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Guo Z, Lei Y, Wang Q. Chinese expert consensus on standard technical specifications for a gut microecomics laboratory (Review). Exp Ther Med 2024; 28:403. [PMID: 39234587 PMCID: PMC11372251 DOI: 10.3892/etm.2024.12692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Accepted: 07/11/2024] [Indexed: 09/06/2024] Open
Abstract
The intestinal microbiota is a complex ecosystem that not only affects various physiological functions, such as metabolism, inflammation and the immune response, but also has an important effect on the development of tumors and response to treatment. The detection of intestinal flora enables the timely identification of disease-related flora abnormalities, which has significant implications for both disease prevention and treatment. In the field of basic and clinical research targeting gut microbiome, there is a need to recognize and understand the laboratory assays for gut microbiomics. Currently, there is no unified standard for the experimental procedure, quality management and report interpretation of intestinal microbiome assay technology. In order to clarify the process, the Tumor and Microecology Committee of China Anti-Cancer Association and the Tumor and Microecology Committee of Hubei Provincial Immunology Society organized relevant experts to discuss and put forward the standard technical specifications for gut microecomics laboratories, which provides a basis for further in-depth research in the field of intestinal microecomics.
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Affiliation(s)
- Zhi Guo
- Department of Hematology, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen, Guangdong 518052, P.R. China
- Institute of Infection, Immunology and Tumor Microenvironment, Hubei Province Key Laboratory of Occupational Hazard Identification and Control, Medical College, Wuhan University of Science and Technology, Wuhan, Hubei 430065, P.R. China
| | - Yumeng Lei
- Institute of Infection, Immunology and Tumor Microenvironment, Hubei Province Key Laboratory of Occupational Hazard Identification and Control, Medical College, Wuhan University of Science and Technology, Wuhan, Hubei 430065, P.R. China
| | - Qiang Wang
- Institute of Infection, Immunology and Tumor Microenvironment, Hubei Province Key Laboratory of Occupational Hazard Identification and Control, Medical College, Wuhan University of Science and Technology, Wuhan, Hubei 430065, P.R. China
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Gao K, Sun B, Zhou G, Cao Z, Xiang L, Yu J, Wang R, Yao Y, Lin F, Li Z, Ren F, Lv Y, Lu Q. Blood-based biomemristor for hyperglycemia and hyperlipidemia monitoring. Mater Today Bio 2024; 28:101169. [PMID: 39183770 PMCID: PMC11342282 DOI: 10.1016/j.mtbio.2024.101169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Revised: 07/25/2024] [Accepted: 07/27/2024] [Indexed: 08/27/2024] Open
Abstract
Thanks to its structural characteristics and signal patterns similar to those of human brain synapses, memristors are widely believed to be applicable for neuromorphic computing. However, to our knowledge, memristors have not been effectively applied in the biomedical field, especially in disease diagnosis and health monitoring. In this work, a blood-based biomemristor was prepared for in vitro detection of hyperglycemia and hyperlipidemia. It was found that the device exhibits excellent resistance switching (RS) behavior at lower voltage biases. Through mechanism analysis, it has been confirmed that the RS behavior is driven by Ohmic conduction and ion rearrangement. Furthermore, the hyperglycemia and hyperlipidemia detection devices were constructed for the first time based on memristor logic circuits, and circuit simulations were conducted. These results confirm the feasibility of blood-based biomemristors in detecting hyperglycemia and hyperlipidemia, providing new prospects for the important application of memristors in the biomedical field.
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Affiliation(s)
- Kaikai Gao
- Department of Geriatric Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
- National Local Joint Engineering Research Center for Precision Surgery and Regenerative Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
- Frontier Institute of Science and Technology (FIST), Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, China
- Micro-and Nano-technology Research Center, State Key Laboratory for Manufacturing Systems Engineering, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, China
| | - Bai Sun
- Department of Geriatric Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
- National Local Joint Engineering Research Center for Precision Surgery and Regenerative Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
- Frontier Institute of Science and Technology (FIST), Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, China
- Micro-and Nano-technology Research Center, State Key Laboratory for Manufacturing Systems Engineering, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, China
| | - Guangdong Zhou
- College of Artificial Intelligence, Brain-inspired Computing & Intelligent Control of Chongqing Key Lab, Southwest University, Chongqing, 400715, China
| | - Zelin Cao
- Department of Geriatric Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
- National Local Joint Engineering Research Center for Precision Surgery and Regenerative Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
- Frontier Institute of Science and Technology (FIST), Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, China
- Micro-and Nano-technology Research Center, State Key Laboratory for Manufacturing Systems Engineering, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, China
| | - Linbiao Xiang
- Department of Geriatric Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
- National Local Joint Engineering Research Center for Precision Surgery and Regenerative Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
| | - Jiawei Yu
- Department of Geriatric Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
- National Local Joint Engineering Research Center for Precision Surgery and Regenerative Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
| | - Ruixin Wang
- Department of Geriatric Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
- National Local Joint Engineering Research Center for Precision Surgery and Regenerative Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
| | - Yingmin Yao
- Department of Geriatric Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
- National Local Joint Engineering Research Center for Precision Surgery and Regenerative Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
| | - Fulai Lin
- Department of Geriatric Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
- National Local Joint Engineering Research Center for Precision Surgery and Regenerative Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
| | - Zhuoqun Li
- Department of Geriatric Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
- National Local Joint Engineering Research Center for Precision Surgery and Regenerative Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
| | - Fenggang Ren
- Department of Geriatric Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
- National Local Joint Engineering Research Center for Precision Surgery and Regenerative Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
| | - Yi Lv
- Department of Geriatric Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
- National Local Joint Engineering Research Center for Precision Surgery and Regenerative Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
| | - Qiang Lu
- Department of Geriatric Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
- National Local Joint Engineering Research Center for Precision Surgery and Regenerative Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
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Li W, Dong H, Niu K, Wang HY, Cheng W, Song H, Ying AK, Zhai X, Li K, Yu H, Guo DS, Wang Y. Analyzing urinary hippuric acid as a metabolic health biomarker through a supramolecular architecture. Talanta 2024; 278:126480. [PMID: 38972275 DOI: 10.1016/j.talanta.2024.126480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 06/10/2024] [Accepted: 06/25/2024] [Indexed: 07/09/2024]
Abstract
The prevalence of metabolic disorders has been found to increase concomitantly with alternations in habitual diet and lifestyle, indicating the importance of metabolic health monitoring for early warning of high-risk status and suggesting effective intervention strategies. Hippuric acid (HA), as one of the most abundant metabolites from the gut microbiota, holds potential as a regulator of metabolic health. Accordingly, it is imperative to establish an efficient, sensitive, and affordable method for large-scale population monitoring, revealing the association between HA level and metabolic disorders. Upon systematic screening of macrocycle•dye reporter pair, a supramolecular architecture (guanidinomethyl-modified calix[5]arene, GMC5A) was employed to sense urinary HA by employing fluorescein (Fl), whose complexation behavior was demonstrated by theoretical calculations, accomplishing quantification of HA in urine from 249 volunteers in the range of 0.10 mM and 10.93 mM. Excitedly, by restricted cubic spline, urinary HA concentration was found to have a significantly negative correlation with the risk of metabolic disorders when it exceeded 0.76 mM, suggesting the importance of dietary habits, especially the consumption of fruits, coffee, and tea, which was unveiled from a simple questionnaire survey. In this study, we accomplished a high throughput and sensitive detection of urinary HA based on supramolecular sensing with the GMC5A•Fl reporter pair, which sheds light on the rapid quantification of urinary HA as an indicator of metabolic health status and early intervention by balancing the daily diet.
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Affiliation(s)
- Wenhui Li
- National Key Laboratory of Chinese Medicine Modernization, State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China
| | - Hua Dong
- First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, Tianjin, 300193, China
| | - Kejing Niu
- National Key Laboratory of Chinese Medicine Modernization, State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China
| | - Huan-Yu Wang
- College of Chemistry, State Key Laboratory of Elemento-Organic Chemistry, Key Laboratory of Functional Polymer Materials (Ministry of Education), Frontiers Science Center for New Organic Matter, Collaborative Innovation Center of Chemical Science and Engineering, Nankai University, Tianjin, 300071, China
| | - Wenqian Cheng
- National Key Laboratory of Chinese Medicine Modernization, State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China
| | - Hualong Song
- First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, Tianjin, 300193, China
| | - An-Kang Ying
- College of Chemistry, State Key Laboratory of Elemento-Organic Chemistry, Key Laboratory of Functional Polymer Materials (Ministry of Education), Frontiers Science Center for New Organic Matter, Collaborative Innovation Center of Chemical Science and Engineering, Nankai University, Tianjin, 300071, China
| | - Xiaobing Zhai
- Faculty of Applied Sciences, Macao Polytechnic University, Macau, China
| | - Kefeng Li
- Faculty of Applied Sciences, Macao Polytechnic University, Macau, China
| | - Huijuan Yu
- National Key Laboratory of Chinese Medicine Modernization, State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China; Haihe Laboratory of Modern Chinese Medicine, Tianjin, 301617, China.
| | - Dong-Sheng Guo
- College of Chemistry, State Key Laboratory of Elemento-Organic Chemistry, Key Laboratory of Functional Polymer Materials (Ministry of Education), Frontiers Science Center for New Organic Matter, Collaborative Innovation Center of Chemical Science and Engineering, Nankai University, Tianjin, 300071, China.
| | - Yuefei Wang
- National Key Laboratory of Chinese Medicine Modernization, State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China; Haihe Laboratory of Modern Chinese Medicine, Tianjin, 301617, China.
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Pu Y, Sun Z, Zhang H, Huang Q, Wang Z, Mei Z, Wang P, Kong M, Yang W, Lin C, Zhou X, Lin S, Huang Q, Huang L, Sun L, Yuan C, Xu Q, Tang H, Wang X, Zheng Y. Gut microbial features and circulating metabolomic signatures of frailty in older adults. NATURE AGING 2024; 4:1249-1262. [PMID: 39054372 DOI: 10.1038/s43587-024-00678-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 07/03/2024] [Indexed: 07/27/2024]
Abstract
Frailty, a multidimensional indicator of suboptimal aging, reflects cumulative declines across multiple physiological systems. Although age-related changes have been reported in gut microbiota, their role in healthy aging remains unclear. In this study, we calculated frailty index (FI) from 33 health-related items to reflect the overall health status of 1,821 older adults (62-96 years, 55% female) and conducted multi-omics analysis using gut metagenomic sequencing data and plasma metabolomic data. We identified 18 microbial species and 17 metabolites shifted along with frailty severity, with stronger links observed in females. The associations of nine species, including various Clostridium species and Faecalibacterium prausnitzii, with FI were reproducible in two external populations. Plasma glycerol levels, white blood cell count and kidney function partially mediated these associations. A composite microbial score derived from FI significantly predicted 2-year mortality (adjusted hazard ratio across extreme quartiles, 2.86; 95% confidence interval, 1.38-5.93), highlighting the potential of microbiota-based strategies for risk stratification in older adults.
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Affiliation(s)
- Yanni Pu
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Zhonghan Sun
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Hui Zhang
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences, Fudan University, Shanghai, China
- School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qingxia Huang
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Zhengdong Wang
- Department of Gastroenterology, Rugao People's Hospital, Rugao, China
| | - Zhendong Mei
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Peilu Wang
- Ministry of Education Key Laboratory of Public Health Safety, School of Public Health, Institute of Nutrition, Fudan University, Shanghai, China
| | - Mengmeng Kong
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Wenjun Yang
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Chenhao Lin
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Xiaofeng Zhou
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Shuchun Lin
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Qiumin Huang
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Lili Huang
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Liang Sun
- Ministry of Education Key Laboratory of Public Health Safety, School of Public Health, Institute of Nutrition, Fudan University, Shanghai, China
| | - Changzheng Yuan
- School of Public Health, Zhejiang University School of Medicine, Hangzhou, China
| | - Qian Xu
- Institute of Gut Microbiota Research and Engineering Development, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Huiru Tang
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, China.
| | - Xiaofeng Wang
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences, Fudan University, Shanghai, China.
- National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai, China.
| | - Yan Zheng
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, China.
- Ministry of Education Key Laboratory of Public Health Safety, School of Public Health, Institute of Nutrition, Fudan University, Shanghai, China.
- National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai, China.
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Ding E, Deng F, Fang J, Liu J, Yan W, Yao Q, Miao K, Wang Y, Sun P, Li C, Liu Y, Dong H, Dong L, Zhang X, Lu Y, Lin X, Ding C, Li T, Shi Y, Cai Y, Liu X, Godri Pollitt KJ, Ji JS, Tong S, Tang S, Shi X. Exposome-Wide Ranking to Uncover Environmental Chemicals Associated with Dyslipidemia: A Panel Study in Healthy Older Chinese Adults from the BAPE Study. ENVIRONMENTAL HEALTH PERSPECTIVES 2024; 132:97005. [PMID: 39240788 PMCID: PMC11379127 DOI: 10.1289/ehp13864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/08/2024]
Abstract
BACKGROUND Environmental contaminants (ECs) are increasingly recognized as crucial drivers of dyslipidemia and cardiovascular disease (CVD), but the comprehensive impact spectrum and interlinking mechanisms remain uncertain. OBJECTIVES We aimed to systematically evaluate the association between exposure to 80 ECs across seven divergent categories and markers of dyslipidemia and investigate their underpinning biomolecular mechanisms via an unbiased integrative approach of internal chemical exposome and multi-omics. METHODS A longitudinal study involving 76 healthy older adults was conducted in Jinan, China, and participants were followed five times from 10 September 2018 to 19 January 2019 in 1-month intervals. A broad spectrum of seven chemical categories covering the prototypes and metabolites of 102 ECs in serum or urine as well as six serum dyslipidemia markers [total cholesterol, high-density lipoprotein cholesterol, low-density lipoprotein cholesterol, apolipoprotein (Apo)A1, ApoB, and ApoE4] were measured. Multi-omics, including the blood transcriptome, serum/urine metabolome, and serum lipidome, were profiled concurrently. Exposome-wide association study and the deletion/substitution/addition algorithms were applied to explore the associations between 80 EC exposures detection frequency > 50 % and dyslipidemia markers. Weighted quantile sum regression was used to assess the mixture effects and relative contributions. Multi-omics profiling, causal inference model, and pathway analysis were conducted to interpret the mediating biomolecules and underlying mechanisms. Examination of cytokines and electrocardiograms was further conducted to validate the observed associations and biomolecular pathways. RESULTS Eight main ECs [1-naphthalene, 1-pyrene, 2-fluorene, dibutyl phosphate, tri-phenyl phosphate, mono-(2-ethyl-5-hydroxyhexyl) phthalate, chromium, and vanadium] were significantly associated with most dyslipidemia markers. Multi-omics indicated that the associations were mediated by endogenous biomolecules and pathways, primarily pertinent to CVD, inflammation, and metabolism. Clinical measures of cytokines and electrocardiograms further cross-validated the association of these exogenous ECs with systemic inflammation and cardiac function, demonstrating their potential mechanisms in driving dyslipidemia pathogenesis. DISCUSSION It is imperative to prioritize mitigating exposure to these ECs in the primary prevention and control of the dyslipidemia epidemic. https://doi.org/10.1289/EHP13864.
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Affiliation(s)
- Enmin Ding
- China CDC Key Laboratory of Environment and Population Health, National Institute of Environmental Health (NIEH), Chinese Center for Disease Control and Prevention (China CDC), Beijing, China
- School of Population Medicine and Public Health, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Fuchang Deng
- China CDC Key Laboratory of Environment and Population Health, National Institute of Environmental Health (NIEH), Chinese Center for Disease Control and Prevention (China CDC), Beijing, China
| | - Jianlong Fang
- China CDC Key Laboratory of Environment and Population Health, National Institute of Environmental Health (NIEH), Chinese Center for Disease Control and Prevention (China CDC), Beijing, China
| | - Juan Liu
- China CDC Key Laboratory of Environment and Population Health, National Institute of Environmental Health (NIEH), Chinese Center for Disease Control and Prevention (China CDC), Beijing, China
| | - Wenyan Yan
- Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Qiao Yao
- China CDC Key Laboratory of Environment and Population Health, National Institute of Environmental Health (NIEH), Chinese Center for Disease Control and Prevention (China CDC), Beijing, China
| | - Ke Miao
- China CDC Key Laboratory of Environment and Population Health, National Institute of Environmental Health (NIEH), Chinese Center for Disease Control and Prevention (China CDC), Beijing, China
| | - Yu Wang
- China CDC Key Laboratory of Environment and Population Health, National Institute of Environmental Health (NIEH), Chinese Center for Disease Control and Prevention (China CDC), Beijing, China
| | - Peijie Sun
- China CDC Key Laboratory of Environment and Population Health, National Institute of Environmental Health (NIEH), Chinese Center for Disease Control and Prevention (China CDC), Beijing, China
| | - Chenfeng Li
- China CDC Key Laboratory of Environment and Population Health, National Institute of Environmental Health (NIEH), Chinese Center for Disease Control and Prevention (China CDC), Beijing, China
| | - Yuanyuan Liu
- China CDC Key Laboratory of Environment and Population Health, National Institute of Environmental Health (NIEH), Chinese Center for Disease Control and Prevention (China CDC), Beijing, China
| | - Haoran Dong
- China CDC Key Laboratory of Environment and Population Health, National Institute of Environmental Health (NIEH), Chinese Center for Disease Control and Prevention (China CDC), Beijing, China
| | - Li Dong
- China CDC Key Laboratory of Environment and Population Health, National Institute of Environmental Health (NIEH), Chinese Center for Disease Control and Prevention (China CDC), Beijing, China
| | - Xu Zhang
- China CDC Key Laboratory of Environment and Population Health, National Institute of Environmental Health (NIEH), Chinese Center for Disease Control and Prevention (China CDC), Beijing, China
| | - Yifu Lu
- China CDC Key Laboratory of Environment and Population Health, National Institute of Environmental Health (NIEH), Chinese Center for Disease Control and Prevention (China CDC), Beijing, China
| | - Xiao Lin
- China CDC Key Laboratory of Environment and Population Health, National Institute of Environmental Health (NIEH), Chinese Center for Disease Control and Prevention (China CDC), Beijing, China
| | - Changming Ding
- China CDC Key Laboratory of Environment and Population Health, National Institute of Environmental Health (NIEH), Chinese Center for Disease Control and Prevention (China CDC), Beijing, China
| | - Tiantian Li
- China CDC Key Laboratory of Environment and Population Health, National Institute of Environmental Health (NIEH), Chinese Center for Disease Control and Prevention (China CDC), Beijing, China
- Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Yali Shi
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Yaqi Cai
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Xiaohui Liu
- National Protein Science Technology Center, Tsinghua University, Beijing, China
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Krystal J Godri Pollitt
- Department of Environmental Health Sciences, Yale School of Public Health, New Haven, Connecticut, USA
| | - John S Ji
- Vanke School of Public Health, Tsinghua University, Beijing, China
| | - Shilu Tong
- China CDC Key Laboratory of Environment and Population Health, National Institute of Environmental Health (NIEH), Chinese Center for Disease Control and Prevention (China CDC), Beijing, China
- Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China
- School of Public Health, Institute of Environment and Population Health, Anhui Medical University, Hefei, China
- School of Public Health and Social Work, Queensland University of Technology, Brisbane, Australia
| | - Song Tang
- China CDC Key Laboratory of Environment and Population Health, National Institute of Environmental Health (NIEH), Chinese Center for Disease Control and Prevention (China CDC), Beijing, China
- Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Xiaoming Shi
- China CDC Key Laboratory of Environment and Population Health, National Institute of Environmental Health (NIEH), Chinese Center for Disease Control and Prevention (China CDC), Beijing, China
- Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, NIEH, China CDC, Beijing, China
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6
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Brochado-Kith O, Rava M, Berenguer J, González-García J, Rojo D, Díez C, Hontañon V, Virseda-Berdices A, Ibañez-Samaniego L, Llop-Herrera E, Olveira A, Pérez-Latorre L, Barbas C, Fernández-Rodríguez A, Resino S, Jiménez-Sousa MA. Altered blood microbiome in patients with HCV-related Child-Pugh class B cirrhosis. J Infect Public Health 2024; 17:102524. [PMID: 39241484 DOI: 10.1016/j.jiph.2024.102524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 08/01/2024] [Accepted: 08/22/2024] [Indexed: 09/09/2024] Open
Abstract
BACKGROUND Altered bacterial translocation is associated with changes in hepatic function and the progression from compensated to decompensated cirrhosis. Child-Turcotte-Pugh (CTP) score is an essential indicator of liver severity. Thus, we aimed to study differences in the blood microbiome together with metabolome profile between HCV-infected patients with CTP class B (CTP-B, significant functional compromise) and patients with CTP class A (CTP-A, well-compensated cirrhosis). METHODS We conducted a cross-sectional study in patients with advanced HCV-related cirrhosis (n = 88) stratified by CTP-B and CTP-A. Bacterial 16S rRNA sequencing was sequenced by MiSeq Illumina technology and non-targeted metabolomics was performed by GC-MS and LC-MS ESI+ and ESI- to complement the analysis. RESULTS Patients with CTP-B had lower levels of richness (Chao1), and alpha diversity (Shannon and Simpson indexes) at phylum level than patients with CTP-A. Likewise, we observed significant differences in beta diversity between groups at phylum, class, and order levels, showing lower diversity in patients with CTP-B. Higher relative abundance of Proteobacteria (p = 0.012), Alphaproteobacteria (p = 0.005), Sphingomonadales (p = 0.012) and Sphingomonadaceae (p = 0.016) were significantly associated with CTP-B. The phylum Proteobacteria was positively correlated with ethanolamine and oleic acid (p = 0.005 and p = 0.004, respectively) and negatively with p-cresol (p = 0.006). In addition, the order Sphingomonadales and the family Sphingomonadaceae was also negatively correlated with p-cresol (p = 0.001 and p = 0.001). CONCLUSIONS Blood microbial diversity was significantly decreased in patients with CTP-B, who presented an enrichment of Proteobacteria, Alphaproteobacteria, Sphingomonadales and Sphingomonadaceae compared to patients with CTP-A.
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Affiliation(s)
- Oscar Brochado-Kith
- Unidad de Infección Viral e Inmunidad, Centro Nacional de Microbiología (CNM), Instituto de Salud Carlos III (ISCIII), Majadahonda, Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid. Spain.
| | - Marta Rava
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid. Spain; Unidad de la Cohorte de la Red de Investigación en Sida (CoRIS). Centro Nacional de Epidemiologia (CNE), Instituto de Salud Carlos III (ISCIII), Madrid, Spain.
| | - Juan Berenguer
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid. Spain; Unidad de Enfermedades Infecciosas/VIH; Hospital General Universitario "Gregorio Marañón", Madrid, Spain; Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain.
| | - Juan González-García
- Servicio de Medicina Interna-Unidad de VIH. Hospital Universitario La Paz, Madrid, Spain; Instituto de Investigación Sanitaria La Paz (IdiPAZ), Madrid, Spain.
| | - David Rojo
- Centre of Metabolomics and Bioanalysis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28060 Boadilla del Monte, Spain.
| | - Cristina Díez
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid. Spain; Unidad de Enfermedades Infecciosas/VIH; Hospital General Universitario "Gregorio Marañón", Madrid, Spain; Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain.
| | - Victor Hontañon
- Servicio de Medicina Interna-Unidad de VIH. Hospital Universitario La Paz, Madrid, Spain; Instituto de Investigación Sanitaria La Paz (IdiPAZ), Madrid, Spain.
| | - Ana Virseda-Berdices
- Unidad de Infección Viral e Inmunidad, Centro Nacional de Microbiología (CNM), Instituto de Salud Carlos III (ISCIII), Majadahonda, Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid. Spain.
| | - Luis Ibañez-Samaniego
- Servicio de Aparato Digestivo, Hospital General Universitario "Gregorio Marañón", Madrid, Spain.
| | - Elba Llop-Herrera
- Departamento de Gastroenterología; Hospital Universitario Puerta de Hierro-Majadahonda; Majadahonda, Madrid; Spain.
| | - Antonio Olveira
- Servicio de Aparato Digestivo, Hospital Universitario La Paz, Madrid, Spain.
| | - Leire Pérez-Latorre
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid. Spain; Unidad de Enfermedades Infecciosas/VIH; Hospital General Universitario "Gregorio Marañón", Madrid, Spain; Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain.
| | - Coral Barbas
- Centre of Metabolomics and Bioanalysis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28060 Boadilla del Monte, Spain.
| | - Amanda Fernández-Rodríguez
- Unidad de Infección Viral e Inmunidad, Centro Nacional de Microbiología (CNM), Instituto de Salud Carlos III (ISCIII), Majadahonda, Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid. Spain.
| | - Salvador Resino
- Unidad de Infección Viral e Inmunidad, Centro Nacional de Microbiología (CNM), Instituto de Salud Carlos III (ISCIII), Majadahonda, Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid. Spain.
| | - María Angeles Jiménez-Sousa
- Unidad de Infección Viral e Inmunidad, Centro Nacional de Microbiología (CNM), Instituto de Salud Carlos III (ISCIII), Majadahonda, Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid. Spain.
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7
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Wang Z, Haslam DE, Sawicki CM, Rivas-Tumanyan S, Hu FB, Liang L, Wong DTW, Joshipura KJ, Bhupathiraju SN. Saliva, Plasma, and Multifluid Metabolomic Signatures of Periodontal Disease, Type 2 Diabetes Progression, and Markers of Glycemia and Dyslipidemia Among Puerto Rican Adults With Overweight and Obesity. J Am Heart Assoc 2024; 13:e033350. [PMID: 39023061 DOI: 10.1161/jaha.123.033350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 05/23/2024] [Indexed: 07/20/2024]
Abstract
BACKGROUND Evidence from cohort studies indicates a bidirectional relationship between periodontal disease and type 2 diabetes (T2D), but the underlying mechanisms remain unknown. In this study, we aimed to (1) identify saliva, plasma, and multifluid metabolomic signatures associated with periodontal disease and (2) determine if these signatures predict T2D progression and cardiometabolic biomarkers at year 3. METHODS AND RESULTS We included participants from the SOALS (San Juan Overweight Adult Longitudinal Study) (n=911). Metabolites from saliva (k=635) and plasma (k=1051) were quantified using liquid chromatography-mass spectrometry. We applied elastic net regression with 10-fold cross-validation to identify baseline metabolomic signatures of periodontal disease. Multivariable Cox proportional hazards regression and linear regression were used to evaluate the association with T2D progression and biomarker concentrations. Metabolomic profiles included highly weighted metabolites related to lysine and pyrimidine metabolism. Periodontal disease or its 3 metabolomic signatures were not associated with T2D progression in 3 years. Prospectively, 1-SD increments in the multifluid and saliva metabolomic signatures were associated with higher low-density lipoprotein (multifluid: 12.9±5.70, P=0.02; saliva: 13.3±5.11, P=0.009). A 1-SD increment in the plasma metabolomic signature was also associated with Homeostatic Model Assessment for Insulin Resistance (2.67±1.14, P=0.02) and triglyceride (0.52±0.18, P=0.002). CONCLUSIONS Although metabolomic signatures of periodontal disease could not predict T2D progression, they were associated with low-density lipoprotein, triglyceride, and Homeostatic Model Assessment for Insulin Resistance levels at year 3.
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Affiliation(s)
- Zicheng Wang
- Department of Epidemiology Harvard T.H. Chan School of Public Health Boston MA USA
| | - Danielle E Haslam
- Department of Nutrition Harvard T.H. Chan School of Public Health Boston MA USA
- Channing Division of Network Medicine Brigham and Women's Hospital and Harvard Medical School Boston MA USA
| | - Caleigh M Sawicki
- Department of Epidemiology Harvard T.H. Chan School of Public Health Boston MA USA
- Channing Division of Network Medicine Brigham and Women's Hospital and Harvard Medical School Boston MA USA
| | | | - Frank B Hu
- Department of Epidemiology Harvard T.H. Chan School of Public Health Boston MA USA
- Department of Nutrition Harvard T.H. Chan School of Public Health Boston MA USA
| | - Liming Liang
- Department of Epidemiology Harvard T.H. Chan School of Public Health Boston MA USA
- Department of Biostatistics Harvard T.H. Chan School of Public Health Boston MA USA
| | - David T W Wong
- School of Dentistry University of California, Los Angeles Los Angeles CA USA
| | - Kaumudi J Joshipura
- Department of Epidemiology Harvard T.H. Chan School of Public Health Boston MA USA
- Ahmedabad University School of Public Health Ahmedabad Gujarat India
| | - Shilpa N Bhupathiraju
- Department of Nutrition Harvard T.H. Chan School of Public Health Boston MA USA
- Channing Division of Network Medicine Brigham and Women's Hospital and Harvard Medical School Boston MA USA
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8
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Cao Q, Liu C, Chen L, Qin Y, Wang T, Wang C. Synergistic impacts of antibiotics and heavy metals on Hermetia illucens: Unveiling dynamics in larval gut bacterial communities and microbial metabolites. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 365:121632. [PMID: 38950506 DOI: 10.1016/j.jenvman.2024.121632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 06/16/2024] [Accepted: 06/26/2024] [Indexed: 07/03/2024]
Abstract
Hermetia illucens larvae showcases remarkable bioremediation capabilities for both antibiotics and heavy metal contaminants. However, the distinctions in larval intestinal microbiota arising from the single and combined effects of antibiotics and heavy metals remain poorly elucidated. In this study, we delved into the details of larval intestinal bacterial communities and microbial metabolites when exposed to single and combined contaminants of oxytetracycline (OTC) and hexavalent chromium (Cr(VI)). After conversion, single contaminant-spiked substrate showed 75.5% of OTC degradation and 95.2% of Cr(VI) reductiuon, while combined contaminant-spiked substrate exhibited 71.3% of OTC degradation and 93.4% of Cr(VI) reductiuon. Single and combined effects led to differences in intestinal bacterial communities, mainly reflected in the genera of Enterococcus, Pseudogracilibacillus, Gracilibacillus, Wohlfahrtiimonas, Sporosarcina, Lysinibacillus, and Myroide. Moreover, these effects also induced differences across various categories of microbial metabolites, which categorized into amino acid and its metabolites, benzene and substituted derivatives, carbohydrates and its metabolites, heterocyclic compounds, hormones and hormone-related compounds, nucleotide and its metabolites, and organic acid and its derivatives. In particular, the differences induced OTC was greater than that of Cr(VI), and combined effects increased the complexity of microbial metabolism compared to that of single contaminant. Correlation analysis indicated that the bacterial genera, Preudogracilibacillus, Enterococcus, Sporosarcina, Lysinibacillus, Wohlfahrtiimonas, Ignatzschineria, and Fusobacterium exhibited significant correlation with significant differential metabolites, these might be used as indicators for the resistance and bioremediation of OTC and Cr(VI) contaminants. These findings are conducive to further understanding that the metabolism of intestinal microbiota determines the resistance of Hermetia illucens to antibiotics and heavy metals.
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Affiliation(s)
- Qingcheng Cao
- Key Laboratory of Green Chemical Process of Ministry of Education, Key Laboratory of Novel Reactor and Green Chemical Technology of Hubei Province, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan, 430205, China
| | - Cuncheng Liu
- Key Laboratory of Green Chemical Process of Ministry of Education, Key Laboratory of Novel Reactor and Green Chemical Technology of Hubei Province, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan, 430205, China; Research Center for Environmental Ecology and Engineering, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan, 430205, China.
| | - Li Chen
- Key Laboratory of Green Chemical Process of Ministry of Education, Key Laboratory of Novel Reactor and Green Chemical Technology of Hubei Province, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan, 430205, China
| | - Yuanhang Qin
- Key Laboratory of Green Chemical Process of Ministry of Education, Key Laboratory of Novel Reactor and Green Chemical Technology of Hubei Province, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan, 430205, China
| | - Tielin Wang
- Key Laboratory of Green Chemical Process of Ministry of Education, Key Laboratory of Novel Reactor and Green Chemical Technology of Hubei Province, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan, 430205, China
| | - Cunwen Wang
- Key Laboratory of Green Chemical Process of Ministry of Education, Key Laboratory of Novel Reactor and Green Chemical Technology of Hubei Province, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan, 430205, China.
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9
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Al Hariri M, Al-Sulaiti H, Anwardeen N, Naja K, A Elrayess M. Comparing the metabolic signatures of obesity defined by waist circumference, waist-hip ratio, or BMI. Obesity (Silver Spring) 2024; 32:1494-1507. [PMID: 38967317 DOI: 10.1002/oby.24070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Revised: 04/04/2024] [Accepted: 04/18/2024] [Indexed: 07/06/2024]
Abstract
OBJECTIVE Measuring obesity is crucial for assessing health risks and developing effective prevention and treatment strategies. The most common methods used to measure obesity include BMI, waist circumference, and waist-hip ratio. This study aimed to determine the metabolic signatures associated with each measure of obesity in the Qatari population. METHODS Metabolomics profiling was conducted to identify, quantify, and characterize metabolites in serum samples from the study participants. Inverse rank normalization, principal component analysis, and orthogonal partial least square-discriminant analysis were used to analyze the metabolomics data. RESULTS This study revealed significant differences in metabolites associated with obesity based on different measurements. In men, phosphatidylcholine and phosphatidylethanolamine metabolites were significantly enriched in individuals classified as having obesity based on the waist-hip ratio. In women, significant changes were observed in leucine, isoleucine, and valine metabolism metabolites. Unique metabolites were found in the different categorization groups that could serve as biomarkers for assessing many obesity-related disorders. CONCLUSIONS This study identified unique metabolic signatures associated with obesity based on different measurements in the Qatari population. These findings contribute to a better understanding of the molecular pathways involved in obesity and may have implications for developing personalized prevention and treatment strategies.
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Affiliation(s)
| | - Haya Al-Sulaiti
- Department of Biomedical Sciences, College of Health Sciences, QU Health Sector, Qatar University, Doha, Qatar
- Biomedical Research Center, Qatar University, Doha, Qatar
| | | | - Khaled Naja
- Biomedical Research Center, Qatar University, Doha, Qatar
| | - Mohamed A Elrayess
- College of Medicine, QU Health Sector, Qatar University, Doha, Qatar
- Biomedical Research Center, Qatar University, Doha, Qatar
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10
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Yu T, Wu B, Zhang D, Deng G, Luo Y, Tang N, Shi Q, Hu F, Zhang G. A novel Bacillus aerolatus CX253 attenuates inflammation induced by Streptococcus pneumoniae in childhood and pregnant rats by regulating gut microbiome. Cell Mol Life Sci 2024; 81:319. [PMID: 39078497 PMCID: PMC11335247 DOI: 10.1007/s00018-024-05232-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 01/20/2024] [Accepted: 04/05/2024] [Indexed: 07/31/2024]
Abstract
Streptococcus pneumoniae (Spn) is the predominant pathogen responsible for community-acquired pneumonia (CAP) in children under five years old, and it can induce over 17% of pregnant women. However, no more effective measures exist to prevent infection induced by Spn in these two special populations. The beneficial microbes can antagonize Spn and provide new targets for preventing pneumococcal infections. This study used 16S rRNA gene sequencing and targeted metabolomics to evaluate the role of the Bacillus aerolatus CX253 (CX253) in alleviating Spn infection. Additionally, the colonization of CX253 was observed in nose, trachea, and lung by using confocal laser scanning microscopy and fluorescent labeling techniques. Compared with the model group, the expression level of interleukin-1β was dropped 1.81-fold and 2.22-fold, and interleukin-6 was decreased 2.39-fold and 1.84-fold. The express of tumor necrosis factor-α was down 2.30-fold and 3.84-fold in prevention group of childhood and pregnant rats, respectively. The 16S rRNA sequencing results showed that CX253 administration alone significantly increased the abundance of Lactobacillus, Limosilactobacillus, and Prevotella in the gut of childhood and pregnant rats. Furthermore, the CX253 increased propionate in the gut of childhood rats and increased propionate and butyrate in the gut of pregnant rats to inhibit pulmonary inflammation. In summary, CX253 attenuated Spn-induced inflammation by regulating the gut microbiota and SCFAs. The research provides valuable information for the prevention of pneumonia.
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Affiliation(s)
- Ting Yu
- Department of Environmental Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, 510515, People's Republic of China
| | - Biru Wu
- Guangdong Provincial Key Laboratory of Construction and Detection in Tissue Engineering, Biomaterials Research Center, School of Biomedical Engineering, Southern Medical University, Guangzhou, 510515, China
| | - Dimei Zhang
- Department of Environmental Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, 510515, People's Republic of China
| | - Guanhua Deng
- Key Laboratory of Occupational Environment and Health, Guangzhou Twelfth People's Hospital, 1Tianqiang St., Huangpu West Ave, Guangzhou, 510620, Guangdong, China.
| | - Yi Luo
- Department of Environmental Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, 510515, People's Republic of China
| | - Ningqianzi Tang
- Department of Environmental Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, 510515, People's Republic of China
| | - Qiankun Shi
- Guangdong Provincial Key Laboratory of Construction and Detection in Tissue Engineering, Biomaterials Research Center, School of Biomedical Engineering, Southern Medical University, Guangzhou, 510515, China
| | - Fang Hu
- Guangdong Provincial Key Laboratory of Construction and Detection in Tissue Engineering, Biomaterials Research Center, School of Biomedical Engineering, Southern Medical University, Guangzhou, 510515, China.
| | - Guoxia Zhang
- Department of Environmental Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, 510515, People's Republic of China.
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11
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Johnson-Martínez JP, Diener C, Levine AE, Wilmanski T, Suskind DL, Ralevski A, Hadlock J, Magis AT, Hood L, Rappaport N, Gibbons SM. Aberrant bowel movement frequencies coincide with increased microbe-derived blood metabolites associated with reduced organ function. Cell Rep Med 2024; 5:101646. [PMID: 39019013 PMCID: PMC11293344 DOI: 10.1016/j.xcrm.2024.101646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 02/22/2024] [Accepted: 06/14/2024] [Indexed: 07/19/2024]
Abstract
Bowel movement frequency (BMF) directly impacts the gut microbiota and is linked to diseases like chronic kidney disease or dementia. In particular, prior work has shown that constipation is associated with an ecosystem-wide switch from fiber fermentation and short-chain fatty acid production to more detrimental protein fermentation and toxin production. Here, we analyze multi-omic data from generally healthy adults to see how BMF affects their molecular phenotypes, in a pre-disease context. Results show differential abundances of gut microbial genera, blood metabolites, and variation in lifestyle factors across BMF categories. These differences relate to inflammation, heart health, liver function, and kidney function. Causal mediation analysis indicates that the association between lower BMF and reduced kidney function is partially mediated by the microbially derived toxin 3-indoxyl sulfate (3-IS). This result, in a generally healthy context, suggests that the accumulation of microbiota-derived toxins associated with abnormal BMF precede organ damage and may be drivers of chronic, aging-related diseases.
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Affiliation(s)
- Johannes P Johnson-Martínez
- Institute for Systems Biology, Seattle, WA 98109, USA; Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
| | - Christian Diener
- Institute for Systems Biology, Seattle, WA 98109, USA; Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
| | - Anne E Levine
- Institute for Systems Biology, Seattle, WA 98109, USA; Seattle Children's Hospital, Seattle, WA 98105, USA
| | | | | | | | - Jennifer Hadlock
- Institute for Systems Biology, Seattle, WA 98109, USA; Department of Biomedical Informatics, University of Washington, Seattle, WA 98104 USA
| | | | - Leroy Hood
- Institute for Systems Biology, Seattle, WA 98109, USA; Department of Bioengineering, University of Washington, Seattle, WA 98195, USA; Phenome Health, Seattle, WA 98109, USA; Department of Immunology, University of Washington, Seattle, WA 98195, USA; Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, WA 98195, USA; Center for Phenomic Health, Buck Institute for Research on Aging, Novato, CA 94945, USA
| | - Noa Rappaport
- Institute for Systems Biology, Seattle, WA 98109, USA; Phenome Health, Seattle, WA 98109, USA; Center for Phenomic Health, Buck Institute for Research on Aging, Novato, CA 94945, USA
| | - Sean M Gibbons
- Institute for Systems Biology, Seattle, WA 98109, USA; Department of Bioengineering, University of Washington, Seattle, WA 98195, USA; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; eScience Institute, University of Washington, Seattle, WA 98195, USA.
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12
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Sun P, Guo X, Ding E, Li C, Ren H, Xu Y, Qian J, Deng F, Shi W, Dong H, Lin EZ, Guo P, Fang J, Zhang Q, Zhao W, Tong S, Lu X, Pollitt KJG, Shi X, Tang S. Association between Personal Abiotic Airborne Exposures and Body Composition Changes among Healthy Adults (60-69 Years Old): A Combined Exposome-Wide and Lipidome Mediation Approach from the China BAPE Study. ENVIRONMENTAL HEALTH PERSPECTIVES 2024; 132:77005. [PMID: 39028628 PMCID: PMC11259245 DOI: 10.1289/ehp13865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 05/25/2024] [Accepted: 06/24/2024] [Indexed: 07/21/2024]
Abstract
BACKGROUND Evidence suggested that abiotic airborne exposures may be associated with changes in body composition. However, more evidence is needed to identify key pollutants linked to adverse health effects and their underlying biomolecular mechanisms, particularly in sensitive older adults. OBJECTIVES Our research aimed to systematically assess the relationship between abiotic airborne exposures and changes in body composition among healthy older adults, as well as the potential mediating mechanisms through the serum lipidome. METHODS From September 2018 to January 2019, we conducted a monthly survey among 76 healthy adults (60-69 years old) in the China Biomarkers of Air Pollutant Exposure (BAPE) study, measuring their personal exposures to 632 abiotic airborne pollutions using MicroPEM and the Fresh Air wristband, 18 body composition indicators from the InBody 770 device, and lipidomics from venous blood samples. We used an exposome-wide association study (ExWAS) and deletion/substitution/addition (DSA) model to unravel complex associations between exposure to contaminant mixtures and body composition, a Bayesian kernel machine regression (BKMR) model to assess the overall effect of key exposures on body composition, and mediation analysis to identify lipid intermediators. RESULTS The ExWAS and DSA model identified that 2,4,5-T methyl ester (2,4,5-TME), 9,10-Anthracenedione (ATQ), 4b,8-dimethyl-2-isopropylphenanthrene, and 4b,5,6,7,8,8a,9,10-octahydro-(DMIP) were associated with increased body fat mass (BFM), fat mass indicators (FMI), percent body fat (PBF), and visceral fat area (VFA) in healthy older adults [Bonferroni-Hochberg false discovery rate ( FD R BH ) < 0.05 ]. The BKMR model demonstrated a positive correlation between contaminants (anthracene, ATQ, copaene, di-epi-α -cedrene, and DMIP) with VFA. Mediation analysis revealed that phosphatidylcholine [PC, PC(16:1e/18:1), PC(16:2e/18:0)] and sphingolipid [SM, SM(d18:2/24:1)] mediated a significant portion, ranging from 12.27% to 26.03% (p-value < 0.05 ), of the observed increase in VFA. DISCUSSION Based on the evidence from multiple model results, ATQ and DMIP were statistically significantly associated with the increased VFA levels of healthy older adults, potentially regulated through lipid intermediators. These findings may have important implications for identifying potentially harmful environmental chemicals and developing targeted strategies for the control and prevention of chronic diseases in the future, particularly as the global population is rapidly aging. https://doi.org/10.1289/EHP13865.
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Affiliation(s)
- Peijie Sun
- China CDC Key Laboratory of Environment and Population Health, National Institute of Environmental Health, Chinese Center for Disease Control and Prevention, Beijing, China
- Department of Toxicology, School of Public Health, China Medical University, Shenyang, China
| | - Xiaojie Guo
- China CDC Key Laboratory of Environment and Population Health, National Institute of Environmental Health, Chinese Center for Disease Control and Prevention, Beijing, China
- Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, Guangdong, China
| | - Enmin Ding
- China CDC Key Laboratory of Environment and Population Health, National Institute of Environmental Health, Chinese Center for Disease Control and Prevention, Beijing, China
- School of Population Medicine and Public Health, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Chenfeng Li
- China CDC Key Laboratory of Environment and Population Health, National Institute of Environmental Health, Chinese Center for Disease Control and Prevention, Beijing, China
- Department of Occupational Health and Environment Health, School of Public Health, Anhui Medical University, Hefei, Anhui, China
| | - Huimin Ren
- China CDC Key Laboratory of Environment and Population Health, National Institute of Environmental Health, Chinese Center for Disease Control and Prevention, Beijing, China
- Department of Toxicology, School of Public Health, China Medical University, Shenyang, China
| | - Yibo Xu
- China CDC Key Laboratory of Environment and Population Health, National Institute of Environmental Health, Chinese Center for Disease Control and Prevention, Beijing, China
- Department of Epidemiology, School of Public Health, China Medical University, Shenyang, China
| | - Jiankun Qian
- China CDC Key Laboratory of Environment and Population Health, National Institute of Environmental Health, Chinese Center for Disease Control and Prevention, Beijing, China
- Department of Toxicology, School of Public Health, China Medical University, Shenyang, China
| | - Fuchang Deng
- China CDC Key Laboratory of Environment and Population Health, National Institute of Environmental Health, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Wanying Shi
- Department of Epidemiology and Health Statistics, School of Public Health, Capital Medical University, and Beijing Municipal Key Laboratory of Clinical Epidemiology, Beijing, China
| | - Haoran Dong
- China CDC Key Laboratory of Environment and Population Health, National Institute of Environmental Health, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Elizabeth Z. Lin
- Department of Environmental Health Sciences, Yale School of Public Health, New Haven, Connecticut, USA
| | - Pengfei Guo
- Department of Environmental Health Sciences, Yale School of Public Health, New Haven, Connecticut, USA
| | - Jianlong Fang
- China CDC Key Laboratory of Environment and Population Health, National Institute of Environmental Health, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Qian Zhang
- Chinese Center for Disease Control and Prevention, National Institute for Nutrition and Health, Beijing, China
| | - Wenhua Zhao
- Chinese Center for Disease Control and Prevention, National Institute for Nutrition and Health, Beijing, China
| | - Shilu Tong
- China CDC Key Laboratory of Environment and Population Health, National Institute of Environmental Health, Chinese Center for Disease Control and Prevention, Beijing, China
- School of Public Health and Social Work, Queensland University of Technology, Brisbane, Australia
| | - Xiaobo Lu
- Department of Toxicology, School of Public Health, China Medical University, Shenyang, China
| | - Krystal J. Godri Pollitt
- Department of Environmental Health Sciences, Yale School of Public Health, New Haven, Connecticut, USA
| | - Xiaoming Shi
- China CDC Key Laboratory of Environment and Population Health, National Institute of Environmental Health, Chinese Center for Disease Control and Prevention, Beijing, China
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute of Environmental Health, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Song Tang
- China CDC Key Laboratory of Environment and Population Health, National Institute of Environmental Health, Chinese Center for Disease Control and Prevention, Beijing, China
- Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China
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13
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Zheng Y, Liu Y, Yang J, Dong L, Zhang R, Tian S, Yu Y, Ren L, Hou W, Zhu F, Mai Y, Han J, Zhang L, Jiang H, Lin L, Lou J, Li R, Lin J, Liu H, Kong Z, Wang D, Dai F, Bao D, Cao Z, Chen Q, Chen Q, Chen X, Gao Y, Jiang H, Li B, Li B, Li J, Liu R, Qing T, Shang E, Shang J, Sun S, Wang H, Wang X, Zhang N, Zhang P, Zhang R, Zhu S, Scherer A, Wang J, Wang J, Huo Y, Liu G, Cao C, Shao L, Xu J, Hong H, Xiao W, Liang X, Lu D, Jin L, Tong W, Ding C, Li J, Fang X, Shi L. Multi-omics data integration using ratio-based quantitative profiling with Quartet reference materials. Nat Biotechnol 2024; 42:1133-1149. [PMID: 37679543 PMCID: PMC11252085 DOI: 10.1038/s41587-023-01934-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 07/31/2023] [Indexed: 09/09/2023]
Abstract
Characterization and integration of the genome, epigenome, transcriptome, proteome and metabolome of different datasets is difficult owing to a lack of ground truth. Here we develop and characterize suites of publicly available multi-omics reference materials of matched DNA, RNA, protein and metabolites derived from immortalized cell lines from a family quartet of parents and monozygotic twin daughters. These references provide built-in truth defined by relationships among the family members and the information flow from DNA to RNA to protein. We demonstrate how using a ratio-based profiling approach that scales the absolute feature values of a study sample relative to those of a concurrently measured common reference sample produces reproducible and comparable data suitable for integration across batches, labs, platforms and omics types. Our study identifies reference-free 'absolute' feature quantification as the root cause of irreproducibility in multi-omics measurement and data integration and establishes the advantages of ratio-based multi-omics profiling with common reference materials.
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Affiliation(s)
- Yuanting Zheng
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China.
| | - Yaqing Liu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Jingcheng Yang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China
- Greater Bay Area Institute of Precision Medicine, Guangzhou, China
| | | | - Rui Zhang
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital, Beijing, China
| | - Sha Tian
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Ying Yu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Luyao Ren
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Wanwan Hou
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Feng Zhu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Yuanbang Mai
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China
| | | | | | | | - Ling Lin
- Zhangjiang Center for Translational Medicine, Shanghai Biotecan Medical Diagnostics Co. Ltd., Shanghai, China
| | - Jingwei Lou
- Zhangjiang Center for Translational Medicine, Shanghai Biotecan Medical Diagnostics Co. Ltd., Shanghai, China
| | - Ruiqiang Li
- Novogene Bioinformatics Institute, Beijing, China
| | - Jingchao Lin
- Metabo-Profile Biotechnology (Shanghai) Co. Ltd., Shanghai, China
| | | | | | - Depeng Wang
- Nextomics Biosciences Institute, Wuhan, China
| | | | - Ding Bao
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Zehui Cao
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Qiaochu Chen
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Qingwang Chen
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Xingdong Chen
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Yuechen Gao
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - He Jiang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Bin Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Bingying Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Jingjing Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China
- Nextomics Biosciences Institute, Wuhan, China
| | - Ruimei Liu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Tao Qing
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Erfei Shang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Jun Shang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Shanyue Sun
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Haiyan Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Xiaolin Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Naixin Zhang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Peipei Zhang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Ruolan Zhang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Sibo Zhu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Andreas Scherer
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- EATRIS ERIC-European Infrastructure for Translational Medicine, Amsterdam, the Netherlands
| | - Jiucun Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Jing Wang
- National Institute of Metrology, Beijing, China
| | - Yinbo Huo
- Key Laboratory of Bioanalysis and Metrology for State Market Regulation, Shanghai Institute of Measurement and Testing Technology, Shanghai, China
| | - Gang Liu
- Key Laboratory of Bioanalysis and Metrology for State Market Regulation, Shanghai Institute of Measurement and Testing Technology, Shanghai, China
| | - Chengming Cao
- Key Laboratory of Bioanalysis and Metrology for State Market Regulation, Shanghai Institute of Measurement and Testing Technology, Shanghai, China
| | - Li Shao
- Key Laboratory of Bioanalysis and Metrology for State Market Regulation, Shanghai Institute of Measurement and Testing Technology, Shanghai, China
| | - Joshua Xu
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, USA
| | - Huixiao Hong
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, USA
| | - Wenming Xiao
- Office of Oncologic Diseases, Office of New Drugs, Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, USA
| | - Xiaozhen Liang
- Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China
| | - Daru Lu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Li Jin
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Weida Tong
- Key Laboratory of Bioanalysis and Metrology for State Market Regulation, Shanghai Institute of Measurement and Testing Technology, Shanghai, China
| | - Chen Ding
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China.
| | - Jinming Li
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital, Beijing, China.
| | - Xiang Fang
- National Institute of Metrology, Beijing, China.
| | - Leming Shi
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China.
- International Human Phenome Institutes (Shanghai), Shanghai, China.
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14
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Zhu D, Wang X, Xi Z, Chen K, Feng Y, Zi C, Pan Z, Ma X, Zeng X, Feng H, Guo D. Diet influences knee osteoarthritis osteophyte formation via gut microbiota and serum metabolites. iScience 2024; 27:110111. [PMID: 38957790 PMCID: PMC11217616 DOI: 10.1016/j.isci.2024.110111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 04/24/2024] [Accepted: 05/23/2024] [Indexed: 07/04/2024] Open
Abstract
Osteophyte formation, a key indicator of osteoarthritis (OA) severity, remains poorly understood in its relation to gut microbiota and metabolites in knee osteoarthritis (KOA). We conducted 16S rDNA sequencing and untargeted metabolomics on fecal and serum samples from 20 healthy volunteers, 80 KOA patients in Guangdong, and 100 in Inner Mongolia, respectively. Through bioinformatics analysis, we identified 3 genera and 5 serum metabolites associated with KOA osteophyte formation. Blautia abundance negatively correlated with meat, cheese, and bean consumption. The 5 serum metabolites negatively correlated with dairy, beef, cheese, sugar, and salt intake, yet positively with age and oil consumption. Higher Blautia levels in the gut may contribute to KOA osteophyte formation, with serum metabolites LTB4 and PGD2 potentially serving as biomarkers. KOA patients in Inner Mongolia exhibited lower Blautia levels and reduced expression of 5 serum metabolites, possibly due to cheese consumption habits, resulting in less osteophyte formation.
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Affiliation(s)
- Dandan Zhu
- Guangdong Center for Clinical Laboratory, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong 510080, China
| | - Xiaochao Wang
- The Second Clinical Medical College of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510405, China
| | - Zhihui Xi
- School of Medicine, South China University of Technology, Guangzhou, Guangdong 510006, China
- Department of Gastrointestinal Surgery, Department of General Surgery, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong 510080, China
| | - Kunling Chen
- Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Yatian Feng
- Rehabilitation department, The Second People’s Hospital of Baiyun District, Guangzhou, Guangdong 510450, China
| | - Chunjian Zi
- The Second Clinical Medical College of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510405, China
| | - Zhijian Pan
- The Second Clinical Medical College of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510405, China
| | - Xinyu Ma
- The Second Clinical Medical College of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510405, China
| | - Xiaolong Zeng
- Department of Orthopaedic Surgery, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510120, China
| | - Huolun Feng
- School of Medicine, South China University of Technology, Guangzhou, Guangdong 510006, China
- Department of Gastrointestinal Surgery, Department of General Surgery, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong 510080, China
| | - Da Guo
- Department of Orthopaedic Surgery, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, Guangdong 510120, China
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15
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Park Y, Ahn JB, Kim DH, Park IS, Son M, Kim JH, Ma HW, Kim SW, Cheon JH. Integrated Analysis of Microbiome and Metabolome Reveals Disease-Specific Profiles in Inflammatory Bowel Diseases and Intestinal Behçet's Disease. Int J Mol Sci 2024; 25:6697. [PMID: 38928402 PMCID: PMC11203907 DOI: 10.3390/ijms25126697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Revised: 06/09/2024] [Accepted: 06/14/2024] [Indexed: 06/28/2024] Open
Abstract
The gut microbial and metabolic characteristics of intestinal Behçet's disease (BD), a condition sharing many clinical similarities with ulcerative colitis (UC) and Crohn's disease (CD), are largely unexplored. This study investigated the gut microbial and metabolic characteristics of intestinal BD as well as potential biomarkers, comparing them with those in UC, CD, and healthy controls. Colon tissue and stool samples from 100 patients (35 UC, 30 CD, and 35 intestinal BD) and 41 healthy volunteers were analyzed using 16S ribosomal RNA sequencing to assess microbial diversity, taxonomic composition, and functional profiling. Plasma metabolomic analyses were performed using gas chromatography and ultra-performance liquid chromatography-mass spectrometry. Results indicated reduced microbial diversity in CD but not in intestinal BD, with intestinal BD showing fewer changes compared to controls yet distinct taxonomic features from UC, CD, and controls. Common alterations across all diseases included a reduction in beneficial bacteria producing short-chain fatty acids. Intestinal BD-specific changes featured a decreased abundance of Bacteroides fragilis. Metabolomic profiles in intestinal BD were similar to those in CD but distinct from those in UC, displaying significant changes in energy metabolism and genetic information processing. This integrative analysis revealed both shared and unique profiles in intestinal BD compared with UC, CD, and controls, advancing our understanding of the distinctive features of these diseases.
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Affiliation(s)
- Yehyun Park
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul 03722, Republic of Korea; (Y.P.); (J.B.A.); (D.H.K.)
- Department of Internal Medicine, Ewha Womans University Seoul Hospital, Seoul 03760, Republic of Korea
| | - Jae Bum Ahn
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul 03722, Republic of Korea; (Y.P.); (J.B.A.); (D.H.K.)
| | - Da Hye Kim
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul 03722, Republic of Korea; (Y.P.); (J.B.A.); (D.H.K.)
| | - I Seul Park
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul 03722, Republic of Korea; (Y.P.); (J.B.A.); (D.H.K.)
- Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Mijeong Son
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul 03722, Republic of Korea; (Y.P.); (J.B.A.); (D.H.K.)
- Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Ji Hyung Kim
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul 03722, Republic of Korea; (Y.P.); (J.B.A.); (D.H.K.)
- Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Hyun Woo Ma
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul 03722, Republic of Korea; (Y.P.); (J.B.A.); (D.H.K.)
- Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Seung Won Kim
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul 03722, Republic of Korea; (Y.P.); (J.B.A.); (D.H.K.)
- Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Jae Hee Cheon
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul 03722, Republic of Korea; (Y.P.); (J.B.A.); (D.H.K.)
- Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
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16
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Rashidi A, Ebadi M, Rehman TU, Elhusseini H, Kazadi D, Halaweish H, Khan MH, Hoeschen A, Cao Q, Luo X, Kabage AJ, Lopez S, Ramamoorthy S, Holtan SG, Weisdorf DJ, Khoruts A, Staley C. Multi-omics Analysis of a Fecal Microbiota Transplantation Trial Identifies Novel Aspects of Acute GVHD Pathogenesis. CANCER RESEARCH COMMUNICATIONS 2024; 4:1454-1466. [PMID: 38767452 PMCID: PMC11164016 DOI: 10.1158/2767-9764.crc-24-0138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 04/23/2024] [Accepted: 05/15/2024] [Indexed: 05/22/2024]
Abstract
Acute GVHD (aGVHD) is a major complication of allogeneic hematopoietic cell transplantation (alloHCT) associated with gut microbiota disruptions. However, whether therapeutic microbiota modulation prevents aGVHD is unknown. We conducted a randomized, placebo-controlled trial of third-party fecal microbiota transplantation (FMT) administered at the peak of microbiota injury in 100 patients with acute myeloid leukemia receiving induction chemotherapy and alloHCT recipients. Despite improvements in microbiome diversity, expansion of commensals, and shrinkage of potential pathogens, aGVHD occurred more frequently after FMT than placebo. Although this unexpected finding could be explained by clinical differences between the two arms, we asked whether a microbiota explanation might be also present. To this end, we performed multi-omics analysis of preintervention and postintervention gut microbiome and serum metabolome. We found that postintervention expansion of Faecalibacterium, a commensal genus with gut-protective and anti-inflammatory properties under homeostatic conditions, predicted a higher risk for aGVHD. Faecalibacterium expansion occurred predominantly after FMT and was due to engraftment of unique donor taxa, suggesting that donor Faecalibacterium-derived antigens might have stimulated allogeneic immune cells. Faecalibacterium and ursodeoxycholic acid (an anti-inflammatory secondary bile acid) were negatively correlated, offering an alternative mechanistic explanation. In conclusion, we demonstrate context dependence of microbiota effects where a normally beneficial bacteria may become detrimental in disease. While FMT is a broad, community-level intervention, it may need precision engineering in ecologically complex settings where multiple perturbations (e.g., antibiotics, intestinal damage, alloimmunity) are concurrently in effect. SIGNIFICANCE Post-FMT expansion of Faecalibacterium, associated with donor microbiota engraftment, predicted a higher risk for aGVHD in alloHCT recipients. Although Faecalibacterium is a commensal genus with gut-protective and anti-inflammatory properties under homeostatic conditions, our findings suggest that it may become pathogenic in the setting of FMT after alloHCT. Our results support a future trial with precision engineering of the FMT product used as GVHD prophylaxis after alloHCT.
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Affiliation(s)
- Armin Rashidi
- Clinical Research Division, Fred Hutchinson Cancer Center; and Division of Oncology, University of Washington, Seattle, Washington
- Division of Hematology, Oncology, and Transplantation, Department of Medicine, University of Minnesota, Minneapolis, Minnesota
| | - Maryam Ebadi
- Department of Radiation Oncology, University of Washington and Fred Hutchinson Cancer Center, Seattle, Washington
| | - Tauseef U. Rehman
- Division of Hematology, Oncology, and Transplantation, Department of Medicine, University of Minnesota, Minneapolis, Minnesota
| | - Heba Elhusseini
- Division of Hematology, Oncology, and Transplantation, Department of Medicine, University of Minnesota, Minneapolis, Minnesota
| | - David Kazadi
- Department of Medicine, University of Minnesota, Minneapolis, Minnesota
| | - Hossam Halaweish
- Department of Surgery, University of Minnesota, Minneapolis, Minnesota
| | - Mohammad H. Khan
- Department of Surgery, University of Minnesota, Minneapolis, Minnesota
| | - Andrea Hoeschen
- Division of Hematology, Oncology, and Transplantation, Department of Medicine, University of Minnesota, Minneapolis, Minnesota
| | - Qing Cao
- Biostatistics Core, Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota
| | - Xianghua Luo
- Biostatistics Core, Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota
- Division of Biostatistics and Health Data Science, School of Public Health, University of Minnesota, Minneapolis, Minnesota
| | - Amanda J. Kabage
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, University of Minnesota, Minneapolis, Minnesota
| | - Sharon Lopez
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, University of Minnesota, Minneapolis, Minnesota
| | | | - Shernan G. Holtan
- Division of Hematology, Oncology, and Transplantation, Department of Medicine, University of Minnesota, Minneapolis, Minnesota
| | - Daniel J. Weisdorf
- Division of Hematology, Oncology, and Transplantation, Department of Medicine, University of Minnesota, Minneapolis, Minnesota
| | - Alexander Khoruts
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, University of Minnesota, Minneapolis, Minnesota
- Biotechnology Institute, University of Minnesota, St. Paul, Minnesota
- Center for Immunology, University of Minnesota, Minneapolis, Minnesota
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17
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Wang P, Sun J, Zhao W, Wang D, Ma Y, Zhao Y, Wang Y, Zhao X. Tomato Pectin Ameliorated Hepatic Steatosis in High-Fat-Diet Mice by Modulating Gut Microbiota and Bile Acid Metabolism. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024. [PMID: 38856079 DOI: 10.1021/acs.jafc.4c01598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Nonalcoholic fatty liver disease (NAFLD) is a worldwide public health issue. Changes in the gut microbiota structure and composition are closely related to host pathophysiology processes. Pectin is associated with several beneficial health effects. In the present study, we aimed at investigating the effect of tomato pectin (TP) on hepatic steatosis and exploring the underlying mechanisms by focusing on the regulation of the gut microbiota-bile acid axis. Our results showed that TP attenuated high-fat diet (HFD)-induced liver steatosis and inflammation. TP administration increased the diversity of gut microbiota, enhancing the abundance of beneficial bacteria and suppressing the abundance of harmful or conditional pathogenic bacteria. Further antibiotic-caused microbiome depletion confirmed that the anti-NAFLD activities of TP were dependent on the regulation of gut microbiota. Besides, TP intervention affected feces bile acid metabolism and caused significant changes in functional conjugated bile acids, which in turn inhibited the ileum FXR/FGF15 signaling, leading to stimulation of the hepatic bile acid (BA) production. Furthermore, TP treatment accelerated BA excretion, promoted BA transportation, inhibited BA reabsorption, and facilitated cholesterol efflux to relieve HFD-induced hyperlipidemia. These findings provide a potential dietary intervention strategy for TP against NAFLD via modulation of cross-talk between BAs and gut bacteria.
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Affiliation(s)
- Pan Wang
- Institute of Agri-food Processing and Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing Key Laboratory of Agricultural Products of Fruits and Vegetables Preservation and Processing, Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture and Rural Affairs, Beijing 100097, China
| | - Jing Sun
- Institute of Agri-food Processing and Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing Key Laboratory of Agricultural Products of Fruits and Vegetables Preservation and Processing, Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture and Rural Affairs, Beijing 100097, China
- College of Food Science, Shenyang Agricultural University, Shenyang, Liaoning 110866, China
| | - Wenting Zhao
- Institute of Agri-food Processing and Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing Key Laboratory of Agricultural Products of Fruits and Vegetables Preservation and Processing, Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture and Rural Affairs, Beijing 100097, China
| | - Dan Wang
- Institute of Agri-food Processing and Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing Key Laboratory of Agricultural Products of Fruits and Vegetables Preservation and Processing, Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture and Rural Affairs, Beijing 100097, China
| | - Yue Ma
- Institute of Agri-food Processing and Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing Key Laboratory of Agricultural Products of Fruits and Vegetables Preservation and Processing, Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture and Rural Affairs, Beijing 100097, China
| | - Yuanyuan Zhao
- Institute of Agri-food Processing and Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing Key Laboratory of Agricultural Products of Fruits and Vegetables Preservation and Processing, Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture and Rural Affairs, Beijing 100097, China
| | - Yubin Wang
- Institute of Agri-food Processing and Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing Key Laboratory of Agricultural Products of Fruits and Vegetables Preservation and Processing, Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture and Rural Affairs, Beijing 100097, China
| | - Xiaoyan Zhao
- Institute of Agri-food Processing and Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing Key Laboratory of Agricultural Products of Fruits and Vegetables Preservation and Processing, Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture and Rural Affairs, Beijing 100097, China
- College of Food Science, Shenyang Agricultural University, Shenyang, Liaoning 110866, China
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18
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Lovrić M, Wang T, Staffe MR, Šunić I, Časni K, Lasky-Su J, Chawes B, Rasmussen MA. A Chemical Structure and Machine Learning Approach to Assess the Potential Bioactivity of Endogenous Metabolites and Their Association with Early Childhood Systemic Inflammation. Metabolites 2024; 14:278. [PMID: 38786755 PMCID: PMC11122766 DOI: 10.3390/metabo14050278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2024] [Revised: 04/29/2024] [Accepted: 05/08/2024] [Indexed: 05/25/2024] Open
Abstract
Metabolomics has gained much attention due to its potential to reveal molecular disease mechanisms and present viable biomarkers. This work uses a panel of untargeted serum metabolomes from 602 children from the COPSAC2010 mother-child cohort. The annotated part of the metabolome consists of 517 chemical compounds curated using automated procedures. We created a filtering method for the quantified metabolites using predicted quantitative structure-bioactivity relationships for the Tox21 database on nuclear receptors and stress response in cell lines. The metabolites measured in the children's serums are predicted to affect specific targeted models, known for their significance in inflammation, immune function, and health outcomes. The targets from Tox21 have been used as targets with quantitative structure-activity relationships (QSARs). They were trained for ~7000 structures, saved as models, and then applied to the annotated metabolites to predict their potential bioactivities. The models were selected based on strict accuracy criteria surpassing random effects. After application, 52 metabolites showed potential bioactivity based on structural similarity with known active compounds from the Tox21 set. The filtered compounds were subsequently used and weighted by their bioactive potential to show an association with early childhood hs-CRP levels at six months in a linear model supporting a physiological adverse effect on systemic low-grade inflammation.
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Affiliation(s)
- Mario Lovrić
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, 2820 Gentofte, Denmark
- Centre for Applied Bioanthropology, Institute for Anthropological Research, 10000 Zagreb, Croatia;
- The Lisbon Council, 1040 Brussels, Belgium
| | - Tingting Wang
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, 2820 Gentofte, Denmark
| | - Mads Rønnow Staffe
- Department of Food Science, University of Copenhagen, 1958 Frederiksberg, Denmark
| | - Iva Šunić
- Centre for Applied Bioanthropology, Institute for Anthropological Research, 10000 Zagreb, Croatia;
| | | | - Jessica Lasky-Su
- Department of Medicine, Boston, MA 02115, USA
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Bo Chawes
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, 2820 Gentofte, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2300 Copenhagen, Denmark
| | - Morten Arendt Rasmussen
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, 2820 Gentofte, Denmark
- Department of Food Science, University of Copenhagen, 1958 Frederiksberg, Denmark
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19
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Luo K, Taryn A, Moon EH, Peters BA, Solomon SD, Daviglus ML, Kansal MM, Thyagarajan B, Gellman MD, Cai J, Burk RD, Knight R, Kaplan RC, Cheng S, Rodriguez CJ, Qi Q, Yu B. Gut microbiota, blood metabolites, and left ventricular diastolic dysfunction in US Hispanics/Latinos. MICROBIOME 2024; 12:85. [PMID: 38725043 PMCID: PMC11084054 DOI: 10.1186/s40168-024-01797-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Accepted: 03/21/2024] [Indexed: 05/12/2024]
Abstract
BACKGROUND Left ventricular diastolic dysfunction (LVDD) is an important precursor of heart failure (HF), but little is known about its relationship with gut dysbiosis and microbial-related metabolites. By leveraging the multi-omics data from the Hispanic Community Health Study/Study of Latinos (HCHS/SOL), a study with population at high burden of LVDD, we aimed to characterize gut microbiota associated with LVDD and identify metabolite signatures of gut dysbiosis and incident LVDD. RESULTS We included up to 1996 Hispanic/Latino adults (mean age: 59.4 years; 67.1% female) with comprehensive echocardiography assessments, gut microbiome, and blood metabolome data. LVDD was defined through a composite criterion involving tissue Doppler assessment and left atrial volume index measurements. Among 1996 participants, 916 (45.9%) had prevalent LVDD, and 212 out of 594 participants without LVDD at baseline developed incident LVDD over a median 4.3 years of follow-up. Using multivariable-adjusted analysis of compositions of microbiomes (ANCOM-II) method, we identified 7 out of 512 dominant gut bacterial species (prevalence > 20%) associated with prevalent LVDD (FDR-q < 0.1), with inverse associations being found for Intestinimonas_massiliensis, Clostridium_phoceensis, and Bacteroide_coprocola and positive associations for Gardnerella_vaginali, Acidaminococcus_fermentans, Pseudomonas_aeruginosa, and Necropsobacter_massiliensis. Using multivariable adjusted linear regression, 220 out of 669 circulating metabolites with detection rate > 75% were associated with the identified LVDD-related bacterial species (FDR-q < 0.1), with the majority being linked to Intestinimonas_massiliensis, Clostridium_phoceensis, and Acidaminococcus_fermentans. Furthermore, 46 of these bacteria-associated metabolites, mostly glycerophospholipids, secondary bile acids, and amino acids, were associated with prevalent LVDD (FDR-q < 0.1), 21 of which were associated with incident LVDD (relative risk ranging from 0.81 [p = 0.001, for guanidinoacetate] to 1.25 [p = 9 × 10-5, for 1-stearoyl-2-arachidonoyl-GPE (18:0/20:4)]). The inclusion of these 21 bacterial-related metabolites significantly improved the prediction of incident LVDD compared with a traditional risk factor model (the area under the receiver operating characteristic curve [AUC] = 0.73 vs 0.70, p = 0.001). Metabolite-based proxy association analyses revealed the inverse associations of Intestinimonas_massilliensis and Clostridium_phoceensis and the positive association of Acidaminococcus_fermentans with incident LVDD. CONCLUSION In this study of US Hispanics/Latinos, we identified multiple gut bacteria and related metabolites linked to LVDD, suggesting their potential roles in this preclinical HF entity. Video Abstract.
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Affiliation(s)
- Kai Luo
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Alkis Taryn
- Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Eun-Hye Moon
- Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Brandilyn A Peters
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Scott D Solomon
- Cardiovascular Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Martha L Daviglus
- Institute for Minority Health Research, University of Illinois Chicago College of Medicine, Chicago, IL, 60612, USA
| | - Mayank M Kansal
- Clinical Medicine, University of Illinois College of Medicine, Chicago, IL, 60612, USA
| | - Bharat Thyagarajan
- Department of Laboratory Medicine & Pathology, University of Minnesota Medical School, Minneapolis, MN, 55455, USA
| | - Marc D Gellman
- Department of Psychology, Clinical Research Building, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA
| | - Jianwen Cai
- Department of Biostatistics, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Robert D Burk
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
- Department of Obstetrics and Gynecology and Women's Health, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
- Department of Pediatrics, Albert Einstein College of Medicine, NY10461, Bronx, USA
| | - Rob Knight
- Center for Microbiome Innovation, University of California, La Jolla, San Diego, CA, 92093, USA
- Department of Bioengineering, University of California, La Jolla, San Diego, CA, 92093, USA
- Department of Pediatrics, University of California, La Jolla, San Diego, CA, 92093, USA
- Department of Computer Science and Engineering, University of California, La Jolla, San Diego, CA, 92093, USA
| | - Robert C Kaplan
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Susan Cheng
- Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Carlos J Rodriguez
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
- Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Qibin Qi
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, 10461, USA.
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA.
| | - Bing Yu
- Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, 77030, USA.
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20
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Predescu E, Vaidean T, Rapciuc AM, Sipos R. Metabolomic Markers in Attention-Deficit/Hyperactivity Disorder (ADHD) among Children and Adolescents-A Systematic Review. Int J Mol Sci 2024; 25:4385. [PMID: 38673970 PMCID: PMC11050195 DOI: 10.3390/ijms25084385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 04/06/2024] [Accepted: 04/11/2024] [Indexed: 04/28/2024] Open
Abstract
Attention-Deficit/Hyperactivity Disorder (ADHD), characterized by clinical diversity, poses diagnostic challenges often reliant on subjective assessments. Metabolomics presents an objective approach, seeking biomarkers for precise diagnosis and targeted interventions. This review synthesizes existing metabolomic insights into ADHD, aiming to reveal biological mechanisms and diagnostic potentials. A thorough PubMed and Web of Knowledge search identified studies exploring blood/urine metabolites in ADHD-diagnosed or psychometrically assessed children and adolescents. Synthesis revealed intricate links between ADHD and altered amino acid metabolism, neurotransmitter dysregulation (especially dopamine and serotonin), oxidative stress, and the kynurenine pathway impacting neurotransmitter homeostasis. Sleep disturbance markers, notably in melatonin metabolism, and stress-induced kynurenine pathway activation emerged. Distinct metabolic signatures, notably in the kynurenine pathway, show promise as potential diagnostic markers. Despite limitations like participant heterogeneity, this review underscores the significance of integrated therapeutic approaches targeting amino acid metabolism, neurotransmitters, and stress pathways. While guiding future research, this overview of the metabolomic findings in ADHD suggests directions for precision diagnostics and personalized ADHD interventions.
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Affiliation(s)
- Elena Predescu
- Department of Neuroscience, Psychiatry and Pediatric Psychiatry, “Iuliu Hatieganu” University of Medicine and Pharmacy, 57 Republicii Street, 400489 Cluj-Napoca, Romania;
| | - Tudor Vaidean
- Clinic of Pediatric Psychiatry and Addiction, Clinical Emergency Hospital for Children, 57 Republicii Street, 400489 Cluj-Napoca, Romania;
| | - Andreea-Marlena Rapciuc
- Clinical Department of Nephrology, County Emergency Clinical Hospital Cluj, 3-5 Clinicilor Street, 400006 Cluj-Napoca, Romania;
| | - Roxana Sipos
- Department of Neuroscience, Psychiatry and Pediatric Psychiatry, “Iuliu Hatieganu” University of Medicine and Pharmacy, 57 Republicii Street, 400489 Cluj-Napoca, Romania;
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21
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Liu X, Tu P, Zhang Y, Xu W, Shan J, Gao B. Aldicarb disturbed bile acid, steroid hormone and oxylipin homeostasis in C57BL/6 J mice. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 275:116285. [PMID: 38564866 DOI: 10.1016/j.ecoenv.2024.116285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 03/26/2024] [Accepted: 03/31/2024] [Indexed: 04/04/2024]
Abstract
Mounting evidence has shown that the gut microbiota plays a key role in human health. The homeostasis of the gut microbiota could be affected by many factors, including environmental chemicals. Aldicarb is a carbamate insecticide used to control a variety of insects and nematode pests in agriculture. Aldicarb is highly toxic and its wide existence has become a global public health concern. In our previous study, we have demonstrated that aldicarb disturbed the gut microbial community structure and composition. However, the impacts of aldicarb on gut microbiota-derived metabolites, bile acids, remain elusive. In present study, we performed targeted metabolomics analysis to explore the effects of aldicarb exposure on bile acids, as well as steroid hormones and oxylipins in the serum, feces and liver of C57BL/6 J mice. Our results showed that aldicarb exposure disturbed the level of various bile acids, steroid hormones and oxylipins in the serum and feces of C57BL/6 J mice. In the liver, the level of cortisol was decreased, meanwhile 15,16-dihydroxyoctadeca-9,12-dienoic acid was increased in aldicarb-treated mice. Metagenomic sequencing analysis showed that the relative abundance of a bile salt hydrolase, choloylglycine hydrolase (EC:3.5.1.24) and a sulfatase enzyme involved in steroid hormone metabolism, arylsulfatase, was significantly increased by aldicarb exposure. Furthermore, correlations were found between gut microbiota and various serum metabolites. The results from this study are helpful to improve the understanding of the impact of carbamate insecticides on host and microbial metabolism.
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Affiliation(s)
- Xin Liu
- Changwang School of Honors, Nanjing University of Information Science and Technology, Nanjing 210044, China.
| | - Pengcheng Tu
- Department of Environmental Health, Zhejiang Provincial Center for Disease Control and Prevention, 3399 Binsheng Road, Hangzhou 310051, China.
| | - Ying Zhang
- West Coast Metabolomics Center, University of California Davis, Davis, CA 95616, USA.
| | - Weichen Xu
- Medical Metabolomics Center, Institute of Pediatrics, Jiangsu Key Laboratory of Pediatric Respiratory Disease, Nanjing University of Chinese Medicine, Nanjing 210023, China.
| | - Jinjun Shan
- Medical Metabolomics Center, Institute of Pediatrics, Jiangsu Key Laboratory of Pediatric Respiratory Disease, Nanjing University of Chinese Medicine, Nanjing 210023, China.
| | - Bei Gao
- School of Marine Sciences, Nanjing University of Information Science and Technology, Nanjing 210044, China; Key Laboratory of Hydrometeorological Disaster Mechanism and Warning of Ministry of Water Resources, Nanjing University of Information Science and Technology, Nanjing 210044, China.
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22
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Zhou X, Shen X, Johnson JS, Spakowicz DJ, Agnello M, Zhou W, Avina M, Honkala A, Chleilat F, Chen SJ, Cha K, Leopold S, Zhu C, Chen L, Lyu L, Hornburg D, Wu S, Zhang X, Jiang C, Jiang L, Jiang L, Jian R, Brooks AW, Wang M, Contrepois K, Gao P, Rose SMSF, Tran TDB, Nguyen H, Celli A, Hong BY, Bautista EJ, Dorsett Y, Kavathas PB, Zhou Y, Sodergren E, Weinstock GM, Snyder MP. Longitudinal profiling of the microbiome at four body sites reveals core stability and individualized dynamics during health and disease. Cell Host Microbe 2024; 32:506-526.e9. [PMID: 38479397 PMCID: PMC11022754 DOI: 10.1016/j.chom.2024.02.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 01/23/2024] [Accepted: 02/20/2024] [Indexed: 03/26/2024]
Abstract
To understand the dynamic interplay between the human microbiome and host during health and disease, we analyzed the microbial composition, temporal dynamics, and associations with host multi-omics, immune, and clinical markers of microbiomes from four body sites in 86 participants over 6 years. We found that microbiome stability and individuality are body-site specific and heavily influenced by the host. The stool and oral microbiome are more stable than the skin and nasal microbiomes, possibly due to their interaction with the host and environment. We identify individual-specific and commonly shared bacterial taxa, with individualized taxa showing greater stability. Interestingly, microbiome dynamics correlate across body sites, suggesting systemic dynamics influenced by host-microbial-environment interactions. Notably, insulin-resistant individuals show altered microbial stability and associations among microbiome, molecular markers, and clinical features, suggesting their disrupted interaction in metabolic disease. Our study offers comprehensive views of multi-site microbial dynamics and their relationship with host health and disease.
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Affiliation(s)
- Xin Zhou
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford Center for Genomics and Personalized Medicine, Stanford, CA 94305, USA; Stanford Diabetes Research Center, Stanford, CA 94305, USA; The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Xiaotao Shen
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford Center for Genomics and Personalized Medicine, Stanford, CA 94305, USA
| | - Jethro S Johnson
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; Oxford Centre for Microbiome Studies, Kennedy Institute of Rheumatology, University of Oxford, Roosevelt Drive, Headington, Oxford OX3 7FY, UK
| | - Daniel J Spakowicz
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; Division of Medical Oncology, Ohio State University Wexner Medical Center, James Cancer Hospital and Solove Research Institute, Columbus, OH 43210, USA
| | | | - Wenyu Zhou
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford Center for Genomics and Personalized Medicine, Stanford, CA 94305, USA
| | - Monica Avina
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Alexander Honkala
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford Healthcare Innovation Labs, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239, USA
| | - Faye Chleilat
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Shirley Jingyi Chen
- Stanford Healthcare Innovation Labs, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Kexin Cha
- Stanford Healthcare Innovation Labs, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Shana Leopold
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Chenchen Zhu
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Lei Chen
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; Shanghai Institute of Immunology, Shanghai Jiao Tong University, Shanghai 200240, PRC
| | - Lin Lyu
- Shanghai Institute of Immunology, Shanghai Jiao Tong University, Shanghai 200240, PRC
| | - Daniel Hornburg
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Si Wu
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Xinyue Zhang
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Chao Jiang
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, PRC
| | - Liuyiqi Jiang
- Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, PRC
| | - Lihua Jiang
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ruiqi Jian
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Andrew W Brooks
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Meng Wang
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Kévin Contrepois
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Peng Gao
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | | | | | - Hoan Nguyen
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Alessandra Celli
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Bo-Young Hong
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; Woody L Hunt School of Dental Medicine, Texas Tech University Health Science Center, El Paso, TX 79905, USA
| | - Eddy J Bautista
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; Corporación Colombiana de Investigación Agropecuaria (Agrosavia), Headquarters-Mosquera, Cundinamarca 250047, Colombia
| | - Yair Dorsett
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; Department of Medicine, University of Connecticut Health Center, Farmington, CT 06032, USA
| | - Paula B Kavathas
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA; Department of Laboratory Medicine, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Yanjiao Zhou
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; Department of Medicine, University of Connecticut Health Center, Farmington, CT 06032, USA
| | - Erica Sodergren
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | | | - Michael P Snyder
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford Center for Genomics and Personalized Medicine, Stanford, CA 94305, USA; Stanford Diabetes Research Center, Stanford, CA 94305, USA; Stanford Healthcare Innovation Labs, Stanford University School of Medicine, Stanford, CA 94305, USA.
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23
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Ai Z, Liu S, Zhang J, Hu Y, Tang P, Cui L, Wang X, Zou H, Li X, Liu J, Nan B, Wang Y. Ginseng Glucosyl Oleanolate from Ginsenoside Ro, Exhibited Anti-Liver Cancer Activities via MAPKs and Gut Microbiota In Vitro/Vivo. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:7845-7860. [PMID: 38501913 DOI: 10.1021/acs.jafc.3c08150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Abstract
Ginseng is widely recognized for its diverse health benefits and serves as a functional food ingredient with global popularity. Ginsenosides with a broad range of pharmacological effects are the most crucial active ingredients in ginseng. This study aimed to derive ginseng glucosyl oleanolate (GGO) from ginsenoside Ro through enzymatic conversion and evaluate its impact on liver cancer in vitro and in vivo. GGO exhibited concentration-dependent HepG2 cell death and markedly inhibited cell proliferation via the MAPK signaling pathway. It also attenuated tumor growth in immunocompromised mice undergoing heterograft transplantation. Furthermore, GGO intervention caused a modulation of gut microbiota composition by specific bacterial populations, including Lactobacillus, Bacteroides, Clostridium, Enterococcus, etc., and ameliorated SCFA metabolism and colonic inflammation. These findings offer promising evidence for the potential use of GGO as a natural functional food ingredient in the prevention and treatment of cancer.
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Affiliation(s)
- Zhiyi Ai
- College of Food Science and Engineering, Jilin Agricultural University, Changchun 130118, China
- Jilin Province Innovation Center for Food Biological Manufacture, Jilin Agricultural University, Changchun 130118, China
| | - Sitong Liu
- College of Food Science and Engineering, Jilin Agricultural University, Changchun 130118, China
- Jilin Province Innovation Center for Food Biological Manufacture, Jilin Agricultural University, Changchun 130118, China
| | - Junshun Zhang
- College of Food Science and Engineering, Jilin Agricultural University, Changchun 130118, China
- Jilin Province Innovation Center for Food Biological Manufacture, Jilin Agricultural University, Changchun 130118, China
| | - Yue Hu
- College of Food Science and Engineering, Jilin Agricultural University, Changchun 130118, China
- Jilin Province Innovation Center for Food Biological Manufacture, Jilin Agricultural University, Changchun 130118, China
| | - Ping Tang
- College of Food Science and Engineering, Jilin Agricultural University, Changchun 130118, China
- Jilin Province Innovation Center for Food Biological Manufacture, Jilin Agricultural University, Changchun 130118, China
| | - Linlin Cui
- College of Food Science and Engineering, Jilin Agricultural University, Changchun 130118, China
- Jilin Province Innovation Center for Food Biological Manufacture, Jilin Agricultural University, Changchun 130118, China
| | - Xinzhu Wang
- College of Food Science and Engineering, Jilin Agricultural University, Changchun 130118, China
- Jilin Province Innovation Center for Food Biological Manufacture, Jilin Agricultural University, Changchun 130118, China
| | - Hongyang Zou
- College of Food Science and Engineering, Jilin Agricultural University, Changchun 130118, China
- Jilin Province Innovation Center for Food Biological Manufacture, Jilin Agricultural University, Changchun 130118, China
| | - Xia Li
- College of Food Science and Engineering, Jilin Agricultural University, Changchun 130118, China
- Jilin Province Innovation Center for Food Biological Manufacture, Jilin Agricultural University, Changchun 130118, China
| | - Jingsheng Liu
- College of Food Science and Engineering, Jilin Agricultural University, Changchun 130118, China
- Jilin Province Innovation Center for Food Biological Manufacture, Jilin Agricultural University, Changchun 130118, China
| | - Bo Nan
- College of Food Science and Engineering, Jilin Agricultural University, Changchun 130118, China
- Jilin Province Innovation Center for Food Biological Manufacture, Jilin Agricultural University, Changchun 130118, China
| | - Yuhua Wang
- College of Food Science and Engineering, Jilin Agricultural University, Changchun 130118, China
- Jilin Province Innovation Center for Food Biological Manufacture, Jilin Agricultural University, Changchun 130118, China
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24
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Tian Q, Greig EE, Walker KA, Fishbein KW, Spencer RG, Resnick SM, Ferrucci L. Plasma metabolomic markers underlying skeletal muscle mitochondrial function relationships with cognition and motor function. Age Ageing 2024; 53:afae079. [PMID: 38615247 DOI: 10.1093/ageing/afae079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Indexed: 04/15/2024] Open
Abstract
BACKGROUND Lower skeletal muscle mitochondrial function is associated with future cognitive impairment and mobility decline, but the biological underpinnings for these associations are unclear. We examined metabolomic markers underlying skeletal muscle mitochondrial function, cognition and motor function. METHODS We analysed data from 560 participants from the Baltimore Longitudinal Study of Aging (mean age: 68.4 years, 56% women, 28% Black) who had data on skeletal muscle oxidative capacity (post-exercise recovery rate of phosphocreatine, kPCr) via 31P magnetic resonance spectroscopy and targeted plasma metabolomics using LASSO model. We then examined which kPCr-related markers were also associated with cognition and motor function in a larger sample (n = 918, mean age: 69.4, 55% women, 27% Black). RESULTS The LASSO model revealed 24 metabolites significantly predicting kPCr, with the top 5 being asymmetric dimethylarginine, lactic acid, lysophosphatidylcholine a C18:1, indoleacetic acid and triacylglyceride (17:1_34:3), also significant in multivariable linear regression. The kPCr metabolite score was associated with cognitive or motor function, with 2.5-minute usual gait speed showing the strongest association (r = 0.182). Five lipids (lysophosphatidylcholine a C18:1, phosphatidylcholine ae C42:3, cholesteryl ester 18:1, sphingomyelin C26:0, octadecenoic acid) and 2 amino acids (leucine, cystine) were associated with both cognitive and motor function measures. CONCLUSION Our findings add evidence to the hypothesis that mitochondrial function is implicated in the pathogenesis of cognitive and physical decline with aging and suggest that targeting specific metabolites may prevent cognitive and mobility decline through their effects on mitochondria. Future omics studies are warranted to confirm these findings and explore mechanisms underlying mitochondrial dysfunction in aging phenotypes.
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Affiliation(s)
- Qu Tian
- Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Erin E Greig
- Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Keenan A Walker
- Laboratory of Behavioral Neuroscience, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Kenneth W Fishbein
- Laboratory of Clinical Investigation, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Richard G Spencer
- Laboratory of Clinical Investigation, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Susan M Resnick
- Laboratory of Behavioral Neuroscience, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Luigi Ferrucci
- Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, MD 21224, USA
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25
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Zhou P, Wang X, Sun M, Yan S. Effects of natural products on functional constipation: analysis of active ingredient and mechanism. NAUNYN-SCHMIEDEBERG'S ARCHIVES OF PHARMACOLOGY 2024; 397:2083-2103. [PMID: 37870581 DOI: 10.1007/s00210-023-02786-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 10/12/2023] [Indexed: 10/24/2023]
Abstract
Constipation is a prevalent clinical ailment of the gastrointestinal system, yet its pathogenesis remains ambiguous. Despite the availability of numerous treatment modalities, they are insufficient in resolving the issue for patients. This work conducted a comprehensive review of the existing literature pertaining to the utilization of natural products for the treatment of constipation, with a focus on the efficacy of natural products in treating constipation, and to provide a comprehensive summary of their underlying mechanisms of action. Upon conducting a thorough review of the extant literature, we found that natural products can effectively treat constipation as modern synthetic drugs and compounded drugs with acetylcholinesterase (AChE) effects, rich in fiber and mucus, and the effects of increasing the tension of the ileum and gastrointestinal tract muscle, mediating signaling pathways, cytokine, excitability of the smooth muscle of the gastrointestinal tract, and regulating the homeostasis of intestinal flora. However, there is a wide variety of natural products, and there are still relatively few studies; the composition of natural products is complex, and the mechanism of action of natural products cannot be clarified. In the future, we need to further improve the detailed mechanism of natural products for the treatment of constipation.
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Affiliation(s)
- Pengfei Zhou
- Department of Anorectal Surgery, Longhua Hospital Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Xiaopeng Wang
- Department of Anorectal surgery, Suzhou TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Suzhou, China
| | - Mingming Sun
- Department of Anorectal surgery, Suzhou TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Suzhou, China
| | - Shuai Yan
- Department of Anorectal surgery, Suzhou TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Suzhou, China.
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26
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Yurkovich JT, Evans SJ, Rappaport N, Boore JL, Lovejoy JC, Price ND, Hood LE. The transition from genomics to phenomics in personalized population health. Nat Rev Genet 2024; 25:286-302. [PMID: 38093095 DOI: 10.1038/s41576-023-00674-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/03/2023] [Indexed: 03/21/2024]
Abstract
Modern health care faces several serious challenges, including an ageing population and its inherent burden of chronic diseases, rising costs and marginal quality metrics. By assessing and optimizing the health trajectory of each individual using a data-driven personalized approach that reflects their genetics, behaviour and environment, we can start to address these challenges. This assessment includes longitudinal phenome measures, such as the blood proteome and metabolome, gut microbiome composition and function, and lifestyle and behaviour through wearables and questionnaires. Here, we review ongoing large-scale genomics and longitudinal phenomics efforts and the powerful insights they provide into wellness. We describe our vision for the transformation of the current health care from disease-oriented to data-driven, wellness-oriented and personalized population health.
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Affiliation(s)
- James T Yurkovich
- Phenome Health, Seattle, WA, USA
- Center for Phenomic Health, The Buck Institute for Research on Aging, Novato, CA, USA
- Department of Bioengineering, University of Texas at Dallas, Richardson, TX, USA
| | - Simon J Evans
- Phenome Health, Seattle, WA, USA
- Center for Phenomic Health, The Buck Institute for Research on Aging, Novato, CA, USA
| | - Noa Rappaport
- Center for Phenomic Health, The Buck Institute for Research on Aging, Novato, CA, USA
- Institute for Systems Biology, Seattle, WA, USA
| | - Jeffrey L Boore
- Phenome Health, Seattle, WA, USA
- Center for Phenomic Health, The Buck Institute for Research on Aging, Novato, CA, USA
| | - Jennifer C Lovejoy
- Phenome Health, Seattle, WA, USA
- Center for Phenomic Health, The Buck Institute for Research on Aging, Novato, CA, USA
- Institute for Systems Biology, Seattle, WA, USA
| | - Nathan D Price
- Institute for Systems Biology, Seattle, WA, USA
- Thorne HealthTech, New York, NY, USA
- Department of Bioengineering, University of Washington, Seattle, WA, USA
- Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, WA, USA
| | - Leroy E Hood
- Phenome Health, Seattle, WA, USA.
- Center for Phenomic Health, The Buck Institute for Research on Aging, Novato, CA, USA.
- Institute for Systems Biology, Seattle, WA, USA.
- Department of Bioengineering, University of Washington, Seattle, WA, USA.
- Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, WA, USA.
- Department of Immunology, University of Washington, Seattle, WA, USA.
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Lv D, Zheng W, Zhang Z, Lin Z, Wu K, Liu H, Liao X, Sun Y. Microbial imidazole propionate affects glomerular filtration rate in patients with diabetic nephropathy through association with HSP90α. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2024; 1871:119703. [PMID: 38453032 DOI: 10.1016/j.bbamcr.2024.119703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 02/23/2024] [Accepted: 02/24/2024] [Indexed: 03/09/2024]
Abstract
Imidazole propionate (ImP) is a detrimental metabolite produced by the fermentation of histidine intermediates via the intestinal flora. Here, the untargeted metabolite analysis of plasma metabolites from patients with diabetic nephropathy (DN), in combination with the Human Metabolome Database, revealed significantly increased levels of ImP in patients with DN, with a positive correlation with patients' blood creatinine concentration and urinary albumin-to-creatinine ratio, and a negative correlation with the glomerular filtration rate. RNA-seq was applied to detect the effects of ImP on renal tissue transcriptome in mice with DN. It demonstrated that ImP exacerbated renal injury in mice with DN and promoted renal tubular epithelial-mesenchymal transition (EMT), leading to renal mesenchymal fibrosis and renal impairment. Furthermore, ImP was found to directly target HAP90α and activate the PI3K-Akt signalling pathway, which is involved in EMT, by the drug affinity response target stability method. The findings showed that ImP may provide a novel target for DN quality, as it can directly bind to and activate HSP90, thereby facilitating the development of DN while acting as a potential indicator for the clinical diagnosis of DN.
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Affiliation(s)
- Dan Lv
- Department of Nephrology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing 400010, China; Department of Neuroscience Research Center, School of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, China
| | - Wenhan Zheng
- Department of Neuroscience Research Center, School of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, China
| | - Zheng Zhang
- Department of Neuroscience Research Center, School of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, China
| | - Ziyue Lin
- Department of Neuroscience Research Center, School of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, China
| | - Keqian Wu
- Department of Neuroscience Research Center, School of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, China
| | - Handeng Liu
- Laboratory of Tissue and Cell Biology, Experimental Teaching Center, Chongqing Medical University, Chongqing 400016, China
| | - Xiaohui Liao
- Department of Nephrology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing 400010, China.
| | - Yan Sun
- Department of Neuroscience Research Center, School of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, China.
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28
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Yin B, Cai Y, Teng T, Wang X, Liu X, Li X, Wang J, Wu H, He Y, Ren F, Kou T, Zhu ZJ, Zhou X. Identifying plasma metabolic characteristics of major depressive disorder, bipolar disorder, and schizophrenia in adolescents. Transl Psychiatry 2024; 14:163. [PMID: 38531835 DOI: 10.1038/s41398-024-02886-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 03/14/2024] [Accepted: 03/19/2024] [Indexed: 03/28/2024] Open
Abstract
Major depressive disorder (MDD), bipolar disorder (BD), and schizophrenia (SCZ) are classified as major mental disorders and together account for the second-highest global disease burden, and half of these patients experience symptom onset in adolescence. Several studies have reported both similar and unique features regarding the risk factors and clinical symptoms of these three disorders. However, it is still unclear whether these disorders have similar or unique metabolic characteristics in adolescents. We conducted a metabolomics analysis of plasma samples from adolescent healthy controls (HCs) and patients with MDD, BD, and SCZ. We identified differentially expressed metabolites between patients and HCs. Based on the differentially expressed metabolites, correlation analysis, metabolic pathway analysis, and potential diagnostic biomarker identification were conducted for disorders and HCs. Our results showed significant changes in plasma metabolism between patients with these mental disorders and HCs; the most distinct changes were observed in SCZ patients. Moreover, the metabolic differences in BD patients shared features with those in both MDD and SCZ, although the BD metabolic profile was closer to that of MDD than to SCZ. Additionally, we identified the metabolites responsible for the similar and unique metabolic characteristics in multiple metabolic pathways. The similar significant differences among the three disorders were found in fatty acid, steroid-hormone, purine, nicotinate, glutamate, tryptophan, arginine, and proline metabolism. Interestingly, we found unique characteristics of significantly altered glycolysis, glycerophospholipid, and sphingolipid metabolism in SCZ; lysine, cysteine, and methionine metabolism in MDD and BD; and phenylalanine, tyrosine, and aspartate metabolism in SCZ and BD. Finally, we identified five panels of potential diagnostic biomarkers for MDD-HC, BD-HC, SCZ-HC, MDD-SCZ, and BD-SCZ comparisons. Our findings suggest that metabolic characteristics in plasma vary across psychiatric disorders and that critical metabolites provide new clues regarding molecular mechanisms in these three psychiatric disorders.
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Affiliation(s)
- Bangmin Yin
- Department of Psychiatry, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Yuping Cai
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
| | - Teng Teng
- Department of Psychiatry, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Xiaolin Wang
- Health Management Center, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Xueer Liu
- Department of Psychiatry, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Xuemei Li
- Department of Psychiatry, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Jie Wang
- Department of Psychiatry, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Hongyan Wu
- Department of Psychiatry, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Yuqian He
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Fandong Ren
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
| | - Tianzhang Kou
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
| | - Zheng-Jiang Zhu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China.
- Shanghai Key Laboratory of Aging Studies, Shanghai, China.
| | - Xinyu Zhou
- Department of Psychiatry, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China.
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29
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Johnson-Martínez JP, Diener C, Levine AE, Wilmanski T, Suskind DL, Ralevski A, Hadlock J, Magis AT, Hood L, Rappaport N, Gibbons SM. Generally-healthy individuals with aberrant bowel movement frequencies show enrichment for microbially-derived blood metabolites associated with reduced kidney function. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.03.04.531100. [PMID: 36945445 PMCID: PMC10028848 DOI: 10.1101/2023.03.04.531100] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]
Abstract
Bowel movement frequency (BMF) has been linked to changes in the composition of the human gut microbiome and to many chronic conditions, like metabolic disorders, neurodegenerative diseases, chronic kidney disease (CKD), and other intestinal pathologies like irritable bowel syndrome and inflammatory bowel disease. Lower BMF (constipation) can lead to compromised intestinal barrier integrity and a switch from saccharolytic to proteolytic fermentation within the microbiota, giving rise to microbially-derived toxins that may make their way into circulation and cause damage to organ systems. However, the connections between BMF, gut microbial metabolism, and the early-stage development and progression of chronic disease remain underexplored. Here, we examined the phenotypic impact of BMF variation in a cohort of generally-healthy, community dwelling adults with detailed clinical, lifestyle, and multi-omic data. We showed significant differences in microbially-derived blood plasma metabolites, gut bacterial genera, clinical chemistries, and lifestyle factors across BMF groups that have been linked to inflammation, cardiometabolic health, liver function, and CKD severity and progression. We found that the higher plasma levels of 3-indoxyl sulfate (3-IS), a microbially-derived metabolite associated with constipation, was in turn negatively associated with estimated glomerular filtration rate (eGFR), a measure of kidney function. Causal mediation analysis revealed that the effect of BMF on eGFR was significantly mediated by 3-IS. Finally, we identify self-reported diet, lifestyle, and psychological factors associated with BMF variation, which indicate several common-sense strategies for mitigating constipation and diarrhea. Overall, we suggest that aberrant BMF is an underappreciated risk factor in the development of chronic diseases, even in otherwise healthy populations.
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Affiliation(s)
- Johannes P. Johnson-Martínez
- Institute for Systems Biology, Seattle, WA 98109, USA
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
| | | | - Anne E. Levine
- Institute for Systems Biology, Seattle, WA 98109, USA
- Seattle Children’s Hospital, Seattle, WA 98105, USA
| | | | | | | | | | | | - Leroy Hood
- Institute for Systems Biology, Seattle, WA 98109, USA
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
- Phenome Health, Seattle, WA 98109
- Department of Immunology, University of Washington, Seattle, WA 98195, USA
- Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, WA 98195, USA
| | - Noa Rappaport
- Institute for Systems Biology, Seattle, WA 98109, USA
| | - Sean M. Gibbons
- Institute for Systems Biology, Seattle, WA 98109, USA
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- eScience Institute, University of Washington, Seattle, WA 98195, USA
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30
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Darmadi D, Pakpahan C, Singh R, Saharan A, Pasaribu WS, Hermansyah H, Rezano A. Inflammatory bowel disease (ulcerative colitis type) severity shows inverse correlation with semen parameters and testosterone levels. Asian J Androl 2024; 26:155-159. [PMID: 37934180 PMCID: PMC10919423 DOI: 10.4103/aja202353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 09/05/2023] [Indexed: 11/08/2023] Open
Abstract
Individuals with inflammatory bowel disease (IBD) have been reported to be at an increased risk of infertility and sexual dysfunction. Although the relationship between them remains unclear, IBD severity is suspected to affect hormone levels and fertility. To analyze the impact of IBD severity on semen parameters and sex hormone levels in ulcerative colitis-type IBD (UC-IBD), we conducted a cross-sectional study involving 120 patients with UC-IBD in Adam Malik General Hospital, Medan, Indonesia. The patients were classified into three groups based on the Mayo score for UC, followed by a comparison of various semen and hormone parameters among these groups. In addition to the cross-sectional analysis, a simple correlation test was conducted irrespective of the patient grouping. Sperm concentration, motility, and morphology were found to decline significantly with an increase in IBD severity. Without classifying patients with IBD into subgroups, the Mayo score showed negative correlations with sperm concentration ( r = -0.375, P < 0.0001), rapid progressive motility ( r = -0.660, P < 0.0001), free testosterone ( r = -0.732, P < 0.0001), and total testosterone ( r = -0.721, P < 0.0001), and positive correlations with immotile sperm ( r = 0.660, P < 0.0001), abnormal morphology ( r = 0.657, P < 0.0001), and sex hormone-binding globulin (SHBG; r = 0.278, P = 0.002). Sperm concentration, motility, and morphology declined significantly with the severity of IBD. This study suggests a significant negative impact of IBD severity on semen quality and sex hormones.
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Affiliation(s)
- Darmadi Darmadi
- Department of Internal Medicine, Faculty of Medicine, Universitas Sumatera Utara, Medan 20155, Indonesia
| | - Cennikon Pakpahan
- Andrology Study Program, Faculty of Medicine, Universitas Airlangga, Surabaya 60132, Indonesia
- Department of Biomedical Sciences, Faculty of Medicine, Universitas Airlangga, Surabaya 60132, Indonesia
| | - Rajender Singh
- Division of Endocrinology, Central Drug Research Institute, Lucknow, Uttar Pradesh 226031, India
| | - Ankur Saharan
- Amity University, Lucknow, Uttar Pradesh 226010, India
| | | | - Hermansyah Hermansyah
- Andrology Study Program, Faculty of Medicine, Universitas Airlangga, Surabaya 60132, Indonesia
| | - Andri Rezano
- Andrology Study Program, Faculty of Medicine, Universitas Airlangga, Surabaya 60132, Indonesia
- Department of Biomedical Sciences, Faculty of Medicine, Universitas Padjadjaran, Sumedang 45363, Indonesia
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Jia Q, Wang H, Wang Y, Xue W, Jiang Q, Wang J, Ning F, Zhu Z, Tian L. Investigation of the mechanism of silica-induced pulmonary fibrosis: The role of lung microbiota dysbiosis and the LPS/TLR4 signaling pathway. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:168948. [PMID: 38048996 DOI: 10.1016/j.scitotenv.2023.168948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 11/25/2023] [Accepted: 11/25/2023] [Indexed: 12/06/2023]
Abstract
The widespread manufacture of silica and its extensive use, and potential release of silica into the environment pose a serious human health hazard. Silicosis, a severe global public health issue, is caused by exposure to silica, leading to persistent inflammation and fibrosis of the lungs. The underlying pathogenic mechanisms of silicosis remain elusive. Lung microbiota dysbiosis is associated with the development of inflammation and fibrosis. However, limited information is currently available regarding the role of lung microbiota in silicosis. The study therefore is designed to conduct a comprehensive analysis of the role of lung microbiota dysbiosis and establish a basis for future investigations into the potential mechanisms underlying silicosis. Here, the pathological and biochemical parameters were used to systematically assessed the degree of inflammation and fibrosis following silica exposure and treatment with combined antibiotics. The underlying mechanisms were studied via integrative multi-omics analyses of the transcriptome and microbiome. Analysis of 16S ribosomal DNA revealed dysbiosis of the microbial community in silicosis, characterized by a predominance of gram-negative bacteria. Exposure to silica has been shown to trigger lung inflammation and fibrosis, leading to an increased concentration of lipopolysaccharides in the bronchoalveolar lavage fluid. Furthermore, Toll-like receptor 4 was identified as a key molecule in the lung microbiota dysbiosis associated with silica-induced lung fibrosis. All of these outcomes can be partially controlled through combined antibiotic administration. The study findings demonstrate that the dysbiosis of lung microbiota enhances silica-induced fibrosis associated with the lipopolysaccharides/Toll-like receptor 4 pathway and provided a promising target for therapeutic intervention of silicosis.
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Affiliation(s)
- Qiyue Jia
- Department of Occupational and Environmental Health, School of Public Health, Capital Medical University, Beijing 100069, China; Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing 100069, China
| | - Hongwei Wang
- Department of Occupational and Environmental Health, School of Public Health, Capital Medical University, Beijing 100069, China; Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing 100069, China
| | - Yan Wang
- Department of Occupational and Environmental Health, School of Public Health, Capital Medical University, Beijing 100069, China; Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing 100069, China
| | - Wenming Xue
- Department of Occupational and Environmental Health, School of Public Health, Capital Medical University, Beijing 100069, China; Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing 100069, China
| | - Qiyue Jiang
- Department of Occupational and Environmental Health, School of Public Health, Capital Medical University, Beijing 100069, China; Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing 100069, China
| | - Jiaxin Wang
- Department of Occupational and Environmental Health, School of Public Health, Capital Medical University, Beijing 100069, China; Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing 100069, China
| | - Fuao Ning
- Department of Occupational and Environmental Health, School of Public Health, Capital Medical University, Beijing 100069, China; Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing 100069, China
| | - Zhonghui Zhu
- Department of Occupational and Environmental Health, School of Public Health, Capital Medical University, Beijing 100069, China; Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing 100069, China.
| | - Lin Tian
- Department of Occupational and Environmental Health, School of Public Health, Capital Medical University, Beijing 100069, China; Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing 100069, China.
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32
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Shtossel O, Koren O, Shai I, Rinott E, Louzoun Y. Gut microbiome-metabolome interactions predict host condition. MICROBIOME 2024; 12:24. [PMID: 38336867 PMCID: PMC10858481 DOI: 10.1186/s40168-023-01737-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 12/10/2023] [Indexed: 02/12/2024]
Abstract
BACKGROUND The effect of microbes on their human host is often mediated through changes in metabolite concentrations. As such, multiple tools have been proposed to predict metabolite concentrations from microbial taxa frequencies. Such tools typically fail to capture the dependence of the microbiome-metabolite relation on the environment. RESULTS We propose to treat the microbiome-metabolome relation as the equilibrium of a complex interaction and to relate the host condition to a latent representation of the interaction between the log concentration of the metabolome and the log frequencies of the microbiome. We develop LOCATE (Latent variables Of miCrobiome And meTabolites rElations), a machine learning tool to predict the metabolite concentration from the microbiome composition and produce a latent representation of the interaction. This representation is then used to predict the host condition. LOCATE's accuracy in predicting the metabolome is higher than all current predictors. The metabolite concentration prediction accuracy significantly decreases cross datasets, and cross conditions, especially in 16S data. LOCATE's latent representation predicts the host condition better than either the microbiome or the metabolome. This representation is strongly correlated with host demographics. A significant improvement in accuracy (0.793 vs. 0.724 average accuracy) is obtained even with a small number of metabolite samples ([Formula: see text]). CONCLUSION These results suggest that a latent representation of the microbiome-metabolome interaction leads to a better association with the host condition than any of the two separated or the simple combination of the two. Video Abstract.
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Affiliation(s)
- Oshrit Shtossel
- Department of Mathematics, Bar-Ilan University, Ramat Gan, 52900, Israel
| | - Omry Koren
- The Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Iris Shai
- Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Ehud Rinott
- Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Yoram Louzoun
- Department of Mathematics, Bar-Ilan University, Ramat Gan, 52900, Israel.
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Zhou X, Shen X, Johnson JS, Spakowicz DJ, Agnello M, Zhou W, Avina M, Honkala A, Chleilat F, Chen SJ, Cha K, Leopold S, Zhu C, Chen L, Lyu L, Hornburg D, Wu S, Zhang X, Jiang C, Jiang L, Jiang L, Jian R, Brooks AW, Wang M, Contrepois K, Gao P, Schüssler-Fiorenza Rose SM, Binh Tran TD, Nguyen H, Celli A, Hong BY, Bautista EJ, Dorsett Y, Kavathas P, Zhou Y, Sodergren E, Weinstock GM, Snyder MP. Longitudinal profiling of the microbiome at four body sites reveals core stability and individualized dynamics during health and disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.01.577565. [PMID: 38352363 PMCID: PMC10862915 DOI: 10.1101/2024.02.01.577565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/26/2024]
Abstract
To understand dynamic interplay between the human microbiome and host during health and disease, we analyzed the microbial composition, temporal dynamics, and associations with host multi-omics, immune and clinical markers of microbiomes from four body sites in 86 participants over six years. We found that microbiome stability and individuality are body-site-specific and heavily influenced by the host. The stool and oral microbiome were more stable than the skin and nasal microbiomes, possibly due to their interaction with the host and environment. Also, we identified individual-specific and commonly shared bacterial taxa, with individualized taxa showing greater stability. Interestingly, microbiome dynamics correlated across body sites, suggesting systemic coordination influenced by host-microbial-environment interactions. Notably, insulin-resistant individuals showed altered microbial stability and associations between microbiome, molecular markers, and clinical features, suggesting their disrupted interaction in metabolic disease. Our study offers comprehensive views of multi-site microbial dynamics and their relationship with host health and disease. Study Highlights The stability of the human microbiome varies among individuals and body sites.Highly individualized microbial genera are more stable over time.At each of the four body sites, systematic interactions between the environment, the host and bacteria can be detected.Individuals with insulin resistance have lower microbiome stability, a more diversified skin microbiome, and significantly altered host-microbiome interactions.
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Xiang L, Du T, Zhang J, Zhang Y, Zhou Y, Zhao Y, Zhou Y, Ma L. Vitamin D 3 supplementation shapes the composition of gut microbiota and improves some obesity parameters induced by high-fat diet in mice. Eur J Nutr 2024; 63:155-172. [PMID: 37740812 DOI: 10.1007/s00394-023-03246-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Accepted: 09/01/2023] [Indexed: 09/25/2023]
Abstract
PURPOSE Individuals with vitamin D (VD) insufficiency have a greater tendency to develop obesity and have increased systemic inflammation. Gut microbiota are involved in the regulation of host inflammation and energy metabolism, which plays a role in the pathogenesis of obesity. Thus, we aimed to evaluate the effects of different doses of VD3 on body weight, serum lipids, inflammatory factors, and intestinal barrier function in obese mice and to explore the regulatory effect of VD3 on gut microbiota in obese mice. METHODS Male C57BL/6 J mice received a normal chow diet (NCD, 10% fat) or high-fat diet (HFD, 60% fat) to induce obesity within 10 weeks. Then, HFD mice were supplemented with 5650, 8475, or 11,300 IU VD3/kg diet for 8 weeks. Finally, 16 s rRNA analysis was performed to analyze gut microbiota composition in cecal contents. In addition, body weight, serum lipids, inflammatory factors, and intestinal barrier function were analyzed. RESULTS VD3 supplementation reduced body weight and the levels of TG, TC, HDL-C, TNF-α, IL-1β and LPS, and increased ZO-1 in HFD-fed mice. Moreover, it increased α-diversity, reduced F/B ratio and altered microbiota composition by increasing relative abundance of Bacteroidetes, Proteobacteria, Desulfovibrio, Dehalobacterium, Odoribacter, and Parabacteroides and reducing relative abundance of Firmicutes and Ruminococcus. There were significant differences between HFD and NCD groups in several metabolic pathways, including endotoxin biosynthesis, tricarboxylic acid cycle, lipid synthesis and metabolism, and glycolysis. CONCLUSIONS Low, medium, and high doses of VD3 inhibited weight gain, reduced levels of blood lipids and inflammatory factors, and improved endotoxemia and gut barrier function in obese mice. It also increased the α-diversity of gut microbiota in obese mice and reduced the relative abundance of some intestinal pathogenic bacteria, increased the relative abundance of some beneficial bacteria, and corrected the intestinal flora disorder of obese mice, with the low- and high-dose groups showing better effects than the medium-dose group.
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Affiliation(s)
- Lian Xiang
- Department of Nutrition and Food Hygiene, School of Public Health, Southwest Medical University, Luzhou, China
| | - Tingwan Du
- Department of Nutrition and Food Hygiene, School of Public Health, Southwest Medical University, Luzhou, China
| | - Jingjing Zhang
- Department of Clinical Nutrition, Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Yuanfan Zhang
- Department of Nutrition and Food Hygiene, School of Public Health, Southwest Medical University, Luzhou, China
| | - Yanqiu Zhou
- Department of Nutrition and Food Hygiene, School of Public Health, Southwest Medical University, Luzhou, China
| | - Yueying Zhao
- Department of Nutrition and Food Hygiene, School of Public Health, Southwest Medical University, Luzhou, China
| | - Yong Zhou
- Department of Medical Cell Biology and Genetics, School of Basic Medical Science, Southwest Medical University, Luzhou, China.
| | - Ling Ma
- Department of Nutrition and Food Hygiene, School of Public Health, Southwest Medical University, Luzhou, China.
- Environmental Health Effects and Risk Assessment Key Laboratory of Luzhou, School of Public Health, Southwest Medical University, Luzhou, China.
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35
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Costello E, Goodrich JA, Patterson WB, Walker DI, Chen J(C, Baumert BO, Rock S, Gilliland FD, Goran MI, Chen Z, Alderete TL, Conti DV, Chatzi L. Proteomic and Metabolomic Signatures of Diet Quality in Young Adults. Nutrients 2024; 16:429. [PMID: 38337712 PMCID: PMC10857402 DOI: 10.3390/nu16030429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 01/27/2024] [Accepted: 01/30/2024] [Indexed: 02/12/2024] Open
Abstract
The assessment of "omics" signatures may contribute to personalized medicine and precision nutrition. However, the existing literature is still limited in the homogeneity of participants' characteristics and in limited assessments of integrated omics layers. Our objective was to use post-prandial metabolomics and fasting proteomics to identify biological pathways and functions associated with diet quality in a population of primarily Hispanic young adults. We conducted protein and metabolite-wide association studies and functional pathway analyses to assess the relationships between a priori diet indices, Healthy Eating Index-2015 (HEI) and Dietary Approaches to Stop Hypertension (DASH) diets, and proteins (n = 346) and untargeted metabolites (n = 23,173), using data from the MetaAIR study (n = 154, 61% Hispanic). Analyses were performed for each diet quality index separately, adjusting for demographics and BMI. Five proteins (ACY1, ADH4, AGXT, GSTA1, F7) and six metabolites (undecylenic acid, betaine, hyodeoxycholic acid, stearidonic acid, iprovalicarb, pyracarbolid) were associated with both diets (p < 0.05), though none were significant after adjustment for multiple comparisons. Overlapping proteins are involved in lipid and amino acid metabolism and in hemostasis, while overlapping metabolites include amino acid derivatives, bile acids, fatty acids, and pesticides. Enriched biological pathways were involved in macronutrient metabolism, immune function, and oxidative stress. These findings in young Hispanic adults contribute to efforts to develop precision nutrition and medicine for diverse populations.
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Affiliation(s)
- Elizabeth Costello
- Department of Population and Public Health Sciences, University of Southern California, Los Angeles, CA 90032, USA; (J.A.G.); (J.C.); (B.O.B.); (S.R.); (F.D.G.); (M.I.G.); (Z.C.); (D.V.C.); (L.C.)
| | - Jesse A. Goodrich
- Department of Population and Public Health Sciences, University of Southern California, Los Angeles, CA 90032, USA; (J.A.G.); (J.C.); (B.O.B.); (S.R.); (F.D.G.); (M.I.G.); (Z.C.); (D.V.C.); (L.C.)
| | - William B. Patterson
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO 80309, USA; (W.B.P.); (T.L.A.)
| | - Douglas I. Walker
- Gangarosa Department of Environmental Health, Emory University, Atlanta, GA 30329, USA;
| | - Jiawen (Carmen) Chen
- Department of Population and Public Health Sciences, University of Southern California, Los Angeles, CA 90032, USA; (J.A.G.); (J.C.); (B.O.B.); (S.R.); (F.D.G.); (M.I.G.); (Z.C.); (D.V.C.); (L.C.)
| | - Brittney O. Baumert
- Department of Population and Public Health Sciences, University of Southern California, Los Angeles, CA 90032, USA; (J.A.G.); (J.C.); (B.O.B.); (S.R.); (F.D.G.); (M.I.G.); (Z.C.); (D.V.C.); (L.C.)
| | - Sarah Rock
- Department of Population and Public Health Sciences, University of Southern California, Los Angeles, CA 90032, USA; (J.A.G.); (J.C.); (B.O.B.); (S.R.); (F.D.G.); (M.I.G.); (Z.C.); (D.V.C.); (L.C.)
| | - Frank D. Gilliland
- Department of Population and Public Health Sciences, University of Southern California, Los Angeles, CA 90032, USA; (J.A.G.); (J.C.); (B.O.B.); (S.R.); (F.D.G.); (M.I.G.); (Z.C.); (D.V.C.); (L.C.)
| | - Michael I. Goran
- Department of Population and Public Health Sciences, University of Southern California, Los Angeles, CA 90032, USA; (J.A.G.); (J.C.); (B.O.B.); (S.R.); (F.D.G.); (M.I.G.); (Z.C.); (D.V.C.); (L.C.)
- Department of Pediatrics, Children’s Hospital Los Angeles, The Saban Research Institute, Los Angeles, CA 90027, USA
| | - Zhanghua Chen
- Department of Population and Public Health Sciences, University of Southern California, Los Angeles, CA 90032, USA; (J.A.G.); (J.C.); (B.O.B.); (S.R.); (F.D.G.); (M.I.G.); (Z.C.); (D.V.C.); (L.C.)
| | - Tanya L. Alderete
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO 80309, USA; (W.B.P.); (T.L.A.)
| | - David V. Conti
- Department of Population and Public Health Sciences, University of Southern California, Los Angeles, CA 90032, USA; (J.A.G.); (J.C.); (B.O.B.); (S.R.); (F.D.G.); (M.I.G.); (Z.C.); (D.V.C.); (L.C.)
| | - Lida Chatzi
- Department of Population and Public Health Sciences, University of Southern California, Los Angeles, CA 90032, USA; (J.A.G.); (J.C.); (B.O.B.); (S.R.); (F.D.G.); (M.I.G.); (Z.C.); (D.V.C.); (L.C.)
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36
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Schillemans T, Yan Y, Ribbenstedt A, Donat-Vargas C, Lindh CH, Kiviranta H, Rantakokko P, Wolk A, Landberg R, Åkesson A, Brunius C. OMICs Signatures Linking Persistent Organic Pollutants to Cardiovascular Disease in the Swedish Mammography Cohort. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:1036-1047. [PMID: 38174696 PMCID: PMC10795192 DOI: 10.1021/acs.est.3c06388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 12/06/2023] [Accepted: 12/07/2023] [Indexed: 01/05/2024]
Abstract
Cardiovascular disease (CVD) development may be linked to persistent organic pollutants (POPs), including organochlorine compounds (OCs) and perfluoroalkyl and polyfluoroalkyl substances (PFAS). To explore underlying mechanisms, we investigated metabolites, proteins, and genes linking POPs with CVD risk. We used data from a nested case-control study on myocardial infarction (MI) and stroke from the Swedish Mammography Cohort - Clinical (n = 657 subjects). OCs, PFAS, and multiomics (9511 liquid chromatography-mass spectrometry (LC-MS) metabolite features; 248 proteins; 8110 gene variants) were measured in baseline plasma. POP-related omics features were selected using random forest followed by Spearman correlation adjusted for confounders. From these, CVD-related omics features were selected using conditional logistic regression. Finally, 29 (for OCs) and 12 (for PFAS) unique features associated with POPs and CVD. One omics subpattern, driven by lipids and inflammatory proteins, associated with MI (OR = 2.03; 95% CI = 1.47; 2.79), OCs, age, and BMI, and correlated negatively with PFAS. Another subpattern, driven by carnitines, associated with stroke (OR = 1.55; 95% CI = 1.16; 2.09), OCs, and age, but not with PFAS. This may imply that OCs and PFAS associate with different omics patterns with opposite effects on CVD risk, but more research is needed to disentangle potential modifications by other factors.
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Affiliation(s)
- Tessa Schillemans
- Cardiovascular
and Nutritional Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm 171 77, Sweden
| | - Yingxiao Yan
- Food
and Nutrition Sciences, Department of Life Sciences, Chalmers University of Technology, Gothenburg 412 96, Sweden
| | - Anton Ribbenstedt
- Food
and Nutrition Sciences, Department of Life Sciences, Chalmers University of Technology, Gothenburg 412 96, Sweden
| | - Carolina Donat-Vargas
- Cardiovascular
and Nutritional Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm 171 77, Sweden
- Barcelona
Institute for Global Health (ISGlobal), Barcelona 08036, Spain
| | - Christian H. Lindh
- Division
of Occupational and Environmental Medicine, Lund University, Lund 221 00, Sweden
| | - Hannu Kiviranta
- Department
of Health Security, National Institute for
Health and Welfare, Kuopio 70701, Finland
| | - Panu Rantakokko
- Department
of Health Security, National Institute for
Health and Welfare, Kuopio 70701, Finland
| | - Alicja Wolk
- Cardiovascular
and Nutritional Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm 171 77, Sweden
| | - Rikard Landberg
- Food
and Nutrition Sciences, Department of Life Sciences, Chalmers University of Technology, Gothenburg 412 96, Sweden
- Department
of Public Health and Clinical Medicine, Umeå University, Umeå 901 87, Sweden
| | - Agneta Åkesson
- Cardiovascular
and Nutritional Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm 171 77, Sweden
| | - Carl Brunius
- Food
and Nutrition Sciences, Department of Life Sciences, Chalmers University of Technology, Gothenburg 412 96, Sweden
- Chalmers
Mass Spectrometry Infrastructure, Department of Life Sciences, Chalmers University of Technology, Gothenburg 412 96, Sweden
- Medical
Epidemiology, Department of Surgical Sciences, Uppsala University, Uppsala 751 05, Sweden
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37
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Ramos Sarmiento K, Carr A, Diener C, Locey KJ, Gibbons SM. Island biogeography theory provides a plausible explanation for why larger vertebrates and taller humans have more diverse gut microbiomes. THE ISME JOURNAL 2024; 18:wrae114. [PMID: 38904949 PMCID: PMC11253425 DOI: 10.1093/ismejo/wrae114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Revised: 05/30/2024] [Accepted: 06/20/2024] [Indexed: 06/22/2024]
Abstract
Prior work has shown a positive scaling relationship between vertebrate body size, human height, and gut microbiome alpha diversity. This observation mirrors commonly observed species area relationships (SARs) in many other ecosystems. Here, we expand these observations to several large datasets, showing that this size-diversity scaling relationship is independent of relevant covariates, like diet, body mass index, age, sex, bowel movement frequency, antibiotic usage, and cardiometabolic health markers. Island biogeography theory (IBT), which predicts that larger islands tend to harbor greater species diversity through neutral demographic processes, provides a simple mechanism for positive SARs. Using a gut-adapted IBT model, we demonstrated that increasing the length of a flow-through ecosystem led to increased species diversity, closely matching our empirical observations. We delve into the possible clinical implications of these SARs in the American Gut cohort. Consistent with prior observations that lower alpha diversity is a risk factor for Clostridioides difficile infection (CDI), we found that individuals who reported a history of CDI were shorter than those who did not and that this relationship was mediated by alpha diversity. We observed that vegetable consumption had a much stronger association with CDI history, which was also partially mediated by alpha diversity. In summary, we find that the positive scaling observed between body size and gut alpha diversity can be plausibly explained by a gut-adapted IBT model, may be related to CDI risk, and vegetable intake appears to independently mitigate this risk, although additional work is needed to validate the potential disease risk implications.
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Affiliation(s)
| | - Alex Carr
- Institute for Systems Biology, Seattle, WA 98109, United States
- Molecular Engineering Graduate Program, University of Washington, Seattle, WA 98195, United States
| | - Christian Diener
- Institute for Systems Biology, Seattle, WA 98109, United States
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, 8010 Graz, Austria
| | - Kenneth J Locey
- Center for Quality, Safety & Value Analytics, Rush University Medical Center, Chicago, IL 60612, United States
| | - Sean M Gibbons
- Institute for Systems Biology, Seattle, WA 98109, United States
- Molecular Engineering Graduate Program, University of Washington, Seattle, WA 98195, United States
- Department of Bioengineering, University of Washington, Seattle, WA 98195, United States
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, United States
- Science Institute, University of Washington, Seattle, WA 98195, United States
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38
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Carr A, Baliga NS, Diener C, Gibbons SM. Personalized Clostridioides difficile engraftment risk prediction and probiotic therapy assessment in the human gut. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.04.28.538771. [PMID: 37162960 PMCID: PMC10168307 DOI: 10.1101/2023.04.28.538771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Clostridioides difficile colonizes up to 30-40% of community-dwelling adults without causing disease. C. difficile infections (CDIs) are the leading cause of antibiotic-associated diarrhea in the U.S. and typically develop in individuals following disruption of the gut microbiota due to antibiotic or chemotherapy treatments. Further treatment of CDI with antibiotics is not always effective and can lead to antibiotic resistance and recurrent infections (rCDI). The most effective treatment for rCDI is the reestablishment of an intact microbiota via fecal microbiota transplants (FMTs). However, the success of FMTs has been difficult to generalize because the microbial interactions that prevent engraftment and facilitate the successful clearance of C. difficile are still only partially understood. Here we show how microbial community-scale metabolic models (MCMMs) accurately predicted known instances of C. difficile colonization susceptibility or resistance in vitro and in vivo. MCMMs provide detailed mechanistic insights into the ecological interactions that govern C. difficile engraftment, like cross-feeding or competition involving metabolites like succinate, trehalose, and ornithine, which differ from person to person. Indeed, three distinct C. difficile metabolic niches emerge from our MCMMs, two associated with positive growth rates and one that represents non-growth, which are consistently observed across 15,204 individuals from five independent cohorts. Finally, we show how MCMMs can predict personalized engraftment and C. difficile growth suppression for a probiotic cocktail (VE303) designed to replace FMTs for the treatment rCDI. Overall, this powerful modeling approach predicts personalized C. difficile engraftment risk and can be leveraged to assess probiotic treatment efficacy. MCMMs could be extended to understand the mechanistic underpinnings of personalized engraftment of other opportunistic bacterial pathogens, beneficial probiotic organisms, or more complex microbial consortia.
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Affiliation(s)
- Alex Carr
- Institute for Systems Biology, Seattle, WA, USA
- Molecular Engineering Program, University of Washington, Seattle, WA, USA
| | - Nitin S. Baliga
- Institute for Systems Biology, Seattle, WA, USA
- Molecular Engineering Program, University of Washington, Seattle, WA, USA
- Departments of Biology and Microbiology, University of Washington, Seattle, WA, USA
- Lawrence Berkeley National Lab, Berkeley, CA, USA
| | - Christian Diener
- Institute for Systems Biology, Seattle, WA, USA
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
| | - Sean M. Gibbons
- Institute for Systems Biology, Seattle, WA, USA
- Molecular Engineering Program, University of Washington, Seattle, WA, USA
- Departments of Bioengineering and Genome Sciences, University of Washington, Seattle, WA, USA
- eScience Institute, University of Washington, Seattle, WA, USA
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39
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Zhang Z, Zhao H, Chen X, Tian G, Liu G, Cai J, Jia G. Implications of Jatropha curcas L. cake feed on swine health: A microbiota-gut-brain axis perspective. Anim Sci J 2024; 95:e13953. [PMID: 38783533 DOI: 10.1111/asj.13953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Revised: 04/15/2024] [Accepted: 04/24/2024] [Indexed: 05/25/2024]
Abstract
The safety of Jatropha curcas L. cake (JCC) in animal feed remains under scrutiny, despite the advent of low phorbol ester (PE) variants. This study investigates the impact of low PE JCC on swine health when used as a protein feed. Pigs were fed a 5% JCC diet with a PE concentration of 0.98 mg/kg, which surprisingly still induced toxicity. Symptoms included depression, decreased food intake, increased diarrhea, along with hypothalamus and colon lesions. The toxicity was associated with a decrease in antioxidant enzymes, an increase in inflammatory cytokines in the hypothalamus, plasma, and colon, and a rise in pro-inflammatory colon microbes and metabolites. Disturbances in neurotransmitters further suggest that this toxicity is related to disruption of the microbiota-gut-brain axis, indicating that JCC's toxic elements are not solely due to PE. The sensitivity of pigs to JCC underscores the need for thorough detoxification prior to its use as feed. These findings significantly contribute to the discourse on the safety of low PE JCC in animal feed, highlighting implications for both the feed industry and public health.
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Affiliation(s)
- Zhenyu Zhang
- Animal Nutrition Institute, Key Laboratory for Animal Disease-Resistance Nutrition of China, Sichuan Agricultural University, Chengdu, Sichuan, China
- Institute of Animal Husbandry and Veterinary Medicine, Meishan Vocational Technical College, Meishan, Sichuan, China
- Agricultural and Rural Bureau of Dongpo District, Meishan, China
| | - Hua Zhao
- Animal Nutrition Institute, Key Laboratory for Animal Disease-Resistance Nutrition of China, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xiaoling Chen
- Animal Nutrition Institute, Key Laboratory for Animal Disease-Resistance Nutrition of China, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Gang Tian
- Animal Nutrition Institute, Key Laboratory for Animal Disease-Resistance Nutrition of China, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Guangmang Liu
- Animal Nutrition Institute, Key Laboratory for Animal Disease-Resistance Nutrition of China, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Jingyi Cai
- Animal Nutrition Institute, Key Laboratory for Animal Disease-Resistance Nutrition of China, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Gang Jia
- Animal Nutrition Institute, Key Laboratory for Animal Disease-Resistance Nutrition of China, Sichuan Agricultural University, Chengdu, Sichuan, China
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40
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Tang X, Zhang L, Ren S, Zhao Y, Zhang Y. Temporal and geographic distribution of gut microbial enterotypes associated with host thermogenesis characteristics in plateau pikas. Microbiol Spectr 2023; 11:e0002023. [PMID: 37815332 PMCID: PMC10715161 DOI: 10.1128/spectrum.00020-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 08/28/2023] [Indexed: 10/11/2023] Open
Abstract
IMPORTANCE The gut microbiotas of small mammals play an important role in host energy homeostasis. However, it is still unknown whether small mammals with different enterotypes show differences in thermogenesis characteristics. Our study confirmed that plateau pikas with different bacterial enterotypes harbored distinct thermogenesis capabilities and employed various strategies against cold environments. Additionally, we also found that pikas with different fungal enterotypes may display differences in coprophagy.
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Affiliation(s)
- Xianjiang Tang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining, China
- University of Chinese Academy of Sciences, College of Life Sciences, Beijing, China
| | - Liangzhi Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining, China
| | - Shi'en Ren
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining, China
- University of Chinese Academy of Sciences, College of Life Sciences, Beijing, China
| | - Yaqi Zhao
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining, China
- University of Chinese Academy of Sciences, College of Life Sciences, Beijing, China
| | - Yanming Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining, China
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41
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Panigrahi G, Candia J, Dorsey TH, Tang W, Ohara Y, Byun JS, Minas TZ, Zhang A, Ajao A, Cellini A, Yfantis HG, Flis AL, Mann D, Ioffe O, Wang XW, Liu H, Loffredo CA, Napoles AM, Ambs S. Diabetes-associated breast cancer is molecularly distinct and shows a DNA damage repair deficiency. JCI Insight 2023; 8:e170105. [PMID: 37906280 PMCID: PMC10795835 DOI: 10.1172/jci.insight.170105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 10/25/2023] [Indexed: 11/02/2023] Open
Abstract
Diabetes commonly affects patients with cancer. We investigated the influence of diabetes on breast cancer biology using a 3-pronged approach that included analysis of orthotopic human tumor xenografts, patient tumors, and breast cancer cells exposed to diabetes/hyperglycemia-like conditions. We aimed to identify shared phenotypes and molecular signatures by investigating the metabolome, transcriptome, and tumor mutational burden. Diabetes and hyperglycemia did not enhance cell proliferation but induced mesenchymal and stem cell-like phenotypes linked to increased mobility and odds of metastasis. They also promoted oxyradical formation and both a transcriptome and mutational signatures of DNA repair deficiency. Moreover, food- and microbiome-derived metabolites tended to accumulate in breast tumors in the presence of diabetes, potentially affecting tumor biology. Breast cancer cells cultured under hyperglycemia-like conditions acquired increased DNA damage and sensitivity to DNA repair inhibitors. Based on these observations, we conclude that diabetes-associated breast tumors may show an increased drug response to DNA damage repair inhibitors.
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Affiliation(s)
- Gatikrushna Panigrahi
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute (NCI), NIH, Bethesda, Maryland, USA
| | - Julián Candia
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute (NCI), NIH, Bethesda, Maryland, USA
- Longitudinal Studies Section, Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, Maryland, USA
| | - Tiffany H. Dorsey
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute (NCI), NIH, Bethesda, Maryland, USA
| | - Wei Tang
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute (NCI), NIH, Bethesda, Maryland, USA
- Data Science & Artificial Intelligence, R&D, AstraZeneca, Gaithersburg, Maryland, USA
| | - Yuuki Ohara
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute (NCI), NIH, Bethesda, Maryland, USA
| | - Jung S. Byun
- Division of Intramural Research, National Institute of Minority Health and Health Disparities, NIH, Bethesda, Maryland, USA
| | - Tsion Zewdu Minas
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute (NCI), NIH, Bethesda, Maryland, USA
| | - Amy Zhang
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute (NCI), NIH, Bethesda, Maryland, USA
| | - Anuoluwapo Ajao
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute (NCI), NIH, Bethesda, Maryland, USA
| | - Ashley Cellini
- Department of Pathology, University of Maryland Medical Center, Baltimore, Maryland, USA
| | - Harris G. Yfantis
- Department of Pathology, University of Maryland Medical Center and Veterans Affairs Maryland Care System, Baltimore, Maryland, USA
| | - Amy L. Flis
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute (NCI), NIH, Bethesda, Maryland, USA
| | - Dean Mann
- Department of Pathology, University of Maryland Medical Center, Baltimore, Maryland, USA
| | - Olga Ioffe
- Department of Pathology, University of Maryland Medical Center, Baltimore, Maryland, USA
| | - Xin W. Wang
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute (NCI), NIH, Bethesda, Maryland, USA
- Liver Cancer Program, Center for Cancer Research, NCI, NIH, Bethesda, Maryland, USA
| | - Huaitian Liu
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute (NCI), NIH, Bethesda, Maryland, USA
| | - Christopher A. Loffredo
- Cancer Prevention and Control Program, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, USA
| | - Anna Maria Napoles
- Division of Intramural Research, National Institute of Minority Health and Health Disparities, NIH, Bethesda, Maryland, USA
| | - Stefan Ambs
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute (NCI), NIH, Bethesda, Maryland, USA
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42
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Tomofuji Y, Kishikawa T, Sonehara K, Maeda Y, Ogawa K, Kawabata S, Oguro-Igashira E, Okuno T, Nii T, Kinoshita M, Takagaki M, Yamamoto K, Arase N, Yagita-Sakamaki M, Hosokawa A, Motooka D, Matsumoto Y, Matsuoka H, Yoshimura M, Ohshima S, Nakamura S, Fujimoto M, Inohara H, Kishima H, Mochizuki H, Takeda K, Kumanogoh A, Okada Y. Analysis of gut microbiome, host genetics, and plasma metabolites reveals gut microbiome-host interactions in the Japanese population. Cell Rep 2023; 42:113324. [PMID: 37935197 DOI: 10.1016/j.celrep.2023.113324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 09/11/2023] [Accepted: 10/06/2023] [Indexed: 11/09/2023] Open
Abstract
Interaction between the gut microbiome and host plays a key role in human health. Here, we perform a metagenome shotgun-sequencing-based analysis of Japanese participants to reveal associations between the gut microbiome, host genetics, and plasma metabolome. A genome-wide association study (GWAS) for microbial species (n = 524) identifies associations between the PDE1C gene locus and Bacteroides intestinalis and between TGIF2 and TGIF2-RAB5IF gene loci and Bacteroides acidifiaciens. In a microbial gene ortholog GWAS, agaE and agaS, which are related to the metabolism of carbohydrates forming the blood group A antigen, are associated with blood group A in a manner depending on the secretor status determined by the East Asian-specific FUT2 variant. A microbiome-metabolome association analysis (n = 261) identifies associations between bile acids and microbial features such as bile acid metabolism gene orthologs including bai and 7β-hydroxysteroid dehydrogenase. Our publicly available data will be a useful resource for understanding gut microbiome-host interactions in an underrepresented population.
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Affiliation(s)
- Yoshihiko Tomofuji
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita 565-0871, Japan; Laboratory for Systems Genetics, RIKEN Center for Integrative Medical Sciences, Tsurumi 230-0045, Japan; Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita 565-0871, Japan; Department of Genome Informatics, Graduate School of Medicine, the University of Tokyo, Tokyo 113-8654, Japan.
| | - Toshihiro Kishikawa
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita 565-0871, Japan; Department of Otorhinolaryngology-Head and Neck Surgery, Osaka University Graduate School of Medicine, Suita 565-0871, Japan; Department of Head and Neck Surgery, Aichi Cancer Center Hospital, Nagoya 464-8681, Japan
| | - Kyuto Sonehara
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita 565-0871, Japan; Laboratory for Systems Genetics, RIKEN Center for Integrative Medical Sciences, Tsurumi 230-0045, Japan; Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita 565-0871, Japan; Department of Genome Informatics, Graduate School of Medicine, the University of Tokyo, Tokyo 113-8654, Japan
| | - Yuichi Maeda
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita 565-0871, Japan; Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita 565-0871, Japan; Laboratory of Immune Regulation, Department of Microbiology and Immunology, Osaka University Graduate School of Medicine, Suita 565-0871, Japan
| | - Kotaro Ogawa
- Department of Neurology, Osaka University Graduate School of Medicine, Suita 565-0871, Japan
| | - Shuhei Kawabata
- Department of Neurosurgery, Osaka University Graduate School of Medicine, Suita 565-0871, Japan
| | - Eri Oguro-Igashira
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita 565-0871, Japan; Laboratory of Immune Regulation, Department of Microbiology and Immunology, Osaka University Graduate School of Medicine, Suita 565-0871, Japan
| | - Tatsusada Okuno
- Department of Neurology, Osaka University Graduate School of Medicine, Suita 565-0871, Japan
| | - Takuro Nii
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita 565-0871, Japan; Laboratory of Immune Regulation, Department of Microbiology and Immunology, Osaka University Graduate School of Medicine, Suita 565-0871, Japan
| | - Makoto Kinoshita
- Department of Neurology, Osaka University Graduate School of Medicine, Suita 565-0871, Japan
| | - Masatoshi Takagaki
- Department of Neurosurgery, Osaka University Graduate School of Medicine, Suita 565-0871, Japan
| | - Kenichi Yamamoto
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita 565-0871, Japan; Department of Pediatrics, Osaka University Graduate School of Medicine, Suita 565-0871, Japan; Laboratory of Statistical Immunology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita 565-0871, Japan
| | - Noriko Arase
- Department of Dermatology, Osaka University Graduate School of Medicine, Suita 565-0871, Japan
| | - Mayu Yagita-Sakamaki
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita 565-0871, Japan; Laboratory of Immune Regulation, Department of Microbiology and Immunology, Osaka University Graduate School of Medicine, Suita 565-0871, Japan
| | - Akiko Hosokawa
- Department of Neurology, Osaka University Graduate School of Medicine, Suita 565-0871, Japan; Department of Neurology, Suita Municipal Hospital, Suita 564-8567, Japan
| | - Daisuke Motooka
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita 565-0871, Japan; Department of Infection Metagenomics, Research Institute for Microbial Diseases, Osaka University, Suita 565-0871, Japan
| | - Yuki Matsumoto
- Department of Infection Metagenomics, Research Institute for Microbial Diseases, Osaka University, Suita 565-0871, Japan
| | - Hidetoshi Matsuoka
- Department of Rheumatology and Allergology, NHO Osaka Minami Medical Center, Kawachinagano 586-8521, Japan
| | - Maiko Yoshimura
- Department of Rheumatology and Allergology, NHO Osaka Minami Medical Center, Kawachinagano 586-8521, Japan
| | - Shiro Ohshima
- Department of Rheumatology and Allergology, NHO Osaka Minami Medical Center, Kawachinagano 586-8521, Japan
| | - Shota Nakamura
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita 565-0871, Japan; Department of Infection Metagenomics, Research Institute for Microbial Diseases, Osaka University, Suita 565-0871, Japan; Center for Infectious Disease Education and Research, Osaka University, Suita 565-0871, Japan
| | - Manabu Fujimoto
- Department of Dermatology, Osaka University Graduate School of Medicine, Suita 565-0871, Japan
| | - Hidenori Inohara
- Department of Otorhinolaryngology-Head and Neck Surgery, Osaka University Graduate School of Medicine, Suita 565-0871, Japan
| | - Haruhiko Kishima
- Department of Neurosurgery, Osaka University Graduate School of Medicine, Suita 565-0871, Japan
| | - Hideki Mochizuki
- Department of Neurology, Osaka University Graduate School of Medicine, Suita 565-0871, Japan
| | - Kiyoshi Takeda
- Laboratory of Immune Regulation, Department of Microbiology and Immunology, Osaka University Graduate School of Medicine, Suita 565-0871, Japan; Center for Infectious Disease Education and Research, Osaka University, Suita 565-0871, Japan; WPI Immunology Frontier Research Center, Osaka University, Suita 565-0871, Japan
| | - Atsushi Kumanogoh
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita 565-0871, Japan; Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita 565-0871, Japan; Department of Immunopathology, Immunology Frontier Research Center, Osaka University, Suita 565-0871, Japan
| | - Yukinori Okada
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita 565-0871, Japan; Laboratory for Systems Genetics, RIKEN Center for Integrative Medical Sciences, Tsurumi 230-0045, Japan; Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita 565-0871, Japan; Department of Genome Informatics, Graduate School of Medicine, the University of Tokyo, Tokyo 113-8654, Japan; Laboratory of Statistical Immunology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita 565-0871, Japan; Center for Infectious Disease Education and Research, Osaka University, Suita 565-0871, Japan; Premium Research Institute for Human Metaverse Medicine (WPI-PRIMe), Osaka University, Suita 565-0871, Japan.
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Verhaar BJH, Mosterd CM, Collard D, Galenkamp H, Muller M, Rampanelli E, van Raalte DH, Nieuwdorp M, van den Born BJH. Sex differences in associations of plasma metabolites with blood pressure and heart rate variability: The HELIUS study. Atherosclerosis 2023; 384:117147. [PMID: 37286456 DOI: 10.1016/j.atherosclerosis.2023.05.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 04/27/2023] [Accepted: 05/17/2023] [Indexed: 06/09/2023]
Abstract
BACKGROUND AND AIMS Since plasma metabolites can modulate blood pressure (BP) and vary between men and women, we examined sex differences in plasma metabolite profiles associated with BP and sympathicovagal balance. Our secondary aim was to investigate associations between gut microbiota composition and plasma metabolites predictive of BP and heart rate variability (HRV). METHODS From the HELIUS cohort, we included 196 women and 173 men. Office systolic BP and diastolic BP were recorded, and heart rate variability (HRV) and baroreceptor sensitivity (BRS) were calculated using finger photoplethysmography. Plasma metabolomics was measured using untargeted LC-MS/MS. Gut microbiota composition was determined using 16S sequencing. We used machine learning models to predict BP and HRV from metabolite profiles, and to predict metabolite levels from gut microbiota composition. RESULTS In women, best predicting metabolites for systolic BP included dihomo-lineoylcarnitine, 4-hydroxyphenylacetateglutamine and vanillactate. In men, top predictors included sphingomyelins, N-formylmethionine and conjugated bile acids. Best predictors for HRV in men included phenylacetate and gentisate, which were associated with lower HRV in men but not in women. Several of these metabolites were associated with gut microbiota composition, including phenylacetate, multiple sphingomyelins and gentisate. CONCLUSIONS Plasma metabolite profiles are associated with BP in a sex-specific manner. Catecholamine derivatives were more important predictors for BP in women, while sphingomyelins were more important in men. Several metabolites were associated with gut microbiota composition, providing potential targets for intervention.
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Affiliation(s)
- Barbara J H Verhaar
- Department of Internal and Vascular Medicine, Amsterdam UMC, Location AMC, Amsterdam, the Netherlands; Department of Internal Medicine - Geriatrics, Amsterdam UMC, Location VUmc, Amsterdam Cardiovascular Sciences, Amsterdam, the Netherlands.
| | - Charlotte M Mosterd
- Department of Internal and Vascular Medicine, Amsterdam UMC, Location AMC, Amsterdam, the Netherlands; Diabetes Center, Department of Internal Medicine, Amsterdam UMC, Location VUmc, Amsterdam, the Netherlands
| | - Didier Collard
- Department of Internal and Vascular Medicine, Amsterdam UMC, Location AMC, Amsterdam, the Netherlands
| | - Henrike Galenkamp
- Department of Public and Occupational Health, Amsterdam UMC, Location AMC, Amsterdam, the Netherlands; Amsterdam Public Health Research Institute, Health Behaviors and Chronic Diseases, Amsterdam, the Netherlands
| | - Majon Muller
- Department of Internal Medicine - Geriatrics, Amsterdam UMC, Location VUmc, Amsterdam Cardiovascular Sciences, Amsterdam, the Netherlands
| | - Elena Rampanelli
- Department of Internal and Vascular Medicine, Amsterdam UMC, Location AMC, Amsterdam, the Netherlands
| | - Daniël H van Raalte
- Department of Internal and Vascular Medicine, Amsterdam UMC, Location AMC, Amsterdam, the Netherlands; Diabetes Center, Department of Internal Medicine, Amsterdam UMC, Location VUmc, Amsterdam, the Netherlands
| | - Max Nieuwdorp
- Department of Internal and Vascular Medicine, Amsterdam UMC, Location AMC, Amsterdam, the Netherlands; Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Sahlgrenska Academy, Goteborgs Universitet, Gothenburg, Sweden
| | - Bert-Jan H van den Born
- Department of Internal and Vascular Medicine, Amsterdam UMC, Location AMC, Amsterdam, the Netherlands; Department of Public and Occupational Health, Amsterdam UMC, Location AMC, Amsterdam, the Netherlands
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44
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Feng J, Yang K, Liu X, Song M, Zhan P, Zhang M, Chen J, Liu J. Machine learning: a powerful tool for identifying key microbial agents associated with specific cancer types. PeerJ 2023; 11:e16304. [PMID: 37901464 PMCID: PMC10601900 DOI: 10.7717/peerj.16304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 09/26/2023] [Indexed: 10/31/2023] Open
Abstract
Machine learning (ML) includes a broad class of computer programs that improve with experience and shows unique strengths in performing tasks such as clustering, classification and regression. Over the past decade, microbial communities have been implicated in influencing the onset, progression, metastasis, and therapeutic response of multiple cancers. Host-microbe interaction may be a physiological pathway contributing to cancer development. With the accumulation of a large number of high-throughput data, ML has been successfully applied to the study of human cancer microbiomics in an attempt to reveal the complex mechanism behind cancer. In this review, we begin with a brief overview of the data sources included in cancer microbiomics studies. Then, the characteristics of the ML algorithm are briefly introduced. Secondly, the application progress of ML in cancer microbiomics is also reviewed. Finally, we highlight the challenges and future prospects facing ML in cancer microbiomics. On this basis, we conclude that the development of cancer microbiomics can not be achieved without ML, and that ML can be used to develop tumor-targeting microbial therapies, ultimately contributing to personalized and precision medicine.
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Affiliation(s)
- Jia Feng
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Sichuan Province Engineering Technology Research Center of Molecular Diagnosis of Clinical Diseases, Molecular Diagnosis of Clinical Diseases Key Laboratory of Luzhou, Sichuan, China
| | - Kailan Yang
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Sichuan Province Engineering Technology Research Center of Molecular Diagnosis of Clinical Diseases, Molecular Diagnosis of Clinical Diseases Key Laboratory of Luzhou, Sichuan, China
| | - Xuexue Liu
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Sichuan Province Engineering Technology Research Center of Molecular Diagnosis of Clinical Diseases, Molecular Diagnosis of Clinical Diseases Key Laboratory of Luzhou, Sichuan, China
| | - Min Song
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Sichuan Province Engineering Technology Research Center of Molecular Diagnosis of Clinical Diseases, Molecular Diagnosis of Clinical Diseases Key Laboratory of Luzhou, Sichuan, China
| | - Ping Zhan
- Department of Obstetrics, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
| | - Mi Zhang
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Sichuan Province Engineering Technology Research Center of Molecular Diagnosis of Clinical Diseases, Molecular Diagnosis of Clinical Diseases Key Laboratory of Luzhou, Sichuan, China
| | - Jinsong Chen
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Sichuan Province Engineering Technology Research Center of Molecular Diagnosis of Clinical Diseases, Molecular Diagnosis of Clinical Diseases Key Laboratory of Luzhou, Sichuan, China
| | - Jinbo Liu
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Sichuan Province Engineering Technology Research Center of Molecular Diagnosis of Clinical Diseases, Molecular Diagnosis of Clinical Diseases Key Laboratory of Luzhou, Sichuan, China
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45
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Astarita G, Kelly RS, Lasky-Su J. Metabolomics and lipidomics strategies in modern drug discovery and development. Drug Discov Today 2023; 28:103751. [PMID: 37640150 PMCID: PMC10543515 DOI: 10.1016/j.drudis.2023.103751] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 08/09/2023] [Accepted: 08/21/2023] [Indexed: 08/31/2023]
Abstract
Metabolomics and lipidomics have an increasingly pivotal role in drug discovery and development. In the context of drug discovery, monitoring changes in the levels or composition of metabolites and lipids relative to genetic variations yields functional insights, bolstering human genetics and (meta)genomic methodologies. This approach also sheds light on potential novel targets for therapeutic intervention. In the context of drug development, metabolite and lipid biomarkers contribute to enhanced success rates, promising a transformative impact on precision medicine. In this review, we deviate from analytical chemist-focused perspectives, offering an overview tailored to drug discovery. We provide introductory insight into state-of-the-art mass spectrometry (MS)-based metabolomics and lipidomics techniques utilized in drug discovery and development, drawing from the collective expertise of our research teams. We comprehensively outline the application of metabolomics and lipidomics in advancing drug discovery and development, spanning fundamental research, target identification, mechanisms of action, and the exploration of biomarkers.
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Affiliation(s)
- Giuseppe Astarita
- Georgetown University, Washington, DC, USA; Arkuda Therapeutics, Watertown, MA, USA.
| | - Rachel S Kelly
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Jessica Lasky-Su
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
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46
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Du J, Zhang C, Liu F, Liu X, Wang D, Zhao D, Shui G, Zhao Y, Yan C. Distinctive metabolic remodeling in TYMP deficiency beyond mitochondrial dysfunction. J Mol Med (Berl) 2023; 101:1237-1253. [PMID: 37603049 DOI: 10.1007/s00109-023-02358-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 07/09/2023] [Accepted: 08/14/2023] [Indexed: 08/22/2023]
Abstract
Mitochondrial neurogastrointestinal encephalomyopathy (MNGIE) is caused by mutations in the TYMP gene, which encodes thymidine phosphorylase (TP). As a cytosolic metabolic enzyme, TP defects affect biological processes that are thought to not be limited to the abnormal replication of mitochondrial DNA. This study aimed to elucidate the characteristic metabolic alterations and associated homeostatic regulation caused by TYMP deficiency. The pathogenicity of novel TYMP variants was evaluated in terms of clinical features, genetic analysis, and structural instability. We analyzed plasma samples from three patients with MNGIE; three patients with m.3243A > G mitochondrial encephalopathy, lactic acidosis, and stroke-like episodes (MELAS); and four healthy controls (HC) using both targeted and untargeted metabolomics techniques. Transcriptomics analysis and bioenergetic studies were performed on skin fibroblasts from participants in these three groups. A TYMP overexpression experiment was conducted to rescue the observed changes. Compared with controls, specific alterations in nucleosides, bile acids, and steroid metabolites were identified in the plasma of MNGIE patients. Comparable mitochondrial dysfunction was present in fibroblasts from patients with TYMP deficiency and in those from patients with the m.3243A > G mutation. Distinctively decreased sterol regulatory element binding protein (SREBP) regulated cholesterol metabolism and fatty acid (FA) biosynthesis as well as reduced FA degradation were revealed in fibroblasts with TYMP deficiency. The restoration of thymidine phosphorylase activity rescued the observed changes in MNGIE fibroblasts. Our findings indicated that more widespread metabolic disturbance may be caused by TYMP deficiency in addition to mitochondrial dysfunction, which expands our knowledge of the biochemical outcome of TYMP deficiency. KEY MESSAGES: Distinct metabolic profiles in patients with TYMP deficiency compared to those with m.3243A > G mutation. TYMP deficiency leads to a global disruption of nucleoside metabolism. Cholesterol and fatty acid metabolism are inhibited in individuals with MNGIE. TYMP is functionally related to SREBP-regulated pathways. Potential metabolite biomarkers that could be valuable clinical tools to improve the diagnosis of MNGIE.
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Affiliation(s)
- Jixiang Du
- Department of Neurology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250012, China
| | - Chao Zhang
- Key Laboratory of Experimental Teratology, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, 250012, China
| | - Fuchen Liu
- Department of Neurology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250012, China
| | - Xihan Liu
- Key Laboratory of Experimental Teratology, Ministry of Education, Department of Cell Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, 250012, China
| | - Dongdong Wang
- Department of Neurology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250012, China
| | - Dandan Zhao
- Department of Neurology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250012, China
| | - Guanghou Shui
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of the Chinese Academy of Sciences, Beijing, 101408, China
| | - Yuying Zhao
- Department of Neurology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250012, China
| | - Chuanzhu Yan
- Department of Neurology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250012, China.
- Qingdao Key Lab of Mitochondrial Medicine, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Qingdao, 266103, China.
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47
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Zubiri-Gaitán A, Blasco A, Hernández P. Plasma metabolomic profiling in two rabbit lines divergently selected for intramuscular fat content. Commun Biol 2023; 6:893. [PMID: 37653068 PMCID: PMC10471702 DOI: 10.1038/s42003-023-05266-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 08/21/2023] [Indexed: 09/02/2023] Open
Abstract
This study provides a thorough comparison of the plasma metabolome of two rabbit lines divergently selected for intramuscular fat content (IMF). The divergent selection led to a correlated response in the overall adiposity, turning these lines into a valuable animal material to study also the genetics of obesity. Over 900 metabolites were detected, and the adjustment of multivariate models, both discriminant and linear, allowed to identify 322 with differential abundances between lines, which also adjusted linearly to the IMF content. The most affected pathways were those of lipids and amino acids, with differences between lines ranging from 0.23 to 6.04 standard deviations, revealing a limited capacity of the low-IMF line to obtain energy from lipids, and a greater branched-chain amino acids catabolism in the high-IMF line related to its increased IMF content. Additionally, changes in metabolites derived from microbial activity supported its relevant role in the lipid deposition. Future research will focus on the analysis of the metabolomic profile of the cecum content, and on the integration of the several -omics datasets available for these lines, to help disentangle the host and microbiome biological mechanisms involved in the IMF deposition.
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Affiliation(s)
- Agostina Zubiri-Gaitán
- Institute for Animal Science and Technology, Universitat Politècnica de València, Valencia, Spain.
| | - Agustín Blasco
- Institute for Animal Science and Technology, Universitat Politècnica de València, Valencia, Spain
| | - Pilar Hernández
- Institute for Animal Science and Technology, Universitat Politècnica de València, Valencia, Spain.
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Lan J, Greter G, Streckenbach B, Wanner B, Arnoldini M, Zenobi R, Slack E. Non-invasive monitoring of microbiota and host metabolism using secondary electrospray ionization-mass spectrometry. CELL REPORTS METHODS 2023; 3:100539. [PMID: 37671025 PMCID: PMC10475793 DOI: 10.1016/j.crmeth.2023.100539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 05/08/2023] [Accepted: 06/28/2023] [Indexed: 09/07/2023]
Abstract
The metabolic "handshake" between the microbiota and its mammalian host is a complex, dynamic process with major influences on health. Dissecting the interaction between microbial species and metabolites found in host tissues has been a challenge due to the requirement for invasive sampling. Here, we demonstrate that secondary electrospray ionization-mass spectrometry (SESI-MS) can be used to non-invasively monitor metabolic activity of the intestinal microbiome of a live, awake mouse. By comparing the headspace metabolome of individual gut bacterial culture with the "volatilome" (metabolites released to the atmosphere) of gnotobiotic mice, we demonstrate that the volatilome is characteristic of the dominant colonizing bacteria. Combining SESI-MS with feeding heavy-isotope-labeled microbiota-accessible sugars reveals the presence of microbial cross-feeding within the animal intestine. The microbiota is, therefore, a major contributor to the volatilome of a living animal, and it is possible to capture inter-species interaction within the gut microbiota using volatilome monitoring.
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Affiliation(s)
- Jiayi Lan
- Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
| | - Giorgia Greter
- Department of Health Sciences and Technology, ETH Zurich, 8093 Zurich, Switzerland
| | - Bettina Streckenbach
- Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
| | | | - Markus Arnoldini
- Department of Health Sciences and Technology, ETH Zurich, 8093 Zurich, Switzerland
| | - Renato Zenobi
- Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
| | - Emma Slack
- Department of Health Sciences and Technology, ETH Zurich, 8093 Zurich, Switzerland
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49
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Sarmiento KR, Carr A, Diener C, Locey KJ, Gibbons SM. Island biogeography theory and the gut: why taller people tend to harbor more diverse gut microbiomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.08.552554. [PMID: 37609334 PMCID: PMC10441360 DOI: 10.1101/2023.08.08.552554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Prior work has shown a positive scaling relationship between vertebrate body size and gut microbiome alpha-diversity. This observation mirrors commonly observed species area relationships (SAR) in many other ecosystems. Here, we show a similar scaling relationship between human height and gut microbiome alpha-diversity across two large, independent cohorts, controlling for a wide range of relevant covariates, such as body mass index, age, sex, and bowel movement frequency. Island Biogeography Theory (IBT), which predicts that larger islands tend to harbor greater species diversity through neutral demographic processes, provides a simple mechanism for these positive SARs. Using an individual-based model of IBT adapted to the gut, we demonstrate that increasing the length of a flow-through ecosystem is associated with increased species diversity. We delve into the possible clinical implications of these SARs in the American Gut Cohort. Consistent with prior observations that lower alpha-diversity is a risk factor for Clostridioides difficile infection (CDI), we found that individuals who reported a history of CDI were shorter than those who did not and that this relationship appeared to be mediated by alpha-diversity. We also observed that vegetable consumption mitigated this risk increase, also by mediation through alpha-diversity. In summary, we find that body size and gut microbiome diversity show a robust positive association, that this macroecological scaling relationship is related to CDI risk, and that greater vegetable intake can mitigate this effect.
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Affiliation(s)
| | - Alex Carr
- Institute for Systems Biology, Seattle, WA 98109, USA
- Molecular Engineering Graduate Program, University of Washington, Seattle, WA 98195, USA
| | | | - Kenneth J. Locey
- Center for Quality, Safety & Value Analytics, Rush University Medical Center, Chicago, IL 60612, USA
| | - Sean M. Gibbons
- Institute for Systems Biology, Seattle, WA 98109, USA
- Molecular Engineering Graduate Program, University of Washington, Seattle, WA 98195, USA
- Department of Biological Engineering, University of Washington, Seattle, WA 98195, USA
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- eScience Institute, University of Washington, Seattle, WA 98195, USA
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50
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Ujlaki G, Kovács T, Vida A, Kókai E, Rauch B, Schwarcz S, Mikó E, Janka E, Sipos A, Hegedűs C, Uray K, Nagy P, Bai P. Identification of Bacterial Metabolites Modulating Breast Cancer Cell Proliferation and Epithelial-Mesenchymal Transition. Molecules 2023; 28:5898. [PMID: 37570868 PMCID: PMC10420980 DOI: 10.3390/molecules28155898] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 07/27/2023] [Accepted: 08/02/2023] [Indexed: 08/13/2023] Open
Abstract
Breast cancer patients are characterized by the oncobiotic transformation of multiple microbiome communities, including the gut microbiome. Oncobiotic transformation of the gut microbiome impairs the production of antineoplastic bacterial metabolites. The goal of this study was to identify bacterial metabolites with antineoplastic properties. We constructed a 30-member bacterial metabolite library and screened the library compounds for effects on cell proliferation and epithelial-mesenchymal transition. The metabolites were applied to 4T1 murine breast cancer cells in concentrations corresponding to the reference serum concentrations. However, yric acid, glycolic acid, d-mannitol, 2,3-butanediol, and trans-ferulic acid exerted cytostatic effects, and 3-hydroxyphenylacetic acid, 4-hydroxybenzoic acid, and vanillic acid exerted hyperproliferative effects. Furthermore, 3-hydroxyphenylacetic acid, 4-hydroxybenzoic acid, 2,3-butanediol, and hydrocinnamic acid inhibited epithelial-to-mesenchymal (EMT) transition. We identified redox sets among the metabolites (d-mannitol-d-mannose, 1-butanol-butyric acid, ethylene glycol-glycolic acid-oxalic acid), wherein only one partner within the set (d-mannitol, butyric acid, glycolic acid) possessed bioactivity in our system, suggesting that changes to the local redox potential may affect the bacterial secretome. Of the nine bioactive metabolites, 2,3-butanediol was the only compound with both cytostatic and anti-EMT properties.
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Affiliation(s)
- Gyula Ujlaki
- Department of Medical Chemistry, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (G.U.); (T.K.); (A.V.); (E.K.); (B.R.); (S.S.); (E.M.); (A.S.); (C.H.); (K.U.)
| | - Tünde Kovács
- Department of Medical Chemistry, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (G.U.); (T.K.); (A.V.); (E.K.); (B.R.); (S.S.); (E.M.); (A.S.); (C.H.); (K.U.)
| | - András Vida
- Department of Medical Chemistry, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (G.U.); (T.K.); (A.V.); (E.K.); (B.R.); (S.S.); (E.M.); (A.S.); (C.H.); (K.U.)
| | - Endre Kókai
- Department of Medical Chemistry, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (G.U.); (T.K.); (A.V.); (E.K.); (B.R.); (S.S.); (E.M.); (A.S.); (C.H.); (K.U.)
| | - Boglára Rauch
- Department of Medical Chemistry, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (G.U.); (T.K.); (A.V.); (E.K.); (B.R.); (S.S.); (E.M.); (A.S.); (C.H.); (K.U.)
| | - Szandra Schwarcz
- Department of Medical Chemistry, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (G.U.); (T.K.); (A.V.); (E.K.); (B.R.); (S.S.); (E.M.); (A.S.); (C.H.); (K.U.)
| | - Edit Mikó
- Department of Medical Chemistry, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (G.U.); (T.K.); (A.V.); (E.K.); (B.R.); (S.S.); (E.M.); (A.S.); (C.H.); (K.U.)
| | - Eszter Janka
- Department of Dermatology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary;
| | - Adrienn Sipos
- Department of Medical Chemistry, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (G.U.); (T.K.); (A.V.); (E.K.); (B.R.); (S.S.); (E.M.); (A.S.); (C.H.); (K.U.)
| | - Csaba Hegedűs
- Department of Medical Chemistry, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (G.U.); (T.K.); (A.V.); (E.K.); (B.R.); (S.S.); (E.M.); (A.S.); (C.H.); (K.U.)
| | - Karen Uray
- Department of Medical Chemistry, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (G.U.); (T.K.); (A.V.); (E.K.); (B.R.); (S.S.); (E.M.); (A.S.); (C.H.); (K.U.)
| | - Péter Nagy
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary;
| | - Peter Bai
- Department of Medical Chemistry, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (G.U.); (T.K.); (A.V.); (E.K.); (B.R.); (S.S.); (E.M.); (A.S.); (C.H.); (K.U.)
- MTA-DE Lendület Laboratory of Cellular Metabolism, 4032 Debrecen, Hungary
- Research Center for Molecular Medicine, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
- ELKH-DE Cell Biology and Signaling Research Group ELKH, 4032 Debrecen, Hungary
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