1.Identification of natural product-based drug combination (NPDC) using artificial intelligence.
Tianle NIU ; Yimiao ZHU ; Minjie MOU ; Tingting FU ; Hao YANG ; Huaicheng SUN ; Yuxuan LIU ; Feng ZHU ; Yang ZHANG ; Yanxing LIU
Chinese Journal of Natural Medicines (English Ed.) 2025;23(11):1377-1390
Natural product-based drug combinations (NPDCs) present distinctive advantages in treating complex diseases. While high-throughput screening (HTS) and conventional computational methods have partially accelerated synergistic drug combination discovery, their applications remain constrained by experimental data fragmentation, high costs, and extensive combinatorial space. Recent developments in artificial intelligence (AI), encompassing traditional machine learning and deep learning algorithms, have been extensively applied in NPDC identification. Through the integration of multi-source heterogeneous data and autonomous feature extraction, prediction accuracy has markedly improved, offering a robust technical approach for novel NPDC discovery. This review comprehensively examines recent advances in AI-driven NPDC prediction, presents relevant data resources and algorithmic frameworks, and evaluates current limitations and future prospects. AI methodologies are anticipated to substantially expedite NPDC discovery and inform experimental validation.
Artificial Intelligence
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Biological Products/chemistry*
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Humans
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Drug Combinations
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Drug Discovery/methods*
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Machine Learning
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Algorithms
2.Comparison of automatic tube voltage modulation combined with an artificial intelligence iterative reconstruction algorithm versus conventional scanning protocol in contrast-enhanced thoracic-abdominal-pelvic CT
Wei DING ; Ziyan LIU ; Zepeng MA ; Tianle ZHANG ; Yongxia ZHAO
Chinese Journal of Radiological Medicine and Protection 2025;45(7):692-698
Objective:To evaluate the image quality and radiation dose in contrast-enhanced thoracic-abdominal-pelvic CT using automatic tube voltage modulation (ATVM) coupled with artificial intelligence iterative reconstruction (AIIR) versus routine tube voltage combined with Karl-3D iterative reconstruction (Karl-3D IR), and to determine the optimal noise level for AIIR in contrast-enhanced thoracic-abdominal-pelvic CT.Methods:A total of 100 patients who underwent contrast-enhanced thoracic-abdominal-pelvic CT examination in the Affiliated Hospital of Hebei University from April to October, 2023 were randomly divided into group A and group B using a random number table, with 50 patients in each group. Group A was scanned using ATVM, and images were reconstructed using AIIR with 1-5 noise levels. Group B was scanned using tube voltage 120 kVp and images were reconstructed with Karl-3D IR and noise level 5. The single-to-noise ratio (SNR), contrast-to-noise ratio (CNR), effective dose (E), and size-specific dose estimate (SSDE) were recorded or calculated for all patients or images. Subjective evaluations of all images were performed. The quality of the reconstructed images using AIIR with 1-5 noise levels were compared and the optimal noise level of AIIR for image reconstruction was determined. Image quality and radiation dose were statistically analyzed for Group A (image reconstruction with optimal AIIR noise level) and Group B.Results:The mean SNR and mean CNR of the reconstructed images using AIIR with noise levels 1, 2, and 3 in group A were higher than those using AIIR with noise levels 4 and 5. The images reconstructed using AIIR with noise levels 3 and 4 scored higher in subjective assessment than those reconstructed using AIIR with noise levels 1, 2, and 5. Therefore, noise level 3 was optimal for AIIR in reconstruction of contrast-enhanced thoracic-abdominal-pelvic CT images. The mean SNR, mean CNR, and subjective evaluation score of group A using AIIR with noise level 3 were higher than those of group B using Karl-3D IR with noise level 5 ( P<0.001). The mean SSDE and the mean E of group A were reduced by 46% and 41%, respectively, compared with those of group B. Conclusions:ATVM technology combined with the AIIR algorithm can improve image quality and reduced patient radiation dose in contrast-enhanced thoracic-abdominal-pelvic CT. Noise level 3 is optimal for AIIR in the reconstruction of arterial-phase and venous-phase contrast-enhanced thoracic-abdominal-pelvic CT images.
3.Discovery of selective HDAC6 inhibitors driven by artificial intelligence and molecular dynamics simulation approaches.
Xingang LIU ; Hao YANG ; Xinyu LIU ; Minjie MOU ; Jie LIU ; Wenying YAN ; Tianle NIU ; Ziyang ZHANG ; He SHI ; Xiangdong SU ; Xuedong LI ; Yang ZHANG ; Qingzhong JIA
Journal of Pharmaceutical Analysis 2025;15(8):101338-101338
Increasing evidence showed that histone deacetylase 6 (HDAC6) dysfunction is directly associated with the onset and progression of various diseases, especially cancers, making the development of HDAC6-targeted anti-tumor agents a research hotspot. In this study, artificial intelligence (AI) technology and molecular simulation strategies were fully integrated to construct an efficient and precise drug screening pipeline, which combined Voting strategy based on compound-protein interaction (CPI) prediction models, cascade molecular docking, and molecular dynamic (MD) simulations. The biological potential of the screened compounds was further evaluated through enzymatic and cellular activity assays. Among the identified compounds, Cmpd.18 exhibited more potent HDAC6 enzyme inhibitory activity (IC50 = 5.41 nM) than that of tubastatin A (TubA) (IC50 = 15.11 nM), along with a favorable subtype selectivity profile (selectivity index ≈ 117.23 for HDAC1), which was further verified by the Western blot analysis. Additionally, Cmpd.18 induced G2/M phase arrest and promoted apoptosis in HCT-116 cells, exerting desirable antiproliferative activity (IC50 = 2.59 μM). Furthermore, based on long-term MD simulation trajectory, the key residues facilitating Cmpd.18's binding were identified by decomposition free energy analysis, thereby elucidating its binding mechanism. Moreover, the representative conformation analysis also indicated that Cmpd.18 could stably bind to the active pocket in an effective conformation, thus demonstrating the potential for in-depth research of the 2-(2-phenoxyethyl)pyridazin-3(2H)-one scaffold.
4.Discovery of selective HDAC6 inhibitors driven by artificial intelligence and molecular dynamics simulation approaches
Xingang LIU ; Hao YANG ; Xinyu LIU ; Minjie MOU ; Jie LIU ; Wenying YAN ; Tianle NIU ; Ziyang ZHANG ; He SHI ; Xiangdong SU ; Xuedong LI ; Yang ZHANG ; Qingzhong JIA
Journal of Pharmaceutical Analysis 2025;15(8):1860-1872
Increasing evidence showed that histone deacetylase 6(HDAC6)dysfunction is directly associated with the onset and progression of various diseases,especially cancers,making the development of HDAC6-targeted anti-tumor agents a research hotspot.In this study,artificial intelligence(AI)technology and molecular simulation strategies were fully integrated to construct an efficient and precise drug screening pipeline,which combined Voting strategy based on compound-protein interaction(CPI)prediction models,cascade molecular docking,and molecular dynamic(MD)simulations.The biological potential of the screened compounds was further evaluated through enzymatic and cellular activity assays.Among the identified compounds,Cmpd.18 exhibited more potent HDAC6 enzyme inhibitory activity(IC50=5.41 nM)than that of tubastatin A(TubA)(IC50=15.11 nM),along with a favorable subtype selectivity profile(selectivity index ≈ 117.23 for HDAC1),which was further verified by the Western blot analysis.Additionally,Cmpd.18 induced G2/M phase arrest and promoted apoptosis in HCT-116 cells,exerting desirable antiproliferative activity(IC50=2.59 μM).Furthermore,based on long-term MD simulation trajectory,the key residues facilitating Cmpd.18's binding were identified by decomposition free energy analysis,thereby elucidating its binding mechanism.Moreover,the representative conformation analysis also indicated that Cmpd.18 could stably bind to the active pocket in an effective conformation,thus demonstrating the potential for in-depth research of the 2-(2-phenoxyethyl)pyridazin-3(2H)-one scaffold.
5.Expression and clinical value of the complement C3 and the S100 calcium binding protein A10 in children with traumatic brain injury
Yuan WEI ; Zhengzhong HAN ; Tianle LIU ; Zhengwei LI ; Bingxin ZHU ; Liping SHENG ; Lei ZHU
Chinese Journal of Applied Clinical Pediatrics 2025;40(12):933-938
Objective:To investigate the expression and clinical significance of the complement C3 and the S100 calcium binding protein A10 (S100A10) in children with traumatic brain injury (TBI).Methods:This case-control study included 129 TBI children admitted to the Affiliated Xuzhou Children′s Hospital of Xuzhou Medical University from January 2023 to November 2024.The patients were divided into a mild group (85 cases) and a moderate-to-severe group (44 cases).Thirty children with inguinal hernia but no underlying diseases admitted to the hospital during the same period were enrolled as the control group A. Twenty children whose lumbar puncture examination showed normal cerebrospinal fluid results and imaging tests showed no central nervous system disorder were included in the control group B. The children with moderate-to-severe TBI were followed up for 1 month after injury and further divided into good and poor prognosis groups.One-way (repeated-measures) analysis of variance (ANOVA) and t-tests were used to compare differences in complement C3 and S100A10 levels in serum and cerebrospinal fluid among groups.The correlation analysis was performed using the Spearman rank correlation method.Receiver operating characteristic (ROC) curves were drawn to evaluate the value of complements C3 and S100A10 proteins for predicting TBI severity. Results:The serum complement C3 levels in control group A, mild TBI, and moderate-to-severe TBI groups were (1.15±0.26) g/L, (1.02±0.09) g/L, (0.87±0.15) g/L, respectively.The difference in serum complement C3 levels was statistically significant among these three groups ( F=53.661, P<0.001).The serum S100A10 levels in control group A, mild TBI, and moderate-to-severe TBI groups were (0.09±0.03) μg/L, (0.17±0.04) μg/L, (0.32±0.11) μg/L, respectively.The difference in serum S100A10 levels was statistically significant among these three groups ( F=71.093, P<0.001).The levels of complement C3 and S100A10 in the cerebrospinal fluid (30 min post-operation) of children with severe TBI were significantly higher than those in the control group B, with statistically significant differences (all P<0.01).Correlation analysis revealed that Glasgow Coma Scale scores showed a positive correlation with serum complement C3 levels and a negative correlation with S100A10 levels ( r=0.592, -0.705; all P<0.001).The serum complement C3 and S100A10 levels were (0.90±0.13) g/L and (0.30±0.10) μg/L in the good prognosis group, and (0.74±0.16) g/L and (0.42±0.11) μg/L in the poor prognosis group, respectively.Both serum complement C3 and S100A10 levels were statistically significantly different between good and poor prognosis groups ( t=3.025, -3.014; all P<0.01).The complement C3 level in the cerebrospinal fluid of severe TBI children was (0.093±0.007) g/L 30 min after operation, and it gradually increased to reach the first peak at day 3 and the second peak at day 5 postoperatively[(0.112±0.005) g/L and (0.120±0.010) g/L, respectively].The difference in the complement C3 level in the cerebrospinal fluid of severe TBI children was significant between 30 min and 3-5 d after operation ( F=42.756, P<0.01).The S100A10 level in the cerebrospinal fluid of severe TBI children was (2.56±0.31) μg/L 30 min after operation, and then it showed a sustained increase, reaching (4.09±0.13) μg/L at day 7 postoperatively.The difference in the S100A10 level in the cerebrospinal fluid of severe TBI children was significant between 30 min and 7 d after operation ( F=110.676, P<0.01).ROC curve analysis showed that the areas under the curve for predicting moderate-to-severe TBI based on serum complement C3 and S100A10 levels were 0.802 and 0.889, respectively (all P<0.01). Conclusions:Serum complement C3 levels are significantly decreased whereas serum S100A10 levels are markedly elevated in pediatric TBI patients.The measurement of serum complement C3 and S100A10 levels can aid in the clinical assessment of the severity and prognosis of TBI children.Both complement C3 and S100A10 levels in cerebrospinal fluid show a significant elevation within 7 days after operation in severe pediatric TBI, which is potentially linked to sustained astrocyte activation.
6.Comparison of automatic tube voltage modulation combined with an artificial intelligence iterative reconstruction algorithm versus conventional scanning protocol in contrast-enhanced thoracic-abdominal-pelvic CT
Wei DING ; Ziyan LIU ; Zepeng MA ; Tianle ZHANG ; Yongxia ZHAO
Chinese Journal of Radiological Medicine and Protection 2025;45(7):692-698
Objective:To evaluate the image quality and radiation dose in contrast-enhanced thoracic-abdominal-pelvic CT using automatic tube voltage modulation (ATVM) coupled with artificial intelligence iterative reconstruction (AIIR) versus routine tube voltage combined with Karl-3D iterative reconstruction (Karl-3D IR), and to determine the optimal noise level for AIIR in contrast-enhanced thoracic-abdominal-pelvic CT.Methods:A total of 100 patients who underwent contrast-enhanced thoracic-abdominal-pelvic CT examination in the Affiliated Hospital of Hebei University from April to October, 2023 were randomly divided into group A and group B using a random number table, with 50 patients in each group. Group A was scanned using ATVM, and images were reconstructed using AIIR with 1-5 noise levels. Group B was scanned using tube voltage 120 kVp and images were reconstructed with Karl-3D IR and noise level 5. The single-to-noise ratio (SNR), contrast-to-noise ratio (CNR), effective dose (E), and size-specific dose estimate (SSDE) were recorded or calculated for all patients or images. Subjective evaluations of all images were performed. The quality of the reconstructed images using AIIR with 1-5 noise levels were compared and the optimal noise level of AIIR for image reconstruction was determined. Image quality and radiation dose were statistically analyzed for Group A (image reconstruction with optimal AIIR noise level) and Group B.Results:The mean SNR and mean CNR of the reconstructed images using AIIR with noise levels 1, 2, and 3 in group A were higher than those using AIIR with noise levels 4 and 5. The images reconstructed using AIIR with noise levels 3 and 4 scored higher in subjective assessment than those reconstructed using AIIR with noise levels 1, 2, and 5. Therefore, noise level 3 was optimal for AIIR in reconstruction of contrast-enhanced thoracic-abdominal-pelvic CT images. The mean SNR, mean CNR, and subjective evaluation score of group A using AIIR with noise level 3 were higher than those of group B using Karl-3D IR with noise level 5 ( P<0.001). The mean SSDE and the mean E of group A were reduced by 46% and 41%, respectively, compared with those of group B. Conclusions:ATVM technology combined with the AIIR algorithm can improve image quality and reduced patient radiation dose in contrast-enhanced thoracic-abdominal-pelvic CT. Noise level 3 is optimal for AIIR in the reconstruction of arterial-phase and venous-phase contrast-enhanced thoracic-abdominal-pelvic CT images.
7.Expression and clinical value of the complement C3 and the S100 calcium binding protein A10 in children with traumatic brain injury
Yuan WEI ; Zhengzhong HAN ; Tianle LIU ; Zhengwei LI ; Bingxin ZHU ; Liping SHENG ; Lei ZHU
Chinese Journal of Applied Clinical Pediatrics 2025;40(12):933-938
Objective:To investigate the expression and clinical significance of the complement C3 and the S100 calcium binding protein A10 (S100A10) in children with traumatic brain injury (TBI).Methods:This case-control study included 129 TBI children admitted to the Affiliated Xuzhou Children′s Hospital of Xuzhou Medical University from January 2023 to November 2024.The patients were divided into a mild group (85 cases) and a moderate-to-severe group (44 cases).Thirty children with inguinal hernia but no underlying diseases admitted to the hospital during the same period were enrolled as the control group A. Twenty children whose lumbar puncture examination showed normal cerebrospinal fluid results and imaging tests showed no central nervous system disorder were included in the control group B. The children with moderate-to-severe TBI were followed up for 1 month after injury and further divided into good and poor prognosis groups.One-way (repeated-measures) analysis of variance (ANOVA) and t-tests were used to compare differences in complement C3 and S100A10 levels in serum and cerebrospinal fluid among groups.The correlation analysis was performed using the Spearman rank correlation method.Receiver operating characteristic (ROC) curves were drawn to evaluate the value of complements C3 and S100A10 proteins for predicting TBI severity. Results:The serum complement C3 levels in control group A, mild TBI, and moderate-to-severe TBI groups were (1.15±0.26) g/L, (1.02±0.09) g/L, (0.87±0.15) g/L, respectively.The difference in serum complement C3 levels was statistically significant among these three groups ( F=53.661, P<0.001).The serum S100A10 levels in control group A, mild TBI, and moderate-to-severe TBI groups were (0.09±0.03) μg/L, (0.17±0.04) μg/L, (0.32±0.11) μg/L, respectively.The difference in serum S100A10 levels was statistically significant among these three groups ( F=71.093, P<0.001).The levels of complement C3 and S100A10 in the cerebrospinal fluid (30 min post-operation) of children with severe TBI were significantly higher than those in the control group B, with statistically significant differences (all P<0.01).Correlation analysis revealed that Glasgow Coma Scale scores showed a positive correlation with serum complement C3 levels and a negative correlation with S100A10 levels ( r=0.592, -0.705; all P<0.001).The serum complement C3 and S100A10 levels were (0.90±0.13) g/L and (0.30±0.10) μg/L in the good prognosis group, and (0.74±0.16) g/L and (0.42±0.11) μg/L in the poor prognosis group, respectively.Both serum complement C3 and S100A10 levels were statistically significantly different between good and poor prognosis groups ( t=3.025, -3.014; all P<0.01).The complement C3 level in the cerebrospinal fluid of severe TBI children was (0.093±0.007) g/L 30 min after operation, and it gradually increased to reach the first peak at day 3 and the second peak at day 5 postoperatively[(0.112±0.005) g/L and (0.120±0.010) g/L, respectively].The difference in the complement C3 level in the cerebrospinal fluid of severe TBI children was significant between 30 min and 3-5 d after operation ( F=42.756, P<0.01).The S100A10 level in the cerebrospinal fluid of severe TBI children was (2.56±0.31) μg/L 30 min after operation, and then it showed a sustained increase, reaching (4.09±0.13) μg/L at day 7 postoperatively.The difference in the S100A10 level in the cerebrospinal fluid of severe TBI children was significant between 30 min and 7 d after operation ( F=110.676, P<0.01).ROC curve analysis showed that the areas under the curve for predicting moderate-to-severe TBI based on serum complement C3 and S100A10 levels were 0.802 and 0.889, respectively (all P<0.01). Conclusions:Serum complement C3 levels are significantly decreased whereas serum S100A10 levels are markedly elevated in pediatric TBI patients.The measurement of serum complement C3 and S100A10 levels can aid in the clinical assessment of the severity and prognosis of TBI children.Both complement C3 and S100A10 levels in cerebrospinal fluid show a significant elevation within 7 days after operation in severe pediatric TBI, which is potentially linked to sustained astrocyte activation.
8.Consensus molecular subtype of colorectal cancer and its clinical application prospects
Tianle JIN ; Yuquan LIU ; Runshi WANG ; Ni HOU ; Jie LI
Journal of Xi'an Jiaotong University(Medical Sciences) 2024;45(4):525-534
Colorectal cancer(CRC)is highly heterogeneous,but traditional TNM staging cannot distinguish the heterogeneity of CRC well,which can no longer meet the treatment needs.Integrating the clinical features,molecular genetic changes in cancer tissue,transcriptome and proteome changes,as well as immune matrix characteristics,the consensus molecular subtype(CMS)of CRC is by far the best description of its heterogeneity.This paper first discusses the molecular genetic changes of three types of CRC cancer tissues(chromosomal instability,microsatellite instability,and CpG island methylation phenotype).Then it systematically elaborates on the clinical characteristics,treatment directions,and prognosis evaluation of CRC patients with different CMS subtypes,as well as their relationship with immunotherapy and changes in gut microbiota.With the continuous improvement of sequencing technology and the prospective precision medicine clinical trial exploration,the"multi-molecule multi-drug"treatment model based on CMS typing will become the core of future precision medicine and personalized medicine.
9.An intervention study of Orff-music therapy for long-term hospitalized patients with schizophrenia
Tianle WANG ; Rizhao LI ; Qiyang HUANG ; Daming LIU ; Dakai XIA ; Ting FENG ; Aroufujiang YIERXIATI ; Jieyi WU ; Bin SUN ; Xinyan ZHENG ; Yingchun DAI
Chinese Journal of Nervous and Mental Diseases 2024;50(3):135-139
Objective This research aims to investigate the impact of Orff music therapy on long-term schizophrenic patients in hospitals.Methods The study was a randomized,single-blind controlled trial conducted from April,2023 to September,2023.From April to September 2023,sixty-eight individuals diagnosed with persistent schizophrenia were enrolled and evenly distributed into a pair of cohorts:a treatment group of thirty-four people receiving the intervention,and an equal number forming the control group for comparative purposes.Individuals enrolled in the experimental arm of the study were administered Orff-music therapy alongside routine rehabilitation treatment across a span of two months.For a period of 8 weeks,the control group was given only standard rehabilitation treatment,whereas the research group underwent Orff-music therapy in addition to the standard rehabilitation treatment.Results Before treatment,there were no significant differences in the positive and negative symptoms scale(PANSS),the inpatient psychosis rehabilitation observe scale(IPROS)and the personal and social performance scale(psp)between two groups.After intervention,the PANSS showed that the changes were better in the study group than in the control group in 3 indicators:negative symptoms(-3.20±4.13 vs.-0.17±2.43,P<0.001),general symptoms(-2.79±3.83 vs.-0.17±2.99,P=0.003)and the total scores(-5.88±6.36 vs.0.00±4.08,P<0.001),but not in positive symptoms(P>0.05).The IPROS showed that the performances of patients in the study group were better than the control group in terms of participation in work therapy(-0.82±2.08 vs.0.23±2.10,P=0.041),socialization(-0.59±1.94 vs.0.53±1.69,P=0.014)and ability to live(-0.94±2.50 vs.0.15±1.48,P=0.033),the changes in scores before and after the intervention were significantly different when compared to the control group.The PSP showed that the changes in scores before and after the treatment of the study group was better than the control group in terms of social activity[0(-1,0)vs.0(0,0),P=0.011],and self-care[0(-1,0)vs.0(-0.25,0),P=0.012]were better than the control group.Conclusion For long-term hospitalized patients with chronic schizophrenia.Orff-music therapy can be a powerful tool for alleviating mental issues,fostering social functioning,and enhancing rehabilitation results.
10.The Association between the Gut Microbiota and Erectile Dysfunction
Tianle ZHU ; Xi LIU ; Peng YANG ; Yukuai MA ; Pan GAO ; Jingjing GAO ; Hui JIANG ; Xiansheng ZHANG
The World Journal of Men's Health 2024;42(4):772-786
Purpose:
Explore the causal relationship between the gut microbiota and erectile dysfunction (ED) at phylum, class, order, family, and genus levels, and identify specific pathogenic bacteria that may be associated with the onset and progression of ED.
Materials and Methods:
The genetic variation data of 196 human gut microbiota incorporated in our study came from the human gut microbiome Genome Wide Association Studies (GWAS) dataset released by the MiBioGen Consortium. The GWAS statistics for ED were extracted from one study by Bovijn et al., which included 223,805 participants of European ancestry, of whom 6,175 were diagnosed with ED. Subsequently, Mendelian randomization (MR) analysis was carried out to explore whether a causal relationship exists between the gut microbiota and ED. Additionally, bidirectional MR analysis was performed to examine the directionality of the causal relationship.
Results:
Through MR analysis, we found that family Lachnospiraceae (odds ratio [OR]: 1.27, 95% confidence interval [CI]: 1.05–1.52, p=0.01) and its subclass genus LachnospiraceaeNC2004 group (OR: 1.17, 95% CI: 1.01–1.37, p=0.04) are associated with a higher risk of ED. In addition, genus Oscillibacter (OR: 1.17, 95% CI: 1.02–1.35, p=0.03), genus Senegalimassilia (OR: 1.32, 95% CI: 1.06–1.64, p=0.01) and genus Tyzzerella3 (OR: 1.14, 95% CI: 1.02–1.27, p=0.02) also increase the risk of ED. In contrast, the inverse variance weighted estimate of genus RuminococcaceaeUCG013 (OR: 0.77, 95% CI: 0.61–0.96, p=0.02) suggests that it has a protective effect against the occurrence of ED.
Conclusions
This study preliminarily identified 6 bacterial taxa that may have a causal relationship with ED, including family Lachnospiraceae, genus Lachnospiraceae NC2004 group, Oscillibacter, Senegalimassilia, Tyzzerella 3 and Ruminococcaceae UCG013. These identified important bacterial taxa may serve as candidates for microbiome intervention in future ED clinical trials.

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