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
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
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
Mining and tailings deposition can cause serious heavy metal(loids)pollution to the surrounding soil environment.Soil microorganisms adapt their metabolism to such conditions,driving alterations in soil function.This ...Mining and tailings deposition can cause serious heavy metal(loids)pollution to the surrounding soil environment.Soil microorganisms adapt their metabolism to such conditions,driving alterations in soil function.This study aims to elucidate the response patterns of nitrogen-cycling microorganisms under long-term heavy metal(loids)exposure.The results showed that the diversity and abundance of nitrogen-cyclingmicroorganisms showed negative feedback to heavy metal(loids)concentrations.Denitrifying microorganisms were shown to be the dominant microorganisms with over 60%of relative abundance and a complex community structure including 27 phyla.Further,the key bacterial species in the denitrification process were calculated using a random forest model,where the top three key species(Pseudomonas stutzei,Sphingobium japonicum and Leifsonia rubra)were found to play a prominent role in nitrite reduction.Functional gene analysis and qPCR revealed that nirK,which is involved in nitrite reduction,significantly accumulated in the most metal-rich soil with the increase of absolute abundance of 63.86%.The experimental results confirmed that the activity of nitrite reductase(Nir)encoded by nirK in the soil was increased at high concentrations of heavy metal(loids).Partial least squares-path model identified three potential modes of nitrite reduction processes being stimulated by heavy metal(loids),the most prominent of which contributed to enhanced nirK abundance and soil Nir activity through positive stimulation of key species.The results provide new insights and preliminary evidence on the stimulation of nitrite reduction processes by heavy metal(loids).展开更多
The mutualistic symbiotic system formed by clumping arbuscular mycorrhizal fungi(AMF)and plants can remediate heavy metal-contaminated soils.However,the specific mechanisms underlying the interaction between AMF and i...The mutualistic symbiotic system formed by clumping arbuscular mycorrhizal fungi(AMF)and plants can remediate heavy metal-contaminated soils.However,the specific mechanisms underlying the interaction between AMF and inter-root microbial communities,particularly their impact on organic phosphorus(P)cycling,remain unclear.This study investigated the gene regulation processes involved in inter-root soil phosphorus cycling in wetland plants,specifically Iris tectorum,following inoculation with AMF under varying concentrations of chromium(Cr)stress.Through macro-genome sequencing,we analyzed the composition and structure of the inter-root soil microbial community associated with Iris tectorum under greenhouse pot conditions.The results demonstrated significant changes in the diversity and composition of the inter-root soil microbial community following AMF inoculation,with Proteobacteria,Actinobacteria,Chloroflexi,Acidobacteria,and Bacteroidetes being the dominant taxa.Under Cr stress,species and gene co-occurrence network analysis revealed that AMF promoted the transformation process of organic phosphorus mineralization and facilitated inorganic phosphorus uptake.Additionally,network analysis of functional genes indicated strong aggregation of(pstS,pstA,pstC,TC.PIT,phoR,pp-gppA)genes,which collectively enhanced phosphorus uptake by plants.These findings shed light on the inter-root soil phosphorus cycling process during the co-remediation of Cr-contaminated soil by AMF-Iris tectorum symbiosis,providing valuable theoretical support for the application of AMF-wetland plant symbiosis systems to remediate heavy metal-contaminated soil.展开更多
Microbial activities are the dynamic core of nutrient cycling in organic substrates,and the exploitation of plant growth-promoting rhizobacteria strains contributes to sustainable agricultural development.This study a...Microbial activities are the dynamic core of nutrient cycling in organic substrates,and the exploitation of plant growth-promoting rhizobacteria strains contributes to sustainable agricultural development.This study aimed to investigate the effect and mechanism of Bacillus velezensis SX13 in nutrient cycling and plant promotion under different substrate supply conditions.The effects of reduced substrate amount(sCK)and inoculation of SX13 strain under both substrate supply conditions(Bv and sBv)on rhizosphere microenvironment and plant growth were investigated using conventional substrate amount(CK)as a control.Results showed no significant difference in the a-diversity indexes(Chao1 and Shannon)of the rhizospheric microbial community among the four treatments.However,nonmetric multidimensional scaling analysis and principal coordinate analysis revealed that compared with CK treatment,the inoculation of SX13strain and reduced substrate supply reshaped the β-diversity structure of microbial communities.Furthermore,inoculation with B.velezensis SX13 under both substrate supply conditions increased the abundance of Proteobacteria(1.64%-2.46%),Acidobacteria(14.09%-43.07%),and Firmicutes(179.29%-861.29%).The results of the Kyoto Encyclopedia of Genes and Genomes(KEGG)pathway enrichment analysis showed that the metabolic pathway with the highest abundance of enriched genes was also the pathway with the most enriched differential genes caused by reducing substrate supply or inoculation of B.velezensis SX13.The rhizosphere inoculation of B.velezensis SX13significantly up-regulated the top genes related to carbohydrate esterases,carbohydrate binding modules,glycoside hydrolases,glycoside transferases,and polysaccharide lyases.As a result,the activities of carbon and nitrogen cycle-related enzymes such as cellobiohydrolase,β-glucosidase,urease,L-leucine amino peptidase,and β-1,4-N-acetylglucosaminidase were increased,which in turn accelerated nutrient cycling.B.velezensis SX13 and its mediated improvement of the rhizospheric microenvironment resulted in the up-regulation of root CsNRT family genes(such as CsNRT1.1,CsNRT1.4a,CsNRT1.4b,CsNRT1.5a,CsNRT1.5b,CsNRT1.5c,and CsNRT1.8),which accelerated nitrogen uptake,accumulation,and utilization efficiency and ultimately improved the yield and quality of cucumber.The effect of SX13 strain was more stable and efficient under conventional substrate supply conditions than under reduced substrate supply conditions.展开更多
Background Pork quality and flavor are critical determinants of consumer preference,yet the role of gut microbiota in shaping meat characteristics remains underexplored.In this study,we investigated how a probiotic co...Background Pork quality and flavor are critical determinants of consumer preference,yet the role of gut microbiota in shaping meat characteristics remains underexplored.In this study,we investigated how a probiotic consortium(FAM:Lactobacillus acidophilus and Bacillus subtilis)modulates the gut-muscle axis to enhance pork flavor.Results In finishing pigs,FAM supplementation significantly increased flavor-associated nucleotides and umamienhancing amino acids in longissimus dorsi muscle.Metagenomic analysis revealed FAM-driven enrichment of glycandegrading Prevotella and short-chain fatty acid-producing Phascolarctobacterium,accompanied by reduced antibiotic resistance genes and virulence factors.Spearman correlation linked Prevotella copri abundance with elevated muscle amino acids,suggesting microbial-encoded CAZymes as key mediators.Conclusions This study provides the first evidence that probiotic-induced gut microbiota remodeling enhances pork flavor through metabolic cross-talk along the gut-muscle axis.The findings suggest a novel strategy for improving pork quality via dietary interventions targeting gut microbiota.展开更多
Background Dietary protein level and amino acid(AA)balance are crucial determinants of animal health and productivity.Supplementing rumen-protected AAs in low-protein diets was considered as an efficient strategy to i...Background Dietary protein level and amino acid(AA)balance are crucial determinants of animal health and productivity.Supplementing rumen-protected AAs in low-protein diets was considered as an efficient strategy to improve the growth performance of ruminants.The colon serves as a crucial conduit for nutrient metabolism during rumen-protected methionine(RPMet)and rumen-protected lysine(RPLys)supplementation,however,it has been challenging to clarify which specific microbiota and their metabolites play a pivotal role in this process.Here,we applied metagenomic and metabolomic approaches to compare the characteristic microbiome and metabolic strategies in the colon of lambs fed a control diet(CON),a low-protein diet(LP)or a LP diet supplemented with RPMet and RPLys(LR).Results The LP treatment decreased the average daily weight gain(ADG)in lambs,while the LR treatment tended to elicit a remission in ADG.The butyrate molar concentration was greater(P<0.05),while acetate molar concentration(P<0.05)was lower for lambs fed the LP and LR diets compared to those fed the CON diet.Moreover,the LP treatment remarkably decreased total AA concentration(P<0.05),while LR treatment showed an improvement in the concentrations of methionine,lysine,leucine,glutamate,and tryptophan.Metagenomic insights proved that the microbial metabolic potentials referring to biosynthesis of volatile fatty acids(VFAs)and AAs in the colon were remarkably altered by three dietary treatments.Metagenomic binning identified distinct microbial markers for the CON group(Alistipes spp.,Phocaeicola spp.,and Ruminococcus spp.),LP group(Fibrobacter spp.,Prevotella spp.,Ruminococcus spp.,and Escherichia coli),and LR group(Akkermansia muciniphila and RUG099 spp.).Conclusions Our findings suggest that RPMet and RPLys supplementation to the low-protein diet could enhance the microbial biosynthesis of butyrate and amino acids,enriche the beneficial bacteria in the colon,and thereby improve the growth performance of lambs.展开更多
Background The ketogenic diet that forces adenosine triphosphate(ATP)production by beta-oxidation of fatty acids instead of carbohydrate glycolysis,has gained consensus on host metabolism.However,the mechanisms how a ...Background The ketogenic diet that forces adenosine triphosphate(ATP)production by beta-oxidation of fatty acids instead of carbohydrate glycolysis,has gained consensus on host metabolism.However,the mechanisms how a ketogenic diet alters gastrointestinal microbiome and its downstream consequences on microbial nutrient availability and energy metabolism remain to be elucidated.Here,we used the sheep model fed with fat-rich diet to evaluate the symbiotic microbiome across three regions of the gastrointestinal tract(rumen,ileum,and colon)to gain a comprehensive understanding of the microbial energy metabolism and microbe-mediated ATP biosynthesis.Results Results showed that sheep fed a fat-rich diet had a greater ADG and increased reliance on fat oxidation for fuel utilization.Metagenomics analysis showed the loss of the specialized fiber-degrading bacteria(genus_Fibrobacter)in the rumen and enrichment of genera RUG420 and Eubacterium,which are involved in lipid metabolism and bile acid processing,in the ileum.A significant functional shift related to energy metabolism was shared across three regions of the gastrointestinal microbiomes.These shifts were dominated by glycolysis/gluconeogenesis and TCA cycle in the rumen and by fatty acid degradation and bile acid transformation in the ileum,indicating adaptation to nutrient availability and energy acquisition.Notably,the abundance of substrate-level phosphorylation(SLP)enzymes was significantly increased in the rumen,ileum and colon,while the ATP-producing capacity through electron transport phosphorylation(ETP)by family_Bacteroidaceae in rumen and Acutalibacteraceae in ileum of sheep with fat-rich diet.Conclusions Altogether,the ATP-related microbiome encoding SLP and ETP in rumen,ileum,and colon contributed 36.95%to the host's weight variation.Our study is the first one demonstrating the microbial potential in the ATP synthesis under the shift in dietary energy source,providing a new perspective on the energy metabolism and precise human macronutrients nutrition.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
Helicobacter pylori(H.pylori)infection plays a critical role in gastric diseases,impacting the microbiota structure in gastric and duodenal ulcers.In their study,Jin et al utilized metagenomic sequencing to analyze mu...Helicobacter pylori(H.pylori)infection plays a critical role in gastric diseases,impacting the microbiota structure in gastric and duodenal ulcers.In their study,Jin et al utilized metagenomic sequencing to analyze mucosal samples from patients with ulcers and healthy controls,revealing significant changes in microbial diversity and composition.This article reviews their findings,emphasizing H.pylori’s role in gastric ulcers and the need for further research on its impact on duodenal ulcers.We evaluate the study’s strengths and limitations,suggesting future research directions to enhance our understanding of H.pylori’s contribution to ulcerative diseases.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
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.
基金supported by the National Natural Science Foundation of China(No.41977029).
文摘Mining and tailings deposition can cause serious heavy metal(loids)pollution to the surrounding soil environment.Soil microorganisms adapt their metabolism to such conditions,driving alterations in soil function.This study aims to elucidate the response patterns of nitrogen-cycling microorganisms under long-term heavy metal(loids)exposure.The results showed that the diversity and abundance of nitrogen-cyclingmicroorganisms showed negative feedback to heavy metal(loids)concentrations.Denitrifying microorganisms were shown to be the dominant microorganisms with over 60%of relative abundance and a complex community structure including 27 phyla.Further,the key bacterial species in the denitrification process were calculated using a random forest model,where the top three key species(Pseudomonas stutzei,Sphingobium japonicum and Leifsonia rubra)were found to play a prominent role in nitrite reduction.Functional gene analysis and qPCR revealed that nirK,which is involved in nitrite reduction,significantly accumulated in the most metal-rich soil with the increase of absolute abundance of 63.86%.The experimental results confirmed that the activity of nitrite reductase(Nir)encoded by nirK in the soil was increased at high concentrations of heavy metal(loids).Partial least squares-path model identified three potential modes of nitrite reduction processes being stimulated by heavy metal(loids),the most prominent of which contributed to enhanced nirK abundance and soil Nir activity through positive stimulation of key species.The results provide new insights and preliminary evidence on the stimulation of nitrite reduction processes by heavy metal(loids).
基金supported by 2024 Guizhou Basic Research Plan(Natural Science)Project,China(Foundation of Guizhou science cooperation-ZK[2024]General 490)the National Natural Science Foundation of China(No.31560107).
文摘The mutualistic symbiotic system formed by clumping arbuscular mycorrhizal fungi(AMF)and plants can remediate heavy metal-contaminated soils.However,the specific mechanisms underlying the interaction between AMF and inter-root microbial communities,particularly their impact on organic phosphorus(P)cycling,remain unclear.This study investigated the gene regulation processes involved in inter-root soil phosphorus cycling in wetland plants,specifically Iris tectorum,following inoculation with AMF under varying concentrations of chromium(Cr)stress.Through macro-genome sequencing,we analyzed the composition and structure of the inter-root soil microbial community associated with Iris tectorum under greenhouse pot conditions.The results demonstrated significant changes in the diversity and composition of the inter-root soil microbial community following AMF inoculation,with Proteobacteria,Actinobacteria,Chloroflexi,Acidobacteria,and Bacteroidetes being the dominant taxa.Under Cr stress,species and gene co-occurrence network analysis revealed that AMF promoted the transformation process of organic phosphorus mineralization and facilitated inorganic phosphorus uptake.Additionally,network analysis of functional genes indicated strong aggregation of(pstS,pstA,pstC,TC.PIT,phoR,pp-gppA)genes,which collectively enhanced phosphorus uptake by plants.These findings shed light on the inter-root soil phosphorus cycling process during the co-remediation of Cr-contaminated soil by AMF-Iris tectorum symbiosis,providing valuable theoretical support for the application of AMF-wetland plant symbiosis systems to remediate heavy metal-contaminated soil.
基金supported by Scientific and Technological Innovative Research Team of Shaanxi Province(Grant No.2021TD-34)China Agriculture Research System(Grant No.CARS-23-D06)Key Research and Development Program of Shaanxi Province in China(Grant No.2022ZDLNY03-11)。
文摘Microbial activities are the dynamic core of nutrient cycling in organic substrates,and the exploitation of plant growth-promoting rhizobacteria strains contributes to sustainable agricultural development.This study aimed to investigate the effect and mechanism of Bacillus velezensis SX13 in nutrient cycling and plant promotion under different substrate supply conditions.The effects of reduced substrate amount(sCK)and inoculation of SX13 strain under both substrate supply conditions(Bv and sBv)on rhizosphere microenvironment and plant growth were investigated using conventional substrate amount(CK)as a control.Results showed no significant difference in the a-diversity indexes(Chao1 and Shannon)of the rhizospheric microbial community among the four treatments.However,nonmetric multidimensional scaling analysis and principal coordinate analysis revealed that compared with CK treatment,the inoculation of SX13strain and reduced substrate supply reshaped the β-diversity structure of microbial communities.Furthermore,inoculation with B.velezensis SX13 under both substrate supply conditions increased the abundance of Proteobacteria(1.64%-2.46%),Acidobacteria(14.09%-43.07%),and Firmicutes(179.29%-861.29%).The results of the Kyoto Encyclopedia of Genes and Genomes(KEGG)pathway enrichment analysis showed that the metabolic pathway with the highest abundance of enriched genes was also the pathway with the most enriched differential genes caused by reducing substrate supply or inoculation of B.velezensis SX13.The rhizosphere inoculation of B.velezensis SX13significantly up-regulated the top genes related to carbohydrate esterases,carbohydrate binding modules,glycoside hydrolases,glycoside transferases,and polysaccharide lyases.As a result,the activities of carbon and nitrogen cycle-related enzymes such as cellobiohydrolase,β-glucosidase,urease,L-leucine amino peptidase,and β-1,4-N-acetylglucosaminidase were increased,which in turn accelerated nutrient cycling.B.velezensis SX13 and its mediated improvement of the rhizospheric microenvironment resulted in the up-regulation of root CsNRT family genes(such as CsNRT1.1,CsNRT1.4a,CsNRT1.4b,CsNRT1.5a,CsNRT1.5b,CsNRT1.5c,and CsNRT1.8),which accelerated nitrogen uptake,accumulation,and utilization efficiency and ultimately improved the yield and quality of cucumber.The effect of SX13 strain was more stable and efficient under conventional substrate supply conditions than under reduced substrate supply conditions.
基金funded by the Key Science and Technology Plan Project of Haikou 546(2023–2024).
文摘Background Pork quality and flavor are critical determinants of consumer preference,yet the role of gut microbiota in shaping meat characteristics remains underexplored.In this study,we investigated how a probiotic consortium(FAM:Lactobacillus acidophilus and Bacillus subtilis)modulates the gut-muscle axis to enhance pork flavor.Results In finishing pigs,FAM supplementation significantly increased flavor-associated nucleotides and umamienhancing amino acids in longissimus dorsi muscle.Metagenomic analysis revealed FAM-driven enrichment of glycandegrading Prevotella and short-chain fatty acid-producing Phascolarctobacterium,accompanied by reduced antibiotic resistance genes and virulence factors.Spearman correlation linked Prevotella copri abundance with elevated muscle amino acids,suggesting microbial-encoded CAZymes as key mediators.Conclusions This study provides the first evidence that probiotic-induced gut microbiota remodeling enhances pork flavor through metabolic cross-talk along the gut-muscle axis.The findings suggest a novel strategy for improving pork quality via dietary interventions targeting gut microbiota.
基金jointly supported by the International Partnership Program of Chinese Academy of Sciences(161343KYSB20200015)Guangxi Provincial Natural Science Foundation of China(2023GXNSFAA026107)+1 种基金the Science and Technology Innovation Program of Hunan Province(2022RC1158)Youth Innovation Promotion Association CAS(2023382)。
文摘Background Dietary protein level and amino acid(AA)balance are crucial determinants of animal health and productivity.Supplementing rumen-protected AAs in low-protein diets was considered as an efficient strategy to improve the growth performance of ruminants.The colon serves as a crucial conduit for nutrient metabolism during rumen-protected methionine(RPMet)and rumen-protected lysine(RPLys)supplementation,however,it has been challenging to clarify which specific microbiota and their metabolites play a pivotal role in this process.Here,we applied metagenomic and metabolomic approaches to compare the characteristic microbiome and metabolic strategies in the colon of lambs fed a control diet(CON),a low-protein diet(LP)or a LP diet supplemented with RPMet and RPLys(LR).Results The LP treatment decreased the average daily weight gain(ADG)in lambs,while the LR treatment tended to elicit a remission in ADG.The butyrate molar concentration was greater(P<0.05),while acetate molar concentration(P<0.05)was lower for lambs fed the LP and LR diets compared to those fed the CON diet.Moreover,the LP treatment remarkably decreased total AA concentration(P<0.05),while LR treatment showed an improvement in the concentrations of methionine,lysine,leucine,glutamate,and tryptophan.Metagenomic insights proved that the microbial metabolic potentials referring to biosynthesis of volatile fatty acids(VFAs)and AAs in the colon were remarkably altered by three dietary treatments.Metagenomic binning identified distinct microbial markers for the CON group(Alistipes spp.,Phocaeicola spp.,and Ruminococcus spp.),LP group(Fibrobacter spp.,Prevotella spp.,Ruminococcus spp.,and Escherichia coli),and LR group(Akkermansia muciniphila and RUG099 spp.).Conclusions Our findings suggest that RPMet and RPLys supplementation to the low-protein diet could enhance the microbial biosynthesis of butyrate and amino acids,enriche the beneficial bacteria in the colon,and thereby improve the growth performance of lambs.
基金supported by Chinese Academy of Sciences(Strategic Priority Research Program Grant No.XDA26040304,XDA26050102)the National Natural Science Foundation of China(32072760)the Natural Science Foundation of Hunan Province of China(2022 JJ10054)。
文摘Background The ketogenic diet that forces adenosine triphosphate(ATP)production by beta-oxidation of fatty acids instead of carbohydrate glycolysis,has gained consensus on host metabolism.However,the mechanisms how a ketogenic diet alters gastrointestinal microbiome and its downstream consequences on microbial nutrient availability and energy metabolism remain to be elucidated.Here,we used the sheep model fed with fat-rich diet to evaluate the symbiotic microbiome across three regions of the gastrointestinal tract(rumen,ileum,and colon)to gain a comprehensive understanding of the microbial energy metabolism and microbe-mediated ATP biosynthesis.Results Results showed that sheep fed a fat-rich diet had a greater ADG and increased reliance on fat oxidation for fuel utilization.Metagenomics analysis showed the loss of the specialized fiber-degrading bacteria(genus_Fibrobacter)in the rumen and enrichment of genera RUG420 and Eubacterium,which are involved in lipid metabolism and bile acid processing,in the ileum.A significant functional shift related to energy metabolism was shared across three regions of the gastrointestinal microbiomes.These shifts were dominated by glycolysis/gluconeogenesis and TCA cycle in the rumen and by fatty acid degradation and bile acid transformation in the ileum,indicating adaptation to nutrient availability and energy acquisition.Notably,the abundance of substrate-level phosphorylation(SLP)enzymes was significantly increased in the rumen,ileum and colon,while the ATP-producing capacity through electron transport phosphorylation(ETP)by family_Bacteroidaceae in rumen and Acutalibacteraceae in ileum of sheep with fat-rich diet.Conclusions Altogether,the ATP-related microbiome encoding SLP and ETP in rumen,ileum,and colon contributed 36.95%to the host's weight variation.Our study is the first one demonstrating the microbial potential in the ATP synthesis under the shift in dietary energy source,providing a new perspective on the energy metabolism and precise human macronutrients nutrition.
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.
文摘Helicobacter pylori(H.pylori)infection plays a critical role in gastric diseases,impacting the microbiota structure in gastric and duodenal ulcers.In their study,Jin et al utilized metagenomic sequencing to analyze mucosal samples from patients with ulcers and healthy controls,revealing significant changes in microbial diversity and composition.This article reviews their findings,emphasizing H.pylori’s role in gastric ulcers and the need for further research on its impact on duodenal ulcers.We evaluate the study’s strengths and limitations,suggesting future research directions to enhance our understanding of H.pylori’s contribution to ulcerative diseases.
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.
