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Sun T, Sun D, Kuang J, Chao X, Guo Y, Li M, Chen T. A cross-omics data analysis strategy for metabolite-microbe pair identification. Proteomics 2024:e2400035. [PMID: 38994817 DOI: 10.1002/pmic.202400035] [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: 01/24/2024] [Revised: 06/22/2024] [Accepted: 07/02/2024] [Indexed: 07/13/2024]
Abstract
Given the pivotal roles of metabolomics and microbiomics, numerous data mining approaches aim to uncover their intricate connections. However, the complex many-to-many associations between metabolome-microbiome profiles yield numerous statistically significant but biologically unvalidated candidates. To address these challenges, we introduce BiOFI, a strategic framework for identifying metabolome-microbiome correlation pairs (Bi-Omics). BiOFI employs a comprehensive scoring system, incorporating intergroup differences, effects on feature correlation networks, and organism abundance. Meanwhile, it establishes a built-in database of metabolite-microbe-KEGG functional pathway linking relationships. Furthermore, BiOFI can rank related feature pairs by combining importance scores and correlation strength. Validation on a dataset of cesarean-section infants confirms the strategy's validity and interpretability. The BiOFI R package is freely accessible at https://github.com/chentianlu/BiOFI.
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Affiliation(s)
- Tao Sun
- Center for Translational Medicine, The Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Dongnan Sun
- Center for Translational Medicine, The Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Junliang Kuang
- Center for Translational Medicine, The Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiaowen Chao
- Center for Translational Medicine, The Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yihan Guo
- School of Medicine, Faculty of Medicine, The University of Queensland, Brisbane, Australia
| | - Mengci Li
- Center for Translational Medicine, The Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Tianlu Chen
- Center for Translational Medicine, The Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
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2
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Gao Y, Chen Q, Liu S, Wang J, Borthwick AGL, Ni J. The mystery of rich human gut antibiotic resistome in the Yellow River with hyper-concentrated sediment-laden flow. WATER RESEARCH 2024; 258:121763. [PMID: 38759286 DOI: 10.1016/j.watres.2024.121763] [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: 03/26/2024] [Revised: 04/30/2024] [Accepted: 05/09/2024] [Indexed: 05/19/2024]
Abstract
Human gut antibiotic resistome widely occur in anoxic environments characterized by high density of bacterial cells and frequent transmission of antibiotic resistance genes (ARGs). Such resistome is greatly diluted, degraded, and restrained in the aerobic habitats within most natural rivers (regarded as "terrestrial guts") connecting continents and the oceans. Here we implemented a large-scale monitoring campaign extending 5,200 km along the Yellow River, and provide the first integral biogeographic pattern for both ARGs and their hosts. We identified plentiful ARGs (24 types and 809 subtypes) and their hosts (24 phyla and 757 MAGs) in three media (water, suspended particulate matter (SPM), and sediment). Unexpectedly, we found diverse human gut bacteria (HGB) acting as supercarriers of ARGs in this oxygen-rich river. We further discovered that numerous microhabitats were created within stratified biofilms that surround SPMs, particularly regarding the aggregation of anaerobic HGB. These microhabitats provide numerous ideal sinks for anaerobic bacteria and facilitate horizontal transfer of ARGs within the stratified biofilms, Furthermore, the stratification of biofilms surrounding SPMs has facilitated synergy between human gut flora and denitrifiers for propagation of ARGs in the anoxic atmospheres, leading to high occurrence of human gut antibiotic resistome. SPMs play active roles in the dynamic interactions of river water and sediment, thus accelerating the evolution of riverine resistome and transmission of human gut antibiotic resistome. This study revealed the special contribution of SPMs to the propagation of ARGs, and highlighted the necessity of making alternative strategies for sustainable management of large rivers with hyper-concentrated sediment-laden flows.
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Affiliation(s)
- Yuan Gao
- School of Water Resources and Environment, China University of Geosciences (Beijing), Beijing 100083, PR China; Key Laboratory of Water and Sediment Sciences, Ministry of Education, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, PR China
| | - Qian Chen
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, PR China; State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, Beijing 100871, PR China
| | - Shufeng Liu
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, PR China
| | - Jiawen Wang
- Eco-environment and Resource Efficiency Research Laboratory, School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen 518055, PR China; Environmental Microbiome and Innovative Genomics Laboratory, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, PR China
| | - Alistair G L Borthwick
- School of Engineering, Computing and Mathematics, University of Plymouth, Plymouth PL4 8AA, United Kingdom
| | - Jinren Ni
- Yellow River Laboratory of Shanxi Province, Shanxi University, Taiyuan 237016, PR China.
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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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Mishra AK, Mahmud I, Lorenzi PL, Jenq RR, Wargo JA, Ajami NJ, Peterson CB. TARO: tree-aggregated factor regression for microbiome data integration. Bioinformatics 2024; 40:btae321. [PMID: 38788190 PMCID: PMC11193058 DOI: 10.1093/bioinformatics/btae321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 03/16/2024] [Accepted: 05/15/2024] [Indexed: 05/26/2024] Open
Abstract
MOTIVATION Although the human microbiome plays a key role in health and disease, the biological mechanisms underlying the interaction between the microbiome and its host are incompletely understood. Integration with other molecular profiling data offers an opportunity to characterize the role of the microbiome and elucidate therapeutic targets. However, this remains challenging to the high dimensionality, compositionality, and rare features found in microbiome profiling data. These challenges necessitate the use of methods that can achieve structured sparsity in learning cross-platform association patterns. RESULTS We propose Tree-Aggregated factor RegressiOn (TARO) for the integration of microbiome and metabolomic data. We leverage information on the taxonomic tree structure to flexibly aggregate rare features. We demonstrate through simulation studies that TARO accurately recovers a low-rank coefficient matrix and identifies relevant features. We applied TARO to microbiome and metabolomic profiles gathered from subjects being screened for colorectal cancer to understand how gut microrganisms shape intestinal metabolite abundances. AVAILABILITY AND IMPLEMENTATION The R package TARO implementing the proposed methods is available online at https://github.com/amishra-stats/taro-package.
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Affiliation(s)
- Aditya K Mishra
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, United States
- Platform for Innovative Microbiome and Translational Research (PRIME-TR), The University of Texas MD Anderson Cancer Center, Houston, TX 77030, United States
| | - Iqbal Mahmud
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, United States
| | - Philip L Lorenzi
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, United States
| | - Robert R Jenq
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, United States
- Platform for Innovative Microbiome and Translational Research (PRIME-TR), The University of Texas MD Anderson Cancer Center, Houston, TX 77030, United States
| | - Jennifer A Wargo
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, United States
- Platform for Innovative Microbiome and Translational Research (PRIME-TR), The University of Texas MD Anderson Cancer Center, Houston, TX 77030, United States
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, United States
| | - Nadim J Ajami
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, United States
- Platform for Innovative Microbiome and Translational Research (PRIME-TR), The University of Texas MD Anderson Cancer Center, Houston, TX 77030, United States
| | - Christine B Peterson
- Platform for Innovative Microbiome and Translational Research (PRIME-TR), The University of Texas MD Anderson Cancer Center, Houston, TX 77030, United States
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, United States
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Challa A, Maras JS, Nagpal S, Tripathi G, Taneja B, Kachhawa G, Sood S, Dhawan B, Acharya P, Upadhyay AD, Yadav M, Sharma R, Bajpai M, Gupta S. Multi-omics analysis identifies potential microbial and metabolite diagnostic biomarkers of bacterial vaginosis. J Eur Acad Dermatol Venereol 2024; 38:1152-1165. [PMID: 38284174 DOI: 10.1111/jdv.19805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 11/06/2023] [Indexed: 01/30/2024]
Abstract
BACKGROUND Bacterial vaginosis (BV) is a common clinical manifestation of a perturbed vaginal ecology associated with adverse sexual and reproductive health outcomes if left untreated. The existing diagnostic modalities are either cumbersome or require skilled expertise, warranting alternate tests. Application of machine-learning tools to heterogeneous and high-dimensional multi-omics datasets finds promising potential in data integration and may aid biomarker discovery. OBJECTIVES The present study aimed to evaluate the potential of the microbiome and metabolome-derived biomarkers in BV diagnosis. Interpretable machine-learning algorithms were used to evaluate the utility of an integrated-omics-derived classification model. METHODS Vaginal samples obtained from reproductive-age group women with (n = 40) and without BV (n = 40) were subjected to 16S rRNA amplicon sequencing and LC-MS-based metabolomics. The vaginal microbiome and metabolome were characterized, and machine-learning analysis was performed to build a classification model using biomarkers with the highest diagnostic accuracy. RESULTS Microbiome-based diagnostic model exhibited a ROC-AUC (10-fold CV) of 0.84 ± 0.21 and accuracy of 0.79 ± 0.18, and important features were Aerococcus spp., Mycoplasma hominis, Sneathia spp., Lactobacillus spp., Prevotella spp., Gardnerella spp. and Fannyhessea vaginae. The metabolome-derived model displayed superior performance with a ROC-AUC of 0.97 ± 0.07 and an accuracy of 0.92 ± 0.08. Beta-leucine, methylimidazole acetaldehyde, dimethylethanolamine, L-arginine and beta cortol were among key predictive metabolites for BV. A predictive model combining both microbial and metabolite features exhibited a high ROC-AUC of 0.97 ± 0.07 and accuracy of 0.94 ± 0.08 with diagnostic performance only slightly superior to the metabolite-based model. CONCLUSION Application of machine-learning tools to multi-omics datasets aid biomarker discovery with high predictive performance. Metabolome-derived classification models were observed to have superior diagnostic performance in predicting BV than microbiome-based biomarkers.
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Affiliation(s)
- A Challa
- Department of Dermatology and Venereology, All India Institute of Medical Sciences, New Delhi, India
| | - J S Maras
- Department of Molecular and Cellular Medicine, Institute of Liver and Biliary Sciences, New Delhi, India
| | - S Nagpal
- TCS Research, Tata Consultancy Services Ltd, Pune, India
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - G Tripathi
- Department of Molecular and Cellular Medicine, Institute of Liver and Biliary Sciences, New Delhi, India
| | - B Taneja
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - G Kachhawa
- Department of Obstetrics and Gynaecology, All India Institute of Medical Sciences, New Delhi, India
| | - S Sood
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - B Dhawan
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - P Acharya
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | - A D Upadhyay
- Department of Biostatistics, All India Institute of Medical Sciences, New Delhi, India
| | - M Yadav
- Department of Molecular and Cellular Medicine, Institute of Liver and Biliary Sciences, New Delhi, India
| | - R Sharma
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - M Bajpai
- Department of Transfusion Medicine, Institute of Liver and Biliary Sciences, New Delhi, India
| | - S Gupta
- Department of Dermatology and Venereology, All India Institute of Medical Sciences, New Delhi, India
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6
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Motil KJ, Beisang A, Smith-Hicks C, Lembo A, Standridge SM, Liu E. Recommendations for the management of gastrointestinal comorbidities with or without trofinetide use in Rett syndrome. Expert Rev Gastroenterol Hepatol 2024; 18:227-237. [PMID: 38869952 DOI: 10.1080/17474124.2024.2368014] [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: 05/21/2024] [Accepted: 06/11/2024] [Indexed: 06/15/2024]
Abstract
INTRODUCTION Although gastrointestinal (GI) comorbidities are experienced by over 90% of individuals with Rett syndrome (RTT), a neurodevelopmental disorder associated with mutations in the MECP2 gene, many neurologists and pediatricians do not rank the management of these comorbidities among the most important treatment goals for RTT. Trofinetide, the first approved pharmacologic treatment for RTT, confers improvements in RTT symptoms but is associated with adverse GI events, primarily diarrhea and vomiting. Treatment strategies for GI comorbidities and drug-associated symptoms in RTT represent an unmet clinical need. AREAS COVERED This perspective covers GI comorbidities experienced by those with RTT, either with or without trofinetide treatment. PubMed literature searches were undertaken on treatment recommendations for the following conditions: constipation, diarrhea, vomiting, aspiration, dysphagia, gastroesophageal reflux, nausea, gastroparesis, gastritis, and abdominal bloating. EXPERT OPINION The authors recommend a proactive approach to management of symptomatic GI comorbidities and drug-associated symptoms in RTT to enhance drug tolerance and improve the quality of life of affected individuals. Management strategies for common GI comorbidities associated with RTT are reviewed based on authors' clinical experience and augmented by recommendations from the literature.
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Affiliation(s)
- Kathleen J Motil
- Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Arthur Beisang
- Department of Pediatrics, Gillette Children's Hospital, Saint Paul, MN, USA
| | - Constance Smith-Hicks
- Center for Synaptic Disorders, Rett and Related Disorders Clinic, Kennedy Krieger Institute, Baltimore, MD, USA
| | - Anthony Lembo
- Digestive Disease Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Shannon M Standridge
- Cincinnati Children's Hospital Medical Center, University of Cincinnati School of Medicine, Cincinnati, OH, USA
| | - Edwin Liu
- Digestive Health Institute, Children's Hospital Colorado, Denver, CO, USA
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Yang M, Cai W, Li X, Deng Y, Li J, Wang X, Zhu L, Wang C, Li X. The Effect of Type 2 Resistant Starch and Indole-3-Propionic Acid on Ameliorating High-Fat-Diet-Induced Hepatic Steatosis and Gut Dysbiosis. Foods 2024; 13:1625. [PMID: 38890854 PMCID: PMC11172015 DOI: 10.3390/foods13111625] [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: 04/20/2024] [Revised: 05/16/2024] [Accepted: 05/21/2024] [Indexed: 06/20/2024] Open
Abstract
Owing to the interplay of genetic and environmental factors, obesity has emerged as a significant global public health concern. To gain enhanced control over obesity, we examined the effects of type 2 resistant starch (RS2) and its promoted microbial-derived metabolite, indole-3-propionic acid (IPA), on hepatic steatosis, antioxidant activity, and gut microbiota in obese mice. Neither RS2 nor low-dose IPA (20 mg kg-1) exhibited a reduction in body weight or improved glucose and lipid metabolism in post-obesity state mice continuously fed the high-fat diet (HFD). However, both interventions improved hepatic steatosis, with RS2 being more effective in all measured parameters, potentially due to changes in gut microbiota and metabolites not solely attributed to IPA. LC-MS/MS analysis revealed increased serum IPA levels in both RS2 and IPA groups, which positively correlated with Bifidobacterium and Clostridium. Moreover, RS2 exhibited a more significant restoration of gut dysbiosis by promoting the abundance of health-promoting bacteria including Faecalibaculum and Bifidobacterium. These findings suggest that the regulatory role of RS2 on tryptophan metabolism only partially explains its prebiotic activity. Future studies should consider increasing the dose of IPA and combining RS2 and IPA to explore their potential interventions in obesity.
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Affiliation(s)
- Min Yang
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, College of Animal Science and Technology and College of Veterinary Medicine, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China; (M.Y.); (W.C.)
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products & Institute of Food Sciences, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (X.L.); (J.L.); (X.W.); (L.Z.)
| | - Wanhao Cai
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, College of Animal Science and Technology and College of Veterinary Medicine, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China; (M.Y.); (W.C.)
| | - Xinxin Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products & Institute of Food Sciences, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (X.L.); (J.L.); (X.W.); (L.Z.)
| | - Yixuan Deng
- The 2nd School of Medicine, Wenzhou Medical University, Chashan University Town, Wenzhou 325035, China;
| | - Jinjun Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products & Institute of Food Sciences, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (X.L.); (J.L.); (X.W.); (L.Z.)
| | - Xin Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products & Institute of Food Sciences, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (X.L.); (J.L.); (X.W.); (L.Z.)
| | - Liying Zhu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products & Institute of Food Sciences, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (X.L.); (J.L.); (X.W.); (L.Z.)
| | - Chong Wang
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, College of Animal Science and Technology and College of Veterinary Medicine, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China; (M.Y.); (W.C.)
| | - Xiaoqiong Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products & Institute of Food Sciences, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (X.L.); (J.L.); (X.W.); (L.Z.)
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8
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Londoño-Osorio S, Leon-Carreño L, Cala MP, Sierra-Zapata L. The gut metabolome in a cohort of pregnant and lactating women from Antioquia-Colombia. Front Mol Biosci 2024; 11:1250413. [PMID: 38803424 PMCID: PMC11128665 DOI: 10.3389/fmolb.2024.1250413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 02/20/2024] [Indexed: 05/29/2024] Open
Abstract
Nutrition during the perinatal period is an essential component of health and one that can severely impact the correct development of a human being and its overall condition, in all the subsequent stages of life. The availability of several compounds, mainly macronutrients and micronutrients, plays a key role in the balanced nutrition of both mother and baby and is a process with direct relation to the gut microbiome. Thus, we hereby refer to the set of small molecules derived from gut microbiome metabolism as the gut metabolome. These continuous processes occurring in the gut of a gestating or lactating mother related to microbial communities and nutrients, can be revealed by metabolomics. In this study, we explore for the first time the gut metabolome of pregnant and lactating women, from our region of Antioquia-Colombia, applying untargeted metabolomics by LC-QTOF-MS, and molecular networking. Regarding the gut metabolome composition of the cohort, we found, key metabolites that can be used as biomarkers of microbiome function, overall metabolic health, dietary intake, pharmacology, and lifestyle. In our cohort, pregnant women evidenced a significantly higher abundance of prostaglandins, alkaloids, corticosteroids, organosilicons, and natural toxins, while in lactating women, lipids stand out. Our results suggest that unveiling the metabolic phenotype of the gut microbiome of an individual, by untargeted metabolomics, allows a broad visualization of the chemical space present in this important niche and enables the recognition of influential indicators of the host's health status and habits, especially of women during this significant perinatal period. This study constitutes the first evidence of the use of untargeted LC-QTOF-MS coupled with molecular networking analysis, of the gut microbiome in a Colombian cohort and establishes a methodology for finding relative abundances of key metabolites, with potential use in nutritional and physiological state assessments, for future personalized health and nutrition practices.
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Affiliation(s)
- Sara Londoño-Osorio
- CIBIOP Research Group, School of Applied Sciences and Engineering, Universidad EAFIT, Medellín, Colombia
| | - Lizeth Leon-Carreño
- MetCore–Metabolomics Core Facility, Vice-Presidency for Research, Universidad de Los Andes, Bogotá, Colombia
| | - Mónica P. Cala
- MetCore–Metabolomics Core Facility, Vice-Presidency for Research, Universidad de Los Andes, Bogotá, Colombia
| | - Laura Sierra-Zapata
- CIBIOP Research Group, School of Applied Sciences and Engineering, Universidad EAFIT, Medellín, Colombia
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9
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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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10
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Delanote J, Correa Rojo A, Wells PM, Steves CJ, Ertaylan G. Systematic identification of the role of gut microbiota in mental disorders: a TwinsUK cohort study. Sci Rep 2024; 14:3626. [PMID: 38351227 PMCID: PMC10864280 DOI: 10.1038/s41598-024-53929-w] [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: 11/11/2022] [Accepted: 02/06/2024] [Indexed: 02/16/2024] Open
Abstract
Mental disorders are complex disorders influenced by multiple genetic, environmental, and biological factors. Specific microbiota imbalances seem to affect mental health status. However, the mechanisms by which microbiota disturbances impact the presence of depression, stress, anxiety, and eating disorders remain poorly understood. Currently, there are no robust biomarkers identified. We proposed a novel pyramid-layer design to accurately identify microbial/metabolomic signatures underlying mental disorders in the TwinsUK registry. Monozygotic and dizygotic twins discordant for mental disorders were screened, in a pairwise manner, for differentially abundant bacterial genera and circulating metabolites. In addition, multivariate analyses were performed, accounting for individual-level confounders. Our pyramid-layer study design allowed us to overcome the limitations of cross-sectional study designs with significant confounder effects and resulted in an association of the abundance of genus Parabacteroides with the diagnosis of mental disorders. Future research should explore the potential role of Parabacteroides as a mediator of mental health status. Our results indicate the potential role of the microbiome as a modifier in mental disorders that might contribute to the development of novel methodologies to assess personal risk and intervention strategies.
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Affiliation(s)
- Julie Delanote
- Sustainable Health, Flemish Institute for Technological Research (VITO), Mol, Belgium
| | - Alejandro Correa Rojo
- Sustainable Health, Flemish Institute for Technological Research (VITO), Mol, Belgium
- Data Science Institute, Interuniversity Institute for Biostatistics and Statistical Bioinformatics (I-BioStat), Hasselt University, Diepenbeek, Belgium
| | - Philippa M Wells
- Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Hospital, 3-4th Floor South Wing Block D, Westminster Bridge Road, London, SE1 7EH, UK
| | - Claire J Steves
- Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Hospital, 3-4th Floor South Wing Block D, Westminster Bridge Road, London, SE1 7EH, UK
- Department of Ageing and Health, St Thomas' Hospital, 9th floor, North Wing, Westminster Bridge Road, London, SE1 7EH, UK
| | - Gökhan Ertaylan
- Sustainable Health, Flemish Institute for Technological Research (VITO), Mol, Belgium.
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Avtanski D, Reddy V, Stojchevski R, Hadzi-Petrushev N, Mladenov M. The Microbiome in the Obesity-Breast Cancer Axis: Diagnostic and Therapeutic Potential. Pathogens 2023; 12:1402. [PMID: 38133287 PMCID: PMC10747404 DOI: 10.3390/pathogens12121402] [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: 11/05/2023] [Revised: 11/25/2023] [Accepted: 11/27/2023] [Indexed: 12/23/2023] Open
Abstract
A growing body of evidence has demonstrated a relationship between the microbiome, adiposity, and cancer development. The microbiome is emerging as an important factor in metabolic disease and cancer pathogenesis. This review aimed to highlight the role of the microbiome in obesity and its association with cancer, with a particular focus on breast cancer. This review discusses how microbiota dysbiosis may contribute to obesity and obesity-related diseases, which are linked to breast cancer. It also explores the potential of the gut microbiome to influence systemic immunity, leading to carcinogenesis via the modulation of immune function. This review underscores the potential use of the microbiome profile as a diagnostic tool and treatment target, with strategies including probiotics, fecal microbiota transplantation, and dietary interventions. However, this emphasizes the need for more research to fully understand the complex relationship between the microbiome, metabolic disorders, and breast cancer. Future studies should focus on elucidating the mechanisms underlying the impact of the microbiome on breast cancer and exploring the potential of the microbiota profile as a biomarker and treatment target.
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Affiliation(s)
- Dimiter Avtanski
- Friedman Diabetes Institute, Lenox Hill Hospital, Northwell Health, New York, NY 10022, USA;
- Feinstein Institutes for Medical Research, Manhasset, NY 11030, USA
- Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY 11549, USA
| | - Varun Reddy
- New York Institute of Technology, College of Osteopathic Medicine, Old Westbury, NY 11545, USA;
| | - Radoslav Stojchevski
- Friedman Diabetes Institute, Lenox Hill Hospital, Northwell Health, New York, NY 10022, USA;
- Feinstein Institutes for Medical Research, Manhasset, NY 11030, USA
- Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY 11549, USA
| | - Nikola Hadzi-Petrushev
- Faculty of Natural Sciences and Mathematics, Institute of Biology, Ss. Cyril and Methodius University, 1000 Skopje, North Macedonia; (N.H.-P.); (M.M.)
| | - Mitko Mladenov
- Faculty of Natural Sciences and Mathematics, Institute of Biology, Ss. Cyril and Methodius University, 1000 Skopje, North Macedonia; (N.H.-P.); (M.M.)
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12
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Nie S, Wang A, Chen X, Gong Y, Yuan Y. Microbial-Related Metabolites May Be Involved in Eight Major Biological Processes and Represent Potential Diagnostic Markers in Gastric Cancer. Cancers (Basel) 2023; 15:5271. [PMID: 37958446 PMCID: PMC10649575 DOI: 10.3390/cancers15215271] [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: 09/09/2023] [Revised: 10/26/2023] [Accepted: 10/30/2023] [Indexed: 11/15/2023] Open
Abstract
Metabolites associated with microbes regulate human immunity, inhibit bacterial colonization, and promote pathogenicity. Integrating microbe and metabolome research in GC provides a direction for understanding the microbe-associated pathophysiological process of metabolic changes and disease occurrence. The present study included 30 GC patients with 30 cancerous tissues and paired non-cancerous tissues (NCs) as controls. LC-MS/MS metabolomics and 16S rRNA sequencing were performed to obtain the metabolic and microbial characteristics. Integrated analysis of the microbes and metabolomes was conducted to explore the coexistence relationship between the microbial and metabolic characteristics of GC and to identify microbial-related metabolite diagnostic markers. The metabolic analysis showed that the overall metabolite distribution differed between the GC tissues and the NC tissues: 25 metabolites were enriched in the NC tissues and 42 metabolites were enriched in the GC tissues. The α and β microbial diversities were higher in the GC tissues than in the NC tissues, with 11 differential phyla and 52 differential genera. In the correlation and coexistence integrated analysis, 66 differential metabolites were correlated and coexisted, with specific differential microbes. The microbes in the GC tissue likely regulated eight metabolic pathways. In the efficacy evaluation of the microbial-related differential metabolites in the diagnosis of GC, 12 differential metabolites (area under the curve [AUC] >0.9) exerted relatively high diagnostic efficiency, and the combined diagnostic efficacy of 5 to 6 microbial-related differential metabolites was higher than the diagnostic efficacy of a single feature. Therefore, microbial diversity and metabolite distribution differed between the GC tissues and the NC tissues. Microbial-related metabolites may be involved in eight major metabolism-based biological processes in GC and represent potential diagnostic markers.
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Affiliation(s)
- Siru Nie
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, The First Hospital of China Medical University, Shenyang 110001, China; (S.N.); (A.W.); (X.C.)
- Key Laboratory of Cancer Etiology and Prevention in Liaoning Education Department, The First Hospital of China Medical University, Shenyang 110001, China
- Key Laboratory of GI Cancer Etiology and Prevention in Liaoning Province, The First Hospital of China Medical University, Shenyang 110001, China
| | - Ang Wang
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, The First Hospital of China Medical University, Shenyang 110001, China; (S.N.); (A.W.); (X.C.)
- Key Laboratory of Cancer Etiology and Prevention in Liaoning Education Department, The First Hospital of China Medical University, Shenyang 110001, China
- Key Laboratory of GI Cancer Etiology and Prevention in Liaoning Province, The First Hospital of China Medical University, Shenyang 110001, China
| | - Xiaohui Chen
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, The First Hospital of China Medical University, Shenyang 110001, China; (S.N.); (A.W.); (X.C.)
- Key Laboratory of Cancer Etiology and Prevention in Liaoning Education Department, The First Hospital of China Medical University, Shenyang 110001, China
- Key Laboratory of GI Cancer Etiology and Prevention in Liaoning Province, The First Hospital of China Medical University, Shenyang 110001, China
| | - Yuehua Gong
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, The First Hospital of China Medical University, Shenyang 110001, China; (S.N.); (A.W.); (X.C.)
- Key Laboratory of Cancer Etiology and Prevention in Liaoning Education Department, The First Hospital of China Medical University, Shenyang 110001, China
- Key Laboratory of GI Cancer Etiology and Prevention in Liaoning Province, The First Hospital of China Medical University, Shenyang 110001, China
| | - Yuan Yuan
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, The First Hospital of China Medical University, Shenyang 110001, China; (S.N.); (A.W.); (X.C.)
- Key Laboratory of Cancer Etiology and Prevention in Liaoning Education Department, The First Hospital of China Medical University, Shenyang 110001, China
- Key Laboratory of GI Cancer Etiology and Prevention in Liaoning Province, The First Hospital of China Medical University, Shenyang 110001, China
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Shao P, Sha Y, Liu X, He Y, Guo X, Hu J, Wang J, Li S, Zhu C, Chen G, Li W. Astragalus additive in feed improved serum immune function, rumen fermentation and the microbiota structure of early-weaned lambs. J Appl Microbiol 2023; 134:lxad278. [PMID: 37994654 DOI: 10.1093/jambio/lxad278] [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: 08/17/2023] [Revised: 11/07/2023] [Accepted: 11/21/2023] [Indexed: 11/24/2023]
Abstract
AIM The purpose of this study was to determine the mechanism of Astragalus activity on the immune function, rumen microbiota structure, and rumen fermentation of early-weaned lambs. METHODS AND RESULTS Thirty healthy early-weaned lambs with similar body weights (17.42 ± 2.02 kg) were selected for the feeding experiment. The control group (KB) was fed a basal diet, and the Astragalus group (HQ) was fed 0.3% Astragalus additive on the basis of a basic diet. The formal trial period was 60 days. The results showed that the concentrations of blood immunoglobulin A (IgA) and immunoglobulin M (IgM) in the HQ group were significantly higher than those in the KB group (P < 0.05). Compared with the KB group, the concentrations of acetic acid, butyric acid, and total volatile fatty acids (VFAs) in the HQ group were higher (P < 0.01). The expression levels of the rumen epithelial-related genes MCT1, MCT4, NHE2, and ZO1 in the Astragalus group were significantly higher than those in the KB group (P < 0.05). 16S rRNA analysis showed that at the phylum level, Bacteroidetes in the HQ group significantly increased (P < 0.01); at the genus level, Prevotella (P < 0.01) and Succiniclasticum (P < 0.01) in the HQ group were found at significantly higher abundances than those in the KB group, and the results of microbiota gene and function prediction showed that "energy metabolism," "glycan biosynthesis and metabolic" pathways were significantly enriched in the HQ group (P < 0.05). CONCLUSION As a feed additive, Astragalus can improve the immunity of early-weaned lambs, the structure of the rumen microbiota of lambs, and the fermentation capacity of the rumen.
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Affiliation(s)
- Pengyang Shao
- College of Animal Science and Technology, Gansu Key Laboratory of Herbivorous Animal Biotechnology, Gansu Agricultural University, Lanzhou 730070, China
| | - Yuzhu Sha
- College of Animal Science and Technology, Gansu Key Laboratory of Herbivorous Animal Biotechnology, Gansu Agricultural University, Lanzhou 730070, China
| | - Xiu Liu
- College of Animal Science and Technology, Gansu Key Laboratory of Herbivorous Animal Biotechnology, Gansu Agricultural University, Lanzhou 730070, China
| | - Yanyu He
- School of Fundamental Sciences, Massey University, Palmerston North 4410, New Zealand
| | - Xinyu Guo
- College of Animal Science and Technology, Gansu Key Laboratory of Herbivorous Animal Biotechnology, Gansu Agricultural University, Lanzhou 730070, China
| | - Jiang Hu
- College of Animal Science and Technology, Gansu Key Laboratory of Herbivorous Animal Biotechnology, Gansu Agricultural University, Lanzhou 730070, China
| | - Jiqing Wang
- College of Animal Science and Technology, Gansu Key Laboratory of Herbivorous Animal Biotechnology, Gansu Agricultural University, Lanzhou 730070, China
| | - Shaobin Li
- College of Animal Science and Technology, Gansu Key Laboratory of Herbivorous Animal Biotechnology, Gansu Agricultural University, Lanzhou 730070, China
| | - Caiye Zhu
- College of Animal Science and Technology, Gansu Key Laboratory of Herbivorous Animal Biotechnology, Gansu Agricultural University, Lanzhou 730070, China
| | - Guoshun Chen
- College of Animal Science and Technology, Gansu Key Laboratory of Herbivorous Animal Biotechnology, Gansu Agricultural University, Lanzhou 730070, China
| | - Wenhao Li
- Academy of Animal Science and Veterinary Medicine, Qinghai University, Xining 810000, China
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Mishra AK, Mahmud I, Lorenzi PL, Jenq RR, Wargo JA, Ajami NJ, Peterson CB. TARO: tree-aggregated factor regression for microbiome data integration. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.17.562792. [PMID: 37904958 PMCID: PMC10614880 DOI: 10.1101/2023.10.17.562792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/01/2023]
Abstract
Motivation Although the human microbiome plays a key role in health and disease, the biological mechanisms underlying the interaction between the microbiome and its host are incompletely understood. Integration with other molecular profiling data offers an opportunity to characterize the role of the microbiome and elucidate therapeutic targets. However, this remains challenging to the high dimensionality, compositionality, and rare features found in microbiome profiling data. These challenges necessitate the use of methods that can achieve structured sparsity in learning cross-platform association patterns. Results We propose Tree-Aggregated factor RegressiOn (TARO) for the integration of microbiome and metabolomic data. We leverage information on the phylogenetic tree structure to flexibly aggregate rare features. We demonstrate through simulation studies that TARO accurately recovers a low-rank coefficient matrix and identifies relevant features. We applied TARO to microbiome and metabolomic profiles gathered from subjects being screened for colorectal cancer to understand how gut microrganisms shape intestinal metabolite abundances. Availability and implementation The R package TARO implementing the proposed methods is available online at https://github.com/amishra-stats/taro-package .
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15
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Larivière-Gauthier G, Kerouanton A, Mompelat S, Bougeard S, Denis M, Fravalo P. Monophasic Variant of Salmonella Typhimurium Infection Affects the Serum Metabolome in Swine. Microorganisms 2023; 11:2565. [PMID: 37894223 PMCID: PMC10608901 DOI: 10.3390/microorganisms11102565] [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: 09/22/2023] [Revised: 10/10/2023] [Accepted: 10/12/2023] [Indexed: 10/29/2023] Open
Abstract
Salmonella is the most relevant foodborne zoonotic agent found in swine, and its presence in French herds is significant. Its carriage is asymptomatic, which makes it difficult to detect during rearing, thus increasing the risk of its presence on pork meat. Studies have shown that enteric infection in animals could be associated with changes in the serum metabolome composition, through the immune response or changes in the digestive microbiota composition. We hypothesized that these changes in the serum metabolome composition could be used as markers for the detection of asymptomatic animals infected by Salmonella. Using untargeted analysis by liquid chromatography coupled with mass spectrometry, we showed that significant differences in the composition of the serum metabolome could be detected between infected or noninfected animals both 1 and 21 days after experimental infection. This serum metabolome composition significantly changed during the 21 days postinfection in the infected animal groups, suggesting an evolution of the impact of infection with time. Despite this evolution, differences in the serum metabolome composition persisted between infected and noninfected animals 21 days after the initial infection. We also showed a possible difference between high-shedding and low-shedding animals 21 days postinfection. Finally, some of the variations in the metabolome were found to be significantly associated with variations of specific members of the fecal microbiota. Thus, excreting and asymptomatic animals, but also high-shedding animals, could be identified on the basis of their serum metabolome composition.
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Affiliation(s)
- Guillaume Larivière-Gauthier
- USC Metabiot, Cnam, 22440 Ploufragan, France;
- USC Metabiot, Anses, Ploufragan-Plouzané-Niort Laboratory, Hygiene and Quality of Poultry and Pig Products Unit, 22440 Ploufragan, France;
| | - Annaëlle Kerouanton
- USC Metabiot, Anses, Ploufragan-Plouzané-Niort Laboratory, Hygiene and Quality of Poultry and Pig Products Unit, 22440 Ploufragan, France;
| | - Sophie Mompelat
- Anses, Fougères Laboratory, Analysis of Residues and Contaminants Unit, 35133 Fougères, France;
| | - Stéphanie Bougeard
- Anses, Ploufragan-Plouzané-Niort Laboratory, Epidemiology, Health and Welfare Unit, 22440 Ploufragan, France;
| | - Martine Denis
- USC Metabiot, Anses, Ploufragan-Plouzané-Niort Laboratory, Hygiene and Quality of Poultry and Pig Products Unit, 22440 Ploufragan, France;
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Gautam A, Bhowmik D, Basu S, Zeng W, Lahiri A, Huson DH, Paul S. Microbiome Metabolome Integration Platform (MMIP): a web-based platform for microbiome and metabolome data integration and feature identification. Brief Bioinform 2023; 24:bbad325. [PMID: 37771003 DOI: 10.1093/bib/bbad325] [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: 04/17/2023] [Revised: 08/12/2023] [Indexed: 09/30/2023] Open
Abstract
A microbial community maintains its ecological dynamics via metabolite crosstalk. Hence, knowledge of the metabolome, alongside its populace, would help us understand the functionality of a community and also predict how it will change in atypical conditions. Methods that employ low-cost metagenomic sequencing data can predict the metabolic potential of a community, that is, its ability to produce or utilize specific metabolites. These, in turn, can potentially serve as markers of biochemical pathways that are associated with different communities. We developed MMIP (Microbiome Metabolome Integration Platform), a web-based analytical and predictive tool that can be used to compare the taxonomic content, diversity variation and the metabolic potential between two sets of microbial communities from targeted amplicon sequencing data. MMIP is capable of highlighting statistically significant taxonomic, enzymatic and metabolic attributes as well as learning-based features associated with one group in comparison with another. Furthermore, MMIP can predict linkages among species or groups of microbes in the community, specific enzyme profiles, compounds or metabolites associated with such a group of organisms. With MMIP, we aim to provide a user-friendly, online web server for performing key microbiome-associated analyses of targeted amplicon sequencing data, predicting metabolite signature, and using learning-based linkage analysis, without the need for initial metabolomic analysis, and thereby helping in hypothesis generation.
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Affiliation(s)
- Anupam Gautam
- Algorithms in Bioinformatics, Institute for Bioinformatics and Medical Informatics, University of Tübingen, Tübingen, Germany
- International Max Planck Research School "From Molecules to Organisms", Max Planck Institute for Biology Tübingen, Tübingen, Germany
- Cluster of Excellence: EXC 2124: Controlling Microbes to Fight Infection, Tübingen, Germany
| | - Debaleena Bhowmik
- Cell Biology and Physiology Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Sayantani Basu
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Wenhuan Zeng
- Algorithms in Bioinformatics, Institute for Bioinformatics and Medical Informatics, University of Tübingen, Tübingen, Germany
- Cluster of Excellence: EXC 2064: Machine Learning: New Perspectives for Science, University of Tübingen, Tübingen, Germany
| | - Abhishake Lahiri
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
- Infectious Diseases and Immunology Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
- Centre for Health Science and Technology, JIS Institute of Advanced Studies and Research Kolkata, JIS University, West Bengal, India
| | - Daniel H Huson
- Algorithms in Bioinformatics, Institute for Bioinformatics and Medical Informatics, University of Tübingen, Tübingen, Germany
- International Max Planck Research School "From Molecules to Organisms", Max Planck Institute for Biology Tübingen, Tübingen, Germany
- Cluster of Excellence: EXC 2124: Controlling Microbes to Fight Infection, Tübingen, Germany
| | - Sandip Paul
- Centre for Health Science and Technology, JIS Institute of Advanced Studies and Research Kolkata, JIS University, West Bengal, India
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Amini Khiabani S, Asgharzadeh M, Samadi Kafil H. Chronic kidney disease and gut microbiota. Heliyon 2023; 9:e18991. [PMID: 37609403 PMCID: PMC10440536 DOI: 10.1016/j.heliyon.2023.e18991] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 07/25/2023] [Accepted: 08/04/2023] [Indexed: 08/24/2023] Open
Abstract
Chronic kidney disease (CKD) refers to a range of various pathophysiological processes correlated with abnormal renal function and a progressive loss in GFR. Just as dysbiosis and altered pathology of the gut are accompanied with hypertension, which is a significant CKD risk factor. Gut dysbiosis in CKD patients is associated with an elevated levels of uremic toxins, which in turn increases the CKD progression. According to research results, the gut-kidney axis has a role in the formation of kidney stones, also in IgAN. A number of researchers have categorized the gut microbiota as enterotypes, and others, skeptical of theory of enterotypes, have suggested biomarkers to describe taxa that related to lifestyle, nutrition, and disease status. Metabolome-microbiome studies have been used to investigate the interactions of host-gut microbiota in terms of the involvement of metabolites in these interactions and are yielded promising results. The correlation between gut microbiota and CKD requires further multi-omic researches. Also, with regard to systems biology, studies on the communication network of proteins and transporters such as SLC and ABC, can help us achieve a deeper understanding of the gut-liver-kidney axis communication and can thus provide promising new horizons in the treatment of CKD patients. Probiotic-based treatment is an approach to reduce uremic poisoning, which is accomplished by swallowing microbes those can catalyze URS in the gut. If further comprehensive studies are carried out, we will know about the probiotics impact in slowing the renal failure progression and reducing inflammatory markers.
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Affiliation(s)
- Siamak Amini Khiabani
- Research center for Pharmaceutical Nanotechnology, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohammad Asgharzadeh
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hossein Samadi Kafil
- Drug Applied Research Center, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
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18
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Zhou D, Song C, Mei Y, Cheng K, Liu F, Cai W, Gao S, Wang Z, Liu Z. A review of Duhuo Jisheng decoction mechanisms in intervertebral disc degeneration in vitro and animal studies. J Orthop Surg Res 2023; 18:436. [PMID: 37322524 DOI: 10.1186/s13018-023-03869-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 05/21/2023] [Indexed: 06/17/2023] Open
Abstract
Intervertebral disc degeneration (IVDD) has become a serious public health problem, placing a heavy burden on society and the healthcare system. Its pathogenesis is not completely clear and may be closely related to mechanical damage, inflammatory factors, oxidative stress and death of nucleus pulposus cells (NPCs). The treatment of IVDD mainly includes conservative treatment and surgery. Conservative treatment is based on hormonal and anti-inflammatory drugs and massage techniques, which can relieve the pain symptoms to a certain extent, but cannot solve the problem from the root cause. Surgical treatment is mainly by removing the herniated nucleus pulposus, but it is more traumatic for IVDD patients, expensive and not suitable for all patients. Therefore, it is extremely important to clarify the pathogenesis of IVDD, to find an effective and convenient treatment and to further elaborate its mechanism of action. The effectiveness of traditional Chinese medicine in the treatment of IVDD has been well demonstrated in clinical medical research. We have been working on the Chinese herbal formula Duhuo Jisheng Decoction, which is a common formula for the treatment of degenerative disc disease. Not only does it have significant clinical effects, but it also has few adverse effects. At present, we found that its mechanism of action mainly involves regulation of inflammatory factors, reduction of apoptosis and pyroptosis of NPCs, inhibition of extracellular matrix degradation, improvement of intestinal flora, etc. However, a few relevant articles have yet comprehensively and systematically summarized the mechanisms by which they exert their effect. Therefore, this paper will comprehensively and systematically explain on it. This is of great clinical significance and social value for elucidating the pathogenesis of IVDD and improving the symptoms of patients, and will provide a theoretical basis and scientific basis for the treatment of IVDD with traditional Chinese medicine.
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Affiliation(s)
- Daqian Zhou
- Department of Orthopedics, The Affiliated Hospital of Traditional Chinese Medicine of Southwest Medical University, Luzhou, 646000, Sichuan Province, China
| | - Chao Song
- Department of Orthopedics, The Affiliated Hospital of Traditional Chinese Medicine of Southwest Medical University, Luzhou, 646000, Sichuan Province, China
| | - Yongliang Mei
- Department of Orthopedics, The Affiliated Hospital of Traditional Chinese Medicine of Southwest Medical University, Luzhou, 646000, Sichuan Province, China
| | - Kang Cheng
- Department of Orthopedics, The Affiliated Hospital of Traditional Chinese Medicine of Southwest Medical University, Luzhou, 646000, Sichuan Province, China
| | - Fei Liu
- Department of Orthopedics, The Affiliated Hospital of Traditional Chinese Medicine of Southwest Medical University, Luzhou, 646000, Sichuan Province, China
| | - Weiye Cai
- Department of Orthopedics, The Affiliated Hospital of Traditional Chinese Medicine of Southwest Medical University, Luzhou, 646000, Sichuan Province, China
| | - Silong Gao
- Department of Orthopedics, The Affiliated Hospital of Traditional Chinese Medicine of Southwest Medical University, Luzhou, 646000, Sichuan Province, China
| | - Zhenlong Wang
- Department of Orthopedics, The Affiliated Hospital of Traditional Chinese Medicine of Southwest Medical University, Luzhou, 646000, Sichuan Province, China.
| | - Zongchao Liu
- Department of Orthopedics, The Affiliated Hospital of Traditional Chinese Medicine of Southwest Medical University, Luzhou, 646000, Sichuan Province, China.
- Luzhou Longmatan District People's Hospital, Luzhou, Sichuan Province, China.
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19
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Wang J, Dong P, Zheng S, Mai Y, Ding J, Pan P, Tang L, Wan Y, Liang H. Advances in gut microbiome in metabonomics perspective: based on bibliometrics methods and visualization analysis. Front Cell Infect Microbiol 2023; 13:1196967. [PMID: 37325519 PMCID: PMC10266355 DOI: 10.3389/fcimb.2023.1196967] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 05/09/2023] [Indexed: 06/17/2023] Open
Abstract
Background and aims Gastrointestinal microbial metabolomics is closely related to the state of the organism and has significant interaction with the pathogenesis of many diseases. Based on the publications in Web of Science Core Collection(WoSCC) from 2004 to 2022, this study conducted a bibliometric analysis of this field, aiming to understand its development trend and frontier, and provide basic information and potential points for in-depth exploration of this field. Methods All articles on gastrointestinal flora and metabolism published from 2004 to 2022 were collected and identified in WoCSS. CiteSpace v.6.1 and VOSviewer v.1.6.15.0 were used to calculate bibliometric indicators, including number of publications and citations, study categories, countries/institutions, authors/co-cited authors, journals/co-cited journals, co-cited references, and keywords. A map was drawn to visualize the data based on the analysis results for a more intuitive view. Results There were 3811 articles in WoSCC that met our criteria. Analysis results show that the number of publications and citations in this field are increasing year by year. China is the country with the highest number of publications and USA owns the highest total link strength and citations. Chinese Acad Sci rank first for the number of institutional publications and total link strength. Journal of Proteome Research has the most publications. Nicholson, Jeremy K. is one of the most important scholars in this field. The most cited reference is "Gut flora metabolism of phosphatidylcholine promotes cardiovascular disease". Burst detection indicates that Urine, spectroscopy, metabonomic and gut microflora are long-standing hot topics in this field, while autism spectrum disorder and omics are likely to be at the forefront of research. The study of related metabolic small molecules and the application of gastrointestinal microbiome metabolomics in various diseases are currently emerging research directions and frontier in this field. Conclusion This study is the first to make a bibliometric analysis of the studies related to gastrointestinal microbial metabolomics and reveal the development trends and current research hotspots in this field. This can contribute to the development of the field by providing relevant scholars with valuable and effective information about the current state of the field.
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Affiliation(s)
- Jieyan Wang
- Department of Urology, The People's Hospital of Longhua, The Affiliated Hospital of Southern Medical University, Shenzen, China
| | - Peng Dong
- College of Anesthesiology, Southern Medical University, Guangzhou, China
- The First School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Shuqian Zheng
- School of Basic Medical Science, Southern Medical University, Guangzhou, China
| | - Yiyin Mai
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Jianan Ding
- School of Basic Medical Science, Southern Medical University, Guangzhou, China
| | - Pinfei Pan
- The First School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Liugang Tang
- Tendon and Injury Department, Sichuan Provincial Orthopedics Hospital, Chengdu, China
| | - Yantong Wan
- Guangdong Provincial Key Laboratory of Proteomics, Southern Medical University, Guangzhou, China
| | - Hui Liang
- Department of Urology, The People's Hospital of Longhua, The Affiliated Hospital of Southern Medical University, Shenzen, China
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20
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Li X, Du Y, Xue C, Kang X, Sun C, Peng H, Fang L, Han Y, Xu X, Zhao C. SIRT2 Deficiency Aggravates Diet-Induced Nonalcoholic Fatty Liver Disease through Modulating Gut Microbiota and Metabolites. Int J Mol Sci 2023; 24:8970. [PMID: 37240315 PMCID: PMC10219207 DOI: 10.3390/ijms24108970] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 05/05/2023] [Accepted: 05/15/2023] [Indexed: 05/28/2023] Open
Abstract
Non-alcoholic fatty liver disease (NAFLD), characterized by excessive lipid accumulation in hepatocytes, is an increasing global healthcare burden. Sirtuin 2 (SIRT2) functions as a preventive molecule for NAFLD with incompletely clarified regulatory mechanisms. Metabolic changes and gut microbiota imbalance are critical to the pathogenesis of NAFLD. However, their association with SIRT2 in NAFLD progression is still unknown. Here, we report that SIRT2 knockout (KO) mice are susceptible to HFCS (high-fat/high-cholesterol/high-sucrose)-induced obesity and hepatic steatosis accompanied with an aggravated metabolic profile, which indicates SIRT2 deficiency promotes NAFLD-NASH (nonalcoholic steatohepatitis) progression. Under palmitic acid (PA), cholesterol (CHO), and high glucose (Glu) conditions, SIRT2 deficiency promotes lipid deposition and inflammation in cultured cells. Mechanically, SIRT2 deficiency induces serum metabolites alteration including upregulation of L-proline and downregulation of phosphatidylcholines (PC), lysophosphatidylcholine (LPC), and epinephrine. Furthermore, SIRT2 deficiency promotes gut microbiota dysbiosis. The microbiota composition clustered distinctly in SIRT2 KO mice with decreased Bacteroides and Eubacterium, and increased Acetatifactor. In clinical patients, SIRT2 is downregulated in the NALFD patients compared with healthy controls, and is associated with exacerbated progression of normal liver status to NAFLD to NASH in clinical patients. In conclusion, SIRT2 deficiency accelerates HFCS-induced NAFLD-NASH progression by inducing alteration of gut microbiota and changes of metabolites.
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Affiliation(s)
- Xingyu Li
- Department of Infectious Diseases, The Third Hospital of Hebei Medical University, Shijiazhuang 050011, China;
- Department of Genetic Engineering, Beijing Institute of Biotechnology, Beijing 100850, China; (Y.D.)
| | - Yimeng Du
- Department of Genetic Engineering, Beijing Institute of Biotechnology, Beijing 100850, China; (Y.D.)
| | - Chunyuan Xue
- Department of Genetic Engineering, Beijing Institute of Biotechnology, Beijing 100850, China; (Y.D.)
| | - Xiaofeng Kang
- Department of Genetic Engineering, Beijing Institute of Biotechnology, Beijing 100850, China; (Y.D.)
| | - Chao Sun
- Department of Genetic Engineering, Beijing Institute of Biotechnology, Beijing 100850, China; (Y.D.)
| | - Huanyan Peng
- Department of Genetic Engineering, Beijing Institute of Biotechnology, Beijing 100850, China; (Y.D.)
| | - Liaoxin Fang
- Department of Genetic Engineering, Beijing Institute of Biotechnology, Beijing 100850, China; (Y.D.)
| | - Yuchen Han
- Department of Genetic Engineering, Beijing Institute of Biotechnology, Beijing 100850, China; (Y.D.)
| | - Xiaojie Xu
- Department of Genetic Engineering, Beijing Institute of Biotechnology, Beijing 100850, China; (Y.D.)
| | - Caiyan Zhao
- Department of Infectious Diseases, The Third Hospital of Hebei Medical University, Shijiazhuang 050011, China;
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21
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Devi MB, Sarma HK, Mukherjee AK, Khan MR. Mechanistic Insights into Immune-Microbiota Interactions and Preventive Role of Probiotics Against Autoimmune Diabetes Mellitus. Probiotics Antimicrob Proteins 2023:10.1007/s12602-023-10087-1. [PMID: 37171690 DOI: 10.1007/s12602-023-10087-1] [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] [Accepted: 05/04/2023] [Indexed: 05/13/2023]
Abstract
Recent studies on genetically susceptible individuals and animal models revealed the potential role of the intestinal microbiota in the pathogenesis of type 1 diabetes (T1D) through complex interactions with the immune system. T1D incidence has been increasing exponentially with modern lifestyle altering normal microbiota composition, causing dysbiosis characterized by an imbalance in the gut microbial community. Dysbiosis has been suggested to be a potential contributing factor in T1D. Moreover, several studies have shown the potential role of probiotics in regulating T1D through various mechanisms. Current T1D therapies target curative measures; however, preventive therapeutics are yet to be proven. This review highlights immune microbiota interaction and the immense role of probiotics and postbiotics as important immunological interventions for reducing the risk of T1D.
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Affiliation(s)
- M Bidyarani Devi
- Molecular Biology and Microbial Biotechnology Laboratory, Life Sciences Division, Institute of Advanced Study in Science and Technology (IASST), Guwahati, Assam, India
- Department of Biotechnology, Gauhati University, Guwahati, Assam, India
| | | | - Ashis K Mukherjee
- Molecular Biology and Microbial Biotechnology Laboratory, Life Sciences Division, Institute of Advanced Study in Science and Technology (IASST), Guwahati, Assam, India
| | - Mojibur R Khan
- Molecular Biology and Microbial Biotechnology Laboratory, Life Sciences Division, Institute of Advanced Study in Science and Technology (IASST), Guwahati, Assam, India.
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22
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Zang H, Wang J, Wang H, Guo J, Li Y, Zhao Y, Song J, Liu F, Liu X, Zhao Y. Metabolic alterations in patients with Helicobacter pylori-related gastritis: The H. pylori-gut microbiota-metabolism axis in progression of the chronic inflammation in the gastric mucosa. Helicobacter 2023:e12984. [PMID: 37186092 DOI: 10.1111/hel.12984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 02/15/2023] [Accepted: 03/13/2023] [Indexed: 05/17/2023]
Abstract
PURPOSE To characterize the serum metabolism in patients with Helicobacter pylori-positive and H. pylori-negative gastritis. METHODS Clinical data and serum gastric function parameters, PGI (pepsinogen I), PGII, PGR (PGI/II), and G-17 (gastrin-17) of 117 patients with chronic gastritis were collected, including 57 H. pylori positive and 60 H. pylori negative subjects. Twenty cases in each group were randomly selected to collect intestinal mucosa specimens and serum samples. The gut microbiota profiles were generated by 16S rRNA gene sequencing, and the serum metabolites were analyzed by a targeted metabolomics approach based on liquid chromatography-mass spectrometry (LC-MS) technology. RESULTS Altered expression of 20 metabolites, including isovaleric acid, was detected in patients with HPAG. Some taxa of Bacteroides, Fusobacterium, and Prevotella in the gut microbiota showed significant correlations with differentially expressed metabolites between H. pylori positive and H. pylori negative individuals. As a result, an H. pylori-gut microbiota-metabolism (HGM) axis was proposed. CONCLUSION Helicobacter pylori infection may influence the progression of mucosal diseases and the emergence of other complications in the host by altering the gut microbiota, and thus affecting the host serum metabolism.
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Affiliation(s)
- Hongmin Zang
- Hebei University of Chinese Medicine, Shijiazhuang, China
- The Traditional Chinese Medicine Hospital of Shijiazhuang, Shijiazhuang, China
| | - Jin Wang
- Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Huijie Wang
- The Traditional Chinese Medicine Hospital of Shijiazhuang, Shijiazhuang, China
| | - Jiaxuan Guo
- The Traditional Chinese Medicine Hospital of Shijiazhuang, Shijiazhuang, China
| | - Yuchan Li
- The Traditional Chinese Medicine Hospital of Shijiazhuang, Shijiazhuang, China
| | - Yinuo Zhao
- School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
| | - Jinzhong Song
- Hebei University of Chinese Medicine, Shijiazhuang, China
- The Traditional Chinese Medicine Hospital of Shijiazhuang, Shijiazhuang, China
| | - Fengshuang Liu
- Hebei University of Chinese Medicine, Shijiazhuang, China
- Hebei Academy of Traditional Chinese Medicine, Shijiazhuang, China
| | - Xuzhao Liu
- North China University of Science and Technology, Tangshan, China
| | - Yubin Zhao
- Hebei University of Chinese Medicine, Shijiazhuang, China
- North China University of Science and Technology, Tangshan, China
- Shijiazhuang People's Hospital, Shijiazhuang, China
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23
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Roshan Lal T, Cechinel LR, Freishtat R, Rastogi D. Metabolic Contributions to Pathobiology of Asthma. Metabolites 2023; 13:212. [PMID: 36837831 PMCID: PMC9962059 DOI: 10.3390/metabo13020212] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 01/11/2023] [Accepted: 01/28/2023] [Indexed: 02/04/2023] Open
Abstract
Asthma is a heterogenous disorder driven by inflammatory mechanisms that result in multiple phenotypes. Given the complex nature of this condition, metabolomics is being used to delineate the pathobiology of asthma. Metabolomics is the study of metabolites in biology, which includes biofluids, cells, and tissues. These metabolites have a vital role in a disease as they contribute to the pathogenesis of said condition. This review describes how macrometabolic and micrometabolic studies pertaining to these metabolites have contributed to our current understanding of asthma, as well as its many phenotypes. One of the main phenotypes this review will discuss in further detail is obesity as well as diabetes. Distinct roles of metabolites in endotyping asthma and their translation to potential therapy development for asthma is also discussed in this review.
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Affiliation(s)
- Tamanna Roshan Lal
- Rare Disease Institute, Children’s National Hospital, Washington, DC 20012, USA
| | - Laura Reck Cechinel
- Departments of Pediatrics and Genomics and Precision Medicine, George Washington University School of Medicine and Health Sciences, Washington, DC 20052, USA
| | - Robert Freishtat
- Departments of Pediatrics and Genomics and Precision Medicine, George Washington University School of Medicine and Health Sciences, Washington, DC 20052, USA
| | - Deepa Rastogi
- Departments of Pediatrics and Genomics and Precision Medicine, George Washington University School of Medicine and Health Sciences, Washington, DC 20052, USA
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24
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Indolepropionic Acid, a Gut Bacteria-Produced Tryptophan Metabolite and the Risk of Type 2 Diabetes and Non-Alcoholic Fatty Liver Disease. Nutrients 2022; 14:nu14214695. [PMID: 36364957 PMCID: PMC9653718 DOI: 10.3390/nu14214695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 10/30/2022] [Accepted: 11/04/2022] [Indexed: 11/09/2022] Open
Abstract
An intricate relationship between gut microbiota, diet, and the human body has recently been extensively investigated. Gut microbiota and gut-derived metabolites, especially, tryptophan derivatives, modulate metabolic and immune functions in health and disease. One of the tryptophan derivatives, indolepropionic acid (IPA), is increasingly being studied as a marker for the onset and development of metabolic disorders, including type 2 diabetes (T2D) and non-alcoholic fatty liver disease (NAFLD). The IPA levels heavily depend on the diet, particularly dietary fiber, and show huge variations among individuals. We suggest that these variations could partially be explained using genetic variants known to be associated with specific diseases such as T2D. In this narrative review, we elaborate on the beneficial effects of IPA in the mitigation of T2D and NAFLD, and further study the putative interactions between IPA and well-known genetic variants (TCF7L2, FTO, and PPARG), known to be associated with the risk of T2D. We have investigated the long-term preventive value of IPA in the development of T2D in the Finnish prediabetic population and the correlation of IPA with phytosterols in obese individuals from an ongoing Kuopio obesity surgery study. The diversity in IPA-linked mechanisms affecting glucose metabolism and liver fibrosis makes it a unique small metabolite and a promising candidate for the reversal or management of metabolic disorders, mainly T2D and NAFLD.
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25
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Takkinsatian P, Mairiang D, Sangkanjanavanich S, Chiewchalermsri C, Tripipitsiriwat A, Sompornrattanaphan M. Dietary Factors Associated with Asthma Development: A Narrative Review and Summary of Current Guidelines and Recommendations. J Asthma Allergy 2022; 15:1125-1141. [PMID: 36046721 PMCID: PMC9420923 DOI: 10.2147/jaa.s364964] [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: 04/24/2022] [Accepted: 08/15/2022] [Indexed: 11/24/2022] Open
Abstract
Asthma is a complex disease, caused by a combination of genetic and environmental factors. The prevalence of asthma is increasing too rapidly to be attributable to genetic factors alone. Thus, environmental factors are becoming increasingly recognized as the cause of asthma. Modifying these environmental factors may be a simple approach for asthma prevention. To date, dietary intervention is an interesting modifiable factor because it can be implemented at the population level. The modification of systemic inflammation, oxidation, and microbial composition might be a mechanistic basis for prevention. This review summarizes the mechanistic basis and evidence from clinical studies on the association between dietary factors and asthma development. We also summarize the recommendations from many organizations and regional guidelines to assist the practicing physician to improve patient care.
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Affiliation(s)
- Preyanit Takkinsatian
- Department of Pediatrics, Faculty of Medicine, Vajira Hospital, Navamindradhiraj University, Bangkok, Thailand
| | - Dara Mairiang
- Department of Pediatrics, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Sasipa Sangkanjanavanich
- Division of Allergy, Immunology, and Rheumatology, Department of Medicine, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand.,Department of Medicine, Phyathai 2 International Hospital, Bangkok, Thailand
| | - Chirawat Chiewchalermsri
- Department of Medicine, Panyananthaphikkhu Chonprathan Medical Center, Srinakharinwirot University, Nonthaburi, Thailand
| | - Athiwat Tripipitsiriwat
- Division of Respiratory Disease and Tuberculosis, Department of Medicine, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Mongkhon Sompornrattanaphan
- Division of Allergy and Clinical Immunology, Department of Medicine, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand
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26
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Beale DJ, Nguyen TV, Shah RM, Bissett A, Nahar A, Smith M, Gonzalez-Astudillo V, Braun C, Baddiley B, Vardy S. Host–Gut Microbiome Metabolic Interactions in PFAS-Impacted Freshwater Turtles (Emydura macquarii macquarii). Metabolites 2022; 12:metabo12080747. [PMID: 36005619 PMCID: PMC9415956 DOI: 10.3390/metabo12080747] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/27/2022] [Accepted: 08/03/2022] [Indexed: 01/09/2023] Open
Abstract
Per-and polyfluoroalkyl substances (PFAS) are a growing concern for humans, wildlife, and more broadly, ecosystem health. Previously, we characterised the microbial and biochemical impact of elevated PFAS on the gut microbiome of freshwater turtles (Emydura macquarii macquarii) within a contaminated catchment in Queensland, Australia. However, the understanding of PFAS impacts on this species and other aquatic organisms is still very limited, especially at the host–gut microbiome molecular interaction level. To this end, the present study aimed to apply these leading-edge omics technologies within an integrated framework that provides biological insight into the host turtle–turtle gut microbiome interactions of PFAS-impacted wild-caught freshwater turtles. For this purpose, faecal samples from PFAS-impacted turtles (n = 5) and suitable PFAS-free reference turtles (n = 5) were collected and analysed. Data from 16S rRNA gene amplicon sequencing and metabolomic profiling of the turtle faeces were integrated using MetOrigin to assign host, microbiome, and co-metabolism activities. Significant variation in microbial composition was observed between the two turtle groups. The PFAS-impacted turtles showed a higher relative abundance of Firmicutes and a lower relative abundance of Bacteroidota than the reference turtles. The faecal metabolome showed several metabolites and pathways significantly affected by PFAS exposure. Turtles exposed to PFAS displayed altered amino acid and butanoate metabolisms, as well as altered purine and pyrimidine metabolism. It is predicted from this study that PFAS-impacted both the metabolism of the host turtle and its gut microbiota which in turn has the potential to influence the host’s physiology and health.
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Affiliation(s)
- David J. Beale
- Land and Water, Commonwealth Scientific and Industrial Research Organisation, Ecosciences Precinct, Dutton Park, QLD 4102, Australia
- Correspondence: ; Tel.: +61-73-833-5774
| | - Thao V. Nguyen
- Land and Water, Commonwealth Scientific and Industrial Research Organisation, Ecosciences Precinct, Dutton Park, QLD 4102, Australia
| | - Rohan M. Shah
- Land and Water, Commonwealth Scientific and Industrial Research Organisation, Ecosciences Precinct, Dutton Park, QLD 4102, Australia
| | - Andrew Bissett
- Oceans and Atmosphere, Commonwealth Scientific and Industrial Research Organisation, Battery Point, TAS 7004, Australia
| | - Akhikun Nahar
- Land and Water, Commonwealth Scientific and Industrial Research Organisation, Research and Innovation Park, Black Mountain, ACT 2601, Australia
| | - Matthew Smith
- NCMI, Commonwealth Scientific and Industrial Research Organisation, Battery Point, TAS 7004, Australia
| | | | - Christoph Braun
- Water Quality and Investigation, Science and Technology Division, Department of Environment and Science, Queensland Government, Dutton Park, QLD 4102, Australia
| | - Brenda Baddiley
- Water Quality and Investigation, Science and Technology Division, Department of Environment and Science, Queensland Government, Dutton Park, QLD 4102, Australia
| | - Suzanne Vardy
- Water Quality and Investigation, Science and Technology Division, Department of Environment and Science, Queensland Government, Dutton Park, QLD 4102, Australia
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Oliveira MET, Paulino GVB, Dos Santos Júnior ED, da Silva Oliveira FA, Melo VMM, Ursulino JS, de Aquino TM, Shetty AK, Landell MF, Gitaí DLG. Multi-omic Analysis of the Gut Microbiome in Rats with Lithium-Pilocarpine-Induced Temporal Lobe Epilepsy. Mol Neurobiol 2022; 59:6429-6446. [PMID: 35962889 DOI: 10.1007/s12035-022-02984-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Accepted: 07/29/2022] [Indexed: 11/25/2022]
Abstract
Evidence supports that the gut microbiota and bacteria-dependent metabolites influence the maintenance of epileptic brain activity. However, the alterations in the gut microbiota between epileptic versus healthy individuals are poorly understood. We used a multi-omic approach to evaluate the changes in the composition of gut metagenome as well in the fecal metabolomic profile in rats before and after being submitted to status epilepticus (SE)-induced temporal lobe epilepsy (TLE). The 16S ribosomal RNA (rRNA) sequencing of fecal samples coupled to bioinformatic analysis revealed taxonomic, compositional, and functional shifts in epileptic rats. The species richness (Chao1 index) was significantly lower in the post-TLE group, and the β-diversity analysis revealed clustering separated from the pre-TLE group. The taxonomic abundance analysis showed a significant increase of phylum Desulfobacterota and a decrease of Patescibacteria in the post-TLE group. The DESEq2 and LEfSe analysis resulted in 18 genera significantly enriched between post-TLE and pre-TLE groups at the genus level. We observed that epileptic rats present a peculiar metabolic phenotype, including a lower concentration of D-glucose and L-lactic acid and a higher concentration of L-glutamic acid and glycine. The microbiota-host metabolic correlation analysis showed that the genera differentially abundant in post-TLE rats are associated with the altered metabolites, especially the proinflammatory Desulfovibrio and Marvinbryantia, which were enriched in epileptic animals and positively correlated with these excitatory neurotransmitters and carbohydrate metabolites. Therefore, our data revealed a correlation between dysbacteriosis in epileptic animals and fecal metabolites that are known to be relevant for maintaining epileptic brain activity by enhancing chronic inflammation, an excitatory-inhibitory imbalance, and/or a metabolic disturbance. These data are promising and suggest that targeting the gut microbiota could provide a novel avenue for preventing and treating acquired epilepsy. However, the causal relationship between these microbial/metabolite components and the SRS occurrence still needs further exploration.
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Affiliation(s)
- Maria Eduarda T Oliveira
- Laboratory of Cellular and Molecular Biology (LBCM), Institute of Biological and Health Sciences, Federal University of Alagoas, Maceió, AL, 57072-900, Brazil
| | - Gustavo V B Paulino
- Laboratory of Molecular Diversity (LDM), Institute of Biological and Health Sciences, Federal University of Alagoas, Maceió, AL, 57072-900, Brazil
| | - Erivaldo D Dos Santos Júnior
- Laboratory of Cellular and Molecular Biology (LBCM), Institute of Biological and Health Sciences, Federal University of Alagoas, Maceió, AL, 57072-900, Brazil
| | - Francisca A da Silva Oliveira
- Laboratory of Microbial Ecology and Biotechnology (Lembiotech), Department of Biology, Universidade Federal Do Ceará, Campus do Pici, Bloco 909, Fortaleza, CE, 60455-760, Brazil
| | - Vânia M M Melo
- Laboratory of Microbial Ecology and Biotechnology (Lembiotech), Department of Biology, Universidade Federal Do Ceará, Campus do Pici, Bloco 909, Fortaleza, CE, 60455-760, Brazil
| | - Jeferson S Ursulino
- Nucleus of Analysis and Research in Nuclear Magnetic Resonance - NAPRMN, Institute of Chemistry and Biotechnology, Federal University of Alagoas, Maceió, AL, 57072-900, Brazil
| | - Thiago M de Aquino
- Nucleus of Analysis and Research in Nuclear Magnetic Resonance - NAPRMN, Institute of Chemistry and Biotechnology, Federal University of Alagoas, Maceió, AL, 57072-900, Brazil
| | - Ashok K Shetty
- Institute for Regenerative Medicine, Department of Molecular and Cellular Medicine, Texas A&M University Health Science Center College of Medicine, College Station, TX, USA
| | - Melissa Fontes Landell
- Laboratory of Molecular Diversity (LDM), Institute of Biological and Health Sciences, Federal University of Alagoas, Maceió, AL, 57072-900, Brazil.
| | - Daniel Leite Góes Gitaí
- Laboratory of Cellular and Molecular Biology (LBCM), Institute of Biological and Health Sciences, Federal University of Alagoas, Maceió, AL, 57072-900, Brazil.
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Feeding Our Microbiota: Stimulation of the Immune/Semiochemical System and the Potential Amelioration of Non-Communicable Diseases. LIFE (BASEL, SWITZERLAND) 2022; 12:life12081197. [PMID: 36013376 PMCID: PMC9410320 DOI: 10.3390/life12081197] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/30/2022] [Accepted: 08/03/2022] [Indexed: 12/12/2022]
Abstract
Non-communicable diseases are those conditions to which causative infectious agents cannot readily be assigned. It is increasingly likely that at least some of these conditions are due to the breakdown of the previously mutualistic intestinal microbiota under the influence of a polluted, biocide-rich, environment. Following the mid-20th century African studies of Denis Burkitt, the environmental cause of conditions such as obesity has been ascribed to the absence of sufficient fibre in the modern diet, however in itself that is insufficient to explain the parallel rise of problems with both the immune system and of mental health. Conversely, Burkitt himself noted that the Maasai, a cattle herding people, remained healthy even with their relatively low intake of dietary fibre. Interestingly, however, Burkitt also emphasised that levels of non-communicable disease within a population rose as faecal weight decreased significantly, to about one third of the levels found in healthy populations. Accordingly, a more cogent explanation for all the available facts is that the fully functioning, adequately diverse microbiome, communicating through what has been termed the microbiota–gut–brain axis, helps to control the passage of food through the digestive tract to provide itself with the nutrition it needs. The method of communication is via the production of semiochemicals, interkingdom signalling molecules, potentially including dopamine. In turn, the microbiome aids the immune system of both adult and, most importantly, the neonate. In this article we consider the role of probiotics and prebiotics, including fermented foods and dietary fibre, in the stimulation of the immune system and of semiochemical production in the gut lumen. Finally, we reprise our suggestion of an ingestible sensor, calibrated to the detection of such semiochemicals, to assess both the effectiveness of individual microbiomes and methods of amelioration of the associated non-communicable diseases.
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The crosstalk of the human microbiome in breast and colon cancer: A metabolomics analysis. Crit Rev Oncol Hematol 2022; 176:103757. [PMID: 35809795 DOI: 10.1016/j.critrevonc.2022.103757] [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: 05/27/2022] [Revised: 06/28/2022] [Accepted: 07/04/2022] [Indexed: 11/20/2022] Open
Abstract
The human microbiome's role in colon and breast cancer is described in this review. Understanding how the human microbiome and metabolomics interact with breast and colon cancer is the chief area of this study. First, the role of the gut and distal microbiome in breast and colon cancer is investigated, and the direct relationship between microbial dysbiosis and breast and colon cancer is highlighted. This work also focuses on the many metabolomic techniques used to locate prospective biomarkers, make an accurate diagnosis, and research new therapeutic targets for cancer treatment. This review clarifies the influence of anti-tumor medications on the microbiota and the proactive measures that can be taken to treat cancer using a variety of therapies, including radiotherapy, chemotherapy, next-generation biotherapeutics, gene-based therapy, integrated omics technology, and machine learning.
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GERSON KD, YANG N, ANTON L, LEVY M, RAVEL J, ELOVITZ MA, BURRIS HH. Second trimester short cervix is associated with decreased abundance of cervicovaginal lipid metabolites. Am J Obstet Gynecol 2022; 227:273.e1-273.e18. [PMID: 35469813 PMCID: PMC9382664 DOI: 10.1016/j.ajog.2022.04.031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 04/10/2022] [Accepted: 04/18/2022] [Indexed: 12/25/2022]
Abstract
BACKGROUND A short cervix is a risk factor for preterm birth. The molecular drivers of a short cervix remain elusive. Metabolites may function as mediators of pathologic processes. OBJECTIVE We sought to determine if a distinct cervicovaginal metabolomic profile is associated with a short cervix (<25 mm) to unveil the potential mechanisms by which premature cervical remodeling leads to a short cervix. STUDY DESIGN This was a secondary analysis of a completed prospective pregnancy cohort. Cervicovaginal fluid was obtained between 20 and 24 weeks' gestation. The participants selected for metabolomic profiling were frequency-matched by birth outcome and cervicovaginal microbiota profile. This analysis included 222 participants with cervical length measured. A short cervix was defined as one having length <25 mm, as measured by transvaginal ultrasound. Unpaired t-tests were performed with a Bonferroni correction for multiple comparisons. RESULTS There were 27 participants with a short cervix, and 195 with normal cervical length. Of the 637 metabolites detected, 26 differed between those with a short cervix and those with normal cervical lengths; 22 were decreased, of which 21 belonged to the lipid metabolism pathway (all P<.000079). Diethanolamine, erythritol, progesterone, and mannitol or sorbitol were increased in the cases of short cervix. Among participants with Lactobacillus-deficient microbiota, only diethanolamine and mannitol or sorbitol differed between short cervix (n=17) and normal cervical length (n=75), both increased. CONCLUSION A short cervix is associated with decreased cervicovaginal lipid metabolites, particularly sphingolipids. This class of lipids stabilizes cell membranes and protects against environmental exposures. Increased diethanolamine-an immunostimulatory xenobiotic-is associated with a short cervix. These observations begin to identify the potential mechanisms by which modifiable environmental factors may invoke cell damage in the setting of biological vulnerability, thus promoting premature cervical remodeling in spontaneous preterm birth.
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Affiliation(s)
- Kristin D. GERSON
- Center for Research on Reproduction and Women’s Health, Department of Obstetrics and Gynecology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA,Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Nancy YANG
- Center for Research on Reproduction and Women’s Health, Department of Obstetrics and Gynecology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Lauren ANTON
- Center for Research on Reproduction and Women’s Health, Department of Obstetrics and Gynecology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Maayan LEVY
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Jacques RAVEL
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Michal A. ELOVITZ
- Center for Research on Reproduction and Women’s Health, Department of Obstetrics and Gynecology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA,Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Heather H. BURRIS
- Center for Research on Reproduction and Women’s Health, Department of Obstetrics and Gynecology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA,Children’s Hospital of Philadelphia, Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
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Lindell AE, Zimmermann-Kogadeeva M, Patil KR. Multimodal interactions of drugs, natural compounds and pollutants with the gut microbiota. Nat Rev Microbiol 2022; 20:431-443. [PMID: 35102308 PMCID: PMC7615390 DOI: 10.1038/s41579-022-00681-5] [Citation(s) in RCA: 81] [Impact Index Per Article: 40.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/04/2022] [Indexed: 02/08/2023]
Abstract
The gut microbiota contributes to diverse aspects of host physiology, ranging from immunomodulation to drug metabolism. Changes in the gut microbiota composition are associated with various diseases as well as with the response to medications. It is therefore important to understand how different lifestyle and environmental factors shape gut microbiota composition. Beyond the commonly considered factor of diet, small-molecule drugs have recently been identified as major effectors of the microbiota composition. Other xenobiotics, such as environmental or chemical pollutants, can also impact gut bacterial communities. Here, we review the mechanisms of interactions between gut bacteria and antibiotics, host-targeted drugs, natural food compounds, food additives and environmental pollutants. While xenobiotics can impact bacterial growth and metabolism, bacteria in turn can bioaccumulate or chemically modify these compounds. These reciprocal interactions can manifest in complex xenobiotic-microbiota-host relationships. Our Review highlights the need to study mechanisms underlying interactions with pollutants and food additives towards deciphering the dynamics and evolution of the gut microbiota.
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Affiliation(s)
- Anna E Lindell
- The Medical Research Council Toxicology Unit, University of Cambridge, Cambridge, UK
| | | | - Kiran R Patil
- The Medical Research Council Toxicology Unit, University of Cambridge, Cambridge, UK.
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Wang L, Li F, Gu B, Qu P, Liu Q, Wang J, Tang J, Cai S, Zhao Q, Ming Z. Metaomics in Clinical Laboratory: Potential Driving Force for Innovative Disease Diagnosis. Front Microbiol 2022; 13:883734. [PMID: 35783436 PMCID: PMC9247514 DOI: 10.3389/fmicb.2022.883734] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 05/18/2022] [Indexed: 11/13/2022] Open
Abstract
Currently, more and more studies suggested that reductionism was lack of holistic and integrative view of biological processes, leading to limited understanding of complex systems like microbiota and the associated diseases. In fact, microbes are rarely present in individuals but normally live in complex multispecies communities. With the recent development of a variety of metaomics techniques, microbes could be dissected dynamically in both temporal and spatial scales. Therefore, in-depth understanding of human microbiome from different aspects such as genomes, transcriptomes, proteomes, and metabolomes could provide novel insights into their functional roles, which also holds the potential in making them diagnostic biomarkers in many human diseases, though there is still a huge gap to fill for the purpose. In this mini-review, we went through the frontlines of the metaomics techniques and explored their potential applications in clinical diagnoses of human diseases, e.g., infectious diseases, through which we concluded that novel diagnostic methods based on human microbiomes shall be achieved in the near future, while the limitations of these techniques such as standard procedures and computational challenges for rapid and accurate analysis of metaomics data in clinical settings were also examined.
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Affiliation(s)
- Liang Wang
- Department of Bioinformatics, School of Medical Informatics and Engineering, Xuzhou Medical University, Xuzhou, China
| | - Fen Li
- Department of Laboratory Medicine, Huaiyin Hospital, Huai’an, China
| | - Bin Gu
- Department of Bioinformatics, School of Medical Informatics and Engineering, Xuzhou Medical University, Xuzhou, China
| | - Pengfei Qu
- The First School of Clinical Medicine, Xuzhou Medical University, Xuzhou, China
| | - Qinghua Liu
- State Key Laboratory of Quality Research in Chinese Medicines, Macau University of Science and Technology, Taipa, Macao SAR, China
| | - Junjiao Wang
- Department of Bioinformatics, School of Medical Informatics and Engineering, Xuzhou Medical University, Xuzhou, China
| | - Jiawei Tang
- Department of Bioinformatics, School of Medical Informatics and Engineering, Xuzhou Medical University, Xuzhou, China
| | - Shubin Cai
- College of Computer Science and Software Engineering, Shenzhen University, Shenzhen, China
| | - Qi Zhao
- School of Computer Science and Software Engineering, University of Science and Technology Liaoning, Anshan, China
- *Correspondence: Qi Zhao,
| | - Zhong Ming
- College of Computer Science and Software Engineering, Shenzhen University, Shenzhen, China
- Zhong Ming,
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Chen M, Guan Y, Huang R, Duan J, Zhou J, Chen T, Wang X, Xia Y, London SJ. Associations between the Maternal Exposome and Metabolome during Pregnancy. ENVIRONMENTAL HEALTH PERSPECTIVES 2022; 130:37003. [PMID: 35254863 PMCID: PMC8901044 DOI: 10.1289/ehp9745] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
BACKGROUND Maternal exposure to environmental chemicals during pregnancy can influence various maternal and offspring health parameters. Modification of maternal metabolism by environmental exposure may be an important pathway for these impacts. However, there is limited evidence regarding exposure to a wide array of chemicals and the metabolome during pregnancy. OBJECTIVES We investigated the relationship between the urinary exposome and metabolome during pregnancy. METHODS Urine samples were collected in the first and third trimesters from 1,024 pregnant women recruited in prenatal clinics in Jiangsu Province, China. The exposome was analyzed using the first trimester sample with ultra-high performance liquid chromatography-high resolution accurate mass spectrometry (UHPLC-HRMS) and inductively coupled plasma mass spectrometry. The metabolome was analyzed using the third trimester sample with UHPLC-HRMS. We evaluated associations between each of 106 exposures in the first trimester with 139 metabolites in the third trimester. RESULTS We identified 1,245 significant associations (p<3.39×10-6, Bonferroni correction) between chemical exposures and maternal metabolism during pregnancy. Among elements, the largest number of the significant metabolic associations were observed for magnesium, and among organic compounds, for 4-tert-octylphenol. We used exposome-metabolome associations to explore mechanisms underlying published associations between prenatal chemical exposures and offspring health outcomes. This integration of the literature with our results suggests that reported associations between 10 analytes and birth weight, gestational age, fat deposition, neurobehavioral development, immunological disorders, and hypertension may be partially mediated by metabolites associated with these exposures. DISCUSSION This high-dimensional analysis of the urinary exposome and metabolome identified many associations between chemical exposures and maternal metabolism during pregnancy. Integration of these associations with the literature on health outcomes of exposure suggests that environmental modulation of the maternal metabolome may play a role in the association between prenatal exposure on pregnancy and child health outcomes. https://doi.org/10.1289/EHP9745.
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Affiliation(s)
- Minjian Chen
- State Key Laboratory of Reproductive Medicine, School of Public Health, Nanjing Medical University, Nanjing, China
- Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Durham, North Carolina, USA
| | - Yusheng Guan
- State Key Laboratory of Reproductive Medicine, School of Public Health, Nanjing Medical University, Nanjing, China
- Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Rui Huang
- State Key Laboratory of Reproductive Medicine, School of Public Health, Nanjing Medical University, Nanjing, China
- Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Jiawei Duan
- State Key Laboratory of Reproductive Medicine, School of Public Health, Nanjing Medical University, Nanjing, China
- Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Jingjing Zhou
- State Key Laboratory of Reproductive Medicine, School of Public Health, Nanjing Medical University, Nanjing, China
- Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Ting Chen
- State Key Laboratory of Reproductive Medicine, School of Public Health, Nanjing Medical University, Nanjing, China
- Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Xinru Wang
- State Key Laboratory of Reproductive Medicine, School of Public Health, Nanjing Medical University, Nanjing, China
- Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Yankai Xia
- State Key Laboratory of Reproductive Medicine, School of Public Health, Nanjing Medical University, Nanjing, China
- Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Stephanie J. London
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Durham, North Carolina, USA
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Wang Y, Gao X, Zhang X, Xiao F, Hu H, Li X, Dong F, Sun M, Xiao Y, Ge T, Li D, Yu G, Liu Z, Zhang T. Microbial and metabolic features associated with outcome of infliximab therapy in pediatric Crohn's disease. Gut Microbes 2022; 13:1-18. [PMID: 33430702 PMCID: PMC7808429 DOI: 10.1080/19490976.2020.1865708] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Gut microbial dysbiosis and altered metabonomics have been implicated in the pathogenesis of Crohn's disease (CD). The aim of our study was to characterize the gut microbiome structure and metabolic activities in pediatric CD patients with different clinical outcomes after infliximab (IFX) therapy. Fecal samples were collected from 20 healthy children and 29 newly diagnosed pediatric CD patients. 16S rRNA/ITS2 gene sequencing and targeted metabolomics analysis were applied to profile the gut bacterial microbiome, mycobiome, and metabolome, respectively. Pediatric CD patients exhibited lower relative abundances of short-chain fatty acids (SCFAs)-producing bacteria including Faecalibacterium, Clostridium clusters IV and XIVb, Roseburia, and Ruminococcus, which were correlated with reduced fecal levels of SCFAs. Decreased unconjugated bile acids (BAs) pool size and a lower unconjugated/conjugated BAs ratio were associated with reduced relative abundances of Bifidobacterium and Clostridium clusters IV and XIVb which contain bile salt hydrolases (BSH) genes. IFX treatment enriched the BSH-producing bacteria in CD subjects, which may explain a decreased level of conjugated BAs and an increase in unconjugated BAs as well as the unconjugated/conjugated BAs ratio. Furthermore, a sustained response (SR) of IFX therapy was associated with higher abundances of Methylobacterium, Sphingomonas, Staphylococcus, and Streptococcus, and higher fecal concentrations of amino acids, including L-aspartic acid, linoleic acid, and L-lactic acid at baseline. Our study suggests that the effects of IFX might be partially mediated by enriching bacteria taxa that producing SCFAs and BSH thereby inhibiting inflammation and restoring the BA metabolism. Some fecal bacteria and metabolites may be predictive of outcomes of IFX therapy for pediatric CD patients.
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Affiliation(s)
- Yizhong Wang
- Department of Gastroenterology, Hepatology and Nutrition, Shanghai Children’s Hospital, Shanghai Jiao Tong University, Shanghai, China,Institue of Pediatric Infection, Immunity and Critical Care Medicine, Shanghai Children’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China,CONTACT Yizhong Wang
| | - Xuefeng Gao
- Hematology-Oncology, International Cancer Center, Shenzhen University General Hospital, Shenzhen University Health Science Center, Shenzhen, China
| | - Xinyue Zhang
- Department of Gastroenterology, Hepatology and Nutrition, Shanghai Children’s Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Fangfei Xiao
- Department of Gastroenterology, Hepatology and Nutrition, Shanghai Children’s Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Hui Hu
- Department of Gastroenterology, Hepatology and Nutrition, Shanghai Children’s Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaolu Li
- Department of Gastroenterology, Hepatology and Nutrition, Shanghai Children’s Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Fang Dong
- Department of Gastroenterology, Hepatology and Nutrition, Shanghai Children’s Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Mingming Sun
- Department of Gastroenterology, The Shanghai Tenth People’s Hospital of Tongji University, Shanghai, China
| | - Yongmei Xiao
- Department of Gastroenterology, Hepatology and Nutrition, Shanghai Children’s Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Ting Ge
- Department of Gastroenterology, Hepatology and Nutrition, Shanghai Children’s Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Dan Li
- Department of Gastroenterology, Hepatology and Nutrition, Shanghai Children’s Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Guangjun Yu
- Institue of Pediatric Infection, Immunity and Critical Care Medicine, Shanghai Children’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhanju Liu
- Department of Gastroenterology, The Shanghai Tenth People’s Hospital of Tongji University, Shanghai, China,Zhanju Liu
| | - Ting Zhang
- Department of Gastroenterology, Hepatology and Nutrition, Shanghai Children’s Hospital, Shanghai Jiao Tong University, Shanghai, China,Institue of Pediatric Infection, Immunity and Critical Care Medicine, Shanghai Children’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China,Ting Zhang Department of Gastroenterology, Hepatology and Nutrition, Shanghai Children’s Hospital, Shanghai Jiao Tong University, Shanghai200062, China
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35
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Renwick VL, Stewart CJ. Exploring functional metabolites in preterm infants. Acta Paediatr 2022; 111:45-53. [PMID: 34626496 DOI: 10.1111/apa.16146] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 10/08/2021] [Indexed: 12/26/2022]
Abstract
AIM Metabolomics is the study of small molecules that represent the functional end points of cellular reactions that can impact health. Necrotising enterocolitis (NEC) and late onset sepsis (LOS) are the main cause of death in preterm infants surviving the initial days of life. METHODS This review will explore and summarise the current literature exploring metabolomics in preterm infants. RESULTS There are a relatively limited number of studies investigating metabolomics in preterm infants with NEC and/or LOS and matched controls. Nonetheless, it is evident across longitudinally age-related metabolomic studies that there are significant changes in metabolite profiles post-partum and over the first year of life. Existing studies have reported associations between the metabolite profiles of serum, urine and stool in health and disease in preterm infants. Although some studies have found selected metabolites are associated with disease, the specific metabolites vary from study to study, and larger studies are required. Excitingly, recent work has also begun to untangle how microbially produced metabolites can impact immunoregulation of the infant. CONCLUSION Metabolic exploration is an emerging research area with huge potential for developing novel biomarkers and better understanding disease processes in preterm infants.
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Affiliation(s)
- Victoria L. Renwick
- Clinical and Translational Research Institute Newcastle University Newcastle upon Tyne UK
| | - Christopher J. Stewart
- Clinical and Translational Research Institute Newcastle University Newcastle upon Tyne UK
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Gerson KD, Liao J, McCarthy C, Burris HH, Korem T, Levy M, Ravel J, Elovitz MA. A non-optimal cervicovaginal microbiota in pregnancy is associated with a distinct metabolomic signature among non-Hispanic Black individuals. Sci Rep 2021; 11:22794. [PMID: 34815499 PMCID: PMC8611022 DOI: 10.1038/s41598-021-02304-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 11/09/2021] [Indexed: 12/13/2022] Open
Abstract
Biomechanical and molecular processes of premature cervical remodeling preceding spontaneous preterm birth (sPTB) likely result from interactions between the cervicovaginal microbiota and host immune responses. A non-optimal cervicovaginal microbiota confers increased risk of sPTB. The cervicovaginal space is metabolically active in pregancy; microbiota can produce, modify, and degrade metabolites within this ecosystem. We establish that cervicovaginal metabolomic output clusters by microbial community in pregnancy among Black individuals, revealing increased metabolism within the amino acid and dipeptide pathways as hallmarks of a non-optimal microbiota. Few differences were detected in metabolomic profiles when stratified by birth outcome. The study raises the possibility that metabolites could distinguish women with greater risk of sPTB among those with similar cervicovaginal microbiota, and that metabolites within the amino acid and carbohydrate pathways may play a role in this distinction.
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Affiliation(s)
- Kristin D Gerson
- Department of OB/GYN, Center for Research on Reproduction and Women's Health, Perelman School of Medicine, University of Pennsylvania, Biomedical Research Building II/III, 1351, 421 Curie Blvd, Philadelphia, PA, 19104-6160, USA.
| | - Jingqiu Liao
- Program for Mathematical Genomics, Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Clare McCarthy
- Department of OB/GYN, Center for Research on Reproduction and Women's Health, Perelman School of Medicine, University of Pennsylvania, Biomedical Research Building II/III, 1351, 421 Curie Blvd, Philadelphia, PA, 19104-6160, USA
| | - Heather H Burris
- Department of OB/GYN, Center for Research on Reproduction and Women's Health, Perelman School of Medicine, University of Pennsylvania, Biomedical Research Building II/III, 1351, 421 Curie Blvd, Philadelphia, PA, 19104-6160, USA
| | - Tal Korem
- Program for Mathematical Genomics, Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, 10032, USA
- Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, NY, 10032, USA
- CIFAR Azrieli Global Scholars Program, CIFAR, Toronto, Canada
| | - Maayan Levy
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Jacques Ravel
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Michal A Elovitz
- Department of OB/GYN, Center for Research on Reproduction and Women's Health, Perelman School of Medicine, University of Pennsylvania, Biomedical Research Building II/III, 1351, 421 Curie Blvd, Philadelphia, PA, 19104-6160, USA
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Sehgal R, Ilha M, Vaittinen M, Kaminska D, Männistö V, Kärjä V, Tuomainen M, Hanhineva K, Romeo S, Pajukanta P, Pihlajamäki J, de Mello VD. Indole-3-Propionic Acid, a Gut-Derived Tryptophan Metabolite, Associates with Hepatic Fibrosis. Nutrients 2021; 13:nu13103509. [PMID: 34684510 PMCID: PMC8538297 DOI: 10.3390/nu13103509] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 09/28/2021] [Accepted: 09/30/2021] [Indexed: 02/06/2023] Open
Abstract
Background and Aims: Gut microbiota-derived metabolites play a vital role in maintenance of human health and progression of disorders, including obesity and type 2 diabetes (T2D). Indole-3-propionic acid (IPA), a gut-derived tryptophan metabolite, has been recently shown to be lower in individuals with obesity and T2D. IPA’s beneficial effect on liver health has been also explored in rodent and cell models. In this study, we investigated the association of IPA with human liver histology and transcriptomics, and the potential of IPA to reduce hepatic stellate cell activation in vitro. Methods: A total of 233 subjects (72% women; age 48.3 ± 9.3 years; BMI 43.1 ± 5.4 kg/m2) undergoing bariatric surgery with detailed liver histology were included. Circulating IPA levels were measured using LC-MS and liver transcriptomics with total RNA-sequencing. LX-2 cells were used to study hepatoprotective effect of IPA in cells activated by TGF-β1. Results: Circulating IPA levels were found to be lower in individuals with liver fibrosis compared to those without fibrosis (p = 0.039 for all participants; p = 0.013 for 153 individuals without T2D). Accordingly, levels of circulating IPA associated with expression of 278 liver transcripts (p < 0.01) that were enriched for the genes regulating hepatic stellate cells (HSCs) activation and hepatic fibrosis signaling. Our results suggest that IPA may have hepatoprotective potential because it is able to reduce cell adhesion, cell migration and mRNA gene expression of classical markers of HSCs activation in LX-2 cells (all p < 0.05). Conclusion: The association of circulating IPA with liver fibrosis and the ability of IPA to reduce activation of LX-2 cells suggests that IPA may have a therapeutic potential. Further molecular studies are needed to investigate the mechanisms how IPA can ameliorate hepatic fibrosis.
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Affiliation(s)
- Ratika Sehgal
- Department of Clinical Nutrition, Institute of Public Health and Clinical Nutrition, University of Eastern Finland, 70211 Kuopio, Finland; (R.S.); (M.I.); (M.V.); (D.K.); (M.T.); (K.H.); (J.P.)
| | - Mariana Ilha
- Department of Clinical Nutrition, Institute of Public Health and Clinical Nutrition, University of Eastern Finland, 70211 Kuopio, Finland; (R.S.); (M.I.); (M.V.); (D.K.); (M.T.); (K.H.); (J.P.)
| | - Maija Vaittinen
- Department of Clinical Nutrition, Institute of Public Health and Clinical Nutrition, University of Eastern Finland, 70211 Kuopio, Finland; (R.S.); (M.I.); (M.V.); (D.K.); (M.T.); (K.H.); (J.P.)
| | - Dorota Kaminska
- Department of Clinical Nutrition, Institute of Public Health and Clinical Nutrition, University of Eastern Finland, 70211 Kuopio, Finland; (R.S.); (M.I.); (M.V.); (D.K.); (M.T.); (K.H.); (J.P.)
| | - Ville Männistö
- Departments of Medicine, University of Eastern Finland and Kuopio University Hospital, 70211 Kuopio, Finland;
| | - Vesa Kärjä
- Department of Pathology, University of Eastern Finland and Kuopio University Hospital, 70211 Kuopio, Finland;
| | - Marjo Tuomainen
- Department of Clinical Nutrition, Institute of Public Health and Clinical Nutrition, University of Eastern Finland, 70211 Kuopio, Finland; (R.S.); (M.I.); (M.V.); (D.K.); (M.T.); (K.H.); (J.P.)
| | - Kati Hanhineva
- Department of Clinical Nutrition, Institute of Public Health and Clinical Nutrition, University of Eastern Finland, 70211 Kuopio, Finland; (R.S.); (M.I.); (M.V.); (D.K.); (M.T.); (K.H.); (J.P.)
- Department of Life Technologies, Food Chemistry and Food Development Unit, University of Turku, 20500 Turku, Finland
| | - Stefano Romeo
- Department of Molecular and Clinical Medicine, University of Gothenburg, 40530 Gothenburg, Sweden;
| | - Päivi Pajukanta
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles (UCLA), Los Angeles, CA 90095, USA;
- Institute for Precision Health, School of Medicine, University of California Los Angeles (UCLA), Los Angeles, CA 90095, USA
| | - Jussi Pihlajamäki
- Department of Clinical Nutrition, Institute of Public Health and Clinical Nutrition, University of Eastern Finland, 70211 Kuopio, Finland; (R.S.); (M.I.); (M.V.); (D.K.); (M.T.); (K.H.); (J.P.)
- Department of Medicine, Endocrinology and Clinical Nutrition, Kuopio University Hospital, 70211 Kuopio, Finland
| | - Vanessa D. de Mello
- Department of Clinical Nutrition, Institute of Public Health and Clinical Nutrition, University of Eastern Finland, 70211 Kuopio, Finland; (R.S.); (M.I.); (M.V.); (D.K.); (M.T.); (K.H.); (J.P.)
- Correspondence:
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Zhao F, An R, Wang L, Shan J, Wang X. Specific Gut Microbiome and Serum Metabolome Changes in Lung Cancer Patients. Front Cell Infect Microbiol 2021; 11:725284. [PMID: 34527604 PMCID: PMC8435782 DOI: 10.3389/fcimb.2021.725284] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 08/10/2021] [Indexed: 12/26/2022] Open
Abstract
Background Lung cancer (LC) is one of the most aggressive, prevalent and fatal malignancies. Gut microbes and their associated metabolites are thought to cause and modulate LC development, albeit influenced by the host genetic make-up and environment. Herein, we identified and classified gut microbiota and serum metabolites associated with LC. Methods Stool samples were collected from 41 LC patients and 40 healthy volunteers. The gut microbiota was analyzed using 16S rRNA gene sequencing. Serum samples were collected from the same LC patients (n=30) and healthy volunteers (n=30) and serum metabolites were analyzed using liquid chromatography-mass spectrometry (LC-MS). Microbiome and metabolome data were analyzed separately and integrated for combined analysis using various bioinformatics methods. Results Serum metabolomics uncovered 870 metabolites regulated in 76 metabolic pathways in both groups. Microbial diversity analyses identified 15967 operational taxonomic units (OTUs) in groups. Of these, the abundance of 232 OTUs was significantly different between HC and LC groups. Also, serum levels of glycerophospholipids (LysoPE 18:3, LysoPC 14:0, LysoPC 18:3), Imidazopyrimidines (Hypoxanthine), AcylGlcADG 66:18; AcylGlcADG (22:6/22:6/22:6) and Acylcarnitine 11:0 were substantially different between HC and LC groups. Combined analysis correlated LC-associated microbes with metabolites, such as Erysipelotrichaceae_UCG_003, Clostridium and Synergistes with glycerophospholipids. Conclusions There is an intricate relationship between gut microbiome and levels of several metabolites such as glycerophospholipids and imidazopyrimidines. Microbial-associated metabolites are potential diagnostic biomarkers and therapeutic targets for LC.
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Affiliation(s)
- Feng Zhao
- Department of Laboratory Medicine, The Fourth School of Clinical Medicine, Zhejiang Chinese Medical University, Hangzhou, China.,Department of Laboratory Medicine, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Rui An
- Department of Laboratory Medicine, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Department of Laboratory Medicine, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Liqian Wang
- Department of Laboratory Medicine, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jikang Shan
- Department of Laboratory Medicine, The Fourth School of Clinical Medicine, Zhejiang Chinese Medical University, Hangzhou, China.,Department of Laboratory Medicine, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xianjun Wang
- Department of Laboratory Medicine, The Fourth School of Clinical Medicine, Zhejiang Chinese Medical University, Hangzhou, China.,Department of Laboratory Medicine, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, China
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Nitroalkene fatty acids modulate bile acid metabolism and lung function in obese asthma. Sci Rep 2021; 11:17788. [PMID: 34493738 PMCID: PMC8423735 DOI: 10.1038/s41598-021-96471-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 08/10/2021] [Indexed: 01/07/2023] Open
Abstract
Bile acid profiles are altered in obese individuals with asthma. Thus, we sought to better understand how obesity-related systemic changes contribute to lung pathophysiology. We also test the therapeutic potential of nitro-oleic acid (NO2-OA), a regulator of metabolic and inflammatory signaling pathways, to mitigate allergen and obesity-induced lung function decline in a murine model of asthma. Bile acids were measured in the plasma of healthy subjects and individuals with asthma and serum and lung tissue of mice with and without allergic airway disease (AAD). Lung function, indices of inflammation and hepatic bile acid enzyme expression were measured in obese mice with house dust mite-induced AAD treated with vehicle or NO2-OA. Serum levels of glycocholic acid and glycoursodeoxycholic acid clinically correlate with body mass index and airway hyperreactivity whereas murine levels of β-muricholic acid and tauro-β-muricholic acid were significantly increased and positively correlated with impaired lung function in obese mice with AAD. NO2-OA reduced murine bile acid levels by modulating hepatic expression of bile acid synthesis enzymes, with a concomitant reduction in small airway resistance and tissue elastance. Bile acids correlate to body mass index and lung function decline and the signaling actions of nitroalkenes can limit AAD by modulating bile acid metabolism, revealing a potential pharmacologic approach to improving the current standard of care.
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Otten AT, Bourgonje AR, Peters V, Alizadeh BZ, Dijkstra G, Harmsen HJM. Vitamin C Supplementation in Healthy Individuals Leads to Shifts of Bacterial Populations in the Gut-A Pilot Study. Antioxidants (Basel) 2021; 10:antiox10081278. [PMID: 34439526 PMCID: PMC8389205 DOI: 10.3390/antiox10081278] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 08/06/2021] [Accepted: 08/10/2021] [Indexed: 12/12/2022] Open
Abstract
Gut microbes are crucial to human health, but microbial composition is often disturbed in a number of human diseases. Accumulating evidence points to nutritional modulation of the gut microbiota as a potentially beneficial therapeutic strategy. Vitamin C (ascorbic acid) may be of particular interest as it has known antioxidant and anti-inflammatory properties. In this study, we investigated whether supplementation with high-dose vitamin C may favourably affect the composition of the gut microbiota. In this pilot study, healthy human participants received 1000 mg vitamin C supplementation daily for two weeks. Gut microbiota composition was analysed before and after intervention by performing faecal 16S rRNA gene sequencing. In total, 14 healthy participants were included. Daily supplementation of high-dose vitamin C led to an increase in the relative abundances of Lachnospiraceae (p < 0.05), whereas decreases were observed for Bacteroidetes (p < 0.01), Enterococci (p < 0.01) and Gemmiger formicilis (p < 0.05). In addition, trends for bacterial shifts were observed for Blautia (increase) and Streptococcus thermophilus (decrease). High-dose vitamin C supplementation for two weeks shows microbiota-modulating effects in healthy individuals, with several beneficial shifts of bacterial populations. This may be relevant as these bacteria have anti-inflammatory properties and strongly associate with gut health.
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Affiliation(s)
- Antonius T. Otten
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, 9713 GZ Groningen, The Netherlands; (A.T.O.); (A.R.B.); (V.P.); (G.D.)
| | - Arno R. Bourgonje
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, 9713 GZ Groningen, The Netherlands; (A.T.O.); (A.R.B.); (V.P.); (G.D.)
| | - Vera Peters
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, 9713 GZ Groningen, The Netherlands; (A.T.O.); (A.R.B.); (V.P.); (G.D.)
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, 9713 GZ Groningen, The Netherlands;
| | - Behrooz Z. Alizadeh
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, 9713 GZ Groningen, The Netherlands;
| | - Gerard Dijkstra
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, 9713 GZ Groningen, The Netherlands; (A.T.O.); (A.R.B.); (V.P.); (G.D.)
| | - Hermie J. M. Harmsen
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, 9713 GZ Groningen, The Netherlands
- Correspondence: ; Tel.: +31-50-361-3480
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Bubier JA, Chesler EJ, Weinstock GM. Host genetic control of gut microbiome composition. Mamm Genome 2021; 32:263-281. [PMID: 34159422 PMCID: PMC8295090 DOI: 10.1007/s00335-021-09884-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 04/07/2021] [Indexed: 02/07/2023]
Abstract
The gut microbiome plays a significant role in health and disease, and there is mounting evidence indicating that the microbial composition is regulated in part by host genetics. Heritability estimates for microbial abundance in mice and humans range from (0.05-0.45), indicating that 5-45% of inter-individual variation can be explained by genetics. Through twin studies, genetic association studies, systems genetics, and genome-wide association studies (GWAS), hundreds of specific host genetic loci have been shown to associate with the abundance of discrete gut microbes. Using genetically engineered knock-out mice, at least 30 specific genes have now been validated as having specific effects on the microbiome. The relationships among of host genetics, microbiome composition, and abundance, and disease is now beginning to be unraveled through experiments designed to test causality. The genetic control of disease and its relationship to the microbiome can manifest in multiple ways. First, a genetic variant may directly cause the disease phenotype, resulting in an altered microbiome as a consequence of the disease phenotype. Second, a genetic variant may alter gene expression in the host, which in turn alters the microbiome, producing the disease phenotype. Finally, the genetic variant may alter the microbiome directly, which can result in the disease phenotype. In order to understand the processes that underlie the onset and progression of certain diseases, future research must take into account the relationship among host genetics, microbiome, and disease phenotype, and the resources needed to study these relationships.
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Affiliation(s)
- Jason A Bubier
- The Jackson Laboratory for Mammalian Genetics, 600 Main Street, Bar Harbor, ME, 04609, USA.
| | - Elissa J Chesler
- The Jackson Laboratory for Mammalian Genetics, 600 Main Street, Bar Harbor, ME, 04609, USA
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Alterations in the Fecal Microbiome and Metabolome of Horses with Antimicrobial-Associated Diarrhea Compared to Antibiotic-Treated and Non-Treated Healthy Case Controls. Animals (Basel) 2021; 11:ani11061807. [PMID: 34204371 PMCID: PMC8235368 DOI: 10.3390/ani11061807] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 05/30/2021] [Indexed: 12/16/2022] Open
Abstract
Diarrhea is an adverse effect of antimicrobial therapy in horses. This matched, case-controlled study compared the fecal microbiome and metabolome of horses on antibiotics that developed diarrhea (AAD, n = 17) to those that did not develop diarrhea (ABX, n = 15) and to a control population not exposed to antibiotics (CON, n = 31). Fecal samples were collected from horses that were matched for diet and antimicrobial agent (including dose, route, and duration of therapy). Illumina sequencing of 16S rRNA genes was performed, and QIIME 2.0 was used to generate alpha and beta diversity metrics. Untargeted metabolomics using GC-MS platforms was performed and analyzed using Metaboanalyst 5.0. Microbiome composition was significantly different in AAD compared to CON (ANOSIM, R = 0.568, p = 0.001) but not to ABX (ANOSIM, R = 0.121, p = 0.0012). AAD and ABX horses had significantly decreased richness and evenness compared to CON horses (p < 0.05). Horses on antimicrobials (AAD and ABX) had significant changes in 14 phyla compared to CON horses. Only Verrucomicrobia distinguished AAD from ABX and CON horses (q = 0.0005). Metabolite profiles of horses with AAD clustered separately from ABX and CON horses. Seven metabolites were found to be significantly different between groups (p < 0.05): L-tyrosine, kynurenic acid, xanthurenic acid, 5-hydroxyindole-3-acetic acid, docosahexaenoic acid ethyl ester, daidzein, and N-acetyltyramine. Metabolite profiles of horses on antimicrobials, especially those with AAD, are altered compared to CON horses.
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Murovec B, Deutsch L, Stres B. General Unified Microbiome Profiling Pipeline (GUMPP) for Large Scale, Streamlined and Reproducible Analysis of Bacterial 16S rRNA Data to Predicted Microbial Metagenomes, Enzymatic Reactions and Metabolic Pathways. Metabolites 2021; 11:336. [PMID: 34074026 PMCID: PMC8225202 DOI: 10.3390/metabo11060336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 05/14/2021] [Accepted: 05/23/2021] [Indexed: 11/23/2022] Open
Abstract
General Unified Microbiome Profiling Pipeline (GUMPP) was developed for large scale, streamlined and reproducible analysis of bacterial 16S rRNA data and prediction of microbial metagenomes, enzymatic reactions and metabolic pathways from amplicon data. GUMPP workflow introduces reproducible data analyses at each of the three levels of resolution (genus; operational taxonomic units (OTUs); amplicon sequence variants (ASVs)). The ability to support reproducible analyses enables production of datasets that ultimately identify the biochemical pathways characteristic of disease pathology. These datasets coupled to biostatistics and mathematical approaches of machine learning can play a significant role in extraction of truly significant and meaningful information from a wide set of 16S rRNA datasets. The adoption of GUMPP in the gut-microbiota related research enables focusing on the generation of novel biomarkers that can lead to the development of mechanistic hypotheses applicable to the development of novel therapies in personalized medicine.
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Affiliation(s)
- Boštjan Murovec
- Faculty of Electrical Engineering, University of Ljubljana, Tržaška 25, SI-1000 Ljubljana, Slovenia;
| | - Leon Deutsch
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia;
| | - Blaž Stres
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia;
- Faculty of Civil and Geodetic Engineering, University of Ljubljana, Jamova 2, SI-1000 Ljubljana, Slovenia
- Department of Automation, Jožef Stefan Institute, Biocybernetics and Robotics, Jamova 39, SI-1000 Ljubljana, Slovenia
- Department of Microbiology, University of Innsbruck, Technikerstrasse 25d, A-6020 Innsbruck, Austria
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Reiman D, Layden BT, Dai Y. MiMeNet: Exploring microbiome-metabolome relationships using neural networks. PLoS Comput Biol 2021; 17:e1009021. [PMID: 33999922 PMCID: PMC8158931 DOI: 10.1371/journal.pcbi.1009021] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 05/27/2021] [Accepted: 04/28/2021] [Indexed: 12/31/2022] Open
Abstract
The advance in microbiome and metabolome studies has generated rich omics data revealing the involvement of the microbial community in host disease pathogenesis through interactions with their host at a metabolic level. However, the computational tools to uncover these relationships are just emerging. Here, we present MiMeNet, a neural network framework for modeling microbe-metabolite relationships. Using ten iterations of 10-fold cross-validation on three paired microbiome-metabolome datasets, we show that MiMeNet more accurately predicts metabolite abundances (mean Spearman correlation coefficients increase from 0.108 to 0.309, 0.276 to 0.457, and -0.272 to 0.264) and identifies more well-predicted metabolites (increase in the number of well-predicted metabolites from 198 to 366, 104 to 143, and 4 to 29) compared to state-of-art linear models for individual metabolite predictions. Additionally, we demonstrate that MiMeNet can group microbes and metabolites with similar interaction patterns and functions to illuminate the underlying structure of the microbe-metabolite interaction network, which could potentially shed light on uncharacterized metabolites through “Guilt by Association”. Our results demonstrated that MiMeNet is a powerful tool to provide insights into the causes of metabolic dysregulation in disease, facilitating future hypothesis generation at the interface of the microbiome and metabolomics. The microbiome has shown to functionally interact with its host or environment at a metabolic level, however the exact nature of these interactions is not well understood. In addition, metabolic dysregulation caused by the microbiome is believed to contribute to the development of diseases such as inflammatory bowel disease, diabetes mellitus, and obesity. In this manuscript, we introduce a computational framework to integrate microbiome and metabolome data to uncover microbe-metabolite interactions in a data-driven manner. Our model uses neural networks to predict metabolite abundances from microbe abundances. The trained models are then used to derive microbe-metabolite feature scores, which are used for clustering microbes and metabolites into functional modules. These module-based interactions are useful in generating biological insights and facilitating hypothesis generation for the investigation of their roles in various metabolic diseases. The software of our model is made freely available to interested researchers.
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Affiliation(s)
- Derek Reiman
- Department of Bioengineering, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Brian T. Layden
- Department of Medicine, Division of Endocrinology, Diabetes, and Metabolism, University of Illinois at Chicago, Chicago, Illinois, United States of America
- Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois, United States of America
| | - Yang Dai
- Department of Bioengineering, University of Illinois at Chicago, Chicago, Illinois, United States of America
- * E-mail:
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Hoque MN, Rahman MS, Ahmed R, Hossain MS, Islam MS, Islam T, Hossain MA, Siddiki AZ. Diversity and genomic determinants of the microbiomes associated with COVID-19 and non-COVID respiratory diseases. GENE REPORTS 2021; 23:101200. [PMID: 33977168 PMCID: PMC8102076 DOI: 10.1016/j.genrep.2021.101200] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 05/03/2021] [Indexed: 12/11/2022]
Abstract
The novel coronavirus disease 2019 (COVID-19) is a rapidly emerging and highly transmissible disease caused by the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2). Understanding the microbiomes associated with the upper respiratory tract infection (URTI), chronic obstructive pulmonary disease (COPD) and COVID-19 diseases has clinical interest. We hypothesize that microbiome diversity and composition, and their genomic features are associated with different pathological conditions of these human respiratory tract diseases. To test this hypothesis, we analyzed 21 RNASeq metagenomic data including eleven COVID-19 (BD = 6 and China = 5), six COPD (UK = 6) and four URTI (USA = 4) samples to unravel the microbiome diversity and related genomic metabolic functions. The metagenomic data mapped to 534 bacterial, 60 archaeal and 61 viral genomes with distinct variation in the microbiome composition across the samples (COVID-19 > COPD > URTI). Notably, 94.57%, 80.0% and 24.59% bacterial, archaeal and viral genera shared between the COVID-19 and non-COVID samples, respectively. However, the COVID-19 related samples had sole association with 16 viral genera other than SARS-CoV-2. Strain-level virome profiling revealed 660 and 729 strains in COVID-19 and non-COVID samples, respectively, and of them 34.50% strains shared between the conditions. Functional annotation of the metagenomic data identified the association of several biochemical pathways related to basic metabolism (amino acid and energy), ABC transporters, membrane transport, virulence, disease and defense, regulation of virulence, programmed cell death, and primary immunodeficiency. We also detected 30 functional gene groups/classes associated with resistance to antibiotics and toxic compounds (RATC) in both COVID-19 and non-COVID microbiomes. Furthermore, we detected comparatively higher abundance of cobalt-zinc-cadmium resistance (CZCR) and multidrug resistance to efflux pumps (MREP) genes in COVID-19 metagenome. The profiles of microbiome diversity and associated microbial genomic features found in both COVID-19 and non-COVID (COPD and URTI) samples might be helpful in developing microbiome-based diagnostics and therapeutics for COVID-19 and non-COVID respiratory diseases. However, future studies might be carried out to explore the microbiome dynamics and the cross-talk between host and microbiomes employing larger volume of samples from different ethnic groups and geoclimatic conditions.
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Affiliation(s)
- M Nazmul Hoque
- Department of Gynecology, Obstetrics and Reproductive Health, Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur 1706, Bangladesh
| | - M Shaminur Rahman
- Department of Microbiology, University of Dhaka, Dhaka 1000, Bangladesh
| | - Rasel Ahmed
- Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh
| | | | | | - Tofazzal Islam
- Institute of Biotechnology and Genetic Engineering (IBGE), BSMRAU, Gazipur 1706, Bangladesh
| | - M Anwar Hossain
- Department of Microbiology, University of Dhaka, Dhaka 1000, Bangladesh.,Vice-Chancellor, Jashore University of Science and Technology, Jashore 7408, Bangladesh
| | - Amam Zonaed Siddiki
- Department of Pathology and Parasitology, Chattogram Veterinary and Animal Sciences University (CVASU), Chattogram 4202, Bangladesh
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Zhou F, Liu B, Liu X, Li Y, Wang L, Huang J, Luo G, Wang X. The Impact of Microbiome and Microbiota-Derived Sodium Butyrate on Drosophila Transcriptome and Metabolome Revealed by Multi-Omics Analysis. Metabolites 2021; 11:298. [PMID: 34066348 PMCID: PMC8148185 DOI: 10.3390/metabo11050298] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 04/15/2021] [Accepted: 04/20/2021] [Indexed: 12/19/2022] Open
Abstract
The host microbiome plays an important role in regulating physiology through microbiota-derived metabolites during host-microbiome interactions. However, molecular mechanism underly host-microbiome interactions remains to be explored. In this study, we used Drosophila as the model to investigate the influence of microbiome and microbiota-derived metabolite sodium butyrate on host transcriptome and metabolome. We established both a sterile Drosophila model and a conventional Drosophila model to demonstrate the role of sodium butyrate. Using multi-omics analysis, we found that microbiome and sodium butyrate could impact host gene expression patterns in both the sterile Drosophila model and the conventional Drosophila model. The analysis of gut microbial using 16S rRNA sequencing showed sodium butyrate treatment also influenced Drosophila bacterial structures. In addition, Drosophila metabolites identified by ultra-high performance liquid chromatography-MS/MS were shown to be affected by sodium butyrate treatment with lipids as the dominant changed components. Our integrative analysis of the transcriptome, the microbiome, and the metabolome data identified candidate transcripts that are coregulated by sodium butyrate. Taken together, our results reveal the impact of the microbiome and microbiota-derived sodium butyrate on host transcriptome and metabolome, and our work provides a better understanding of host-microbiome interactions at the molecular level with multi-omics data.
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Affiliation(s)
- Fan Zhou
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China; (F.Z.); (X.L.); (L.W.); (J.H.)
| | - Biaodi Liu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China; (B.L.); (Y.L.)
| | - Xin Liu
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China; (F.Z.); (X.L.); (L.W.); (J.H.)
| | - Yan Li
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China; (B.L.); (Y.L.)
| | - Luoluo Wang
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China; (F.Z.); (X.L.); (L.W.); (J.H.)
| | - Jia Huang
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China; (F.Z.); (X.L.); (L.W.); (J.H.)
| | - Guanzheng Luo
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China; (B.L.); (Y.L.)
| | - Xiaoyun Wang
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China; (F.Z.); (X.L.); (L.W.); (J.H.)
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Koliada A, Moseiko V, Romanenko M, Lushchak O, Kryzhanovska N, Guryanov V, Vaiserman A. Sex differences in the phylum-level human gut microbiota composition. BMC Microbiol 2021; 21:131. [PMID: 33931023 PMCID: PMC8088078 DOI: 10.1186/s12866-021-02198-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Accepted: 04/16/2021] [Indexed: 12/11/2022] Open
Abstract
Background Evidence was previously provided for sex-related differences in the human gut microbiota composition, and sex-specific discrepancy in hormonal profiles was proposed as a main determinant of these differences. On the basis of these findings, the assumption was made on the role of microbiota in the sexual dimorphism of human diseases. To date, sex differences in fecal microbiota were demonstrated primarily at lower taxonomic levels, whereas phylum-level differences between sexes were reported in few studies only. In the present population-based cross-sectional research, sex differences in the phylum-level human gut microbiota composition were identified in a large (total n = 2301) sample of relatively healthy individuals from Ukraine. Results Relative abundances of Firmicutes and Actinobacteria, as determined by qRT-PCR, were found to be significantly increased, while that of Bacteroidetes was significantly decreased in females compared to males. The Firmicutes to Bacteroidetes (F/B) ratio was significantly increased in females compared to males. Females had 31 % higher odds of having F/B ratio more than 1 than males. This trend was evident in all age groups. The difference between sexes was even more pronounced in the elder individuals (50+): in this age group, female participants had 56 % higher odds of having F/B ratio > 1 than the male ones. Conclusions In conclusion, sex-specific differences in the phylum-level intestinal microbiota composition were observed in the Ukraine population. The F/B ratio was significantly increased in females compared to males. Further investigation is needed to draw strong conclusions regarding the mechanistic basis for sex-specific differences in the gut microbiota composition and regarding the role of these differences in the initiation and progression of human chronic diseases. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-021-02198-y.
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Affiliation(s)
| | | | - Mariana Romanenko
- Institute of Gerontology, Vyshgorodskaya st. 67, 04114, Kyiv, Ukraine
| | - Oleh Lushchak
- Vasyl Stefanyk Precarpathian National University, Ivano-Frankivsk, Ukraine.,Research and Development Institute, Ivano-Frankivsk, Ukraine
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Ramamoorthy S, Levy S, Mohamed M, Abdelghani A, Evans AM, Miller LAD, Mehta L, Moore S, Freinkman E, Hourigan SK. An ambient-temperature storage and stabilization device performs comparably to flash-frozen collection for stool metabolomics in infants. BMC Microbiol 2021; 21:59. [PMID: 33618670 PMCID: PMC7901118 DOI: 10.1186/s12866-021-02104-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 02/02/2021] [Indexed: 02/08/2023] Open
Abstract
Background Stool metabolites provide essential insights into the function of the gut microbiome. The current gold standard for storage of stool samples for metabolomics is flash-freezing at − 80 °C which can be inconvenient and expensive. Ambient temperature storage of stool is more practical, however no available methodologies adequately preserve the metabolomic profile of stool. A novel sampling kit (OMNImet.GUT; DNA Genotek, Inc.) was introduced for ambient temperature storage and stabilization of feces for metabolomics; we aimed to test the performance of this kit vs. flash-freezing. To do this stool was collected from an infant’s diaper was divided into two aliquots: 1) flash-frozen and 2) stored in an OMNImet.GUT tube at ambient temperature for 3–4 days. Samples from the same infant were collected at 2 different time points to assess metabolite changes over time. Subsequently, all samples underwent metabolomic analysis by liquid chromatography – tandem mass spectrometry (LC-MS/MS). Results Paired fecal samples (flash-frozen and ambient temperature) from 16 infants were collected at 2 time points (32 individual samples, 64 aliquots). Similar numbers of metabolites were detected in both the frozen and ambient temperature samples (1126 in frozen, 1107 in ambient temperature, 1064 shared between sample types). Metabolite abundances were strongly correlated between storage methods (median Spearman correlation Rs = 0.785 across metabolites). Hierarchical clustering analysis and principal component analysis showed that samples from the same individuals at a given time point clustered closely, regardless of the storage method. Repeat samples from the same individual were compared by paired t-test, separately for the frozen and OMNImet.GUT. The number of metabolites in each biochemical class that significantly changed (p < 0.05) at timepoint 2 relative to timepoint 1 was similar in flash-frozen versus ambient temperature storage. Changes in microbiota modified metabolites over time were also consistent across both methodologies. Conclusion Ambient temperature storage and stabilization of stool in the OMNImet.GUT device yielded comparable metabolomic results to flash freezing in terms of 1) the identity and abundance of detected biochemicals 2) the distinct metabolomic profiles of subjects and 3) changes in metabolites over time that are plausibly microbiota-induced. This method potentially provides a more convenient, less expensive home collection and storage option for stool metabolomic analysis. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-021-02104-6.
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Affiliation(s)
| | - Shira Levy
- Inova Children's Hospital, 3300 Gallows Rd, Falls Church, VA, 22042, USA
| | - Masouma Mohamed
- Inova Children's Hospital, 3300 Gallows Rd, Falls Church, VA, 22042, USA
| | - Alaa Abdelghani
- Inova Children's Hospital, 3300 Gallows Rd, Falls Church, VA, 22042, USA
| | - Anne M Evans
- Metabolon, 617 Davis Dr UNIT 100, Morrisville, NC, 27560, USA
| | - Luke A D Miller
- Metabolon, 617 Davis Dr UNIT 100, Morrisville, NC, 27560, USA
| | - Lopa Mehta
- Inova Health System, 3300 Gallows Rd, Falls Church, VA, 22042, USA
| | - Sean Moore
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, University of Virginia, 200 Jeanette Lancaster Way, Charlottesville, VA, 22903, USA
| | | | - Suchitra K Hourigan
- Inova Children's Hospital, 3300 Gallows Rd, Falls Church, VA, 22042, USA. .,Pediatric Specialists of Virginia, 3023 Hamaker Ct, Fairfax, VA, 22031, USA.
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Thavamani A, Salem I, Sferra TJ, Sankararaman S. Impact of Altered Gut Microbiota and Its Metabolites in Cystic Fibrosis. Metabolites 2021; 11:metabo11020123. [PMID: 33671639 PMCID: PMC7926988 DOI: 10.3390/metabo11020123] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 02/15/2021] [Accepted: 02/20/2021] [Indexed: 12/14/2022] Open
Abstract
Cystic fibrosis (CF) is the most common lethal, multisystemic genetic disorder in Caucasians. Mutations in the gene encoding the cystic fibrosis transmembrane regulator (CFTR) protein are responsible for impairment of epithelial anionic transport, leading to impaired fluid regulation and pH imbalance across multiple organs. Gastrointestinal (GI) manifestations in CF may begin in utero and continue throughout the life, resulting in a chronic state of an altered intestinal milieu. Inherent dysfunction of CFTR leads to dysbiosis of the gut. This state of dysbiosis is further perpetuated by acquired factors such as use of antibiotics for recurrent pulmonary exacerbations. Since the gastrointestinal microbiome and their metabolites play a vital role in nutrition, metabolic, inflammatory, and immune functions, the gut dysbiosis will in turn impact various manifestations of CF-both GI and extra-GI. This review focuses on the consequences of gut dysbiosis and its metabolic implications on CF disease and possible ways to restore homeostasis.
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Affiliation(s)
- Aravind Thavamani
- Department of Pediatrics, Division of Pediatric Gastroenterology, UH Rainbow Babies & Children’s Hospital, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA; (A.T.); (T.J.S.)
| | - Iman Salem
- Center for Medial Mycology, Case Western Reserve University School of Medicine, UH Cleveland Medical Center, Cleveland, OH 44106, USA;
| | - Thomas J. Sferra
- Department of Pediatrics, Division of Pediatric Gastroenterology, UH Rainbow Babies & Children’s Hospital, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA; (A.T.); (T.J.S.)
| | - Senthilkumar Sankararaman
- Department of Pediatrics, Division of Pediatric Gastroenterology, UH Rainbow Babies & Children’s Hospital, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA; (A.T.); (T.J.S.)
- Correspondence: ; Tel.: +1-216-844-1765
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50
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Audano M, Pedretti S, Ligorio S, Giavarini F, Caruso D, Mitro N. Investigating metabolism by mass spectrometry: From steady state to dynamic view. JOURNAL OF MASS SPECTROMETRY : JMS 2021; 56:e4658. [PMID: 33084147 DOI: 10.1002/jms.4658] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 09/10/2020] [Accepted: 09/14/2020] [Indexed: 06/11/2023]
Abstract
Metabolism is the set of life-sustaining reactions in organisms. These biochemical reactions are organized in metabolic pathways, in which one metabolite is converted through a series of steps catalyzed by enzymes in another chemical compound. Metabolic reactions are categorized as catabolic, the breaking down of metabolites to produce energy, and/or anabolic, the synthesis of compounds that consume energy. The balance between catabolism of the preferential fuel substrate and anabolism defines the overall metabolism of a cell or tissue. Metabolomics is a powerful tool to gain new insights contributing to the identification of complex molecular mechanisms in the field of biomedical research, both basic and translational. The enormous potential of this kind of analyses consists of two key aspects: (i) the possibility of performing so-called targeted and untargeted experiments through which it is feasible to verify or formulate a hypothesis, respectively, and (ii) the opportunity to run either steady-state analyses to have snapshots of the metabolome at a given time under different experimental conditions or dynamic analyses through the use of labeled tracers. In this review, we will highlight the most important practical (e.g., different sample extraction approaches) and conceptual steps to consider for metabolomic analysis, describing also the main application contexts in which it is used. In addition, we will provide some insights into the most innovative approaches and progress in the field of data analysis and processing, highlighting how this part is essential for the proper extrapolation and interpretation of data.
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Affiliation(s)
- Matteo Audano
- DiSFeB, Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milan, 20133, Italy
| | - Silvia Pedretti
- DiSFeB, Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milan, 20133, Italy
| | - Simona Ligorio
- DiSFeB, Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milan, 20133, Italy
| | - Flavio Giavarini
- DiSFeB, Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milan, 20133, Italy
| | - Donatella Caruso
- DiSFeB, Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milan, 20133, Italy
| | - Nico Mitro
- DiSFeB, Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milan, 20133, Italy
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