Increased circulating branched-chain amino acids(BCAAs)have been involved in the pathogenesis of obesity and insulin resistance.However,evidence relating berberine(BBR),gut microbiota,BCAAs,and insulin resis⁃tance is ...Increased circulating branched-chain amino acids(BCAAs)have been involved in the pathogenesis of obesity and insulin resistance.However,evidence relating berberine(BBR),gut microbiota,BCAAs,and insulin resis⁃tance is limited.Here,we showed that BBR could effectively rectify steatohepatitis and glucose intolerance in high-fat diet(HFD)-fed mice.BBR reorganized gut microbiota populations under both the normal chow diet(NCD)and HFD.Particu⁃larly,BBR noticeably decreased the relative abundance of BCAA-producing bacteria,including order Clostridiales;fami⁃lies Streptococcaceae,Clostridiaceae,and Prevotellaceae;and genera Streptococcus and Prevotella.Compared with the HFD group,predictive metagenomics indicated a reduction in the proportion of gut microbiota genes involved in BCAA biosynthesis but the enrichment genes for BCAA degradation and transport by BBR treatment.Accordingly,the elevated serum BCAAs of HFD group were significantly decreased by BBR.Furthermore,the Western blotting results implied that BBR could promote the BCAA catabolism in the liver and epididymal white adipose tissues of HFD-fed mice by acti⁃vation of the multienzyme branched-chain α-ketoacid dehydrogenase complex,whereas by inhibition of the phosphoryla⁃tion state of BCKDHA(E1α subunit)and branched-chain α-ketoacid dehydrogenase kinase.The ex vivo assay further confirmed that BBR could increase BCAA catabolism in both AML12 hepatocytes and 3T3-L1 adipocytes.Finally,data from healthy subjects and diabetics confirmed that BBR could improve glycemic control and modulate circulating BCAAs.Besides,functional microbiomics integrated high-throughput microbial genomics,metabolomics and molecular biotechnology has also been successfully applied to reveal the anti-obesity mechanism of hydroxysafflor yellow A.展开更多
The authors regret that 1.The citation"(Fig.5B)"should be removed from the final paragraph of Section 3.5 in the Results and Discussion,as the summary statement reflects the overall findings and is not exclu...The authors regret that 1.The citation"(Fig.5B)"should be removed from the final paragraph of Section 3.5 in the Results and Discussion,as the summary statement reflects the overall findings and is not exclu-sively represented by Fig.5B.展开更多
Esophageal cancer is a prevalent and aggressive malignancy associated with a poor prognosis.Metabolomics and microbiomics have emerged as promising approaches for investigating the tumor microenvironment and monitorin...Esophageal cancer is a prevalent and aggressive malignancy associated with a poor prognosis.Metabolomics and microbiomics have emerged as promising approaches for investigating the tumor microenvironment and monitoring dynamic changes throughout the treatment process.These methodologies facilitate the direct observation of phenotypic alterations with high sensitivity,throughput,and adaptability across diverse sample types.Microbial genomic data play a crucial role in predicting the metabolic potential of microorganisms,whereas metabolomics offers direct evidence of active metabolic pathways under specific conditions.This review presents novel insights into the pathogenesis,diagnosis,and treatment of esophageal cancer through the application of metabolomics and microbiomics.Future advancements in the integration of multi-omics data are expected to further elucidate the metabolic mechanisms and pathophysiological processes underlying esophageal cancer,thereby laying a robust scientific foundation for early diagnosis,prognostic assessment,and personalized treatment strategies.展开更多
The pathophysiology of many ailments,including neurological,gastrointestinal,and metabolic disorders,is well known to be influenced by intestinal dysbiosis.Clinical research has provided evidence suggesting a strong c...The pathophysiology of many ailments,including neurological,gastrointestinal,and metabolic disorders,is well known to be influenced by intestinal dysbiosis.Clinical research has provided evidence suggesting a strong correlation between dysbiosis of the gut microbiome and colorectal cancer(CRC)development.The active reprogramming of metabolic pathways to boost glycolysis,fatty acid production,lipogenesis,and glutaminolysis constitutes a major metabolic shift in cancer development,including CRC.The complex combination of different factors leads to CRC,making it an environmental disease.These factors include food and lifestyle choices,genetics and family history,age,underlying intestinal diseases,and dysbiosis of the gut microbiota.One of the primary risk factors for carcinoma development is diet,which impacts an individual’s gut microbiome.In addition to impacting CRC formation,the gut microbiome also has immunomodulatory effects,including various immunological interactions and the underlying mechanisms governing them.Microbial interactions in CRC have been extensively studied,yet numerous unresolved queries exist on how gut bacteria can influence treatment.Microbiome-driven immunotherapies,focusing on probiotics,prebiotics,and synbiotics,represent a promising therapeutic avenue.However,large-scale treatment utilization in CRC patients is limited by several issues,including variations in the microbial makeup of each patient’s gut and a lack of established methods.The study highlights the impact of several risk factors,including dysbiosis of the gut microbiome and different approaches to halting and treating CRC progression with a focus on diet changes and modulation of the gut flora.Given the foregoing,we propose that if research gaps are addressed and immunotherapy is paired with microbial interventions,microbiota-based therapeutics could potentially impede the growth of tumors and treat CRC.展开更多
Ciliates are a dominant group in the marine sediment microecosystem,and their interactions with symbiotic prokaryotes are important for understanding the adaptation mechanisms of marine benthic eukaryotes.However,the ...Ciliates are a dominant group in the marine sediment microecosystem,and their interactions with symbiotic prokaryotes are important for understanding the adaptation mechanisms of marine benthic eukaryotes.However,the microbial communities(microbiome)associated with most benthic ciliates and the taxonomic attributes of the dominant symbiotic bacteria are unclear.In this study,we focused on Paraspathidium apofuscum,a ciliate prevalent in marine benthic environments,and comprehensively explored the diversity and cellular location of the microbiomes in two P.apofuscum isolates using single-cell-based full-length16S rRNA amplicon sequencing,phylogenetic analysis,and fluorescence in situ hybridization.The results showed that the P.apofuscum cell surface carried a highly diverse microbiome whose cellular localization was consistent with the positions of the ciliate's somatic dikinetids.The dominant genera in the microbiome,Pseudoalteromonas,Halobacteriovorax and Oceaniserpentilla,were associated with unicellular eukaryotes.In particular,Pseudoalteromonas likely uses ciliate-secreted metabolites as nutrients and plays a role in host physical protection or pathogen resistance.Halobacteriovorax and Oceaniserpentilla are newly discovered or rare bacterial genera innovatively found to have ecological niches in symbiosis with benthic ciliates.Comparison analysis indicates that the microbiomes associated with benthic ciliates display species and population specificity,which are attributed to several factors such as environmental physicochemical properties,host physiological states,and interactions among associated bacteria.This study provides important insights into the environmental adaptation of eukaryotes through a symbiotic mechanism in the marine benthic environment.展开更多
The poultry gut microbiome plays a key role in nutrient digestion,immune function,and overall health.Differences among various farming systems,including conventional,antibiotic-free,free-range,and organic systems,infl...The poultry gut microbiome plays a key role in nutrient digestion,immune function,and overall health.Differences among various farming systems,including conventional,antibiotic-free,free-range,and organic systems,influence microbial composition and function through variations in diet,genetic selection,environmental exposure,and antibiotic use.Conventional systems typically rely on formulated diets and controlled housing conditions,often with routine antimicrobial use.In contrast,organic systems emphasize natural feed ingredients,including roughage,outdoor access,and strict limitations on the use of antibiotics.These divergent practices shape the gut microbiota differently,with organic systems generally associated with greater exposure to environmental microbes and,consequently,greater microbial diversity.However,the implications of this increased diversity for poultry health and performance are complex,as organic systems may also carry a higher risk of pathogen exposure.This review summarizes current findings on the chicken gut microbiome across conventional and alternative production systems(antibiotic-free,freerange,and organic),focusing on microbial diversity,functional potential,and disease resilience.The need for standardized methodologies and consistent nomenclature in microbiome research is also discussed to improve comparability across studies.Understanding how production systems influence the gut microbiota is essential for improving poultry health and productivity while addressing challenges related to antimicrobial resistance and sustainable farming practices.展开更多
The objective of this study was to understand the effect of long-term aconitine(AC)oral administration on the digestive tract and serum metabolism.Subjects consumed either 0.9%Na Cl(n=8)or AC(n=17)gavage designed to r...The objective of this study was to understand the effect of long-term aconitine(AC)oral administration on the digestive tract and serum metabolism.Subjects consumed either 0.9%Na Cl(n=8)or AC(n=17)gavage designed to represent human chronic AC administrations for 13 days.Organ pathology was determined using hematoxylin-eosin staining and immunohistochemistry.Fecal and proximal intestinal content samples were collected to perform shotgun metagenomic sequencing.Serum samples were collected,and untargeted metabolomics was performed.In this study,AC administration induced proximal intestine,liver,and kidney injury.Microbiome composition remained stable after AC exposure,while several microbes presented dynamic alteration.Moreover,AC affected the abundance of the fatty acid biosynthesis rate-limiting gene acc A at day 7.AC induces 30 serum metabolites to significantly change at day 14,including several short-chain acylcarnitines.WGCNA revealed 2 sub-modules associated with the level of several short-chain acylcarnitines.In summary,AC affects the digestive tract and serum metabolism after chronic administration.AC may affect the enrichment of microbial-derived acc A gene.The abundance of serum acylcarnitines detected in the AC group may associate with its anti-heart failure effects.展开更多
Background The rapid emergence of multidrug-resistant Salmonella in poultry demands alternative control strategies beyond conventional antibiotics.In this study,we evaluated a combination of lytic Salmonella-infecting...Background The rapid emergence of multidrug-resistant Salmonella in poultry demands alternative control strategies beyond conventional antibiotics.In this study,we evaluated a combination of lytic Salmonella-infecting bacteriophages(SLAM_phi ST45 and SLAM_phiST56)and a probiotic bacterium Limosilactobacillus reuteri(SLAM_LAR11)in a chick model challenged with Salmonella enterica serovar Typhimurium infection.Results Co-administration with two-phage cocktail and a probiotic showed markedly reduced Salmonella colonization in the gut and systemic organs of chicks,comparable to the effect of phage-only treatment.In contrast with phage-only treatment,the combined therapy significantly improved the rate of body-weight change from the day of infection to necropsy(P<0.0001)and alleviated infection-associated splenomegaly(P=0.028)and hepatomegaly(P=0.011).In the ileum,the villus height-to-crypt depth ratio(VH/CD)increased significantly(P=0.044).In the colon,expression of tight-junction genes OCLN(P=0.014),TJP1(P<0.0001),and MUC2(P=0.011)was elevated,whereas the pro-inflammatory cytokine IL6 was reduced(P=0.018).These improvements were accompanied,in the cecum,by trends toward decreases in Escherichia-Shigella(P=0.09)and Clostridium(P=0.16)and a trend toward an increase in Blautia(P=0.11);additionally,in the ileum,Lactobacillus(P=0.037)and Blautia(P=0.016)increased significantly,yielding a more balanced microbiota than with phage-only treatment.Consistently,levels of functional metabolites,including acetic acid(LDA=3.32)and lactic acid(LDA=5.29),were increased.Conclusion Taken together,these findings demonstrate that phage-probiotic co-administration not only enhances the clearance of multidrug-resistant Salmonella more effectively than phage treatment alone but also promotes intestinal health,highlighting its potential as an antibiotic-alternatives strategy to improve intestinal health and ensure food safety in poultry production systems.展开更多
Microglia,lipids,and their interaction are found to play important roles in post-stroke immunity.Microglia are sensitive to detect environment change in injured brain.Activated microglia undergo phenotypical remodelin...Microglia,lipids,and their interaction are found to play important roles in post-stroke immunity.Microglia are sensitive to detect environment change in injured brain.Activated microglia undergo phenotypical remodeling and trigger complex signal casca d es to regulate immune responses after stroke.Lipids including peripheral lipid metabolism and lipid droplet biogenesis are involved in the control of microglia functions,such as activation,phagocytosis,proliferation,and pro-inflammation.In this review,we explore new scope of microglia and lipids in immune regulation of stro ke.Implication of peripheral lipid metabolism after stroke is mentioned and advances in microglia-lipid inte raction are discussed We give a special focus on how diet and gut microbiome influence neuroinflammation system via gut-brain axis,and how these processes associate with the risk and outcome of stroke.Moreove r,we reviewed the therapeutic targets related to lipid metabolism and microglial modulation after stro ke.These can provide a prospective strategy for more efficient and safer treatment for ischemic and hemorrhagic stroke.展开更多
Microorganisms constitute an essential component in the indoor environment,which is closely related to hu-man health.However,there is limited evidence regarding the associations between indoor airborne microbiome and ...Microorganisms constitute an essential component in the indoor environment,which is closely related to hu-man health.However,there is limited evidence regarding the associations between indoor airborne microbiome and systemic inflammation,as well as whether this association is modified by indoor particulate matter and the underlying mechanisms.In this prospective repeated-measure study among 66 participants,indoor airborne mi-crobiome was characterized using amplicon sequencing and qPCR.Indoor fine particulate matter(PM_(2.5))and inhalable particulate matter(PM10)were measured.Systemic inflammatory biomarkers were assessed,including white blood cell(WBC),neutrophil(NEUT),monocyte,eosinophil counts,and their proportions.Targeted serum amino acid metabolomics were conducted to explore the underlying mechanisms.Linear mixed-effect models re-vealed that bacterial and fungal Simpson diversity were significantly associated with decreased WBC and NEUT.For example,for each interquartile range increase in the bacterial Simpson diversity,WBC and NEUT changed by-4.53%(95%CI:-8.25%,-0.66%)and-5.95%(95%CI:-11.3%,-0.27%),respectively.Notably,increased inflammatory risks of airborne microbial exposure were observed when indoor PM_(2.5) and PM10 levels were below the WHO air quality guidelines.Mediation analyses indicated that dopamine metabolism partially mediated the anti-inflammatory effects of fungal diversity exposure.Overall,our study indicated protection from a diverse indoor microbial environment on cardiovascular health and proposed an underlying mechanism through amino acid metabolism.Additionally,health risks associated with microbial exposure deserve more attention in con-texts of low indoor particulate matter pollution.Further research is necessary to fully disentangle the complex relationships between indoor microbiome,air pollutants,and human health.展开更多
Background Zearalenone(ZEN),a common mycotoxin in ruminant diets,could disturb the rumen ecosystem and impair rumen fermentation.Noticeably,ZEN has been shown to reduce the relative abundances of specific bacterial ta...Background Zearalenone(ZEN),a common mycotoxin in ruminant diets,could disturb the rumen ecosystem and impair rumen fermentation.Noticeably,ZEN has been shown to reduce the relative abundances of specific bacterial taxa that potentially possess quorum sensing(QS)functions,which are deemed essential for the microbial interactions and adaptations during rumen fermentation.Nonetheless,whether QS communications participate in the responses of rumen microbial fermentation to ZEN remains unknown.Therefore,the present trial was performed to explore the potential roles of QS during the alterations of rumen microbial fermentation by ZEN through a rumen simulation technique(RUSITEC)system,in a replicated 4×4 Latin square design.Results ZEN significantly(P<0.05)reduced QS signal autoinducer-2(AI-2),and tended to(P=0.051)downregulate QS signal C4-homoserine lactone(HSL).ZEN also significantly(P<0.05)decreased total volatile fatty acid(TVFA),acetate,propionate,isobutyrate,isovalerate,organic matter disappearance(OMD),neutral detergent fiber disappearance(NDFD),and acid detergent fiber disappearance(ADFD)in different manners.The linear discriminant analysis effect size(LEf Se)analysis indicated significantly(P<0.05)differential enrichments of a series of bacterial taxa such as Butyrivibrio_sp_X503,Rhizobium daejeonense,Hoylesella buccalis,Ezakiella coagulans,Enterococcus cecorum,Ruminococcus_sp_zg-924,Polystyrenella longa,and Methylacidimicrobium fagopyrum across different treatments.The phylogenetic investigation of communities by reconstruction of unobserved states 2(PICRUSt2)analysis suggested that QS were predicted to be significantly(P<0.05)affected by ZEN.The metabolomics analysis detected considerable significantly(P<0.05)differing metabolites and implied that ZEN challenge significantly(P<0.05)influenced the indole alkaloid biosynthesis,biosynthesis of alkaloids derived from shikimate pathway,and sesquiterpenoid and triterpenoid biosynthesis.Significant(P<0.05)interconnections of QS molecules with the differential rumen fermentation traits,differential bacterial taxa,and differential metabolites were exhibited by Spearman analysis.Conclusions ZEN negatively affected the QS signals of AI-2 and C4-HSL,which was found to correlate with the fluctuations in specific rumen fermentation characteristics,ruminal bacterial populations,and ruminal metabolisms.These interrelationships implied the potential involvement of QS in the reactions of rumen microbiota to ZEN contamination,and probably contributed to the inhibition of rumen fermentation.展开更多
Background: The human gut microbiome is an important target for disease treatment and prevention. Various microbial species within the complex ecosystem of the microbiome have been shown to play important roles in dis...Background: The human gut microbiome is an important target for disease treatment and prevention. Various microbial species within the complex ecosystem of the microbiome have been shown to play important roles in disease. Identification of bioactive materials capable of altering the abundances of these species both safely and effectively is a major goal in microbiome research. Many traditional Chinese medicines (TCMs) have been reported to affect the composition of the gut microbiome. Here, we summarize studies that have used TCMs to alter the gut microbiome and discuss the response relationship between TCMs and gut microbial species. Methods: We searched the PubMed, Web of Science, and Knowledge Network databases using the terms “traditional Chinese medicine,” “gut microbiome,” and specific system disease names (endocrine, immune, nervous, cardiovascular, and digestive). Studies were excluded if irrelevant or if the experimental procedures were unclear. Results: TCMs have been reported to affect a wide range of gut microbial taxa spanning major phyla, including Firmicutes, Bacteroidetes, Proteobacteria, Verrucomicrobiota, Actinobacteria, and Fusobacteria. In all, 54 TCMs including compounds and extracts have been tested in rodents and 30 have been examined in human trials. Almost all studies have reported positive results in regulating the gut microbiome as well as modulating corresponding phenotypes, spanning diseases of the endocrine, immune, nervous, cardiovascular, and digestive systems. Gut species, including Akkermansia, Bacteroides, Fusobacterium, Faecalibacterium, and E. coli, were found to be regulated by 19 TCMs. A network was constructed to visualize the interactions between TCMs and these taxa. Conclusion: There exists a complex and close relationship between intestinal microflora and diseases. Sufficient experimental data and studies have proved that the imbalance of intestinal microflora affects health by mediating metabolism, immune regulation, inflammation and signal transduction. Many characteristic alterations of intestinal microflora are positively correlated with diseases, so intestinal microflora has become a potential risk index and treatment target for many diseases. Many TCMs affect the relative abundances of microbial species in the gut, and therefore may be useful for modulating the gut microbiome. This review provides a reference for prioritizing candidate TCMs from the enormous repertoire of such medicines to test which specific gut microbes are targeted.展开更多
Although diet and gut microbial composition have been linked to chronic respiratory diseases,these associations remain difficult to interpret because of confounding and reverse causation.The gut-lung axis provides a p...Although diet and gut microbial composition have been linked to chronic respiratory diseases,these associations remain difficult to interpret because of confounding and reverse causation.The gut-lung axis provides a plausible framework for this interaction,yet direct genetic evidence is limited.Using a two-step,two-sample Mendelian randomization(MR)framework,supplemented by multivariable MR(MVMR)to adjust for pleiotropic effects and Benjamini-Hochberg false discovery rate(FDR)correction for multiple testing,we assessed the causal contributions of dietary habits and gut microbial taxa to major chronic respiratory diseases.We identified 22 dietary factors with causal effects on disease risk and 225 microbial taxa that acted as independent risk or protective contributors.Mediation analyses further showed that the effects of 12 dietary habits were transmitted through 32 specific microbial taxa.Notably,genetically predicted pork intake increased the risk of chronic obstructive pulmonary disease(COPD)(OR=10.53,95%CI[8.54,13.00]),an effect partly mediated by elevated abundance of CAG-485 sp002404675.In contrast,bread consumption conferred protection against asthma(OR=0.68,95%CI[0.64,0.72]),whereas this benefit was offset by approximately 45%through a pathway involving reduced Veillonella abundance.Collectively,these findings provide genetic support for the gut-lung axis and demonstrate that the gut microbiome functions as a causal mediator linking diet to chronic respiratory disease risk.However,since this study was based on individuals of European ancestry,caution is warranted when generalizing these causal estimates to non-European populations,such as East Asian groups.This work suggests new opportunities for microbiota-targeted prevention and therapeutic strategies.展开更多
Amyotrophic lateral sclerosis is a devastating neurodegenerative disease marked by progressive motor neuron degeneration.Despite extensive research,effective treatments remain elusive,underscoring the need to explore ...Amyotrophic lateral sclerosis is a devastating neurodegenerative disease marked by progressive motor neuron degeneration.Despite extensive research,effective treatments remain elusive,underscoring the need to explore the molecular mechanisms driving disease progression.The amyotrophic lateral sclerosis complexity is further compounded by its large heterogeneity,encompassing both genetic and sporadic forms,diverse phenotypic presentations,and highly variable progression rates.A key pathological feature of amyotrophic lateral sclerosis is the aggregation of TAR DNA-binding protein 43,which contributes to cellular toxicity,neuroinflammation,and neuronal dysfunction.This review explores the complex interplay between TAR DNA-binding protein 43 pathology,immunity dysregulation,and the gut-brain axis,with a focus on the role of microbiome-derived metabolites in amyotrophic lateral sclerosis.Neuroinflammation,mediated by both innate and adaptive immunity,plays a central role in disease pathogenesis,with TAR DNA-binding protein 43 influencing immune signaling and exacerbating neurotoxicity.Additionally,disruptions in gut microbiota composition and intestinal barrier integrity,frequently observed in amyotrophic lateral sclerosis patients,suggest a potential role for the gut-brain axis in modulating neurodegenerative processes.By integrating evidence from emerging studies,our aim is to clarify how TAR DNA-binding protein 43 aggregation contributes to neuroinflammation and immune dysfunction while exploring the gut microbiota role as both a modulator and potential biomarker of disease.Understanding these interactions could pave the way for novel therapeutic strategies,including microbiome-targeted interventions such as probiotics,dietary modifications,or immune-modulating therapies.Finally,unraveling the TAR DNA-binding protein 43-immune system-microbiome axis may offer new avenues for personalized treatments aimed at mitigating neuroinflammation,slowing amyotrophic lateral sclerosis progression,and improving patient outcomes and life quality.展开更多
Background Recent studies have suggested a potential role of the oral microbiome in the development of cardiovascular diseases.This study aims to investigate the association between oral microbiota and cardiovascular ...Background Recent studies have suggested a potential role of the oral microbiome in the development of cardiovascular diseases.This study aims to investigate the association between oral microbiota and cardiovascular disease risk,including atrial fibrillation,myocardial infarction,chronic heart failure,and hypertension.Methods We analyzed GWAS data from East Asian populations'oral microbiome,involving 2,017 tongue and 1,915 saliva samples from 2,984 individuals with whole-genome sequencing.Additionally,we sourced cardiovascular disease GWAS data from NBDC,including atrial fibrillation(8,180 cases,28,621 controls),myocardial infarction(14,992 cases,146,214 controls),chronic heart failure(10,540 cases,168,186 controls),and systolic blood pressure(145,505 individuals).Results Several oral microbiota taxa were found to be significantly associated with cardiovascular disease outcomes.Specific microbiota,such as Centipeda,Corynebacterium,and Pseudomonas E,were negatively correlated with heart failure.In contrast,taxa like Neisseria D and Actinomyces were associated with an increased risk of atrial fibrillation and myocardial infarction.Additionally,certain oral microbiota showed correlations with changes in blood pressure,highlighting their potential role in hypertension.Conclusion Our findings suggest that the oral microbiota may influence the development and progression of cardiovascular diseases,providing new insights into the potential impact of oral health on cardiovascular risk.展开更多
Catalpa bungei,a fast-growing timber tree,is threatened by the lepidopteran pest Omphisa plagialis.Previous studies in our laboratory successfully generated transgenic C.bungei lines overexpressing Cry genes(Cry1Ab,Cr...Catalpa bungei,a fast-growing timber tree,is threatened by the lepidopteran pest Omphisa plagialis.Previous studies in our laboratory successfully generated transgenic C.bungei lines overexpressing Cry genes(Cry1Ab,Cry2A,and Cry9-2)that exhibited resistance to O.plagialis,but their potential impact on soil bacterial communities remains unclear.In this study,we analyzed nine transgenic C.bungei lines(three independent lines for each Cry gene)to characterize their rhizosphere bacterial communities using high-throughput sequencing of the 16S ribosomal DNA(rDNA)V4-V5 regions.A total of 628 amplicon sequence variants(ASVs)were shared among all transgenic and wild-type(WT)lines,forming a stable core microbiome dominated by Proteobacteria,Bacteroidota,Acidobacteriota,and Actinobacteriota.Alpha diversity showed no significant differences,while beta diversity revealed minor but distinct compositional shifts.Cry1Ab lines exhibited higher abundances of fast-growing taxa,particularly Proteobacteria and Bacteroidota;Cry2A lines displayed intermediate profiles,whereas Cry9-2 lines were nearly indistinguishable from WT communities.Linear discriminant analysis of the effect size revealed significant enrichment of taxa such as Burkholderiaceae and Ralstonia in the Cry1Ab rhizosphere,in contrast to the higher abundance of Chloroflexi in the WT.Functional predictions indicated consistent metabolic pathways across all treatments,suggesting strong ecological redundancy.This study demonstrates minimal impact on rhizosphere microbial communities in transgenic C.bungei plants.The Cry9-2 construct exhibited superior environmental stability,whereas the Cry1Ab construct caused only slight but ecologically acceptable shifts.These findings support the ecological safety of Bt-transgenic C.bungei and identify Cry9-2 as a particularly favorable candidate for forestry applications.This comparative evaluation of three Cry genes in a tree species provides a framework for future gene-specific biosafety assessments in woody plants.展开更多
Background:The Colorectal Cancer(CRC)pathogenesis and therapeutic efficacy are influenced by the gut microbiome,making it a promising biomarker for predicting treatment responses and adverse effects.This systematic re...Background:The Colorectal Cancer(CRC)pathogenesis and therapeutic efficacy are influenced by the gut microbiome,making it a promising biomarker for predicting treatment responses and adverse effects.This systematic review aims to outline the gut microbiome composition in individuals with CRC undergoing the same therapeutic regimen and evaluate interindividual microbiome profile variations to better understand how these differences may influence therapeutic outcomes.Methods:Key studies investigating the microbiome’s role in therapeutic approaches for CRC were searched in both PubMed and Cochrane databases on 12 and 22 March 2025,respectively.Eligible studies included free full-text English-language randomized clinical trials and human observational studies reporting on gut microbiome composition and treatment outcomes.RoB 2 and ROBINS-I were employed in the evaluation of bias for randomized trials and observational studies,respectively.Data extracted was narratively analyzed.Results:Six studies involving a total of 361 individuals were included.Therapeutic interventions,either standard treatments and/or those targeting the gut microbiome,generally increased probiotic taxa and reduced pro-carcinogenic bacteria.However,no consistent pattern of improved clinical outcomes was observed,suggesting that treatment mechanisms,the tumor’s nature,and individual characteristics play critical roles in microbiome modulation.Conclusion:The gut microbiome holds significant potential in clinical settings.Nonetheless,further research is needed to better understand its functional aspects and to consider the influence of treatment mechanisms,the tumor’s nature,and individual characteristics as modulators,in order to optimize clinical outcomes.展开更多
Wu et al recently applied multi-region 16S rRNA sequencing to characterize the gastric cancer microbiome,demonstrating improved taxonomic resolution and detection sensitivity over conventional single-region approaches...Wu et al recently applied multi-region 16S rRNA sequencing to characterize the gastric cancer microbiome,demonstrating improved taxonomic resolution and detection sensitivity over conventional single-region approaches.While the study represents a valuable methodological step forward,it remains limited by singlecenter design,lack of quantitative calibration,and insufficient control for contamination and inter-laboratory variability.This editorial critically appraises these methodological gaps and emphasizes that future efforts must focus on harmonized,consensus-driven workflows to ensure reproducibility and clinical reliability.The translational potential of multi-region 16S lies in moving from descriptive microbial profiling to actionable clinical integration,particularly for recurrence prediction,treatment-response monitoring,and perioperative complication risk assessment.By addressing these methodological,economic,and ethical challenges,the field can advance toward evidence-based and clinically deployable microbiome-guided precision oncology.展开更多
Background The gayal(Bos frontalis),a semi-domesticated bovine species,demonstrates exceptional adaptability to lignocellulose-rich diets dominated by bamboo,suggesting the presence of a specialized gastrointestinal m...Background The gayal(Bos frontalis),a semi-domesticated bovine species,demonstrates exceptional adaptability to lignocellulose-rich diets dominated by bamboo,suggesting the presence of a specialized gastrointestinal microbiome.However,the functional mechanisms underlying this host-microbiome interaction remain poorly understood.Here,we conducted integrated metagenomic and metatranscriptomic analyses of rumen,cecum,and colon digesta from yellow cattle and gayal raised on the same bamboo-based high-fiber diet.Results The results showed that gayal exhibited superior fiber-degrading capacity relative to yellow cattle,evidenced by significantly higher(P<0.05)fiber digestibility,cellulase and xylanase activities,and increased volatile fatty acids production despite identical feed intake.Microbial community analysis revealed distinct composition in both the rumen and hindgut of gayal compared to yellow cattle,with notable enrichment of taxa specialized in lignocellulose degradation.Metatranscriptomic profiling further identified upregulation of key lignin-modification enzymes,particularly AA6,AA2,and AA3,primarily encoded by Prevotella,Cryptobacteroides,Limimorpha,and Ventricola.These enzymes are known to modify lignin structure to increase polysaccharide accessibility.These results demonstrate that gayal hosts a unique and metabolically active gastrointestinal microbiome capable of efficient lignocellulose deconstruction through a coordinated enzymatic cascade,especially effective in dismantling lignin barriers.Conclusions This study provides novel insights into host-microbiome co-adaptation to fibrous feeds and highlights the potential of gayal-derived microbial consortia and enzymes for improving roughage utilization in ruminant agriculture.展开更多
Objective Previous Mendelian randomization(MR)studies have suggested an association between the gut microbiome and metabolic-associated fatty liver disease(MAFLD).However,the reliance on 16S rRNA sequencing data has l...Objective Previous Mendelian randomization(MR)studies have suggested an association between the gut microbiome and metabolic-associated fatty liver disease(MAFLD).However,the reliance on 16S rRNA sequencing data has led to inconsistent findings and limited species-level insights.To address this,we conducted a de novo MR analysis using species-level shotgun metagenomic data,combined it with a meta-analysis to consolidate the existing evidence,and explored metabolite-mediated pathways.Methods Bidirectional MR analyses were performed between 883 gut microbiota taxa(derived from shotgun metagenomic genome-wide association study)and MAFLD.Published MR studies(up to December 1,2024)were identified using PubMed,Embase,Web of Science,and the Cochrane Library for meta-analysis.Multivariable MR(MVMR)and mediation analyses were applied to assess the mediating effects of 1,400 blood metabolites.Results The de novo MR identified 25 MAFLD-associated microbial taxa.Integration with 7 published studies revealed 34 causal taxa,including 10 at the species level.Among the 1,400 metabolites,53 showed causal links with MAFLD.MVMR and mediation analyses identified deoxycholate as a mediator of the effect of Bifidobacterium on MAFLD risk(22.06%mediation proportion).Conclusion This study elucidated the connections between species-level gut microbiota and MAFLD,highlighting the interplay between microbiota,metabolites,and disease pathogenesis.These findings provide novel insights into the potential therapeutic targets for MAFLD.展开更多
文摘Increased circulating branched-chain amino acids(BCAAs)have been involved in the pathogenesis of obesity and insulin resistance.However,evidence relating berberine(BBR),gut microbiota,BCAAs,and insulin resis⁃tance is limited.Here,we showed that BBR could effectively rectify steatohepatitis and glucose intolerance in high-fat diet(HFD)-fed mice.BBR reorganized gut microbiota populations under both the normal chow diet(NCD)and HFD.Particu⁃larly,BBR noticeably decreased the relative abundance of BCAA-producing bacteria,including order Clostridiales;fami⁃lies Streptococcaceae,Clostridiaceae,and Prevotellaceae;and genera Streptococcus and Prevotella.Compared with the HFD group,predictive metagenomics indicated a reduction in the proportion of gut microbiota genes involved in BCAA biosynthesis but the enrichment genes for BCAA degradation and transport by BBR treatment.Accordingly,the elevated serum BCAAs of HFD group were significantly decreased by BBR.Furthermore,the Western blotting results implied that BBR could promote the BCAA catabolism in the liver and epididymal white adipose tissues of HFD-fed mice by acti⁃vation of the multienzyme branched-chain α-ketoacid dehydrogenase complex,whereas by inhibition of the phosphoryla⁃tion state of BCKDHA(E1α subunit)and branched-chain α-ketoacid dehydrogenase kinase.The ex vivo assay further confirmed that BBR could increase BCAA catabolism in both AML12 hepatocytes and 3T3-L1 adipocytes.Finally,data from healthy subjects and diabetics confirmed that BBR could improve glycemic control and modulate circulating BCAAs.Besides,functional microbiomics integrated high-throughput microbial genomics,metabolomics and molecular biotechnology has also been successfully applied to reveal the anti-obesity mechanism of hydroxysafflor yellow A.
文摘The authors regret that 1.The citation"(Fig.5B)"should be removed from the final paragraph of Section 3.5 in the Results and Discussion,as the summary statement reflects the overall findings and is not exclu-sively represented by Fig.5B.
基金supported by the National Natural Science Foundation of China(No.82072557)National Key Research and Development Program of China(No.2021YFC2500900)+5 种基金Fundamental Research Funds for the Central Universities(Grant No.YG2023QNB04)Shanghai Municipal Education Commission-Gaofeng Clinical Medicine Grant of China(No.20172005)support was provided by the Program of Shanghai Academic Research Leader from the Science and Technology Commission of Shanghai Municipality,China(No.20XD1402300)Novel Interdisciplinary Research Project from the Shanghai Municipal Health Commission,China(No.2022JC023)Interdisciplinary Program of Shanghai Jiao Tong University,China(No.YG2023ZD04)Clinical Research Project in Health Services of the Shanghai Municipal Health Commission of China(No.202240089).
文摘Esophageal cancer is a prevalent and aggressive malignancy associated with a poor prognosis.Metabolomics and microbiomics have emerged as promising approaches for investigating the tumor microenvironment and monitoring dynamic changes throughout the treatment process.These methodologies facilitate the direct observation of phenotypic alterations with high sensitivity,throughput,and adaptability across diverse sample types.Microbial genomic data play a crucial role in predicting the metabolic potential of microorganisms,whereas metabolomics offers direct evidence of active metabolic pathways under specific conditions.This review presents novel insights into the pathogenesis,diagnosis,and treatment of esophageal cancer through the application of metabolomics and microbiomics.Future advancements in the integration of multi-omics data are expected to further elucidate the metabolic mechanisms and pathophysiological processes underlying esophageal cancer,thereby laying a robust scientific foundation for early diagnosis,prognostic assessment,and personalized treatment strategies.
文摘The pathophysiology of many ailments,including neurological,gastrointestinal,and metabolic disorders,is well known to be influenced by intestinal dysbiosis.Clinical research has provided evidence suggesting a strong correlation between dysbiosis of the gut microbiome and colorectal cancer(CRC)development.The active reprogramming of metabolic pathways to boost glycolysis,fatty acid production,lipogenesis,and glutaminolysis constitutes a major metabolic shift in cancer development,including CRC.The complex combination of different factors leads to CRC,making it an environmental disease.These factors include food and lifestyle choices,genetics and family history,age,underlying intestinal diseases,and dysbiosis of the gut microbiota.One of the primary risk factors for carcinoma development is diet,which impacts an individual’s gut microbiome.In addition to impacting CRC formation,the gut microbiome also has immunomodulatory effects,including various immunological interactions and the underlying mechanisms governing them.Microbial interactions in CRC have been extensively studied,yet numerous unresolved queries exist on how gut bacteria can influence treatment.Microbiome-driven immunotherapies,focusing on probiotics,prebiotics,and synbiotics,represent a promising therapeutic avenue.However,large-scale treatment utilization in CRC patients is limited by several issues,including variations in the microbial makeup of each patient’s gut and a lack of established methods.The study highlights the impact of several risk factors,including dysbiosis of the gut microbiome and different approaches to halting and treating CRC progression with a focus on diet changes and modulation of the gut flora.Given the foregoing,we propose that if research gaps are addressed and immunotherapy is paired with microbial interventions,microbiota-based therapeutics could potentially impede the growth of tumors and treat CRC.
基金supported by the National Natural Science Foundation of China(Nos.42176163 and 31970398)。
文摘Ciliates are a dominant group in the marine sediment microecosystem,and their interactions with symbiotic prokaryotes are important for understanding the adaptation mechanisms of marine benthic eukaryotes.However,the microbial communities(microbiome)associated with most benthic ciliates and the taxonomic attributes of the dominant symbiotic bacteria are unclear.In this study,we focused on Paraspathidium apofuscum,a ciliate prevalent in marine benthic environments,and comprehensively explored the diversity and cellular location of the microbiomes in two P.apofuscum isolates using single-cell-based full-length16S rRNA amplicon sequencing,phylogenetic analysis,and fluorescence in situ hybridization.The results showed that the P.apofuscum cell surface carried a highly diverse microbiome whose cellular localization was consistent with the positions of the ciliate's somatic dikinetids.The dominant genera in the microbiome,Pseudoalteromonas,Halobacteriovorax and Oceaniserpentilla,were associated with unicellular eukaryotes.In particular,Pseudoalteromonas likely uses ciliate-secreted metabolites as nutrients and plays a role in host physical protection or pathogen resistance.Halobacteriovorax and Oceaniserpentilla are newly discovered or rare bacterial genera innovatively found to have ecological niches in symbiosis with benthic ciliates.Comparison analysis indicates that the microbiomes associated with benthic ciliates display species and population specificity,which are attributed to several factors such as environmental physicochemical properties,host physiological states,and interactions among associated bacteria.This study provides important insights into the environmental adaptation of eukaryotes through a symbiotic mechanism in the marine benthic environment.
基金supported by funds of the Federal Ministry of Agriculture,Food and Regional Identity(BMLEH)based on a decision of the parliament of the Federal Republic of Germany via the Federal Office for Agriculture and Food(BLE)under the Federal Programme for Ecological Farming and Other Forms of Sustainable Agriculture(FKZ 2821OE034)。
文摘The poultry gut microbiome plays a key role in nutrient digestion,immune function,and overall health.Differences among various farming systems,including conventional,antibiotic-free,free-range,and organic systems,influence microbial composition and function through variations in diet,genetic selection,environmental exposure,and antibiotic use.Conventional systems typically rely on formulated diets and controlled housing conditions,often with routine antimicrobial use.In contrast,organic systems emphasize natural feed ingredients,including roughage,outdoor access,and strict limitations on the use of antibiotics.These divergent practices shape the gut microbiota differently,with organic systems generally associated with greater exposure to environmental microbes and,consequently,greater microbial diversity.However,the implications of this increased diversity for poultry health and performance are complex,as organic systems may also carry a higher risk of pathogen exposure.This review summarizes current findings on the chicken gut microbiome across conventional and alternative production systems(antibiotic-free,freerange,and organic),focusing on microbial diversity,functional potential,and disease resilience.The need for standardized methodologies and consistent nomenclature in microbiome research is also discussed to improve comparability across studies.Understanding how production systems influence the gut microbiota is essential for improving poultry health and productivity while addressing challenges related to antimicrobial resistance and sustainable farming practices.
基金supported by the CAMS Innovation Fund for Medical Sciences(2019-I2M-5-055)the National Natural Science Foundation of China(82471925)。
文摘The objective of this study was to understand the effect of long-term aconitine(AC)oral administration on the digestive tract and serum metabolism.Subjects consumed either 0.9%Na Cl(n=8)or AC(n=17)gavage designed to represent human chronic AC administrations for 13 days.Organ pathology was determined using hematoxylin-eosin staining and immunohistochemistry.Fecal and proximal intestinal content samples were collected to perform shotgun metagenomic sequencing.Serum samples were collected,and untargeted metabolomics was performed.In this study,AC administration induced proximal intestine,liver,and kidney injury.Microbiome composition remained stable after AC exposure,while several microbes presented dynamic alteration.Moreover,AC affected the abundance of the fatty acid biosynthesis rate-limiting gene acc A at day 7.AC induces 30 serum metabolites to significantly change at day 14,including several short-chain acylcarnitines.WGCNA revealed 2 sub-modules associated with the level of several short-chain acylcarnitines.In summary,AC affects the digestive tract and serum metabolism after chronic administration.AC may affect the enrichment of microbial-derived acc A gene.The abundance of serum acylcarnitines detected in the AC group may associate with its anti-heart failure effects.
基金supported by the National Research Foundation of Korea(NRF)grant funded by the National Research Foundation of Korea Grantfunded by the Korean government(MEST)(NRF-2021R1A2C3011051)by the Korea government(MSIT)(No.RS-2023-00218476)。
文摘Background The rapid emergence of multidrug-resistant Salmonella in poultry demands alternative control strategies beyond conventional antibiotics.In this study,we evaluated a combination of lytic Salmonella-infecting bacteriophages(SLAM_phi ST45 and SLAM_phiST56)and a probiotic bacterium Limosilactobacillus reuteri(SLAM_LAR11)in a chick model challenged with Salmonella enterica serovar Typhimurium infection.Results Co-administration with two-phage cocktail and a probiotic showed markedly reduced Salmonella colonization in the gut and systemic organs of chicks,comparable to the effect of phage-only treatment.In contrast with phage-only treatment,the combined therapy significantly improved the rate of body-weight change from the day of infection to necropsy(P<0.0001)and alleviated infection-associated splenomegaly(P=0.028)and hepatomegaly(P=0.011).In the ileum,the villus height-to-crypt depth ratio(VH/CD)increased significantly(P=0.044).In the colon,expression of tight-junction genes OCLN(P=0.014),TJP1(P<0.0001),and MUC2(P=0.011)was elevated,whereas the pro-inflammatory cytokine IL6 was reduced(P=0.018).These improvements were accompanied,in the cecum,by trends toward decreases in Escherichia-Shigella(P=0.09)and Clostridium(P=0.16)and a trend toward an increase in Blautia(P=0.11);additionally,in the ileum,Lactobacillus(P=0.037)and Blautia(P=0.016)increased significantly,yielding a more balanced microbiota than with phage-only treatment.Consistently,levels of functional metabolites,including acetic acid(LDA=3.32)and lactic acid(LDA=5.29),were increased.Conclusion Taken together,these findings demonstrate that phage-probiotic co-administration not only enhances the clearance of multidrug-resistant Salmonella more effectively than phage treatment alone but also promotes intestinal health,highlighting its potential as an antibiotic-alternatives strategy to improve intestinal health and ensure food safety in poultry production systems.
基金Shanghai Municipal Health Commission,No.20224Z0008(to PY)the National Natural Science Foundation of China,No.82101412(to MZ)+1 种基金the Science Foundation of Naval Medical Center of PLA,No.23M2702(to MZ)National Key Research and Development Program of China,No.2023YFC2506506(QL)。
文摘Microglia,lipids,and their interaction are found to play important roles in post-stroke immunity.Microglia are sensitive to detect environment change in injured brain.Activated microglia undergo phenotypical remodeling and trigger complex signal casca d es to regulate immune responses after stroke.Lipids including peripheral lipid metabolism and lipid droplet biogenesis are involved in the control of microglia functions,such as activation,phagocytosis,proliferation,and pro-inflammation.In this review,we explore new scope of microglia and lipids in immune regulation of stro ke.Implication of peripheral lipid metabolism after stroke is mentioned and advances in microglia-lipid inte raction are discussed We give a special focus on how diet and gut microbiome influence neuroinflammation system via gut-brain axis,and how these processes associate with the risk and outcome of stroke.Moreove r,we reviewed the therapeutic targets related to lipid metabolism and microglial modulation after stro ke.These can provide a prospective strategy for more efficient and safer treatment for ischemic and hemorrhagic stroke.
基金supported by the National Key Research and Development Program of China(No.2022YFC3702704)the National Natural Science Foundation of China(Nos.22376005,22076006 and 82073506).
文摘Microorganisms constitute an essential component in the indoor environment,which is closely related to hu-man health.However,there is limited evidence regarding the associations between indoor airborne microbiome and systemic inflammation,as well as whether this association is modified by indoor particulate matter and the underlying mechanisms.In this prospective repeated-measure study among 66 participants,indoor airborne mi-crobiome was characterized using amplicon sequencing and qPCR.Indoor fine particulate matter(PM_(2.5))and inhalable particulate matter(PM10)were measured.Systemic inflammatory biomarkers were assessed,including white blood cell(WBC),neutrophil(NEUT),monocyte,eosinophil counts,and their proportions.Targeted serum amino acid metabolomics were conducted to explore the underlying mechanisms.Linear mixed-effect models re-vealed that bacterial and fungal Simpson diversity were significantly associated with decreased WBC and NEUT.For example,for each interquartile range increase in the bacterial Simpson diversity,WBC and NEUT changed by-4.53%(95%CI:-8.25%,-0.66%)and-5.95%(95%CI:-11.3%,-0.27%),respectively.Notably,increased inflammatory risks of airborne microbial exposure were observed when indoor PM_(2.5) and PM10 levels were below the WHO air quality guidelines.Mediation analyses indicated that dopamine metabolism partially mediated the anti-inflammatory effects of fungal diversity exposure.Overall,our study indicated protection from a diverse indoor microbial environment on cardiovascular health and proposed an underlying mechanism through amino acid metabolism.Additionally,health risks associated with microbial exposure deserve more attention in con-texts of low indoor particulate matter pollution.Further research is necessary to fully disentangle the complex relationships between indoor microbiome,air pollutants,and human health.
基金financially supported by the National Natural Science Foundation of China(Grant No.32302764)Hunan Provincial Natural Science Foundation(Grant No.2024JJ5179)+1 种基金Key laboratory for the feed and biology technique of Xinjiang Uygur Autonomous Region(Grant No.XJSLSW-2023001)Hunan Herbivores Industry Technological System(Grant No.HARS-08)。
文摘Background Zearalenone(ZEN),a common mycotoxin in ruminant diets,could disturb the rumen ecosystem and impair rumen fermentation.Noticeably,ZEN has been shown to reduce the relative abundances of specific bacterial taxa that potentially possess quorum sensing(QS)functions,which are deemed essential for the microbial interactions and adaptations during rumen fermentation.Nonetheless,whether QS communications participate in the responses of rumen microbial fermentation to ZEN remains unknown.Therefore,the present trial was performed to explore the potential roles of QS during the alterations of rumen microbial fermentation by ZEN through a rumen simulation technique(RUSITEC)system,in a replicated 4×4 Latin square design.Results ZEN significantly(P<0.05)reduced QS signal autoinducer-2(AI-2),and tended to(P=0.051)downregulate QS signal C4-homoserine lactone(HSL).ZEN also significantly(P<0.05)decreased total volatile fatty acid(TVFA),acetate,propionate,isobutyrate,isovalerate,organic matter disappearance(OMD),neutral detergent fiber disappearance(NDFD),and acid detergent fiber disappearance(ADFD)in different manners.The linear discriminant analysis effect size(LEf Se)analysis indicated significantly(P<0.05)differential enrichments of a series of bacterial taxa such as Butyrivibrio_sp_X503,Rhizobium daejeonense,Hoylesella buccalis,Ezakiella coagulans,Enterococcus cecorum,Ruminococcus_sp_zg-924,Polystyrenella longa,and Methylacidimicrobium fagopyrum across different treatments.The phylogenetic investigation of communities by reconstruction of unobserved states 2(PICRUSt2)analysis suggested that QS were predicted to be significantly(P<0.05)affected by ZEN.The metabolomics analysis detected considerable significantly(P<0.05)differing metabolites and implied that ZEN challenge significantly(P<0.05)influenced the indole alkaloid biosynthesis,biosynthesis of alkaloids derived from shikimate pathway,and sesquiterpenoid and triterpenoid biosynthesis.Significant(P<0.05)interconnections of QS molecules with the differential rumen fermentation traits,differential bacterial taxa,and differential metabolites were exhibited by Spearman analysis.Conclusions ZEN negatively affected the QS signals of AI-2 and C4-HSL,which was found to correlate with the fluctuations in specific rumen fermentation characteristics,ruminal bacterial populations,and ruminal metabolisms.These interrelationships implied the potential involvement of QS in the reactions of rumen microbiota to ZEN contamination,and probably contributed to the inhibition of rumen fermentation.
基金funding by National Natural Science Foundation of China(No.82174492)National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion Project(N o.ZJJBGS2024002-1).
文摘Background: The human gut microbiome is an important target for disease treatment and prevention. Various microbial species within the complex ecosystem of the microbiome have been shown to play important roles in disease. Identification of bioactive materials capable of altering the abundances of these species both safely and effectively is a major goal in microbiome research. Many traditional Chinese medicines (TCMs) have been reported to affect the composition of the gut microbiome. Here, we summarize studies that have used TCMs to alter the gut microbiome and discuss the response relationship between TCMs and gut microbial species. Methods: We searched the PubMed, Web of Science, and Knowledge Network databases using the terms “traditional Chinese medicine,” “gut microbiome,” and specific system disease names (endocrine, immune, nervous, cardiovascular, and digestive). Studies were excluded if irrelevant or if the experimental procedures were unclear. Results: TCMs have been reported to affect a wide range of gut microbial taxa spanning major phyla, including Firmicutes, Bacteroidetes, Proteobacteria, Verrucomicrobiota, Actinobacteria, and Fusobacteria. In all, 54 TCMs including compounds and extracts have been tested in rodents and 30 have been examined in human trials. Almost all studies have reported positive results in regulating the gut microbiome as well as modulating corresponding phenotypes, spanning diseases of the endocrine, immune, nervous, cardiovascular, and digestive systems. Gut species, including Akkermansia, Bacteroides, Fusobacterium, Faecalibacterium, and E. coli, were found to be regulated by 19 TCMs. A network was constructed to visualize the interactions between TCMs and these taxa. Conclusion: There exists a complex and close relationship between intestinal microflora and diseases. Sufficient experimental data and studies have proved that the imbalance of intestinal microflora affects health by mediating metabolism, immune regulation, inflammation and signal transduction. Many characteristic alterations of intestinal microflora are positively correlated with diseases, so intestinal microflora has become a potential risk index and treatment target for many diseases. Many TCMs affect the relative abundances of microbial species in the gut, and therefore may be useful for modulating the gut microbiome. This review provides a reference for prioritizing candidate TCMs from the enormous repertoire of such medicines to test which specific gut microbes are targeted.
文摘Although diet and gut microbial composition have been linked to chronic respiratory diseases,these associations remain difficult to interpret because of confounding and reverse causation.The gut-lung axis provides a plausible framework for this interaction,yet direct genetic evidence is limited.Using a two-step,two-sample Mendelian randomization(MR)framework,supplemented by multivariable MR(MVMR)to adjust for pleiotropic effects and Benjamini-Hochberg false discovery rate(FDR)correction for multiple testing,we assessed the causal contributions of dietary habits and gut microbial taxa to major chronic respiratory diseases.We identified 22 dietary factors with causal effects on disease risk and 225 microbial taxa that acted as independent risk or protective contributors.Mediation analyses further showed that the effects of 12 dietary habits were transmitted through 32 specific microbial taxa.Notably,genetically predicted pork intake increased the risk of chronic obstructive pulmonary disease(COPD)(OR=10.53,95%CI[8.54,13.00]),an effect partly mediated by elevated abundance of CAG-485 sp002404675.In contrast,bread consumption conferred protection against asthma(OR=0.68,95%CI[0.64,0.72]),whereas this benefit was offset by approximately 45%through a pathway involving reduced Veillonella abundance.Collectively,these findings provide genetic support for the gut-lung axis and demonstrate that the gut microbiome functions as a causal mediator linking diet to chronic respiratory disease risk.However,since this study was based on individuals of European ancestry,caution is warranted when generalizing these causal estimates to non-European populations,such as East Asian groups.This work suggests new opportunities for microbiota-targeted prevention and therapeutic strategies.
文摘Amyotrophic lateral sclerosis is a devastating neurodegenerative disease marked by progressive motor neuron degeneration.Despite extensive research,effective treatments remain elusive,underscoring the need to explore the molecular mechanisms driving disease progression.The amyotrophic lateral sclerosis complexity is further compounded by its large heterogeneity,encompassing both genetic and sporadic forms,diverse phenotypic presentations,and highly variable progression rates.A key pathological feature of amyotrophic lateral sclerosis is the aggregation of TAR DNA-binding protein 43,which contributes to cellular toxicity,neuroinflammation,and neuronal dysfunction.This review explores the complex interplay between TAR DNA-binding protein 43 pathology,immunity dysregulation,and the gut-brain axis,with a focus on the role of microbiome-derived metabolites in amyotrophic lateral sclerosis.Neuroinflammation,mediated by both innate and adaptive immunity,plays a central role in disease pathogenesis,with TAR DNA-binding protein 43 influencing immune signaling and exacerbating neurotoxicity.Additionally,disruptions in gut microbiota composition and intestinal barrier integrity,frequently observed in amyotrophic lateral sclerosis patients,suggest a potential role for the gut-brain axis in modulating neurodegenerative processes.By integrating evidence from emerging studies,our aim is to clarify how TAR DNA-binding protein 43 aggregation contributes to neuroinflammation and immune dysfunction while exploring the gut microbiota role as both a modulator and potential biomarker of disease.Understanding these interactions could pave the way for novel therapeutic strategies,including microbiome-targeted interventions such as probiotics,dietary modifications,or immune-modulating therapies.Finally,unraveling the TAR DNA-binding protein 43-immune system-microbiome axis may offer new avenues for personalized treatments aimed at mitigating neuroinflammation,slowing amyotrophic lateral sclerosis progression,and improving patient outcomes and life quality.
基金supported by the National Natural Science Foundation of China(Grant No.82500432)the Heilongjiang Provincial Health Commission Scientific Research Project(Grant No.20240303010111).
文摘Background Recent studies have suggested a potential role of the oral microbiome in the development of cardiovascular diseases.This study aims to investigate the association between oral microbiota and cardiovascular disease risk,including atrial fibrillation,myocardial infarction,chronic heart failure,and hypertension.Methods We analyzed GWAS data from East Asian populations'oral microbiome,involving 2,017 tongue and 1,915 saliva samples from 2,984 individuals with whole-genome sequencing.Additionally,we sourced cardiovascular disease GWAS data from NBDC,including atrial fibrillation(8,180 cases,28,621 controls),myocardial infarction(14,992 cases,146,214 controls),chronic heart failure(10,540 cases,168,186 controls),and systolic blood pressure(145,505 individuals).Results Several oral microbiota taxa were found to be significantly associated with cardiovascular disease outcomes.Specific microbiota,such as Centipeda,Corynebacterium,and Pseudomonas E,were negatively correlated with heart failure.In contrast,taxa like Neisseria D and Actinomyces were associated with an increased risk of atrial fibrillation and myocardial infarction.Additionally,certain oral microbiota showed correlations with changes in blood pressure,highlighting their potential role in hypertension.Conclusion Our findings suggest that the oral microbiota may influence the development and progression of cardiovascular diseases,providing new insights into the potential impact of oral health on cardiovascular risk.
基金funded by the Chinese Academy of Forestry-Special funds for basic scientific research service expenses of the central level public welfare research institutes(Grant No.CAFYBB2020QD001)the National Natural Science Foundation of China(Grant Nos.32101550,32271917)+1 种基金Jiangsu Agricultural Science and Technology Innovation Fund(Grant No.CX(24)3052)National Forestry and Grassland Administration’s Center for Science and Technology Development Projects(Grant No.KJZXSA202202).
文摘Catalpa bungei,a fast-growing timber tree,is threatened by the lepidopteran pest Omphisa plagialis.Previous studies in our laboratory successfully generated transgenic C.bungei lines overexpressing Cry genes(Cry1Ab,Cry2A,and Cry9-2)that exhibited resistance to O.plagialis,but their potential impact on soil bacterial communities remains unclear.In this study,we analyzed nine transgenic C.bungei lines(three independent lines for each Cry gene)to characterize their rhizosphere bacterial communities using high-throughput sequencing of the 16S ribosomal DNA(rDNA)V4-V5 regions.A total of 628 amplicon sequence variants(ASVs)were shared among all transgenic and wild-type(WT)lines,forming a stable core microbiome dominated by Proteobacteria,Bacteroidota,Acidobacteriota,and Actinobacteriota.Alpha diversity showed no significant differences,while beta diversity revealed minor but distinct compositional shifts.Cry1Ab lines exhibited higher abundances of fast-growing taxa,particularly Proteobacteria and Bacteroidota;Cry2A lines displayed intermediate profiles,whereas Cry9-2 lines were nearly indistinguishable from WT communities.Linear discriminant analysis of the effect size revealed significant enrichment of taxa such as Burkholderiaceae and Ralstonia in the Cry1Ab rhizosphere,in contrast to the higher abundance of Chloroflexi in the WT.Functional predictions indicated consistent metabolic pathways across all treatments,suggesting strong ecological redundancy.This study demonstrates minimal impact on rhizosphere microbial communities in transgenic C.bungei plants.The Cry9-2 construct exhibited superior environmental stability,whereas the Cry1Ab construct caused only slight but ecologically acceptable shifts.These findings support the ecological safety of Bt-transgenic C.bungei and identify Cry9-2 as a particularly favorable candidate for forestry applications.This comparative evaluation of three Cry genes in a tree species provides a framework for future gene-specific biosafety assessments in woody plants.
基金supported by FCT/MCTES UIDP/05608/2020(https://doi.org/10.54499/UIDP/05608/2020)UIDB/05608/2020(https://doi.org/10.54499/UIDB/05608/2020).
文摘Background:The Colorectal Cancer(CRC)pathogenesis and therapeutic efficacy are influenced by the gut microbiome,making it a promising biomarker for predicting treatment responses and adverse effects.This systematic review aims to outline the gut microbiome composition in individuals with CRC undergoing the same therapeutic regimen and evaluate interindividual microbiome profile variations to better understand how these differences may influence therapeutic outcomes.Methods:Key studies investigating the microbiome’s role in therapeutic approaches for CRC were searched in both PubMed and Cochrane databases on 12 and 22 March 2025,respectively.Eligible studies included free full-text English-language randomized clinical trials and human observational studies reporting on gut microbiome composition and treatment outcomes.RoB 2 and ROBINS-I were employed in the evaluation of bias for randomized trials and observational studies,respectively.Data extracted was narratively analyzed.Results:Six studies involving a total of 361 individuals were included.Therapeutic interventions,either standard treatments and/or those targeting the gut microbiome,generally increased probiotic taxa and reduced pro-carcinogenic bacteria.However,no consistent pattern of improved clinical outcomes was observed,suggesting that treatment mechanisms,the tumor’s nature,and individual characteristics play critical roles in microbiome modulation.Conclusion:The gut microbiome holds significant potential in clinical settings.Nonetheless,further research is needed to better understand its functional aspects and to consider the influence of treatment mechanisms,the tumor’s nature,and individual characteristics as modulators,in order to optimize clinical outcomes.
文摘Wu et al recently applied multi-region 16S rRNA sequencing to characterize the gastric cancer microbiome,demonstrating improved taxonomic resolution and detection sensitivity over conventional single-region approaches.While the study represents a valuable methodological step forward,it remains limited by singlecenter design,lack of quantitative calibration,and insufficient control for contamination and inter-laboratory variability.This editorial critically appraises these methodological gaps and emphasizes that future efforts must focus on harmonized,consensus-driven workflows to ensure reproducibility and clinical reliability.The translational potential of multi-region 16S lies in moving from descriptive microbial profiling to actionable clinical integration,particularly for recurrence prediction,treatment-response monitoring,and perioperative complication risk assessment.By addressing these methodological,economic,and ethical challenges,the field can advance toward evidence-based and clinically deployable microbiome-guided precision oncology.
基金funded by the Joint Funds of the National Natural Science Foundation of China(U2202203)。
文摘Background The gayal(Bos frontalis),a semi-domesticated bovine species,demonstrates exceptional adaptability to lignocellulose-rich diets dominated by bamboo,suggesting the presence of a specialized gastrointestinal microbiome.However,the functional mechanisms underlying this host-microbiome interaction remain poorly understood.Here,we conducted integrated metagenomic and metatranscriptomic analyses of rumen,cecum,and colon digesta from yellow cattle and gayal raised on the same bamboo-based high-fiber diet.Results The results showed that gayal exhibited superior fiber-degrading capacity relative to yellow cattle,evidenced by significantly higher(P<0.05)fiber digestibility,cellulase and xylanase activities,and increased volatile fatty acids production despite identical feed intake.Microbial community analysis revealed distinct composition in both the rumen and hindgut of gayal compared to yellow cattle,with notable enrichment of taxa specialized in lignocellulose degradation.Metatranscriptomic profiling further identified upregulation of key lignin-modification enzymes,particularly AA6,AA2,and AA3,primarily encoded by Prevotella,Cryptobacteroides,Limimorpha,and Ventricola.These enzymes are known to modify lignin structure to increase polysaccharide accessibility.These results demonstrate that gayal hosts a unique and metabolically active gastrointestinal microbiome capable of efficient lignocellulose deconstruction through a coordinated enzymatic cascade,especially effective in dismantling lignin barriers.Conclusions This study provides novel insights into host-microbiome co-adaptation to fibrous feeds and highlights the potential of gayal-derived microbial consortia and enzymes for improving roughage utilization in ruminant agriculture.
基金supported by grants from the National Natural Science Foundation of China(82270924)the CAMS Innovation Fund for Medical Sciences(CIFMS 2021-I2M-1-016)the National High Level Hospital Clinical Research Funding(2022-PUMCH-C-014,2025-PUMCH-C-041).
文摘Objective Previous Mendelian randomization(MR)studies have suggested an association between the gut microbiome and metabolic-associated fatty liver disease(MAFLD).However,the reliance on 16S rRNA sequencing data has led to inconsistent findings and limited species-level insights.To address this,we conducted a de novo MR analysis using species-level shotgun metagenomic data,combined it with a meta-analysis to consolidate the existing evidence,and explored metabolite-mediated pathways.Methods Bidirectional MR analyses were performed between 883 gut microbiota taxa(derived from shotgun metagenomic genome-wide association study)and MAFLD.Published MR studies(up to December 1,2024)were identified using PubMed,Embase,Web of Science,and the Cochrane Library for meta-analysis.Multivariable MR(MVMR)and mediation analyses were applied to assess the mediating effects of 1,400 blood metabolites.Results The de novo MR identified 25 MAFLD-associated microbial taxa.Integration with 7 published studies revealed 34 causal taxa,including 10 at the species level.Among the 1,400 metabolites,53 showed causal links with MAFLD.MVMR and mediation analyses identified deoxycholate as a mediator of the effect of Bifidobacterium on MAFLD risk(22.06%mediation proportion).Conclusion This study elucidated the connections between species-level gut microbiota and MAFLD,highlighting the interplay between microbiota,metabolites,and disease pathogenesis.These findings provide novel insights into the potential therapeutic targets for MAFLD.
