases in 14 metagenomes of Antarctic microbial mats. The samples were obtained from different sites, representing diverse biogeographic regions of maritime and continental Antarctica. A protocol was designed based on generation of Hidden Markov Models from the four beta-lactamase classes by Ambler classification, using sequences from the Comprehensive Antibiotic Resistance Database (CARD). The models were used as queries for metagenome analysis and recovered contigs were subsequently annotated using RAST. According to our analysis, 14 metagenomes analyzed contain A, B and C beta-lactamase genes. Class D genes, however, were identified in 11 metagenomes. The most abundant was class C (46.8%), followed by classes B (35.5%), A (14.2%) and D (3.5%). A considerable number of sequences formed clusters which included, in some cases, contigs from different metagenomes. These assemblies are clearly separated from reference clusters, previously identified using CARD beta-lactamase sequences. While bacterial antibiotic resistance is a major challenge of public health worldwide, our results suggest that environmental diversity of beta-lactamase genes is higher than that currently reported, although this should be complemented with gene function analysis.展开更多
Cold seeps in the deep sea are closely linked to energy exploration as well as global climate change.The alkane-dominated chemical energy-driven model makes cold seeps an oasis of deep-sea life,showcasing an unparalle...Cold seeps in the deep sea are closely linked to energy exploration as well as global climate change.The alkane-dominated chemical energy-driven model makes cold seeps an oasis of deep-sea life,showcasing an unparalleled reservoir of microbial genetic diversity.Here,by analyzing 113 metagenomes collected from 14 global sites across 5 cold seep types,we present a comprehensive Cold Seep Microbiomic Database(CSMD)to archive the genomic and functional diversity of cold seep microbiomes.The CSMD includes over 49 million non-redundant genes and 3175 metagenome-assembled genomes,which represent 1895 species spanning 105 phyla.In addition,beta diversity analysis indicates that both the sampling site and cold seep type have a substantial impact on the prokaryotic microbiome community composition.Heterotrophic and anaerobic metabolisms are prevalent in microbial communities,accompanied by considerable mixotrophs and facultative anaerobes,highlighting the versatile metabolic potential in cold seeps.Furthermore,secondary metabolic gene cluster analysis indicates that at least 98.81%of the sequences potentially encode novel natural products,with ribosomally synthesized and post-translationally modified peptides being the predominant type widely distributed in archaea and bacteria.Overall,the CSMD represents a valuable resource that would enhance the understanding and utilization of global cold seep microbiomes.展开更多
Dietary fat content can reduce the methane production of dairy cows;however,the relevance fatty acid(FA)composition has towards this inhibitory effect is debatable.Furthermore,in-depth studies elucidating the effects ...Dietary fat content can reduce the methane production of dairy cows;however,the relevance fatty acid(FA)composition has towards this inhibitory effect is debatable.Furthermore,in-depth studies elucidating the effects of unsaturated fatty acids(UFA)on rumen function and the mechanism of reducing methane(CH_(4))production are lacking.This study exposed 10 Holstein cows with the same parity,similar milk yield to two total mixed rations:low unsaturated FA(LUFA)and high unsaturated FA(HUFA)with similar fat content.The LUFA group mainly added fat powder(C16:0>90%),and the HUFA group mainly replaced fat powder with extruded flaxseed.The experiment lasted 26 d,the last 5 d of which,gas exchange in respiratory chambers was conducted to measure gas emissions.We found that an increase in the UFA in diet did not affect milk production(P>0.05)and could align the profile of milk FAs more closely with modern human nutritional requirements.Furthermore,we found that increasing the UFA content in the diet lead to a decrease in the abundance of Methanobrevibacter in the rumen(|linear discriminant analysis[LDA]score|>2 and P 2 and P<0.05),which ultimately decreased CH4 production(P<0.05).Our results illustrated the mechanism involving decreased CH4 production when fed a UFA diet in dairy cows.We believe that our study provides new evidence to explore CH4 emission reduction measures for dairy cows.展开更多
Background:In the dynamic progression of root canal infections,the resultant change in environmental conditions directs the adaptation of the microbiome in terms of richness,evenness,and diversity.Objective:The goal o...Background:In the dynamic progression of root canal infections,the resultant change in environmental conditions directs the adaptation of the microbiome in terms of richness,evenness,and diversity.Objective:The goal of this study is to contrast the interradicular bacterial community structures of teeth in acute and chronic stages and investigate potential microorganisms associated with persistent apical periapical infections.Methods:Interradicular samples were collected from 10 teeth in the apical periodontitis group and 10 teeth in the chronic apical periodontitis group.High-throughput next-generation sequencing(NGS)–based microbial identification through the Illumina platform was used to characterize the complex intraradicular microbial communities in acute and chronic root canal infections.Results:Bacteria were the major domain,with a prevalence of>97%(acute cases:98.11%and chronic cases:97.6%)compared to eukaryotes and archaea.Bacterial diversity was relatively higher in acute compared to chronic conditions under 10 and 9 phyla,79 and 64 genera,and 172 and 135 species,respectively.These endodontically infecting bacteria belonged to Firmicutes(47.21%),Bacteroidetes(20.07%),and Proteobacteria(10.72%)in acute conditions,while in the chronic stage,Firmicutes(40.85%),Proteobacteria(27.80%),and Actinobacteria(14.79%)were abundant.The phylum Candidatus Saccharibacteria was exclusively found in acute samples.Spirochaetes and Synergistetes were found predominantly in acute infections compared to chronic infections.Bacillus and Lactobacillus were found in equal and highest abundance under the phylum Firmicutes in both conditions.Conclusion:This study provides information on the differential microbial community present in the apical root canal system of teeth with acute and chronic apical periodontitis and contributes to new approaches or channels for future research on preventive measures and therapeutic protocols during disease progression and treatment.However,functional characterization and detection of antimicrobial resistance in these two clinical conditions can supplement these findings for deciding routine drug treatment for periodontal infections.展开更多
Wu et al recently applied multi-region 16S rRNA sequencing to characterize the gastric cancer microbiome,demonstrating improved taxonomic resolution and detection sensitivity over conventional single-region approaches...Wu et al recently applied multi-region 16S rRNA sequencing to characterize the gastric cancer microbiome,demonstrating improved taxonomic resolution and detection sensitivity over conventional single-region approaches.While the study represents a valuable methodological step forward,it remains limited by singlecenter design,lack of quantitative calibration,and insufficient control for contamination and inter-laboratory variability.This editorial critically appraises these methodological gaps and emphasizes that future efforts must focus on harmonized,consensus-driven workflows to ensure reproducibility and clinical reliability.The translational potential of multi-region 16S lies in moving from descriptive microbial profiling to actionable clinical integration,particularly for recurrence prediction,treatment-response monitoring,and perioperative complication risk assessment.By addressing these methodological,economic,and ethical challenges,the field can advance toward evidence-based and clinically deployable microbiome-guided precision oncology.展开更多
Blood deficiency syndrome(BDS)refers to a pathological state with blood dysfunction and organ dystrophy in traditional Chinese medicine.Danggui Wuji granules(DWG)was developed from a formula containing Angelicae Sinen...Blood deficiency syndrome(BDS)refers to a pathological state with blood dysfunction and organ dystrophy in traditional Chinese medicine.Danggui Wuji granules(DWG)was developed from a formula containing Angelicae Sinensis Radix and Musculus et Os Galli Domestici.Herein,we investigated the mechanism of DWG in treating BDS by modulating gut microbiota.We found that DWG protected mice from BDS by elevating the levels of red blood cell count,hemoglobin,and hematocrit in peripheral blood and increasing the erythrocyte membrane Na+-K+-ATPase activity.Danggui Wuji granules changed the composition and metabolites of colonic flora.Notably,Lactobacillus,Muribaculaceae,and Alistipes were the main genera showing changes after DWG treatment.Our findings revealed that DWG presented a positive therapeutic effect on BDS in mice by regulating the gut microbiota and metabolites.The protective mechanism of DWG was associated with pathways such as metabolic pathways,biosynthesis of secondary metabolites,ABC transporters,ribosome,thyroid hormone synthesis,lysine degradation,galactose metabolism,tyrosine metabolism,etc.展开更多
Background:Accurately and efficiently extracting microbial genomic sequences from complex metagenomic data is crucial for advancing our understanding in fields such as clinical diagnostics,environmental microbiology,a...Background:Accurately and efficiently extracting microbial genomic sequences from complex metagenomic data is crucial for advancing our understanding in fields such as clinical diagnostics,environmental microbiology,and biodiversity.As sequencing technologies evolve,this task becomes increasingly challenging due to the intricate nature of microbial communities and the vast amount of data generated.Especially in intensive care units(ICUs),infections caused by antibiotic-resistant bacteria are increasingly prevalent among critically ill patients,significantly impacting the effectiveness of treatments and patient prognoses.Therefore,obtaining timely and accurate information about infectious pathogens is of paramount importance for the treatment of patients with severe infections,which enables precisely targeted anti-infection therapies,and a tool that can extract microbial genomic sequences from metagenomic dataset would be of help.Methods:We developed MetaGeneMiner to help with retrieving specific microbial genomic sequences from metagenomes using a k-mer-based approach.It facilitates the rapid and accurate identification and analysis of pathogens.The tool is designed to be user-friendly and efficient on standard personal computers,allowing its use across a wide variety of settings.We validated MetaGeneMiner using eight metagenomic samples from ICU patients,which demonstrated its efficiency and accuracy.Results:The software extensively retrieved coding sequences of pathogens Acinetobacter baumannii and herpes simplex virus type 1 and detected a variety of resistance genes.All documentation and source codes for MetaGeneMiner are freely available at https://gitee.com/sculab/MetaGeneMiner.Conclusions:It is foreseeable that MetaGeneMiner possesses the potential for applications across multiple domains,including clinical diagnostics,environmental microbiology,gut microbiome research,as well as biodiversity and conservation biology.Particularly in ICU settings,MetaGeneMiner introduces a novel,rapid,and precise method for diagnosing and treating infections in critically ill patients.This tool is capable of efficiently identifying infectious pathogens,guiding personalized and precise treatment strategies,and monitoring the development of antibiotic resistance,significantly impacting the diagnosis and treatment of severe infections.展开更多
Microbes are increasingly being implicated in autoimmune disease.This calls for a re-evaluation of how these chronic inflammatory illnesses are routinely treated.The standard of care for autoimmune disease remains the...Microbes are increasingly being implicated in autoimmune disease.This calls for a re-evaluation of how these chronic inflammatory illnesses are routinely treated.The standard of care for autoimmune disease remains the use of medications that slow the immune response,while treatments aimed at eradicating microbes seek the exact opposite-stimulation of the innate immune response.Immunostimulation is complicated by a cascade of sequelae,including exacerbated inflammation,which occurs in response to microbial death.Over the past 8 years,we have collaborated with American and international clinical professionals to research a model-based treatment for inflammatory disease.This intervention,designed to stimulate the innate immune response,has required a reevaluation of disease progression and amelioration.Paramount is the inherent conflict between palliation and microbicidal efficacy.Increased microbicidal activity was experienced as immunopathology-a temporary worsening of symptoms.Further studies are needed,but they will require careful planning to manage this immunopathology.展开更多
基金supported by the National Natural Science Foundation of China (No. 41430643)
文摘The anaerobic/anoxic/oxic（A2O） process is globally one of the widely used biological sewage treatment processes. This is the first report of a metagenomic analysis using Illumina sequencing of full-scale A2O sludge from a municipal sewage treatment plant.With more than 530,000 clean reads from different taxa and metabolic categories, the metagenome results allow us to gain insight into the functioning of the biological community of the A2O sludge. There are 51 phyla and nearly 900 genera identified from the A2O activated sludge ecosystem. Proteobacteria, Bacteroidetes, Nitrospirae and Chloroflexi are predominant phyla in the activated sludge, suggesting that these organisms play key roles in the biodegradation processes in the A2O sewage treatment system.Nitrospira, Thauera, Dechloromonas and Ignavibacterium, which have abilities to metabolize nitrogen and aromatic compounds, are most prevalent genera. The percent of nitrogen and phosphorus metabolism in the A2O sludge is 2.72% and 1.48%, respectively. In the current A2O sludge, the proportion of Candidatus Accumulibacter is 1.37%, which is several times more than that reported in a recent study of A2O sludge. Among the four processes of nitrogen metabolism, denitrification related genes had the highest number of sequences（76.74%）, followed by ammonification（15.77%）, nitrogen fixation（3.88%） and nitrification（3.61%）. In phylum Planctomycetes, four genera（Planctomyces, Pirellula, Gemmata and Singulisphaera） are included in the top 30 abundant genera, suggesting the key role of ANAMMOX in nitrogen metabolism in the A2O sludge.
基金Supported by the Knowledge Innovation Program of Chinese Academy of Sciences (No. KSCX2-YW-G-073)
文摘In this study, the 454 pyrosequencing technology was used to analyze the DNA of the Microcystis aeruginosa symbiosis system from cyanobacterial algal blooms in Taihu Lake, China. We generated 183 228 reads with an average length of 248 bp. Running the 454 assembly algorithm over our sequences yielded 22 239 significant contigs. After excluding the M. aeruginosa sequences, we obtained 1 322 assembled contigs longer than 1 000 bp. Taxonomic analysis indicated that four kingdoms were represented in the community: Archaea (n = 9; 0.01%), Bacteria (n = 98 921; 99.6%), Eukaryota (n = 373; 3.7%), and Viruses (n = 18; 0.02%). The bacterial sequences were predominantly Alphaproteobacteria (n = 41 805; 83.3%), Betaproteobacteria (n = 5 254; 10.5%) and Gammaproteobacteria (n = 1 180; 2.4%). Gene annotations and assignment of COG (clusters of orthologous groups) functional categories indicate that a large number of the predicted genes are involved in metabolic, genetic, and environmental information processes. Our results demonstrate the extraordinary diversity of a microbial community in an ectosymbiotic system and further establish the tremendous utility of pyrosequencing.
基金Supported by the Strategic Priority Research Program of Chinese Academy of Sciences(No.XDA11030404)the National High Technology Research and Development Program of China(863 Program)(Nos.2012AA092103,2014AA093501,2014AA093505)+1 种基金the Knowledge Innovation Program of Chinese Academy of Sciences(No.KZCX2-YW-JC201)the Open Project Program of Key Laboratory of Marine Bio-Resources Sustainable Utilization,South China Sea Institute of Oceanology,Chinese Academy of Sciences(No.LMB121006)
文摘Lipolytic enzymes, including esterases and lipases, represent a group of hydrolases that catalyze the cleavage and formation of ester bonds. A novel esterase gene, scsEst01, was cloned from a South China Sea sediment metagenome. The scsEst01 gene consisted of 921 bp encoding 307 amino acid residues. The predicted amino acid sequence shared less than 90% identity with other lipolytic enzymes in the NCBI nonredundant protein database. Scs Est01 was successfully co-expressed in E scherichia coli BL21(DE3) with chaperones(dnaK-dna J-grp E) to prevent the formation of inclusion bodies. The recombinant protein was purified on an immobilized metal ion affinity column containing chelating Sepharose charged with Ni2 +. The enzyme was characterized using p-nitrophenol butyrate as a substrate. Scs Est01 had the highest lipolytic activity at 35℃ and p H 8.0, indicative of a meso-thermophilic alkaline esterase. Scs Est01 was thermostable at 20℃. The lipolytic activity of scs Est01 was strongly increased by Fe2 +, Mn 2+ and 1% Tween 80 or Tween 20.
文摘With the aim of identifying novel thermostable esterases, comprehensive sequence databases and cloned fosmid libraries of metagenomes derived from an offshore oil reservoir on the Norwegian Continental Shelf were screened for enzyme candidates using both sequence-and function-based screening. From several candidates identified in both approaches, one enzyme discovered by the functional approach was verified as a novel esterase and subjected to a deeper characterization. The enzyme was successfully over-produced in Escherichia coli and was shown to be thermostable up to 90°C, with the highest esterase activity on short-chain ester substrates and with tolerance to solvents and metal ions. The fact that the thermostable enzyme was solely found by functional screening of the oil reservoir metagenomes illustrates the importance of this approach as a complement to purely sequence-based screening, in which the enzyme candidate was not detected. In addition, this example indicates the large potential of deep-sub-surface oil reservoir metagenomes as a source of novel, thermostable enzymes of potential relevance for industrial applications.
基金supported by the Laboratory of Lingnan Modern Agriculture Project, China (NT2021006)the Foundation for Innovative Research Groups of the National Natural Science Foundation of China (32121004)the Local Innovative and Research Teams Project of Guangdong Pearl River Talents Program, China (2019BT02N054)。
文摘Antimicrobial resistance has become a global problem that poses great threats to human health. Antimicrobials are widely used in broiler chicken production and consequently affect their gut microbiota and resistome. To better understand how continuous antimicrobial use in farm animals alters their microbial ecology, we used a metagenomic approach to investigate the effects of pulsed antimicrobial administration on the bacterial community, antibiotic resistance genes(ARGs) and ARG bacterial hosts in the feces of broiler chickens. Chickens received three 5-day courses of individual or combined antimicrobials, including amoxicillin, chlortetracycline and florfenicol. The florfenicol administration significantly increased the abundance of mcr-1 gene accompanied by floR gene, while amoxicillin significantly increased the abundance of genes encoding the AcrAB-tolC multidrug efflux pump(marA, soxS, sdiA, rob, evgS and phoP).These three antimicrobials all led to an increase in Proteobacteria. The increase in ARG host, Escherichia, was mainly attributed to the β-lactam, chloramphenicol and tetracycline resistance genes harbored by Escherichia under the pulsed antimicrobial treatments. These results indicated that pulsed antimicrobial administration with amoxicillin,chlortetracycline, florfenicol or their combinations significantly increased the abundance of Proteobacteria and enhanced the abundance of particular ARGs. The ARG types were occupied by the multidrug resistance genes and had significant correlations with the total ARGs in the antimicrobial-treated groups. The results of this study provide comprehensive insight into pulsed antimicrobial-mediated alteration of chicken fecal microbiota and resistome.
基金supported by the National Research Foundation (NRF) of Korea (No. NRF-040920150076)
文摘White sand heath forests(WS) or kerangas, an unusual variant of tropical forests in Borneo, characterized by open scrubby vegetation, low productivity, and distinctive plant species composition and soil microbial community, are regarded as a stressful lowpH and/or nutrient environment. We investigated whether the functional soil metagenome also shows a predicted set of indicators of stressful conditions in WS. Based on stress-tolerant strategies exhibited by larger organisms, we hypothesized that genes for stress tolerance, dormancy, sporulation, and nutrient processing are more abundant in the soil microbiota of WS. We also hypothesized that there is less evidence of biotic interaction in white sand soils, with lower connectivity and fewer genes related to organismic interactions. In Brunei, we sampled soils from a WS and a normal primary dipterocarp forest, together with an inland heath, an intermediate forest type. Soil DNA was extracted, and shotgun sequencing was performed using Illumina HiSeq platform, with classification by the Metagenomics Rapid Annotation using Subsystem Technology(MG-RAST). The results, on one hand, supported our hypothesis(on greater abundance of dormancy, virulence, and sporulation-related genes). However, some aspects of our results showed no significant difference(specifically in stress tolerance, antibiotic resistance, viruses, and clustered regularly interspaced short palindrome repeats(CRISPRs)). It appears that in certain respects, the extreme white sand environment produces the predicted strategy of less biotic interaction, but exhibits high soil microbiota connectivity and functional diversity.
基金supported by the Research Development Fund(RDF-23-01-067)the Summer Undergraduate Research Fellowship(SURF)Program(SURF-2023-0079)from Xi'an Jiaotong-Liverpool University to M.T.
文摘Wild bees are ecologically vital but increasingly threatened by anthropogenic activities,leading to uncertain survival and health outcomes in urban environments.The gut microbiome contains features indicating host health and reflecting long-term evolutionary adaptation and acute reactions to real-time stressors.Moving beyond bacteria,we propose a comprehensive analysis integrating diet,bacteriome,virome,resistome,and their association to understand the survival status of urban lives better.We conducted a study on mason bees(Osmia excavata)across 10 urban agricultural sites in Suzhou,China,using shotgun gut metagenome sequencing for data derived from total gut DNA.Our findings revealed that most ingested pollen originated from Brassica crops and the unexpected garden tree Plantanus,indicating that floral resources at the 10 sites supported Osmia but with limited plant diversity.Varied city landscapes revealed site-specific flowers that all contributed to Osmia sustenance.The gut bacterial community,dominated by Gammaproteobacteria,showed remarkable structural stability across 8 sites but suggested perturbations at 2 sites.Antibiotic resistance gene profiles highly varied across 10 sites with prevalent unclassified drug classes,highlighting environmental threats to both bees and humans.The virome analysis identified honeybee pathogens,suggesting potential virus spillover.Many unknown bacteriophages were detected,some of which targeted the core gut bacteria,underscoring their role in maintaining gut homeostasis.These multifaceted metagenomic insights hold the potential to predict bee health and identify environmental threats,thereby guiding probiotic development and city management for effective bee conservation.
基金supported by the National Natural Science Foundation of China (Grant No. 30770298)
文摘The plankton community plays an especially important role in the functioning of aquatic ecosystems and also in biogeochemical cycles. Since the beginning of marine research expeditions in the 1870s, an enormous number of planktonic organisms have been described and studied. Plankton investigation has become one of the most important areas of aquatic ecological study, as well as a crucial component of aquatic environmental evaluation. Nonetheless, traditional investigations have mainly focused on morphospecies composition, abundances and dynamics, which primarily depend on morphological identification and counting under microscopes. However, for many species/groups, with few readily observable characteristics, morphological identification and counting have historically been a difficult task. Over the past decades, microbiologists have endeavored to apply and extend molecular techniques to address questions in microbial ecology. These culture-independent studies have generated new insights into microbial ecology. One such strategy, metagenome-based analysis, has also proved to be a powerful tool for plankton research. This mini-review presents a brief history of plankton research using morphological and metagenome-based approaches and the potential applications and further directions of metagenomic analyses in plankton ecological studies are discussed. The use of metagenome-based approaches for plankton ecological study in aquatic ecosystems is encouraged.
基金supported by the National ‘‘Twelfth Five-Year’’ Plan for Science and Technology of China(2012BAI06B02)the National Natural Science Foundation of China(91231119, 30970667 and 11021463)the National Basic Research Program of China (2011CB707500)
文摘Using high-throughput sequencing on metagenome to analyze marine microbial community, it is one of current main issues in the field of environmental microbe research. In this paper, we conducted the functional analysis on seven samples of metagenomic data from different depth seawater in Hawaii. The results of gene prediction and function annotation indicate that there are large amounts of potential novel genes of which functions remain unknown at present. Based on the gene annotation, codon usage bias is studied on ribosomal protein-related genes and shows an evident influence by the marine extreme environment. Furthermore, focusing on the marine environmental differences such as light intensity, dissolved oxygen, temperature and pressure among various depths, comparative analysis is carried out on related genes and metabolic pathways. Thus, the understanding as well as new insights into the correlation between marine environment and microbes are proposed at molecular level. Therefore, the studies herein afford a clue to reveal the special living strategies of microbial community from sea surface to deep sea.
文摘Estimating taxonomic content constitutes a key problem in metagenomic sequencing data analysis.However,extracting such content from high-throughput data of next-generation sequencing is very time-consuming with the currently available software.Here,we present CloudLCA,a parallel LCA algorithm that significantly improves the efficiency of determining taxonomic composition in metagenomic data analysis.Results show that CloudLCA(1)has a running time nearly linear with the increase of dataset magnitude,(2)displays linear speedup as the number of processors grows,especially for large datasets,and(3)reaches a speed of nearly 215 million reads each minute on a cluster with ten thin nodes.In comparison with MEGAN,a well-known metagenome analyzer,the speed of CloudLCA is up to 5 more times faster,and its peak memory usage is approximately 18.5%that of MEGAN,running on a fat node.CloudLCA can be run on one multiprocessor node or a cluster.It is expected to be part of MEGAN to accelerate analyzing reads,with the same output generated as MEGAN,which can be import into MEGAN in a direct way to finish the following analysis.Moreover,CloudLCA is a universal solution for finding the lowest common ancestor,and it can be applied in other fields requiring an LCA algorithm.
文摘In this study,we introduce a novel bioinformatics program,Spore-associated Symbiotic Microbes Position-specific Function(SeSaMe PS Function),for position-specific functional analysis of short sequences derived from metagenome sequencing data of the arbuscular mycorrhizal fungi.The unique advantage of the program lies in databases created based on genus-specific sequence properties derived from protein secondary structure,namely amino acid usages,codon usages,and codon contexts of 3-codon DNA 9-mers.SeSaMe PS Function searches a query sequence against reference sequence database,identifies 3-codon DNA 9-mers with structural roles,and creates a comparative dataset containing the codon usage biases of the 3-codon DNA 9-mers from 54 bacterial and fungal genera.The program applies correlation principal component analysis in conjunction with K-means clustering method to the comparative dataset.3-codon DNA 9-mers clustered as a sole member or with only a few members are often structurally and functionally distinctive sites that provide useful insights into important molecular interactions.The program provides a versatile means for studying functions of short sequences from metagenome sequencing and has a wide spectrum of applications.SeSaMe PS Function is freely accessible at www.fungalsesame.org.
文摘Analysis of environmental samples for bacterial antibiotic resistance genes may have different objectives and analysis strategies. In some cases, the purpose was to study diversity and evolution of genes that could be grouped within a mechanism of antibiotic resistance. Different protocols have been designed for detection and confirmation that a functional gene was found. In this study, we present a sequence-based screening of candidate genes encoding beta-lactamases in 14 metagenomes of Antarctic microbial mats. The samples were obtained from different sites, representing diverse biogeographic regions of maritime and continental Antarctica. A protocol was designed based on generation of Hidden Markov Models from the four beta-lactamase classes by Ambler classification, using sequences from the Comprehensive Antibiotic Resistance Database (CARD). The models were used as queries for metagenome analysis and recovered contigs were subsequently annotated using RAST. According to our analysis, 14 metagenomes analyzed contain A, B and C beta-lactamase genes. Class D genes, however, were identified in 11 metagenomes. The most abundant was class C (46.8%), followed by classes B (35.5%), A (14.2%) and D (3.5%). A considerable number of sequences formed clusters which included, in some cases, contigs from different metagenomes. These assemblies are clearly separated from reference clusters, previously identified using CARD beta-lactamase sequences. While bacterial antibiotic resistance is a major challenge of public health worldwide, our results suggest that environmental diversity of beta-lactamase genes is higher than that currently reported, although this should be complemented with gene function analysis.
基金support from the Senior User Project of RV KEXUE(Grant No.KEXUE2019GZ05)the Center for Ocean Mega-Science,Chinese Academy of Sciences+2 种基金funding support from the Second Tibetan Plateau Scientific Expedition and Research Program(Grant No.2021QZKK0100)the National Key R&D Program of China(Grant No.2022YFF1002801)the National Natural Science Foundation of China(Grant No.92251302).
文摘Cold seeps in the deep sea are closely linked to energy exploration as well as global climate change.The alkane-dominated chemical energy-driven model makes cold seeps an oasis of deep-sea life,showcasing an unparalleled reservoir of microbial genetic diversity.Here,by analyzing 113 metagenomes collected from 14 global sites across 5 cold seep types,we present a comprehensive Cold Seep Microbiomic Database(CSMD)to archive the genomic and functional diversity of cold seep microbiomes.The CSMD includes over 49 million non-redundant genes and 3175 metagenome-assembled genomes,which represent 1895 species spanning 105 phyla.In addition,beta diversity analysis indicates that both the sampling site and cold seep type have a substantial impact on the prokaryotic microbiome community composition.Heterotrophic and anaerobic metabolisms are prevalent in microbial communities,accompanied by considerable mixotrophs and facultative anaerobes,highlighting the versatile metabolic potential in cold seeps.Furthermore,secondary metabolic gene cluster analysis indicates that at least 98.81%of the sequences potentially encode novel natural products,with ribosomally synthesized and post-translationally modified peptides being the predominant type widely distributed in archaea and bacteria.Overall,the CSMD represents a valuable resource that would enhance the understanding and utilization of global cold seep microbiomes.
基金supported by the National Key R&D Program of China (No.2022YFD1301001).
文摘Dietary fat content can reduce the methane production of dairy cows;however,the relevance fatty acid(FA)composition has towards this inhibitory effect is debatable.Furthermore,in-depth studies elucidating the effects of unsaturated fatty acids(UFA)on rumen function and the mechanism of reducing methane(CH_(4))production are lacking.This study exposed 10 Holstein cows with the same parity,similar milk yield to two total mixed rations:low unsaturated FA(LUFA)and high unsaturated FA(HUFA)with similar fat content.The LUFA group mainly added fat powder(C16:0>90%),and the HUFA group mainly replaced fat powder with extruded flaxseed.The experiment lasted 26 d,the last 5 d of which,gas exchange in respiratory chambers was conducted to measure gas emissions.We found that an increase in the UFA in diet did not affect milk production(P>0.05)and could align the profile of milk FAs more closely with modern human nutritional requirements.Furthermore,we found that increasing the UFA content in the diet lead to a decrease in the abundance of Methanobrevibacter in the rumen(|linear discriminant analysis[LDA]score|>2 and P 2 and P<0.05),which ultimately decreased CH4 production(P<0.05).Our results illustrated the mechanism involving decreased CH4 production when fed a UFA diet in dairy cows.We believe that our study provides new evidence to explore CH4 emission reduction measures for dairy cows.
基金funded by the Siksha‘O’Anusandhan(Deemed to be University).
文摘Background:In the dynamic progression of root canal infections,the resultant change in environmental conditions directs the adaptation of the microbiome in terms of richness,evenness,and diversity.Objective:The goal of this study is to contrast the interradicular bacterial community structures of teeth in acute and chronic stages and investigate potential microorganisms associated with persistent apical periapical infections.Methods:Interradicular samples were collected from 10 teeth in the apical periodontitis group and 10 teeth in the chronic apical periodontitis group.High-throughput next-generation sequencing(NGS)–based microbial identification through the Illumina platform was used to characterize the complex intraradicular microbial communities in acute and chronic root canal infections.Results:Bacteria were the major domain,with a prevalence of>97%(acute cases:98.11%and chronic cases:97.6%)compared to eukaryotes and archaea.Bacterial diversity was relatively higher in acute compared to chronic conditions under 10 and 9 phyla,79 and 64 genera,and 172 and 135 species,respectively.These endodontically infecting bacteria belonged to Firmicutes(47.21%),Bacteroidetes(20.07%),and Proteobacteria(10.72%)in acute conditions,while in the chronic stage,Firmicutes(40.85%),Proteobacteria(27.80%),and Actinobacteria(14.79%)were abundant.The phylum Candidatus Saccharibacteria was exclusively found in acute samples.Spirochaetes and Synergistetes were found predominantly in acute infections compared to chronic infections.Bacillus and Lactobacillus were found in equal and highest abundance under the phylum Firmicutes in both conditions.Conclusion:This study provides information on the differential microbial community present in the apical root canal system of teeth with acute and chronic apical periodontitis and contributes to new approaches or channels for future research on preventive measures and therapeutic protocols during disease progression and treatment.However,functional characterization and detection of antimicrobial resistance in these two clinical conditions can supplement these findings for deciding routine drug treatment for periodontal infections.
文摘Wu et al recently applied multi-region 16S rRNA sequencing to characterize the gastric cancer microbiome,demonstrating improved taxonomic resolution and detection sensitivity over conventional single-region approaches.While the study represents a valuable methodological step forward,it remains limited by singlecenter design,lack of quantitative calibration,and insufficient control for contamination and inter-laboratory variability.This editorial critically appraises these methodological gaps and emphasizes that future efforts must focus on harmonized,consensus-driven workflows to ensure reproducibility and clinical reliability.The translational potential of multi-region 16S lies in moving from descriptive microbial profiling to actionable clinical integration,particularly for recurrence prediction,treatment-response monitoring,and perioperative complication risk assessment.By addressing these methodological,economic,and ethical challenges,the field can advance toward evidence-based and clinically deployable microbiome-guided precision oncology.
基金This work was supported by National Research and Development Project of China(grant no.2023YFF0724803)Scientific and technological innovation project of China Academy of Chinese Medical Sciences(grant no.CI2021B015)The Fundamental Research Funds for the Central Public Welfare Research Institutes(grant no.ZZ15-WT-04,ZZ15-WT-08).
文摘Blood deficiency syndrome(BDS)refers to a pathological state with blood dysfunction and organ dystrophy in traditional Chinese medicine.Danggui Wuji granules(DWG)was developed from a formula containing Angelicae Sinensis Radix and Musculus et Os Galli Domestici.Herein,we investigated the mechanism of DWG in treating BDS by modulating gut microbiota.We found that DWG protected mice from BDS by elevating the levels of red blood cell count,hemoglobin,and hematocrit in peripheral blood and increasing the erythrocyte membrane Na+-K+-ATPase activity.Danggui Wuji granules changed the composition and metabolites of colonic flora.Notably,Lactobacillus,Muribaculaceae,and Alistipes were the main genera showing changes after DWG treatment.Our findings revealed that DWG presented a positive therapeutic effect on BDS in mice by regulating the gut microbiota and metabolites.The protective mechanism of DWG was associated with pathways such as metabolic pathways,biosynthesis of secondary metabolites,ABC transporters,ribosome,thyroid hormone synthesis,lysine degradation,galactose metabolism,tyrosine metabolism,etc.
基金supported by grants from the National Natural Science Foundation of China(Nos.32071666 and 32271552)the Science&Technology Fundamental Resources Investigation Program(No.2022FY101000).
文摘Background:Accurately and efficiently extracting microbial genomic sequences from complex metagenomic data is crucial for advancing our understanding in fields such as clinical diagnostics,environmental microbiology,and biodiversity.As sequencing technologies evolve,this task becomes increasingly challenging due to the intricate nature of microbial communities and the vast amount of data generated.Especially in intensive care units(ICUs),infections caused by antibiotic-resistant bacteria are increasingly prevalent among critically ill patients,significantly impacting the effectiveness of treatments and patient prognoses.Therefore,obtaining timely and accurate information about infectious pathogens is of paramount importance for the treatment of patients with severe infections,which enables precisely targeted anti-infection therapies,and a tool that can extract microbial genomic sequences from metagenomic dataset would be of help.Methods:We developed MetaGeneMiner to help with retrieving specific microbial genomic sequences from metagenomes using a k-mer-based approach.It facilitates the rapid and accurate identification and analysis of pathogens.The tool is designed to be user-friendly and efficient on standard personal computers,allowing its use across a wide variety of settings.We validated MetaGeneMiner using eight metagenomic samples from ICU patients,which demonstrated its efficiency and accuracy.Results:The software extensively retrieved coding sequences of pathogens Acinetobacter baumannii and herpes simplex virus type 1 and detected a variety of resistance genes.All documentation and source codes for MetaGeneMiner are freely available at https://gitee.com/sculab/MetaGeneMiner.Conclusions:It is foreseeable that MetaGeneMiner possesses the potential for applications across multiple domains,including clinical diagnostics,environmental microbiology,gut microbiome research,as well as biodiversity and conservation biology.Particularly in ICU settings,MetaGeneMiner introduces a novel,rapid,and precise method for diagnosing and treating infections in critically ill patients.This tool is capable of efficiently identifying infectious pathogens,guiding personalized and precise treatment strategies,and monitoring the development of antibiotic resistance,significantly impacting the diagnosis and treatment of severe infections.
文摘Microbes are increasingly being implicated in autoimmune disease.This calls for a re-evaluation of how these chronic inflammatory illnesses are routinely treated.The standard of care for autoimmune disease remains the use of medications that slow the immune response,while treatments aimed at eradicating microbes seek the exact opposite-stimulation of the innate immune response.Immunostimulation is complicated by a cascade of sequelae,including exacerbated inflammation,which occurs in response to microbial death.Over the past 8 years,we have collaborated with American and international clinical professionals to research a model-based treatment for inflammatory disease.This intervention,designed to stimulate the innate immune response,has required a reevaluation of disease progression and amelioration.Paramount is the inherent conflict between palliation and microbicidal efficacy.Increased microbicidal activity was experienced as immunopathology-a temporary worsening of symptoms.Further studies are needed,but they will require careful planning to manage this immunopathology.
