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
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
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: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
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
Ulcerative colitis(UC)is a recurrent inflammatory bowel disease that imposes a severe burden on families and society.In recent years,exploiting the potential of marine bioactive peptides for the treatment of diseases ...Ulcerative colitis(UC)is a recurrent inflammatory bowel disease that imposes a severe burden on families and society.In recent years,exploiting the potential of marine bioactive peptides for the treatment of diseases has become a topic of intense research interest.This study revealed the mechanism underlying the protective effect of the dominant polypeptide PKKVV(Pro-Lys-Lys-Val-Val)of Rhopilema esculentum cnidoblasts against DSS-induced UC through a combined analysis of the metagenome and serum metabolome.Specifically,the polypeptide composition of R.esculentum cnidoblasts was determined by matrix-assisted laser desorption ionization time-of-flight mass spectrometry(MALDI-TOF/TOF-MS).Molecular docking showed that the dominant peptide PKKVV could bind better with tumor necrosis factor-α(TNF-α)than the original ligand.Subsequent animal experiments suggested that PKKVV could modulate disorganized gut microorganisms in mice with UC;affect serum metabolites through the arachidonic acid,glycerophospholipid and linoleic acid metabolism pathways;and further alleviate UC symptoms.This study provides a reference for the comprehensive development of marine bioactive substances and nonpharmaceutical treatments for UC.展开更多
BACKGROUND Fecal microbiota transplantation(FMT)is a promising therapeutic approach for treating Crohn’s disease(CD).The new method of FMT,based on the automatic washing process,was named as washed microbiota transpl...BACKGROUND Fecal microbiota transplantation(FMT)is a promising therapeutic approach for treating Crohn’s disease(CD).The new method of FMT,based on the automatic washing process,was named as washed microbiota transplantation(WMT).Most existing studies have focused on observing the clinical phenomena.However,the mechanism of action of FMT for the effective management of CD-particularly in-depth multi-omics analysis involving the metagenome,metatranscriptome,and metabolome-has not yet been reported.AIM To assess the efficacy of WMT for CD and explore alterations in the microbiome and metabolome in response to WMT.METHODS We conducted a prospective,open-label,single-center clinical study.Eleven CD patients underwent WMT.Their clinical responses(defined as a decrease in their CD Activity Index score of>100 points)and their microbiome(metagenome,metatranscriptome)and metabolome profiles were evaluated three months after the procedure.RESULTS Seven of the 11 patients(63.6%)showed an optimal clinical response three months post-WMT.Gut microbiome diversity significantly increased after WMT,consistent with improved clinical symptoms.Comparison of the metagenome and metatranscriptome analyses revealed consistent alterations in certain strains,such as Faecalibac-terium prausnitzii,Roseburia intestinalis,and Escherichia coli.In addition,metabolomics analyses demonstrated that CD patients had elevated levels of various amino acids before treatment compared to the donors.However,levels of vital amino acids that may be associated with disease progression(e.g.,L-glutamic acid,gamma-glutamyl-leucine,and prolyl-glutamine)were reduced after WMT.CONCLUSION WMT demonstrated therapeutic efficacy in CD treatment,likely due to the effective reconstruction of the patient’s microbiome.Multi-omics techniques can effectively help decipher the potential mechanisms of WMT in treating CD.展开更多
A growing body of evidence suggests that the gut microbiota contributes to the development of neurodegenerative diseases via the microbiota-gut-brain axis.As a contributing factor,microbiota dysbiosis always occurs in...A growing body of evidence suggests that the gut microbiota contributes to the development of neurodegenerative diseases via the microbiota-gut-brain axis.As a contributing factor,microbiota dysbiosis always occurs in pathological changes of neurodegenerative diseases,such as Alzheimer’s disease,Parkinson’s disease,and amyotrophic lateral sclerosis.High-throughput sequencing technology has helped to reveal that the bidirectional communication between the central nervous system and the enteric nervous system is facilitated by the microbiota’s diverse microorganisms,and for both neuroimmune and neuroendocrine systems.Here,we summarize the bioinformatics analysis and wet-biology validation for the gut metagenomics in neurodegenerative diseases,with an emphasis on multi-omics studies and the gut virome.The pathogen-associated signaling biomarkers for identifying brain disorders and potential therapeutic targets are also elucidated.Finally,we discuss the role of diet,prebiotics,probiotics,postbiotics and exercise interventions in remodeling the microbiome and reducing the symptoms of neurodegenerative diseases.展开更多
BACKGROUND Helicobacter pylori(H.pylori)infection is closely associated with gastrointestinal diseases.Our preliminary studies have indicated that H.pylori infection had a significant impact on the mucosal microbiome ...BACKGROUND Helicobacter pylori(H.pylori)infection is closely associated with gastrointestinal diseases.Our preliminary studies have indicated that H.pylori infection had a significant impact on the mucosal microbiome structure in patients with gastric ulcer(GU)or duodenal ulcer(DU).AIM To investigate the contributions of H.pylori infection and the mucosal microbiome to the pathogenesis and progression of ulcerative diseases.METHODS Patients with H.pylori infection and either GU or DU,and healthy individuals without H.pylori infection were included.Gastric or duodenal mucosal samples was obtained and subjected to metagenomic sequencing.The compositions of the microbial communities and their metabolic functions in the mucosal tissues were analyzed.RESULTS Compared with that in the healthy individuals,the gastric mucosal microbiota in the H.pylori-positive patients with GU was dominated by H.pylori,with signi-ficantly reduced biodiversity.The intergroup differential functions,which were enriched in the H.pylori-positive GU patients,were all derived from H.pylori,particularly those concerning transfer RNA queuosine-modification and the synthesis of demethylmenaquinones or menaquinones.A significant enrichment of the uibE gene was detected in the synthesis pathway.There was no significant difference in microbial diversity between the H.pylori-positive DU patients and healthy controls.CONCLUSION H.pylori infection significantly alters the gastric microbiota structure,diversity,and biological functions,which may be important contributing factors for GU.展开更多
Free amino acid(FAA)is the important component of vinegar that infl uences quality perception and consumer acceptance.FAA is one of the major metabolites produced by microorganisms;however,the microbial metabolic netw...Free amino acid(FAA)is the important component of vinegar that infl uences quality perception and consumer acceptance.FAA is one of the major metabolites produced by microorganisms;however,the microbial metabolic network on FAA biosynthesis remains unclear.Through metagenomic analysis,this work aimed to elucidate the roles of microbes in FAA biosynthesis during Monascus rice vinegar fermentation.Taxonomic profiles from functional analyses showed 14 dominant genera with high contributions to the metabolism pathways.The metabolic network for FAA biosynthesis was then constructed,and the microbial distribution in different metabolic pathways was illuminated.The results revealed that 5 functional genera were closely involved in FAA biosynthesis.This study illuminated the metabolic roles of microorganisms in FAA biosynthesis and provided crucial insights into the functional attributes of microbiota in vinegar fermentation.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
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
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
Background Dietary supplementation of xylooligosac charides(XOS) has been found to influence gut health by manipulating cecal microbiota and producing microbe-origin metabolites.But no study investigated and compared ...Background Dietary supplementation of xylooligosac charides(XOS) has been found to influence gut health by manipulating cecal microbiota and producing microbe-origin metabolites.But no study investigated and compared the effect of in ovo feeding of xylobiose(XOS2) and xy lotriose(XOS3) in chickens.This study investigated the effect of in ovo feeding of these XOS compounds on post-hatch gut health parameters in chickens.A total of 144 fertilized chicken eggs were divided into three groups:a) non-injected control(CON),b) XOS2,and c) XOS3.On the 17^(th) embryonic day,the eggs of the XOS2 and XOS3 groups were injected with 3 mg of XOS2 and XOS3 diluted in 0.5 mL of 0.85% normal saline through the amniotic sac.After hatching,the chicks were raised for 21 d.Blood was collected on d 14 to measure plasma immunoglobulin.Cecal digests were collected for measuring short-chain fatty acids(SCFA) on d 14 and 21,and for microbial ecology and microbial metabolic pathway analyses on d 7 and 21.Results The results were considered significantly different at P<0.05.ELISA quantified plasma IgA and IgG on d 14chickens,revealing no differences among the treatments.Gas chromatography results showed no significant differences in the concentrations of cecal SCFAs on d 14 but significant differences on d 21.However;the SCFA concentrations were lower in the XOS3 than in the CON group on d 21.The cecal metagenomics data showed that the abundance of the family Clostridiaceae significantly decreased on d 7,and the abundance of the family Oscillospiraceae increased on d 21 in the XOS2 compared to the CON.There was a reduction in the relative abundance of genus Clostridium sense stricto 1 in the XOS2 compared to the CON on d 7 and the genus Ruminococcus,torques in both XOS2 and XOS3 groups compared to the CON on d 21.The XOS2 and XOS3 groups reduced the genes for chondroitin sulfate degradation Ⅰ and L-histidine degradation Ⅰpathways,which contribute to improved gut health,respectivelyc in the microbiome on d 7.In contrast,on d 21,the XOS2 and XOS3 groups enriched the thiamin salvage Ⅱ,L-isoleucine biosynthesis Ⅳ,and O-antigen building blocks biosynthesis(E. coli) pathways,which are indicative of improved gut health.Unlike the XOS3 and CON,the microbiome enriched the pathways associated with energy enhancement,including flavin biosynthesis Ⅰ,sucrose degradation Ⅲ,and Calvin-Benson-Bassham cycle pathways,in the XOS2 group on d 21.Conclusion In ovo XOS2 and XOS3 feeding promoted beneficial bacterial growth and reduced harmful bacteria at the family and genus levels.The metagenomic-based microbial metabolic pathway profiling predicted a favorable change in the availability of cecal metabolites in the XOS2 and XOS3 groups.The modulation of microbiota and metabolic pathways suggests that in ovo XOS2 and XOS3 feeding improved gut health during the post-hatch period of broilers.展开更多
This study demonstrates the feasibility and effectiveness of utilizing native soils as a resource for inocula to produce n-caproate through the chain elongation(CE)platform,offering new insights into anaerobic soil pr...This study demonstrates the feasibility and effectiveness of utilizing native soils as a resource for inocula to produce n-caproate through the chain elongation(CE)platform,offering new insights into anaerobic soil processes.The results reveal that all five of the tested soil types exhibit CE activity when supplied with high concentrations of ethanol and acetate,highlighting the suitability of soil as an ideal source for n-caproate production.Compared with anaerobic sludge and pit mud,the native soil CE system exhibited higher selectivity(60.53%),specificity(82.32%),carbon distribution(60.00%),electron transfer efficiency(165.00%),and conductivity(0.59 ms∙cm^(-1)).Kinetic analysis further confirmed the superiority of soil in terms of a shorter lag time and higher yield.A microbial community analysis indicated a positive correlation between the relative abundances of Pseudomonas,Azotobacter,and Clostridium and n-caproate production.Moreover,metagenomics analysis revealed a higher abundance of functional genes in key microbial species,providing direct insights into the pathways involved in n-caproate formation,including in situ CO_(2)utilization,ethanol oxidation,fatty acid biosynthesis(FAB),and reverse beta-oxidation(RBO).The numerous functions in FAB and RBO are primarily associated with Pseudomonas,Clostridium,Rhodococcus,Stenotrophomonas,and Geobacter,suggesting that these genera may play roles that are involved or associated with the CE process.Overall,this innovative inoculation strategy offers an efficient microbial source for n-caproate production,underscoring the importance of considering CE activity in anaerobic soil microbial ecology and holding potential for significant economic and environmental benefits through soil consortia exploration.展开更多
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 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.
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.
基金sponsored by the National Key R&D Program of China (2018YFD0901102)the Natural Science Foundation of Zhejiang Province (LQ22D060002)+2 种基金the Fund of State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products (ZS20190105)the Fundamental Research Funds for the Provincial Universities of Zhejiang (SJLY2021015)the K.C.Wong Magna Fund of Ningbo University。
文摘Ulcerative colitis(UC)is a recurrent inflammatory bowel disease that imposes a severe burden on families and society.In recent years,exploiting the potential of marine bioactive peptides for the treatment of diseases has become a topic of intense research interest.This study revealed the mechanism underlying the protective effect of the dominant polypeptide PKKVV(Pro-Lys-Lys-Val-Val)of Rhopilema esculentum cnidoblasts against DSS-induced UC through a combined analysis of the metagenome and serum metabolome.Specifically,the polypeptide composition of R.esculentum cnidoblasts was determined by matrix-assisted laser desorption ionization time-of-flight mass spectrometry(MALDI-TOF/TOF-MS).Molecular docking showed that the dominant peptide PKKVV could bind better with tumor necrosis factor-α(TNF-α)than the original ligand.Subsequent animal experiments suggested that PKKVV could modulate disorganized gut microorganisms in mice with UC;affect serum metabolites through the arachidonic acid,glycerophospholipid and linoleic acid metabolism pathways;and further alleviate UC symptoms.This study provides a reference for the comprehensive development of marine bioactive substances and nonpharmaceutical treatments for UC.
基金Supported by the Innovation Platform for Academicians of Hainan Province,No.YSPTZX202313Hainan Province Clinical Medical Center,No.2021818+3 种基金Hainan Provincial Health Industry Research Project,No.22A200078Hainan Provincial Postgraduate Innovation Research Project,No.Qhyb2022-133Hainan Medical University Graduate Student Innovative Research Project,No.HYYB2022A18Nanjing Medical University Fan Daiming Research Funds for Holistic Integrative Medicine,No.2020-3HIM.
文摘BACKGROUND Fecal microbiota transplantation(FMT)is a promising therapeutic approach for treating Crohn’s disease(CD).The new method of FMT,based on the automatic washing process,was named as washed microbiota transplantation(WMT).Most existing studies have focused on observing the clinical phenomena.However,the mechanism of action of FMT for the effective management of CD-particularly in-depth multi-omics analysis involving the metagenome,metatranscriptome,and metabolome-has not yet been reported.AIM To assess the efficacy of WMT for CD and explore alterations in the microbiome and metabolome in response to WMT.METHODS We conducted a prospective,open-label,single-center clinical study.Eleven CD patients underwent WMT.Their clinical responses(defined as a decrease in their CD Activity Index score of>100 points)and their microbiome(metagenome,metatranscriptome)and metabolome profiles were evaluated three months after the procedure.RESULTS Seven of the 11 patients(63.6%)showed an optimal clinical response three months post-WMT.Gut microbiome diversity significantly increased after WMT,consistent with improved clinical symptoms.Comparison of the metagenome and metatranscriptome analyses revealed consistent alterations in certain strains,such as Faecalibac-terium prausnitzii,Roseburia intestinalis,and Escherichia coli.In addition,metabolomics analyses demonstrated that CD patients had elevated levels of various amino acids before treatment compared to the donors.However,levels of vital amino acids that may be associated with disease progression(e.g.,L-glutamic acid,gamma-glutamyl-leucine,and prolyl-glutamine)were reduced after WMT.CONCLUSION WMT demonstrated therapeutic efficacy in CD treatment,likely due to the effective reconstruction of the patient’s microbiome.Multi-omics techniques can effectively help decipher the potential mechanisms of WMT in treating CD.
基金financially supported by the National Natural Science Foundation of China,No.32002235(to MT)the Science and Technology Foundation of Taian of Shandong Province,No.2020NS216(to XL)。
文摘A growing body of evidence suggests that the gut microbiota contributes to the development of neurodegenerative diseases via the microbiota-gut-brain axis.As a contributing factor,microbiota dysbiosis always occurs in pathological changes of neurodegenerative diseases,such as Alzheimer’s disease,Parkinson’s disease,and amyotrophic lateral sclerosis.High-throughput sequencing technology has helped to reveal that the bidirectional communication between the central nervous system and the enteric nervous system is facilitated by the microbiota’s diverse microorganisms,and for both neuroimmune and neuroendocrine systems.Here,we summarize the bioinformatics analysis and wet-biology validation for the gut metagenomics in neurodegenerative diseases,with an emphasis on multi-omics studies and the gut virome.The pathogen-associated signaling biomarkers for identifying brain disorders and potential therapeutic targets are also elucidated.Finally,we discuss the role of diet,prebiotics,probiotics,postbiotics and exercise interventions in remodeling the microbiome and reducing the symptoms of neurodegenerative diseases.
基金Supported by Wenling Science and Technology Program,China,No.2020S0180101Science and Technology Program of Traditional Chinese Medicine in Zhejiang Province,China,No.2023ZL784.
文摘BACKGROUND Helicobacter pylori(H.pylori)infection is closely associated with gastrointestinal diseases.Our preliminary studies have indicated that H.pylori infection had a significant impact on the mucosal microbiome structure in patients with gastric ulcer(GU)or duodenal ulcer(DU).AIM To investigate the contributions of H.pylori infection and the mucosal microbiome to the pathogenesis and progression of ulcerative diseases.METHODS Patients with H.pylori infection and either GU or DU,and healthy individuals without H.pylori infection were included.Gastric or duodenal mucosal samples was obtained and subjected to metagenomic sequencing.The compositions of the microbial communities and their metabolic functions in the mucosal tissues were analyzed.RESULTS Compared with that in the healthy individuals,the gastric mucosal microbiota in the H.pylori-positive patients with GU was dominated by H.pylori,with signi-ficantly reduced biodiversity.The intergroup differential functions,which were enriched in the H.pylori-positive GU patients,were all derived from H.pylori,particularly those concerning transfer RNA queuosine-modification and the synthesis of demethylmenaquinones or menaquinones.A significant enrichment of the uibE gene was detected in the synthesis pathway.There was no significant difference in microbial diversity between the H.pylori-positive DU patients and healthy controls.CONCLUSION H.pylori infection significantly alters the gastric microbiota structure,diversity,and biological functions,which may be important contributing factors for GU.
基金The authors are grateful for the financial support from National Natural Science Foundation of China(32001728).
文摘Free amino acid(FAA)is the important component of vinegar that infl uences quality perception and consumer acceptance.FAA is one of the major metabolites produced by microorganisms;however,the microbial metabolic network on FAA biosynthesis remains unclear.Through metagenomic analysis,this work aimed to elucidate the roles of microbes in FAA biosynthesis during Monascus rice vinegar fermentation.Taxonomic profiles from functional analyses showed 14 dominant genera with high contributions to the metabolism pathways.The metabolic network for FAA biosynthesis was then constructed,and the microbial distribution in different metabolic pathways was illuminated.The results revealed that 5 functional genera were closely involved in FAA biosynthesis.This study illuminated the metabolic roles of microorganisms in FAA biosynthesis and provided crucial insights into the functional attributes of microbiota in vinegar fermentation.
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 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 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.
基金supported by the USDA National Institute for Food and Agriculture,Hatch-Multistate Fund,managed by the College of Tropical Agriculture and Human Resources,University of Hawaii at Manoa,Honolulu,HI,USA。
文摘Background Dietary supplementation of xylooligosac charides(XOS) has been found to influence gut health by manipulating cecal microbiota and producing microbe-origin metabolites.But no study investigated and compared the effect of in ovo feeding of xylobiose(XOS2) and xy lotriose(XOS3) in chickens.This study investigated the effect of in ovo feeding of these XOS compounds on post-hatch gut health parameters in chickens.A total of 144 fertilized chicken eggs were divided into three groups:a) non-injected control(CON),b) XOS2,and c) XOS3.On the 17^(th) embryonic day,the eggs of the XOS2 and XOS3 groups were injected with 3 mg of XOS2 and XOS3 diluted in 0.5 mL of 0.85% normal saline through the amniotic sac.After hatching,the chicks were raised for 21 d.Blood was collected on d 14 to measure plasma immunoglobulin.Cecal digests were collected for measuring short-chain fatty acids(SCFA) on d 14 and 21,and for microbial ecology and microbial metabolic pathway analyses on d 7 and 21.Results The results were considered significantly different at P<0.05.ELISA quantified plasma IgA and IgG on d 14chickens,revealing no differences among the treatments.Gas chromatography results showed no significant differences in the concentrations of cecal SCFAs on d 14 but significant differences on d 21.However;the SCFA concentrations were lower in the XOS3 than in the CON group on d 21.The cecal metagenomics data showed that the abundance of the family Clostridiaceae significantly decreased on d 7,and the abundance of the family Oscillospiraceae increased on d 21 in the XOS2 compared to the CON.There was a reduction in the relative abundance of genus Clostridium sense stricto 1 in the XOS2 compared to the CON on d 7 and the genus Ruminococcus,torques in both XOS2 and XOS3 groups compared to the CON on d 21.The XOS2 and XOS3 groups reduced the genes for chondroitin sulfate degradation Ⅰ and L-histidine degradation Ⅰpathways,which contribute to improved gut health,respectivelyc in the microbiome on d 7.In contrast,on d 21,the XOS2 and XOS3 groups enriched the thiamin salvage Ⅱ,L-isoleucine biosynthesis Ⅳ,and O-antigen building blocks biosynthesis(E. coli) pathways,which are indicative of improved gut health.Unlike the XOS3 and CON,the microbiome enriched the pathways associated with energy enhancement,including flavin biosynthesis Ⅰ,sucrose degradation Ⅲ,and Calvin-Benson-Bassham cycle pathways,in the XOS2 group on d 21.Conclusion In ovo XOS2 and XOS3 feeding promoted beneficial bacterial growth and reduced harmful bacteria at the family and genus levels.The metagenomic-based microbial metabolic pathway profiling predicted a favorable change in the availability of cecal metabolites in the XOS2 and XOS3 groups.The modulation of microbiota and metabolic pathways suggests that in ovo XOS2 and XOS3 feeding improved gut health during the post-hatch period of broilers.
基金supported by the National Natural Science Foundation of China(52000132 and 51978201)Open Project of State Key Laboratory of Urban Water Resource and Environment,Harbin Institute of Technology(HC202241)the Fundamental Research Funds for the Central Universities.
文摘This study demonstrates the feasibility and effectiveness of utilizing native soils as a resource for inocula to produce n-caproate through the chain elongation(CE)platform,offering new insights into anaerobic soil processes.The results reveal that all five of the tested soil types exhibit CE activity when supplied with high concentrations of ethanol and acetate,highlighting the suitability of soil as an ideal source for n-caproate production.Compared with anaerobic sludge and pit mud,the native soil CE system exhibited higher selectivity(60.53%),specificity(82.32%),carbon distribution(60.00%),electron transfer efficiency(165.00%),and conductivity(0.59 ms∙cm^(-1)).Kinetic analysis further confirmed the superiority of soil in terms of a shorter lag time and higher yield.A microbial community analysis indicated a positive correlation between the relative abundances of Pseudomonas,Azotobacter,and Clostridium and n-caproate production.Moreover,metagenomics analysis revealed a higher abundance of functional genes in key microbial species,providing direct insights into the pathways involved in n-caproate formation,including in situ CO_(2)utilization,ethanol oxidation,fatty acid biosynthesis(FAB),and reverse beta-oxidation(RBO).The numerous functions in FAB and RBO are primarily associated with Pseudomonas,Clostridium,Rhodococcus,Stenotrophomonas,and Geobacter,suggesting that these genera may play roles that are involved or associated with the CE process.Overall,this innovative inoculation strategy offers an efficient microbial source for n-caproate production,underscoring the importance of considering CE activity in anaerobic soil microbial ecology and holding potential for significant economic and environmental benefits through soil consortia exploration.
