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
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
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
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
Soil cadmium(Cd)contamination poses significant risks to human health and environmental sustainability.Despite advances in bioremediation,effective bioagents with clear mechanistic insights for Cd detoxification are l...Soil cadmium(Cd)contamination poses significant risks to human health and environmental sustainability.Despite advances in bioremediation,effective bioagents with clear mechanistic insights for Cd detoxification are lacking.We first deciphered the whole-genome sequence of a novel Cd-tolerant Trichoderma nigricans T32781 and its in vivo heavy metal tolerance.In five independent pot and field trials,we revealed the T32781-induced alleviation mechanisms of plant-microbe-soil interactions in wheat and barley in response to Cd toxicity using a combination of agronomic,physiological,microbiome and metabolome approaches.We discovered that T32781 inoculation in soil significantly increased grain yield and decreased grain Cd concentration in barley and wheat exposed to different soil Cd levels.T32781 predominantly colonized soils,mitigating Cd toxicity by reducing soil Cd availability and promoting beneficial soil microbial communities and metabolites.These beneficial effects were further validated in the field,where the exogenous application of key metabolites induced by T32781 inoculation in soils and plants significantly increased grain yield and reduced grain Cd concentration in barley.This work highlights the potential of T32781 to enhance plantmicrobe-soil interactions and support sustainable and safe crop production in Cd-contaminated soils,addressing the increasing global demand for cereal production for food and feed.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 gut microbiome has emerged as a critical modulator of cancer immunotherapy response.However,the mechanisms by which gut-associated metabolites influence checkpoint blockade efficacy in prostate cancer(P...Background:The gut microbiome has emerged as a critical modulator of cancer immunotherapy response.However,the mechanisms by which gut-associated metabolites influence checkpoint blockade efficacy in prostate cancer(PC)remain not fully explored.The study aimed to explore how gut metabolites regulate death-ligand 1(PD-L1)blockade via exosomes and boost immune checkpoint inhibitors(ICIs)in PC.Methods:We recruited 70 PC patients to set up into five subgroups.The integrated multi-omics analysis was performed.In parallel,we validated the function of gut microbiome-associated metabolites on PD-L1 production and immunotherapy treatment efficacy in PC cell lines and transgenic adenocarcinoma of the mouse prostate(TRAMP)models.Results:We identified two metabolites,16(R)-Hydroxyeicosatetraenoic acid(16(R)-HETE)and 6-Keto-Prostaglandin E1(6-Keto-PGE1),that positively correlated with the plasma exosomal PD-L1 levels.The in vitro experiments found that both 16(R)-HETE and 6-Keto-PGE1 can enhance PD-L1 expression at the mRNA,protein,and exosome levels in both human and mouse PC cell lines,which were also validated in vivo based on subcutaneous mouse models.Both metabolites significantly promoted the anti-PD-L1 efficacy against PC in situ on a TRAMP mouse model.Conclusions:Targeting the“gut-tumor metabolic axis”is a promising strategy to improve the efficacy of immune checkpoint inhibitors in tumors.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
Inter-individual heterogeneity in drug response is a serious problem that affects the patient＇s wellbeing and poses enormous clinical and financial burdens on a societal level. Pharmacogenomics has been at the forefr...Inter-individual heterogeneity in drug response is a serious problem that affects the patient＇s wellbeing and poses enormous clinical and financial burdens on a societal level. Pharmacogenomics has been at the forefront of research into the impact of individual genetic background on drug response variability or drug toxicity, and recently the gut microbiome, which has also been called the second genome, has been recog- nized as an important player in this respect. Moreover, the microbiome is a very attractive target for improving drug efficacy and safety due to the opportunities to manipulate its composition. Pharmacomicrobiomics is an emerging field that investigates the interplay of microbiome variation and drugs response and disposi- tion （absorption, distribution, metabolism and excretion）. In this review, we provide a historical overview and examine current state-of-the-art knowledge on the complex interactions between gut microbiome, host and drugs. We argue that combining pharmacogenomics and pharmacomicrobiomics will provide an important foundation for making major advances in personalized medicine.展开更多
The microbiome refers to the collective genomes of all resident microorganisms of a particular organism,environment,or ecosystem.Plant surfaces and interior parts are populated by myriads of bacteria,fungi,and microbe...The microbiome refers to the collective genomes of all resident microorganisms of a particular organism,environment,or ecosystem.Plant surfaces and interior parts are populated by myriads of bacteria,fungi,and microbes from other kingdoms, which can have considerable effects on plant growth,disease resistance,abiotic stress tolerance,and nutrient uptake.展开更多
Colorectal cancer(CRC)is a common malignant tumor with a high mortality rate worldwide.Advanced CRC often leads to liver metastasis,which has a poor prognosis,highlighting the need to investigate the underlying mechan...Colorectal cancer(CRC)is a common malignant tumor with a high mortality rate worldwide.Advanced CRC often leads to liver metastasis,which has a poor prognosis,highlighting the need to investigate the underlying mechanisms.Omics,encompassing genomics,epigenomics,transcriptomics,proteomics,metabolomics,and microbiomics,enables comprehensive molecular analysis of cells and tissues.Tumor-omics research has advanced rapidly,with growing attention on CRC-related omics.However,systematic reviews on omics research specific to colorectal cancer liver metastasis(CRLM)are limited.This review summarizes the current status and progress of multi-omics research on CRLM and discusses the application of multi-omics technologies in basic research and the significant clinical implications.展开更多
Background Sow longevity and reproductivity are essential in the modern swine industry.Although many studies have focused on the genetic and genomic factors for selection,little is known about the associations between...Background Sow longevity and reproductivity are essential in the modern swine industry.Although many studies have focused on the genetic and genomic factors for selection,little is known about the associations between the microbiome and sows with longevity in reproduction.Results In this study,we collected and sequenced rectal and vaginal swabs from 48 sows,nine of which completed up to four parities(U4P group),exhibiting reproductive longevity.We first identified predictors of sow longevity in the rectum(e.g.,Akkermansia)and vagina(e.g.,Lactobacillus)of the U4P group using RandomForest in the early breeding stage of the first parity.Interestingly,these bacteria in the U4P group showed decreased predicted KEGG gene abundance involved in the biosynthesis of amino acids.Then,we tracked the longitudinal changes of the micro-biome over four parities in the U4P sows.LEfSe analysis revealed parity-associated bacteria that existed in both the rectum and vagina(e.g.,Streptococcus in Parity 1,Lactobacillus in Parity 2,Veillonella in Parity 4).We also identi-fied patterns of bacterial change between the early breeding stage(d 0)and d 110,such as Streptococcus,which was decreased in all four parties.Furthermore,sows in the U4P group with longevity potential also showed better reproductive performance.Finally,we discovered bacterial predictors(e.g.,Prevotellaceae NK3B31 group)for the total number of piglets born throughout the four parities in both the rectum and vagina.Conclusions This study highlights how the rectal and vaginal microbiome in sows with longevity in reproduc-tion changes within four parities.The identification of parity-associated,pregnancy-related,and reproductive performance-correlated bacteria provides the foundation for targeted microbiome modulation to improve animal production.展开更多
PURPOSE:To investigate the differences in gut microbial characteristics between two traditional Chinese syndromes of premature ovarian insufficiency(POI).METHODS:Forty women with POI were recruited from the Department...PURPOSE:To investigate the differences in gut microbial characteristics between two traditional Chinese syndromes of premature ovarian insufficiency(POI).METHODS:Forty women with POI were recruited from the Department of Traditional Chinese Medicine at Shenzhen Maternity and Child Healthcare Hospital between June and December 2020.Women with POI were divided into the kidney deficiency and blood stasis syndrome(SDBS)and Qi and blood deficiency syndrome(QBDS)groups.Gut microbial community profiles were analyzed by 16S rRNA gene sequencing using an Illumina Mi Seq system.A retrospective study comparing hormone levels and gut microbiota information was performed between the SDBS and QBDS groups.RESULTS:Compared with the QBDS group,the serum levels of estradiol(E2)and anti-Müllerian hormone(AMH)were significantly decreased in the SDBS group.The quantities of Adlercreutzia,Eggerthella,Klebsiella,and Paraprevotella significantly increased in the SDBS group,whereas Lactobacillus decreased significantly.Moreover,alterations in the microbiome in the SDBS and QBDS groups were closely related to the levels of E2 and AMH.The area under the receiver operating characteristic curve for the classification of the two syndromes by the gut microbiome was 0.71.CONCLUSIONS:There were significant differences in the dominant microbiota between the SDBS and QBDS groups,and the change in Proteobacteria in the QBDS group was more significant.The characteristics of gut microbiota help us differentiate between the SDBS and QBDS groups,which may provide a basis for the objectification of TCM syndrome types.展开更多
Phyllosphere microbiome plays an irreplaceable role in maintaining plant health under stress,but its structure and functions in heavy metal-hyperaccumulating plants remain elusive.Here,the phyllosphere microbiome,inha...Phyllosphere microbiome plays an irreplaceable role in maintaining plant health under stress,but its structure and functions in heavy metal-hyperaccumulating plants remain elusive.Here,the phyllosphere microbiome,inhabiting hyperaccumulating(HE)and non-hyperaccumulating ecotype(NHE)of Sedum alfredii grown in soils with varying heavy metal concentration,was characterized.Compared with NHE,the microbial communityα-diversity was greater in HE.Core phyllosphere taxa with high relative abundance(>10%),including Streptomyces and Nocardia(bacteria),Cladosporium and Acremonium(fungi),were significantly related to cadmium(Cd)and zinc(Zn)concentration and biomass of host plants.Moreover,microbial co-occurrence networks in HE exhibited greater complexity than those in NHE.Additionally,proportions of positive associations in HE bacterial networks increased with the rising heavy metal concentration,indicating a higher resistance of HE phyllosphere microbiome to heavy metal stress.Furthermore,in contrast to NHE,microbial community functions,primarily involved in heavy metal stress resistance,were more abundant in HE,in which microbiome assisted hosts to resist heavy metal stress better.Collectively,this study indicated that phyllosphere microbiome of the hyperaccumulator played an indispensable role in assisting hosts to resist heavy metal stress,and provided new insights into phyllosphere microbial application potential in phytoremediation.展开更多
The gut microbiome comprises a vast community of microbes inhabiting the human alimentary canal,playing a crucial role in various physiological functions.These microbes generally live in harmony with the host;however,...The gut microbiome comprises a vast community of microbes inhabiting the human alimentary canal,playing a crucial role in various physiological functions.These microbes generally live in harmony with the host;however,when dysbiosis occurs,it can contribute to the pathogenesis of diseases,including osteoporosis.Osteoporosis,a systemic skeletal disease characterized by reduced bone mass and increased fracture risk,has attracted significant research attention concerning the role of gut microbes in its development.Advances in molecular biology have highlighted the influence of gut microbiota on osteoporosis through mechanisms involving immunoregulation,modulation of the gut-brain axis,and regulation of the intestinal barrier and nutrient absorption.These microbes can enhance bone mass by inhibiting osteoclast differentiation,inducing apoptosis,reducing bone resorption,and promoting osteoblast proliferation and maturation.Despite these promising findings,the therapeutic effectiveness of targeting gut microbes in osteoporosis requires further investigation.Notably,gut microbiota has been increasingly studied for their potential in early diagnosis,intervention,and as an adjunct therapy for osteoporosis,suggesting a growing utility in improving bone health.Further research is essential to fully elucidate the therapeutic potential and clinical application of gut microbiome modulation in the management of osteoporosis.展开更多
BACKGROUND Colorectal cancer is the third most common malignancy and the fourth leading cause of cancer-related deaths worldwide.Several studies have shown an association between gut microbiota and colorectal cancer.G...BACKGROUND Colorectal cancer is the third most common malignancy and the fourth leading cause of cancer-related deaths worldwide.Several studies have shown an association between gut microbiota and colorectal cancer.Gut microbiota is unique and can be influenced by geographic factors and habits.This study aimed to determine the diversity and composition of colonic mucosal microbiota in patients with and without colorectal cancer.AIM To determine the diversity and composition of colonic mucosal microbiota in patients with and without colorectal cancer in Indonesia.METHODS This case-control study included 59 subjects(35 colorectal cancer patients and 24 non-colorectal cancer patients indicated for colonoscopy at Dr.Cipto Mangunkusumo Gastrointestinal Endoscopy Center and Fatmawati Hospital.Microbiota examination was performed using 16S rRNA sequencing.Bioinformatics analysis was performed using the wf-metagenomics pipeline from EPI2Me-Labs(Oxford Nanopore Technologies platform).RESULTS Patients with colorectal cancer had a higher median index value on the Shannon index(3.28 vs 2.82,P>0.05)and a lower value on the Simpson index(0.050 vs 0.060,P>0.05).Significant differences in beta diversity were observed at the genus(P=0.002)and species levels(P=0.001).Firmicutes,Proteobacteria,Bacteroidetes,and Fusobacteria were the dominant phyla.The genera Bacteroides,Campylobacter,Peptostreptococcus,and Parvimonas were found more frequently in colorectal cancer,while Faecalibacterium,Haemophilus,and Phocaeicola were more frequently found in non-colorectal cancer.The relative abundance of Fusobacterium nucleatum,Bacteroides fragilis,Enterococcus faecalis,Campylobacter hominis,and Enterococcus faecalis species was significantly elevated in patients with colorectal cancer.Meanwhile,Faecalibacterium prausnitzii,Faecalibacterium duncaniae,and Prevotella copri were more commonly found in non-colorectal cancer.CONCLUSION Patients with colorectal cancer exhibit distinct differences in the composition and diversity of their colonic mucosal microbiota compared to those with non-colorectal cancer.This study was reviewed and approved by the Ethics Committee of Faculty of Medicine,Universitas Indonesia(No.KET-1517/UN2.F1/ETIK/PPM.00.02/2023).展开更多
The intricate interplay between natural compounds like curcumin and the gut microbiome has gained significant attention in recent years due to their potential therapeutic implications in various health conditions.Curc...The intricate interplay between natural compounds like curcumin and the gut microbiome has gained significant attention in recent years due to their potential therapeutic implications in various health conditions.Curcumin,a polyphenolic compound derived from turmeric,exhibits diverse pharmacological properties,including anti-inflammatory,antioxidant,and anticancer effects.Understanding how curcumin modulates gut microbiota composition and function is crucial for elucidating its therapeutic mechanisms.This review examines the current literature on the interactions between curcumin and the gut microbiome.A systematic search of relevant databases was conducted to identify studies investigating the effects of curcumin on gut microbial diversity and abundance.Key findings from studies exploring curcumin's efficacy in neurological disorders,gastrointestinal diseases,and metabolic dysfunction are synthesized and discussed.Studies have demonstrated that curcumin supplementation can modulate gut microbiota composition and function,leading to beneficial effects on gut health and homeostasis.Mechanisms underlying curcumin's therapeutic effects include immune modulation,neuroprotection,and inflammation regulation.However,challenges such as poor bioavailability and safety concerns remain significant hurdles to overcome.The interactions between curcumin and the gut microbiome hold promise for therapeutic interventions in a diverse range of health conditions.Further research is needed to optimize curcumin formulations,improve bioavailability,and address safety concerns.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.
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.
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.
基金supported by the National Natural Science Foundation of China(NSFC-ASRT International Joint Research Project 3211101286)Zhejiang Science and Technology Major Program on Agricultural New Variety Breeding,China(2021C02064-3)。
文摘Soil cadmium(Cd)contamination poses significant risks to human health and environmental sustainability.Despite advances in bioremediation,effective bioagents with clear mechanistic insights for Cd detoxification are lacking.We first deciphered the whole-genome sequence of a novel Cd-tolerant Trichoderma nigricans T32781 and its in vivo heavy metal tolerance.In five independent pot and field trials,we revealed the T32781-induced alleviation mechanisms of plant-microbe-soil interactions in wheat and barley in response to Cd toxicity using a combination of agronomic,physiological,microbiome and metabolome approaches.We discovered that T32781 inoculation in soil significantly increased grain yield and decreased grain Cd concentration in barley and wheat exposed to different soil Cd levels.T32781 predominantly colonized soils,mitigating Cd toxicity by reducing soil Cd availability and promoting beneficial soil microbial communities and metabolites.These beneficial effects were further validated in the field,where the exogenous application of key metabolites induced by T32781 inoculation in soils and plants significantly increased grain yield and reduced grain Cd concentration in barley.This work highlights the potential of T32781 to enhance plantmicrobe-soil interactions and support sustainable and safe crop production in Cd-contaminated soils,addressing the increasing global demand for cereal production for food and feed.
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supported by Tianjian advanced biomedical laboratory key research and development projectHenan Province Natural Science Foundation(Grant Number 242300421283)Major Science and Technology Project of Henan Province(221100310200)。
文摘Background:The gut microbiome has emerged as a critical modulator of cancer immunotherapy response.However,the mechanisms by which gut-associated metabolites influence checkpoint blockade efficacy in prostate cancer(PC)remain not fully explored.The study aimed to explore how gut metabolites regulate death-ligand 1(PD-L1)blockade via exosomes and boost immune checkpoint inhibitors(ICIs)in PC.Methods:We recruited 70 PC patients to set up into five subgroups.The integrated multi-omics analysis was performed.In parallel,we validated the function of gut microbiome-associated metabolites on PD-L1 production and immunotherapy treatment efficacy in PC cell lines and transgenic adenocarcinoma of the mouse prostate(TRAMP)models.Results:We identified two metabolites,16(R)-Hydroxyeicosatetraenoic acid(16(R)-HETE)and 6-Keto-Prostaglandin E1(6-Keto-PGE1),that positively correlated with the plasma exosomal PD-L1 levels.The in vitro experiments found that both 16(R)-HETE and 6-Keto-PGE1 can enhance PD-L1 expression at the mRNA,protein,and exosome levels in both human and mouse PC cell lines,which were also validated in vivo based on subcutaneous mouse models.Both metabolites significantly promoted the anti-PD-L1 efficacy against PC in situ on a TRAMP mouse model.Conclusions:Targeting the“gut-tumor metabolic axis”is a promising strategy to improve the efficacy of immune checkpoint inhibitors in tumors.
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.
文摘Inter-individual heterogeneity in drug response is a serious problem that affects the patient＇s wellbeing and poses enormous clinical and financial burdens on a societal level. Pharmacogenomics has been at the forefront of research into the impact of individual genetic background on drug response variability or drug toxicity, and recently the gut microbiome, which has also been called the second genome, has been recog- nized as an important player in this respect. Moreover, the microbiome is a very attractive target for improving drug efficacy and safety due to the opportunities to manipulate its composition. Pharmacomicrobiomics is an emerging field that investigates the interplay of microbiome variation and drugs response and disposi- tion （absorption, distribution, metabolism and excretion）. In this review, we provide a historical overview and examine current state-of-the-art knowledge on the complex interactions between gut microbiome, host and drugs. We argue that combining pharmacogenomics and pharmacomicrobiomics will provide an important foundation for making major advances in personalized medicine.
文摘The microbiome refers to the collective genomes of all resident microorganisms of a particular organism,environment,or ecosystem.Plant surfaces and interior parts are populated by myriads of bacteria,fungi,and microbes from other kingdoms, which can have considerable effects on plant growth,disease resistance,abiotic stress tolerance,and nutrient uptake.
基金supported by grants from the Natural Science Foundation of Chongqing(Grant No.CSTB2024NSCQ-MSX0478).
文摘Colorectal cancer(CRC)is a common malignant tumor with a high mortality rate worldwide.Advanced CRC often leads to liver metastasis,which has a poor prognosis,highlighting the need to investigate the underlying mechanisms.Omics,encompassing genomics,epigenomics,transcriptomics,proteomics,metabolomics,and microbiomics,enables comprehensive molecular analysis of cells and tissues.Tumor-omics research has advanced rapidly,with growing attention on CRC-related omics.However,systematic reviews on omics research specific to colorectal cancer liver metastasis(CRLM)are limited.This review summarizes the current status and progress of multi-omics research on CRLM and discusses the application of multi-omics technologies in basic research and the significant clinical implications.
基金funded by the National Key Research and Development Program of China (2023YFE0124400)the Specific university discipline construction project (2023B10564001)+1 种基金grants administered by the Arkansas Biosciences Institute and the USDAa core grant (P20GM121293, proteogenomics core)。
文摘Background Sow longevity and reproductivity are essential in the modern swine industry.Although many studies have focused on the genetic and genomic factors for selection,little is known about the associations between the microbiome and sows with longevity in reproduction.Results In this study,we collected and sequenced rectal and vaginal swabs from 48 sows,nine of which completed up to four parities(U4P group),exhibiting reproductive longevity.We first identified predictors of sow longevity in the rectum(e.g.,Akkermansia)and vagina(e.g.,Lactobacillus)of the U4P group using RandomForest in the early breeding stage of the first parity.Interestingly,these bacteria in the U4P group showed decreased predicted KEGG gene abundance involved in the biosynthesis of amino acids.Then,we tracked the longitudinal changes of the micro-biome over four parities in the U4P sows.LEfSe analysis revealed parity-associated bacteria that existed in both the rectum and vagina(e.g.,Streptococcus in Parity 1,Lactobacillus in Parity 2,Veillonella in Parity 4).We also identi-fied patterns of bacterial change between the early breeding stage(d 0)and d 110,such as Streptococcus,which was decreased in all four parties.Furthermore,sows in the U4P group with longevity potential also showed better reproductive performance.Finally,we discovered bacterial predictors(e.g.,Prevotellaceae NK3B31 group)for the total number of piglets born throughout the four parities in both the rectum and vagina.Conclusions This study highlights how the rectal and vaginal microbiome in sows with longevity in reproduc-tion changes within four parities.The identification of parity-associated,pregnancy-related,and reproductive performance-correlated bacteria provides the foundation for targeted microbiome modulation to improve animal production.
基金Sanming Project of Medicine in Shenzhen:the First Affiliated Hospital of Guangzhou University of Traditional Chinese Medicine,Luo Songping National Famous Chinese Medicine Practitioner Female Reproductive Disorders Prevention and Treatment Team(SZZYSM202311010)Guangdong Provincial Administration of Traditional Chinese Medicine:Investigation of the Mechanism of Regulating Ren-Tong-Du Acupuncture on Ovarian Granulosa Cells in Polycystic Ovary Syndrome based on Activin A/Smads Signalling Pathway(No.20181229)+1 种基金Guangdong Provincial Administration of Traditional Chinese Medicine:Evaluation of the Efficacy of Menstrual Regulation and Pregnancy Promotion by Acupuncture in the Treatment of Premature Ovarian Insufficiency(No.20201294)Shenzhen Science and Innovation Commission:Investigating the Mechanism of Action of Acupuncture in Regulating the Gut Microbiome to Inhibit Apoptosis of Ovarian Granulosa Cells in Premature Ovarian Insufficiency Mice based on the Rictor/Torepamycin Target Protein C2 Pathway(No.JCYJ20210324130001004)。
文摘PURPOSE:To investigate the differences in gut microbial characteristics between two traditional Chinese syndromes of premature ovarian insufficiency(POI).METHODS:Forty women with POI were recruited from the Department of Traditional Chinese Medicine at Shenzhen Maternity and Child Healthcare Hospital between June and December 2020.Women with POI were divided into the kidney deficiency and blood stasis syndrome(SDBS)and Qi and blood deficiency syndrome(QBDS)groups.Gut microbial community profiles were analyzed by 16S rRNA gene sequencing using an Illumina Mi Seq system.A retrospective study comparing hormone levels and gut microbiota information was performed between the SDBS and QBDS groups.RESULTS:Compared with the QBDS group,the serum levels of estradiol(E2)and anti-Müllerian hormone(AMH)were significantly decreased in the SDBS group.The quantities of Adlercreutzia,Eggerthella,Klebsiella,and Paraprevotella significantly increased in the SDBS group,whereas Lactobacillus decreased significantly.Moreover,alterations in the microbiome in the SDBS and QBDS groups were closely related to the levels of E2 and AMH.The area under the receiver operating characteristic curve for the classification of the two syndromes by the gut microbiome was 0.71.CONCLUSIONS:There were significant differences in the dominant microbiota between the SDBS and QBDS groups,and the change in Proteobacteria in the QBDS group was more significant.The characteristics of gut microbiota help us differentiate between the SDBS and QBDS groups,which may provide a basis for the objectification of TCM syndrome types.
基金supported by the National Natural Science Foundation of China(Nos.42177008,and 42377005)the fellowship of China Postdoctoral Science Foundation(No.2022M712770)the Fundamental Research Funds for the Central Universities.
文摘Phyllosphere microbiome plays an irreplaceable role in maintaining plant health under stress,but its structure and functions in heavy metal-hyperaccumulating plants remain elusive.Here,the phyllosphere microbiome,inhabiting hyperaccumulating(HE)and non-hyperaccumulating ecotype(NHE)of Sedum alfredii grown in soils with varying heavy metal concentration,was characterized.Compared with NHE,the microbial communityα-diversity was greater in HE.Core phyllosphere taxa with high relative abundance(>10%),including Streptomyces and Nocardia(bacteria),Cladosporium and Acremonium(fungi),were significantly related to cadmium(Cd)and zinc(Zn)concentration and biomass of host plants.Moreover,microbial co-occurrence networks in HE exhibited greater complexity than those in NHE.Additionally,proportions of positive associations in HE bacterial networks increased with the rising heavy metal concentration,indicating a higher resistance of HE phyllosphere microbiome to heavy metal stress.Furthermore,in contrast to NHE,microbial community functions,primarily involved in heavy metal stress resistance,were more abundant in HE,in which microbiome assisted hosts to resist heavy metal stress better.Collectively,this study indicated that phyllosphere microbiome of the hyperaccumulator played an indispensable role in assisting hosts to resist heavy metal stress,and provided new insights into phyllosphere microbial application potential in phytoremediation.
文摘The gut microbiome comprises a vast community of microbes inhabiting the human alimentary canal,playing a crucial role in various physiological functions.These microbes generally live in harmony with the host;however,when dysbiosis occurs,it can contribute to the pathogenesis of diseases,including osteoporosis.Osteoporosis,a systemic skeletal disease characterized by reduced bone mass and increased fracture risk,has attracted significant research attention concerning the role of gut microbes in its development.Advances in molecular biology have highlighted the influence of gut microbiota on osteoporosis through mechanisms involving immunoregulation,modulation of the gut-brain axis,and regulation of the intestinal barrier and nutrient absorption.These microbes can enhance bone mass by inhibiting osteoclast differentiation,inducing apoptosis,reducing bone resorption,and promoting osteoblast proliferation and maturation.Despite these promising findings,the therapeutic effectiveness of targeting gut microbes in osteoporosis requires further investigation.Notably,gut microbiota has been increasingly studied for their potential in early diagnosis,intervention,and as an adjunct therapy for osteoporosis,suggesting a growing utility in improving bone health.Further research is essential to fully elucidate the therapeutic potential and clinical application of gut microbiome modulation in the management of osteoporosis.
文摘BACKGROUND Colorectal cancer is the third most common malignancy and the fourth leading cause of cancer-related deaths worldwide.Several studies have shown an association between gut microbiota and colorectal cancer.Gut microbiota is unique and can be influenced by geographic factors and habits.This study aimed to determine the diversity and composition of colonic mucosal microbiota in patients with and without colorectal cancer.AIM To determine the diversity and composition of colonic mucosal microbiota in patients with and without colorectal cancer in Indonesia.METHODS This case-control study included 59 subjects(35 colorectal cancer patients and 24 non-colorectal cancer patients indicated for colonoscopy at Dr.Cipto Mangunkusumo Gastrointestinal Endoscopy Center and Fatmawati Hospital.Microbiota examination was performed using 16S rRNA sequencing.Bioinformatics analysis was performed using the wf-metagenomics pipeline from EPI2Me-Labs(Oxford Nanopore Technologies platform).RESULTS Patients with colorectal cancer had a higher median index value on the Shannon index(3.28 vs 2.82,P>0.05)and a lower value on the Simpson index(0.050 vs 0.060,P>0.05).Significant differences in beta diversity were observed at the genus(P=0.002)and species levels(P=0.001).Firmicutes,Proteobacteria,Bacteroidetes,and Fusobacteria were the dominant phyla.The genera Bacteroides,Campylobacter,Peptostreptococcus,and Parvimonas were found more frequently in colorectal cancer,while Faecalibacterium,Haemophilus,and Phocaeicola were more frequently found in non-colorectal cancer.The relative abundance of Fusobacterium nucleatum,Bacteroides fragilis,Enterococcus faecalis,Campylobacter hominis,and Enterococcus faecalis species was significantly elevated in patients with colorectal cancer.Meanwhile,Faecalibacterium prausnitzii,Faecalibacterium duncaniae,and Prevotella copri were more commonly found in non-colorectal cancer.CONCLUSION Patients with colorectal cancer exhibit distinct differences in the composition and diversity of their colonic mucosal microbiota compared to those with non-colorectal cancer.This study was reviewed and approved by the Ethics Committee of Faculty of Medicine,Universitas Indonesia(No.KET-1517/UN2.F1/ETIK/PPM.00.02/2023).
文摘The intricate interplay between natural compounds like curcumin and the gut microbiome has gained significant attention in recent years due to their potential therapeutic implications in various health conditions.Curcumin,a polyphenolic compound derived from turmeric,exhibits diverse pharmacological properties,including anti-inflammatory,antioxidant,and anticancer effects.Understanding how curcumin modulates gut microbiota composition and function is crucial for elucidating its therapeutic mechanisms.This review examines the current literature on the interactions between curcumin and the gut microbiome.A systematic search of relevant databases was conducted to identify studies investigating the effects of curcumin on gut microbial diversity and abundance.Key findings from studies exploring curcumin's efficacy in neurological disorders,gastrointestinal diseases,and metabolic dysfunction are synthesized and discussed.Studies have demonstrated that curcumin supplementation can modulate gut microbiota composition and function,leading to beneficial effects on gut health and homeostasis.Mechanisms underlying curcumin's therapeutic effects include immune modulation,neuroprotection,and inflammation regulation.However,challenges such as poor bioavailability and safety concerns remain significant hurdles to overcome.The interactions between curcumin and the gut microbiome hold promise for therapeutic interventions in a diverse range of health conditions.Further research is needed to optimize curcumin formulations,improve bioavailability,and address safety concerns.
