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Zhao Q, Chen Y, Huang W, Zhou H, Zhang W. Drug-microbiota interactions: an emerging priority for precision medicine. Signal Transduct Target Ther 2023; 8:386. [PMID: 37806986 PMCID: PMC10560686 DOI: 10.1038/s41392-023-01619-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 07/20/2023] [Accepted: 08/24/2023] [Indexed: 10/10/2023] Open
Abstract
Individual variability in drug response (IVDR) can be a major cause of adverse drug reactions (ADRs) and prolonged therapy, resulting in a substantial health and economic burden. Despite extensive research in pharmacogenomics regarding the impact of individual genetic background on pharmacokinetics (PK) and pharmacodynamics (PD), genetic diversity explains only a limited proportion of IVDR. The role of gut microbiota, also known as the second genome, and its metabolites in modulating therapeutic outcomes in human diseases have been highlighted by recent studies. Consequently, the burgeoning field of pharmacomicrobiomics aims to explore the correlation between microbiota variation and IVDR or ADRs. This review presents an up-to-date overview of the intricate interactions between gut microbiota and classical therapeutic agents for human systemic diseases, including cancer, cardiovascular diseases (CVDs), endocrine diseases, and others. We summarise how microbiota, directly and indirectly, modify the absorption, distribution, metabolism, and excretion (ADME) of drugs. Conversely, drugs can also modulate the composition and function of gut microbiota, leading to changes in microbial metabolism and immune response. We also discuss the practical challenges, strategies, and opportunities in this field, emphasizing the critical need to develop an innovative approach to multi-omics, integrate various data types, including human and microbiota genomic data, as well as translate lab data into clinical practice. To sum up, pharmacomicrobiomics represents a promising avenue to address IVDR and improve patient outcomes, and further research in this field is imperative to unlock its full potential for precision medicine.
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Affiliation(s)
- Qing Zhao
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, PR China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, 110 Xiangya Road, Changsha, 410078, PR China
- Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha, 410078, PR China
- National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha, 410008, PR China
| | - Yao Chen
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, PR China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, 110 Xiangya Road, Changsha, 410078, PR China
- Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha, 410078, PR China
- National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha, 410008, PR China
| | - Weihua Huang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, PR China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, 110 Xiangya Road, Changsha, 410078, PR China
- Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha, 410078, PR China
- National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha, 410008, PR China
| | - Honghao Zhou
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, PR China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, 110 Xiangya Road, Changsha, 410078, PR China
- Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha, 410078, PR China
- National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha, 410008, PR China
| | - Wei Zhang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, PR China.
- The First Affiliated Hospital of Shantou University Medical College, Shantou, 515041, PR China.
- The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, 510080, PR China.
- Central Laboratory of Hunan Cancer Hospital, Central South University, 283 Tongzipo Road, Changsha, 410013, PR China.
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2
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Jagirdhar GSK, Perez JA, Perez AB, Surani S. Integration and implementation of precision medicine in the multifaceted inflammatory bowel disease. World J Gastroenterol 2023; 29:5211-5225. [PMID: 37901450 PMCID: PMC10600960 DOI: 10.3748/wjg.v29.i36.5211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 07/31/2023] [Accepted: 09/06/2023] [Indexed: 09/20/2023] Open
Abstract
Inflammatory bowel disease (IBD) is a complex disease with variability in genetic, environmental, and lifestyle factors affecting disease presentation and course. Precision medicine has the potential to play a crucial role in managing IBD by tailoring treatment plans based on the heterogeneity of clinical and temporal variability of patients. Precision medicine is a population-based approach to managing IBD by integrating environmental, genomic, epigenomic, transcriptomic, proteomic, and metabolomic factors. It is a recent and rapidly developing medicine. The widespread adoption of precision medicine worldwide has the potential to result in the early detection of diseases, optimal utilization of healthcare resources, enhanced patient outcomes, and, ultimately, improved quality of life for individuals with IBD. Though precision medicine is promising in terms of better quality of patient care, inadequacies exist in the ongoing research. There is discordance in study conduct, and data collection, utilization, interpretation, and analysis. This review aims to describe the current literature on precision medicine, its multiomics approach, and future directions for its application in IBD.
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Affiliation(s)
| | - Jose Andres Perez
- Department of Medicine, Saint Francis Health Systems, Tulsa, OK 74133, United States
| | - Andrea Belen Perez
- Department of Research, Columbia University, New York, NY 10027, United States
| | - Salim Surani
- Department of Medicine and Pharmacology, Texas A&M University, College Station, TX 77413, United States
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3
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Valles-Colomer M, Menni C, Berry SE, Valdes AM, Spector TD, Segata N. Cardiometabolic health, diet and the gut microbiome: a meta-omics perspective. Nat Med 2023; 29:551-561. [PMID: 36932240 DOI: 10.1038/s41591-023-02260-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 02/16/2023] [Indexed: 03/19/2023]
Abstract
Cardiometabolic diseases have become a leading cause of morbidity and mortality globally. They have been tightly linked to microbiome taxonomic and functional composition, with diet possibly mediating some of the associations described. Both the microbiome and diet are modifiable, which opens the way for novel therapeutic strategies. High-throughput omics techniques applied on microbiome samples (meta-omics) hold the unprecedented potential to shed light on the intricate links between diet, the microbiome, the metabolome and cardiometabolic health, with a top-down approach. However, effective integration of complementary meta-omic techniques is an open challenge and their application on large cohorts is still limited. Here we review meta-omics techniques and discuss their potential in this context, highlighting recent large-scale efforts and the novel insights they provided. Finally, we look to the next decade of meta-omics research and discuss various translational and clinical pathways to improving cardiometabolic health.
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Affiliation(s)
- Mireia Valles-Colomer
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Cristina Menni
- Department of Twin Research, King's College London, London, UK
| | - Sarah E Berry
- Department of Nutritional Sciences, King's College London, London, UK
| | - Ana M Valdes
- School of Medicine, University of Nottingham, Nottingham, UK
- Nottingham National Institute for Health Research Biomedical Research Centre, Nottingham, UK
| | - Tim D Spector
- Department of Twin Research, King's College London, London, UK
| | - Nicola Segata
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy.
- European Institute of Oncology, Scientific Institute for Research, Hospitalization and Healthcare, Milan, Italy.
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4
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Fekete EE, Figeys D, Zhang X. Microbiota-directed biotherapeutics: considerations for quality and functional assessment. Gut Microbes 2023; 15:2186671. [PMID: 36896938 PMCID: PMC10012963 DOI: 10.1080/19490976.2023.2186671] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/11/2023] Open
Abstract
Mounting evidence points to causative or correlative roles of gut microbiome in the development of a myriad of diseases ranging from gastrointestinal diseases, metabolic diseases to neurological disorders and cancers. Consequently, efforts have been made to develop and apply therapeutics targeting the human microbiome, in particular the gut microbiota, for treating diseases and maintaining wellness. Here we summarize the current development of gut microbiota-directed therapeutics with a focus on novel biotherapeutics, elaborate the need of advanced -omics approaches for evaluating the microbiota-type biotherapeutics, and discuss the clinical and regulatory challenges. We also discuss the development and potential application of ex vivo microbiome assays and in vitro intestinal cellular models in this context. Altogether, this review aims to provide a broad view of promises and challenges of the emerging field of microbiome-directed human healthcare.
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Affiliation(s)
- Emily Ef Fekete
- Regulatory Research Division, Centre for Oncology, Radiopharmaceuticals and Research, Biologic and Radiopharmaceutical Drugs Directorate, Health Products and Food Branch, Health Canada, Ottawa, Canada
| | - Daniel Figeys
- School of Pharmaceutical Sciences, Faculty of Medicine, University of Ottawa, Ottawa, Canada.,Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Canada
| | - Xu Zhang
- Regulatory Research Division, Centre for Oncology, Radiopharmaceuticals and Research, Biologic and Radiopharmaceutical Drugs Directorate, Health Products and Food Branch, Health Canada, Ottawa, Canada.,School of Pharmaceutical Sciences, Faculty of Medicine, University of Ottawa, Ottawa, Canada
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Delhove J, Alawami M, Macowan M, Lester SE, Nguyen PT, Jersmann HPA, Reynolds PN, Roscioli E. Organotypic sinonasal airway culture systems are predictive of the mucociliary phenotype produced by bronchial airway epithelial cells. Sci Rep 2022; 12:19225. [PMID: 36357550 PMCID: PMC9648462 DOI: 10.1038/s41598-022-23667-y] [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: 06/02/2022] [Accepted: 11/03/2022] [Indexed: 11/12/2022] Open
Abstract
Differentiated air-liquid interface models are the current standard to assess the mucociliary phenotype using clinically-derived samples in a controlled environment. However, obtaining basal progenitor airway epithelial cells (AEC) from the lungs is invasive and resource-intensive. Hence, we applied a tissue engineering approach to generate organotypic sinonasal AEC (nAEC) epithelia to determine whether they are predictive of bronchial AEC (bAEC) models. Basal progenitor AEC were isolated from healthy participants using a cytological brushing method and differentiated into epithelia on transwells until the mucociliary phenotype was observed. Tissue architecture was assessed using H&E and alcian blue/Verhoeff-Van Gieson staining, immunofluorescence (for cilia via acetylated α-tubulin labelling) and scanning electron microscopy. Differentiation and the formation of tight-junctions were monitored over the culture period (day 1-32) by quantifying trans-epithelial electrical resistance. End point (day 32) tight junction protein expression was assessed using Western blot analysis of ZO-1, Occludin-1 and Claudin-1. Reverse transcription qPCR-array was used to assess immunomodulatory and autophagy-specific transcript profiles. All outcome measures were assessed using R-statistical software. Mucociliary architecture was comparable for nAEC and bAEC-derived cultures, e.g. cell density P = 0.55, epithelial height P = 0.88 and cilia abundance P = 0.41. Trans-epithelial electrical resistance measures were distinct from day 1-14, converged over days 16-32, and were statistically similar over the entire culture period (global P < 0.001). This agreed with end-point (day 32) measures of tight junction protein abundance which were non-significant for each analyte (P > 0.05). Transcript analysis for inflammatory markers demonstrated significant variation between nAEC and bAEC epithelial cultures, and favoured increased abundance in the nAEC model (e.g. TGFβ and IL-1β; P < 0.05). Conversely, the abundance of autophagy-related transcripts were comparable and the range of outcome measures for either model exhibited a considerably more confined uncertainty distribution than those observed for the inflammatory markers. Organotypic air-liquid interface models of nAEC are predictive of outcomes related to barrier function, mucociliary architecture and autophagy gene activity in corresponding bAEC models. However, inflammatory markers exhibited wide variation which may be explained by the sentinel immunological surveillance role of the sinonasal epithelium.
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Affiliation(s)
- Juliette Delhove
- grid.1010.00000 0004 1936 7304Adelaide Medical School, University of Adelaide, Adelaide, SA Australia ,grid.1694.aRespiratory and Sleep Medicine, Women’s and Children’s Hospital, Adelaide, SA Australia
| | - Moayed Alawami
- grid.1010.00000 0004 1936 7304Adelaide Medical School, University of Adelaide, Adelaide, SA Australia ,grid.460761.20000 0001 0323 4206Respiratory Department, Lyell McEwin Hospital, Adelaide, SA Australia
| | - Matthew Macowan
- grid.1010.00000 0004 1936 7304Adelaide Medical School, University of Adelaide, Adelaide, SA Australia ,grid.1002.30000 0004 1936 7857Department of Immunology and Pathology, Monash University, Melbourne, VIC Australia
| | - Susan E. Lester
- grid.1010.00000 0004 1936 7304Adelaide Medical School, University of Adelaide, Adelaide, SA Australia ,grid.278859.90000 0004 0486 659XDepartment of Rheumatology, The Queen Elizabeth Hospital, Adelaide, SA Australia
| | - Phan T. Nguyen
- grid.1010.00000 0004 1936 7304Adelaide Medical School, University of Adelaide, Adelaide, SA Australia ,grid.416075.10000 0004 0367 1221Department of Thoracic Medicine, Royal Adelaide Hospital, Adelaide, SA Australia
| | - Hubertus P. A. Jersmann
- grid.1010.00000 0004 1936 7304Adelaide Medical School, University of Adelaide, Adelaide, SA Australia ,grid.416075.10000 0004 0367 1221Department of Thoracic Medicine, Royal Adelaide Hospital, Adelaide, SA Australia
| | - Paul N. Reynolds
- grid.1010.00000 0004 1936 7304Adelaide Medical School, University of Adelaide, Adelaide, SA Australia ,grid.416075.10000 0004 0367 1221Department of Thoracic Medicine, Royal Adelaide Hospital, Adelaide, SA Australia
| | - Eugene Roscioli
- grid.1010.00000 0004 1936 7304Adelaide Medical School, University of Adelaide, Adelaide, SA Australia ,grid.416075.10000 0004 0367 1221Department of Thoracic Medicine, Royal Adelaide Hospital, Adelaide, SA Australia ,Adelaide Health and Medical Science, Building, Corner of North Terrace and George St, Adelaide, SA 5005 Australia
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Intercontinental Gut Microbiome Variances in IBD. Int J Mol Sci 2022; 23:ijms231810868. [PMID: 36142786 PMCID: PMC9506019 DOI: 10.3390/ijms231810868] [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: 08/29/2022] [Revised: 09/14/2022] [Accepted: 09/15/2022] [Indexed: 11/17/2022] Open
Abstract
The development of biomarkers for inflammatory bowel disease (IBD) diagnosis would be relevant in a generalized context. However, intercontinental investigation on these microbial biomarkers remains scarce. We examined taxonomic microbiome variations in IBD using published DNA shotgun metagenomic data. For this purpose, we used sequenced data from our previous Spanish Crohn’s disease (CD) and ulcerative colitis (UC) cohort, downloaded sequence data from a Chinese CD cohort, and downloaded taxonomic and functional profiling tables from a USA CD and UC cohort. At the global level, geographical location and disease phenotype were the main explanatory covariates of microbiome variations. In healthy controls (HC) and UC, geography turned out to be the most important factor, while disease intestinal location was the most important one in CD. Disease severity correlated with lower alpha-diversity in UC but not in CD. Across geography, alpha-diversity was significantly different independently of health status, except for CD. Despite recruitment from different countries and with different disease severity scores, CD patients may harbor a very similar microbial taxonomic profile. Our study pointed out that geographic location, disease activity status, and other environmental factors are important contributing factors in microbiota changes in IBD. We therefore strongly recommend taking these factors into consideration for future IBD studies to obtain globally valid and reproducible biomarkers.
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7
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Chatterjee G, Negi S, Basu S, Faintuch J, O'Donovan A, Shukla P. Microbiome systems biology advancements for natural well-being. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 838:155915. [PMID: 35568180 DOI: 10.1016/j.scitotenv.2022.155915] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Revised: 05/09/2022] [Accepted: 05/09/2022] [Indexed: 06/15/2023]
Abstract
Throughout the years all data from epidemiological, physiological and omics have suggested that the microbial communities play a considerable role in modulating human health. The population of microorganisms residing in the human intestine collectively known as microbiota presents a genetic repertoire that is higher in magnitude than the human genome. They play an essential role in host immunity and neuronal signaling. Rapid enhancement of sequence based screening and development of humanized gnotobiotic model has sparked a great deal of interest among scientists to probe the dynamic interactions of the commensal bacteria. This review focuses on systemic analysis of the gut microbiome to decipher the complexity of the host-microbe intercommunication and gives a special emphasis on the evolution of targeted precision medicine through microbiome engineering. In addition, we have also provided a comprehensive description of how interconnection between metabolism and biochemical reactions in a specific organism can be obtained from a metabolic network or a flux balance analysis and combining multiple datasets helps in the identification of a particular metabolite. The review highlights how genetic modification of the critical components and programming the resident microflora can be employed for targeted precision medicine. Inspite of the ongoing debate on the utility of gut microbiome we have explored on the probable new therapeutic avenues like FMT (Fecal microbiota transplant) can be utilized. This review also recapitulates integrating human-relevant 3D cellular models coupled with computational models and the metadata obtained from interventional and epidemiological studies may decipher the complex interactome of diet-microbiota-disease pathophysiology. In addition, it will also open new avenues for the development of therapeutics derived from microbiome or implementation of personalized nutrition. In addition, the identification of biomarkers can also help towards the development of new diagnostic tools and eventually will lead to strategic management of the disease. Inspite of the ongoing debate on the utility of the gut microbiome we have explored how probable new therapeutic avenues like FMT (Fecal microbiota transplant) can be utilized. This review also summarises integrating human-relevant 3D cellular models coupled with computational models and the metadata obtained from interventional and epidemiological studies may decipher the complex interactome of diet- microbiota-disease pathophysiology. In addition, it will also open new avenues for the development of therapeutics derived from the microbiome or implementation of personalized nutrition. In addition, the identification of biomarkers can also help towards the development of new diagnostic tools and eventually will lead to strategic management of disease.
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Affiliation(s)
| | - Sangeeta Negi
- NMC Biolab, New Mexico Consortium, Los Alamos, NM, USA; Los Alamos National Laboratory, Los Alamos, NM 87544, USA
| | - Supratim Basu
- NMC Biolab, New Mexico Consortium, Los Alamos, NM, USA
| | - Joel Faintuch
- Department of Gastroenterology, Sao Paulo University Medical School, São Paulo, SP 01246-903, Brazil
| | | | - Pratyoosh Shukla
- Enzyme Technology and Protein Bioinformatics Laboratory, School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi 221005, India.
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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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9
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Cerk K, Aguilera‐Gómez M. Microbiota analysis for risk assessment: evaluation of hazardous dietary substances and its potential role on the gut microbiome variability and dysbiosis. EFSA J 2022; 20:e200404. [PMID: 35634548 PMCID: PMC9131584 DOI: 10.2903/j.efsa.2022.e200404] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The expansion of fields related to probiotics, microbiome‐targeted interventions and an evolving landscape for implementation across policy, industry and end users, signifies an era of important clinical translational changes. Characteristics and perception of traditional probiotics stemmed from the historical long‐term use of fermented products. Although the distinction between probiotic microorganisms and fermentation‐associated microbes is important, it is often confused as not all fermented foods are probiotic supplements. Current innovation in area of biotechnology and bioinformatics is emerging outside of the classical definitions and new probiotics will emerge from novel sources, challenging scientific as well as regulatory instructions. At the same time, the search for individual and group microbiome signatures – biomarkers in order to predict disease incidence, progression and response to treatment is a key area of microbiological and multidisciplinary research, enabled by efficient and powerful processing of large data sets. However, the regulation of marketed beneficial microbes and probiotics differs among countries and the basic level of classification, which depend on probiotic classification is not globally harmonised. At the same time, the regulation is very demanding to evaluate the safety of products on the market, so that only those products with scientific evidence benefits can obtain positive recognition in ways of health claims. Collaborative experimental and theoretical approaches and case studies have assisted the progress in this crosscutting area of research. There is a requirement to clearly specify criteria and provide details about ways and approaches of achieving those criteria with the intention that manufacturers can benefit from a transparent way of communicating product quality to end users.
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Feakins R, Torres J, Borralho-Nunes P, Burisch J, Cúrdia Gonçalves T, De Ridder L, Driessen A, Lobatón T, Menchén L, Mookhoek A, Noor N, Svrcek M, Villanacci V, Zidar N, Tripathi M. ECCO Topical Review on Clinicopathological Spectrum and Differential Diagnosis of Inflammatory Bowel Disease. J Crohns Colitis 2022; 16:343-368. [PMID: 34346490 DOI: 10.1093/ecco-jcc/jjab141] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
INTRODUCTION Many diseases can imitate inflammatory bowel disease [IBD] clinically and pathologically. This review outlines the differential diagnosis of IBD and discusses morphological pointers and ancillary techniques that assist with the distinction between IBD and its mimics. METHODS European Crohn's and Colitis Organisation [ECCO] Topical Reviews are the result of an expert consensus. For this review, ECCO announced an open call to its members and formed three working groups [WGs] to study clinical aspects, pathological considerations, and the value of ancillary techniques. All WGs performed a systematic literature search. RESULTS Each WG produced a draft text and drew up provisional Current Practice Position [CPP] statements that highlighted the most important conclusions. Discussions and a preliminary voting round took place, with subsequent revision of CPP statements and text and a further meeting to agree on final statements. CONCLUSIONS Clinicians and pathologists encounter a wide variety of mimics of IBD, including infection, drug-induced disease, vascular disorders, diverticular disease, diversion proctocolitis, radiation damage, and immune disorders. Reliable distinction requires a multidisciplinary approach.
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Affiliation(s)
- Roger Feakins
- Department of Cellular Pathology, Royal Free Hospital, London, and University College London, UK
| | - Joana Torres
- Department of Gastroenterology, Hospital Beatriz Ângelo, Loures, Portugal
| | - Paula Borralho-Nunes
- Department of Pathology, Hospital Cuf Descobertas, Lisboa and Faculdade de Medicina da Universidade de Lisboa, Lisbon, Portugal
| | - Johan Burisch
- Gastrounit, Medical Division, Hvidovre Hospital, University of Copenhagen, Denmark
| | - Tiago Cúrdia Gonçalves
- Department of Gastroenterology, Hospital da Senhora da Oliveira, Guimarães, Portugal.,School of Medicine, University of Minho, Braga/Guimarães, Portugal.,ICVS/3B's-PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Lissy De Ridder
- Department of Paediatric Gastroenterology, Erasmus MC Sophia Children's Hospital, University Medical Center Rotterdam, The Netherlands
| | - Ann Driessen
- Department of Pathology, University Hospital Antwerp, University Antwerp, Edegem, Belgium
| | - Triana Lobatón
- Department of Gastroenterology, Ghent University Hospital, Ghent, Belgium
| | - Luis Menchén
- Department of Digestive System Medicine, Hospital General Universitario-Insitituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain.,Department of Medicine, Universidad Complutense, Madrid, Spain.,Centro de Investigación Biomédica En Red de Enfermedades Hepáticas y Digestivas [CIBEREHD], Madrid, Spain
| | - Aart Mookhoek
- Department of Pathology, Amsterdam UMC, Amsterdam, The Netherlands
| | - Nurulamin Noor
- Department of Gastroenterology, Addenbrooke's Hospital, Cambridge University Hospitals NHS Trust, Cambridge, UK
| | - Magali Svrcek
- Department of Pathology, Sorbonne Université, AP-HP, Saint-Antoine Hospital, Paris, France
| | - Vincenzo Villanacci
- Department of Histopathology, Spedali Civili and University of Brescia, Brescia, Italy
| | - Nina Zidar
- Institute of Pathology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Monika Tripathi
- Department of Histopathology, Cambridge Biomedical Campus, Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
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11
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Chen D, Fulmer C, Gordon IO, Syed S, Stidham RW, Vande Casteele N, Qin Y, Falloon K, Cohen BL, Wyllie R, Rieder F. Application of Artificial Intelligence to Clinical Practice in Inflammatory Bowel Disease - What the Clinician Needs to Know. J Crohns Colitis 2021; 16:460-471. [PMID: 34558619 PMCID: PMC8919817 DOI: 10.1093/ecco-jcc/jjab169] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Artificial intelligence [AI] techniques are quickly spreading across medicine as an analytical method to tackle challenging clinical questions. What were previously thought of as highly complex data sources, such as images or free text, are now becoming manageable. Novel analytical methods merge the latest developments in information technology infrastructure with advances in computer science. Once primarily associated with Silicon Valley, AI techniques are now making their way into medicine, including in the field of inflammatory bowel diseases [IBD]. Understanding potential applications and limitations of these techniques can be difficult, in particular for busy clinicians. In this article, we explain the basic terminologies and provide a particular focus on the foundations behind state-of-the-art AI methodologies in both imaging and text. We explore the growing applications of AI in medicine, with a specific focus on IBD to inform the practising gastroenterologist and IBD specialist. Finally, we outline possible future uses of these technologies in daily clinical practice.
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Affiliation(s)
- David Chen
- Medical Operations, Cleveland Clinic Foundation, Cleveland, OH, USA,Department of Gastroenterology, Hepatology and Nutrition, Digestive Diseases and Surgery Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Clifton Fulmer
- Department of Pathology, Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Ilyssa O Gordon
- Department of Pathology, Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Sana Syed
- Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, School of Medicine, University of Virginia, Charlottesville, VA, USA,School of Data Science, University of Virginia, Charlottesville, VA, USA
| | - Ryan W Stidham
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Michigan Medicine, Ann Arbor, MI, USA,Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | | | - Yi Qin
- Department of Gastroenterology, Hepatology and Nutrition, Digestive Diseases and Surgery Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Katherine Falloon
- Department of Gastroenterology, Hepatology and Nutrition, Digestive Diseases and Surgery Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Benjamin L Cohen
- Department of Gastroenterology, Hepatology and Nutrition, Digestive Diseases and Surgery Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Robert Wyllie
- Medical Operations, Cleveland Clinic Foundation, Cleveland, OH, USA,Department of Pediatric Gastroenterology, Hepatology, and Nutrition, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Florian Rieder
- Corresponding author: Florian Rieder, MD, Department of Inflammation and Immunity, and Department of Gastroenterology, Hepatology, & Nutrition, Cleveland Clinic Foundation, 9500 Euclid Ave., Cleveland, OH 44195, USA. Tel: (216) 445-5631; Fax: (216) 636-0104; E-mail:
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12
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Zhu X, Li B, Lou P, Dai T, Chen Y, Zhuge A, Yuan Y, Li L. The Relationship Between the Gut Microbiome and Neurodegenerative Diseases. Neurosci Bull 2021; 37:1510-1522. [PMID: 34216356 PMCID: PMC8490573 DOI: 10.1007/s12264-021-00730-8] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 03/25/2021] [Indexed: 02/07/2023] Open
Abstract
Many recent studies have shown that the gut microbiome plays important roles in human physiology and pathology. Also, microbiome-based therapies have been used to improve health status and treat diseases. In addition, aging and neurodegenerative diseases, including Alzheimer's disease and Parkinson's disease, have become topics of intense interest in biomedical research. Several researchers have explored the links between these topics to study the potential pathogenic or therapeutic effects of intestinal microbiota in disease. But the exact relationship between neurodegenerative diseases and gut microbiota remains unclear. As technology advances, new techniques for studying the microbiome will be developed and refined, and the relationship between diseases and gut microbiota will be revealed. This article summarizes the known interactions between the gut microbiome and neurodegenerative diseases, highlighting assay techniques for the gut microbiome, and we also discuss the potential therapeutic role of microbiome-based therapies in diseases.
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Affiliation(s)
- Xueling Zhu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China.,Research Units of Infectious Disease and Microecology, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Bo Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China.,Research Units of Infectious Disease and Microecology, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Pengcheng Lou
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China.,Research Units of Infectious Disease and Microecology, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Tingting Dai
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China.,Research Units of Infectious Disease and Microecology, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Yang Chen
- The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Aoxiang Zhuge
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China.,Research Units of Infectious Disease and Microecology, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Yin Yuan
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China.,Research Units of Infectious Disease and Microecology, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Lanjuan Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China. .,Research Units of Infectious Disease and Microecology, Chinese Academy of Medical Sciences, Beijing, 100730, China.
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13
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López-Moreno A, Acuña I, Torres-Sánchez A, Ruiz-Moreno Á, Cerk K, Rivas A, Suárez A, Monteoliva-Sánchez M, Aguilera M. Next Generation Probiotics for Neutralizing Obesogenic Effects: Taxa Culturing Searching Strategies. Nutrients 2021; 13:1617. [PMID: 34065873 PMCID: PMC8151043 DOI: 10.3390/nu13051617] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 05/06/2021] [Accepted: 05/08/2021] [Indexed: 12/12/2022] Open
Abstract
The combination of diet, lifestyle, and the exposure to food obesogens categorized into "microbiota disrupting chemicals" (MDC) could determine obesogenic-related dysbiosis and modify the microbiota diversity that impacts on individual health-disease balances, inducing altered pathogenesis phenotypes. Specific, complementary, and combined treatments are needed to face these altered microbial patterns and the specific misbalances triggered. In this sense, searching for next-generation beneficial microbes or next-generation probiotics (NGP) by microbiota culturing, and focusing on their demonstrated, extensive scope and well-defined functions could contribute to counteracting and repairing the effects of obesogens. Therefore, this review presents a perspective through compiling information and key strategies for directed searching and culturing of NGP that could be administered for obesity and endocrine-related dysbiosis by (i) observing the differential abundance of specific microbiota taxa in obesity-related patients and analyzing their functional roles, (ii) developing microbiota-directed strategies for culturing these taxa groups, and (iii) applying the successful compiled criteria from recent NGP clinical studies. New isolated or cultivable microorganisms from healthy gut microbiota specifically related to obesogens' neutralization effects might be used as an NGP single strain or in consortia, both presenting functions and the ability to palliate metabolic-related disorders. Identification of holistic approaches for searching and using potential NGP, key aspects, the bias, gaps, and proposals of solutions are also considered in this review.
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Affiliation(s)
- Ana López-Moreno
- Department of Microbiology, Faculty of Pharmacy, Campus of Cartuja, University of Granada, 18071 Granada, Spain; (Á.R.-M.); (K.C.); (M.M.-S.)
- Center of Biomedical Research, Institute of Nutrition and Food Technology “José Mataix”, University of Granada, Armilla, 18016 Granada, Spain; (I.A.); (A.S.)
| | - Inmaculada Acuña
- Center of Biomedical Research, Institute of Nutrition and Food Technology “José Mataix”, University of Granada, Armilla, 18016 Granada, Spain; (I.A.); (A.S.)
- Department of Biochemistry and Molecular Biology, Faculty of Pharmacy, Campus of Cartuja, University of Granada, 18071 Granada, Spain
| | - Alfonso Torres-Sánchez
- Department of Microbiology, Faculty of Pharmacy, Campus of Cartuja, University of Granada, 18071 Granada, Spain; (Á.R.-M.); (K.C.); (M.M.-S.)
| | - Ángel Ruiz-Moreno
- Department of Microbiology, Faculty of Pharmacy, Campus of Cartuja, University of Granada, 18071 Granada, Spain; (Á.R.-M.); (K.C.); (M.M.-S.)
| | - Klara Cerk
- Department of Microbiology, Faculty of Pharmacy, Campus of Cartuja, University of Granada, 18071 Granada, Spain; (Á.R.-M.); (K.C.); (M.M.-S.)
| | - Ana Rivas
- IBS, Instituto de Investigación Biosanitaria, 18012 Granada, Spain;
- Department of Nutrition and Food Science, Campus of Cartuja, University of Granada, 18071 Granada, Spain
| | - Antonio Suárez
- Center of Biomedical Research, Institute of Nutrition and Food Technology “José Mataix”, University of Granada, Armilla, 18016 Granada, Spain; (I.A.); (A.S.)
- Department of Biochemistry and Molecular Biology, Faculty of Pharmacy, Campus of Cartuja, University of Granada, 18071 Granada, Spain
| | - Mercedes Monteoliva-Sánchez
- Department of Microbiology, Faculty of Pharmacy, Campus of Cartuja, University of Granada, 18071 Granada, Spain; (Á.R.-M.); (K.C.); (M.M.-S.)
- Center of Biomedical Research, Institute of Nutrition and Food Technology “José Mataix”, University of Granada, Armilla, 18016 Granada, Spain; (I.A.); (A.S.)
| | - Margarita Aguilera
- Department of Microbiology, Faculty of Pharmacy, Campus of Cartuja, University of Granada, 18071 Granada, Spain; (Á.R.-M.); (K.C.); (M.M.-S.)
- Center of Biomedical Research, Institute of Nutrition and Food Technology “José Mataix”, University of Granada, Armilla, 18016 Granada, Spain; (I.A.); (A.S.)
- IBS, Instituto de Investigación Biosanitaria, 18012 Granada, Spain;
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14
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Gupta V, Mohsen W, Chapman TP, Satsangi J. Predicting Outcome in Acute Severe Colitis-Controversies in Clinical Practice in 2021. J Crohns Colitis 2021; 15:1211-1221. [PMID: 33388777 PMCID: PMC7799290 DOI: 10.1093/ecco-jcc/jjaa265] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Acute severe ulcerative colitis [ASUC] remains a common medical emergency, with 25% of patients with ulcerative colitis experiencing at least one event in their disease course. Despite advances in medical therapy, ASUC continues to be associated with considerable morbidity and mortality, with up to 30% of patients requiring colectomy during initial admission. Our aim was to review the current controversies and recent progress in risk stratification, prediction of outcome, and personalisation of care in ASUC. We re-assess the use of Truelove and Witts' criteria, serum biomarkers, and the use of composite clinical indices in current clinical practice. We explore the potential for endoscopic prediction using defined validated indices for accurate and early prognostication, and the need to define outcome. We also consider the impact of the current COVID-19 pandemic. Finally, we discuss the current research agenda, including the application of new and emerging biomarkers coupled with multi-omics and the implications in management and optimisation of outcome. Research priorities for the prediction of outcome in acute severe colitis include the following. 1. Development of an accurate admission score to guide early medical rescue therapy or colectomy. 2. Utility of point-of-care faecal calprotectin, with determination of optimal cut-off values. 3. Role of serum and faecal infliximab levels to both predict outcome and guide accelerated infliximab dosing. 4. Role of novel biomarkers, including serum calprotectin, in predicting response to corticosteroids or rescue therapy. 5. Specific predictors of response to ciclosporin and infliximab to allow rationalisation of drug use. 6. Utility of validated endoscopic scores. 7. Utility of radiological assessment beyond use of plain abdominal X-ray. 8. The use of multiomics and machine learning to predict risk of Acute Severe Colitis in patients with Ulcerative Colitis.
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Affiliation(s)
- Vipin Gupta
- Translational Gastroenterology Unit, Nuffield Department of Experimental Medicine, University of Oxford, Oxford, UK,Department Of Gastroenterology, University Hospital of Wales, Cardiff and Vale University Health Board, Cardiff, UK
| | - Waled Mohsen
- Translational Gastroenterology Unit, Nuffield Department of Experimental Medicine, University of Oxford, Oxford, UK,Digestive Diseases Unit, Gold Coast University Hospital, Queensland, Australia,Corresponding author: Waled Mohsen,
| | - Thomas P Chapman
- Translational Gastroenterology Unit, Nuffield Department of Experimental Medicine, University of Oxford, Oxford, UK,Department of Gastroenterology, Western Sussex Hospitals NHS Foundation Trust, Worthing, UK
| | - Jack Satsangi
- Translational Gastroenterology Unit, Nuffield Department of Experimental Medicine, University of Oxford, Oxford, UK
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15
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Yang L, Hou K, Zhang B, Ouyang C, Lin A, Xu S, Ke D, Fang L, Chen Q, Wu J, Yan C, Lian Y, Jiang T, He J, Wang H, Fu Y, Xiao C, Chen Z. Preservation of the fecal samples at ambient temperature for microbiota analysis with a cost-effective and reliable stabilizer EffcGut. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 741:140423. [PMID: 32615432 DOI: 10.1016/j.scitotenv.2020.140423] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 05/31/2020] [Accepted: 06/20/2020] [Indexed: 02/05/2023]
Abstract
With the increasing researches on the role of gut microbiota in human health and disease, appropriate storage method of fecal samples at ambient temperature would conveniently guarantee the precise and reliable microbiota results. Nevertheless, less choice of stabilizer that is cost-efficient and feasible to be used in longer preservation period obstructed the large-scale metagenomics studies. Here, we evaluated the efficacy of a guanidine isothiocyanate-based reagent method EffcGut and compared it with the other already used storage method by means of 16S rRNA gene sequencing technology. We found that guanidine isothiocyanate-based reagent method at ambient temperature was not inferior to OMNIgene·GUT OM-200 and it could retain the similar bacterial community as that of -80 °C within 24 weeks. Furthermore, bacterial diversity and community structure difference were compared among different sample fraction (supernatant, suspension and precipitate) preserved in EffcGut and -80 °C. We found that supernatant under the preservation of EffcGut retained the similar community structure and composition as that of the low temperature preservation method.
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Affiliation(s)
- Luxi Yang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, School of Life Sciences, Xiamen University, Xiamen, China; Institute for Microbial Ecology, School of Medicine, Xiamen University, Xiamen, China
| | - Kaijian Hou
- Department of Endocrine and Metabolic Diseases, Longhu Hospital, the First Affiliated Hospital of Shantou University Medical College, China
| | - Bangzhou Zhang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, School of Life Sciences, Xiamen University, Xiamen, China; Institute for Microbial Ecology, School of Medicine, Xiamen University, Xiamen, China
| | - Cong Ouyang
- Xiamen Treatgut Biotechnology Co., Ltd., Xiamen, China
| | - Aiqiang Lin
- Xiamen Treatgut Biotechnology Co., Ltd., Xiamen, China
| | - Shuangbin Xu
- Xiamen Treatgut Biotechnology Co., Ltd., Xiamen, China
| | - Dongxian Ke
- Xiamen Treatgut Biotechnology Co., Ltd., Xiamen, China
| | - Lujing Fang
- Xiamen Treatgut Biotechnology Co., Ltd., Xiamen, China
| | - Qiongyun Chen
- Institute for Microbial Ecology, School of Medicine, Xiamen University, Xiamen, China
| | - Jingtong Wu
- Institute for Microbial Ecology, School of Medicine, Xiamen University, Xiamen, China
| | - Changsheng Yan
- Institute for Microbial Ecology, School of Medicine, Xiamen University, Xiamen, China
| | - Yifan Lian
- Institute for Microbial Ecology, School of Medicine, Xiamen University, Xiamen, China
| | - Tao Jiang
- Xiamen Treatgut Biotechnology Co., Ltd., Xiamen, China
| | - Jianquan He
- Department of Rehabilitation, Zhongshan Hospital, Xiamen University, China
| | - Han Wang
- Xiamen Treatgut Biotechnology Co., Ltd., Xiamen, China
| | - Yousi Fu
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, School of Life Sciences, Xiamen University, Xiamen, China
| | | | - Zhangran Chen
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, School of Life Sciences, Xiamen University, Xiamen, China; Institute for Microbial Ecology, School of Medicine, Xiamen University, Xiamen, China.
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16
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Zhang X, Li L, Butcher J, Stintzi A, Figeys D. Advancing functional and translational microbiome research using meta-omics approaches. MICROBIOME 2019; 7:154. [PMID: 31810497 PMCID: PMC6898977 DOI: 10.1186/s40168-019-0767-6] [Citation(s) in RCA: 127] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 11/11/2019] [Indexed: 05/05/2023]
Abstract
The gut microbiome has emerged as an important factor affecting human health and disease. The recent development of -omics approaches, including phylogenetic marker-based microbiome profiling, shotgun metagenomics, metatranscriptomics, metaproteomics, and metabolomics, has enabled efficient characterization of microbial communities. These techniques can provide strain-level taxonomic resolution of the taxa present in microbiomes, assess the potential functions encoded by the microbial community and quantify the metabolic activities occurring within a complex microbiome. The application of these meta-omics approaches to clinical samples has identified microbial species, metabolic pathways, and metabolites that are associated with the development and treatment of human diseases. These findings have further facilitated microbiome-targeted drug discovery and efforts to improve human health management. Recent in vitro and in vivo investigations have uncovered the presence of extensive drug-microbiome interactions. These interactions have also been shown to be important contributors to the disparate patient responses to treatment that are often observed during disease therapy. Therefore, developing techniques or frameworks that enable rapid screening, detailed evaluation, and accurate prediction of drug/host-microbiome interactions is critically important in the modern era of microbiome research and precision medicine. Here we review the current status of meta-omics techniques, including integrative multi-omics approaches, for characterizing the microbiome's functionality in the context of health and disease. We also summarize and discuss new frameworks for applying meta-omics approaches and microbiome assays to study drug-microbiome interactions. Lastly, we discuss and exemplify strategies for implementing microbiome-based precision medicines using these meta-omics approaches and high throughput microbiome assays.
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Affiliation(s)
- Xu Zhang
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario Canada
| | - Leyuan Li
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario Canada
| | - James Butcher
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario Canada
| | - Alain Stintzi
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario Canada
| | - Daniel Figeys
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario Canada
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17
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Peters DL, Wang W, Zhang X, Ning Z, Mayne J, Figeys D. Metaproteomic and Metabolomic Approaches for Characterizing the Gut Microbiome. Proteomics 2019; 19:e1800363. [PMID: 31321880 DOI: 10.1002/pmic.201800363] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 06/27/2019] [Indexed: 12/14/2022]
Abstract
The gut microbiome has been shown to play a significant role in human healthy and diseased states. The dynamic signaling that occurs between the host and microbiome is critical for the maintenance of host homeostasis. Analyzing the human microbiome with metaproteomics, metabolomics, and integrative multi-omics analyses can provide significant information on markers for healthy and diseased states, allowing for the eventual creation of microbiome-targeted treatments for diseases associated with dysbiosis. Metaproteomics enables functional activity information to be gained from the microbiome samples, while metabolomics provides insight into the overall metabolic states affecting/representing the host-microbiome interactions. Combining these functional -omic platforms together with microbiome composition profiling allows for a holistic overview on the functional and metabolic state of the microbiome and its influence on human health. Here the benefits of metaproteomics, metabolomics, and the integrative multi-omic approaches to investigating the gut microbiome in the context of human health and diseases are reviewed.
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Affiliation(s)
- Danielle L Peters
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON, KIH 8M5, Canada
| | - Wenju Wang
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON, KIH 8M5, Canada
| | - Xu Zhang
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON, KIH 8M5, Canada
| | - Zhibin Ning
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON, KIH 8M5, Canada
| | - Janice Mayne
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON, KIH 8M5, Canada
| | - Daniel Figeys
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON, KIH 8M5, Canada.,Canadian Institute for Advanced Research, 661 University Ave, Toronto, ON, M5G 1M1, Canada.,The University of Ottawa and Shanghai Institute of Materia Medica Joint Research Center on Systems and Personalized Pharmacology, 451 Smyth Road, Ottawa, ON, KIH 8M5, Canada
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18
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Falony G, Vandeputte D, Caenepeel C, Vieira-Silva S, Daryoush T, Vermeire S, Raes J. The human microbiome in health and disease: hype or hope. Acta Clin Belg 2019; 74:53-64. [PMID: 30810508 DOI: 10.1080/17843286.2019.1583782] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
OBJECTIVES The prognostic, diagnostic, and therapeutic potential of the human gut microbiota is widely recognised. However, translation of microbiome findings to clinical practice is challenging. Here, we discuss current knowledge and applications in the field. METHODS We revisit some recent advances in the field of faecal microbiome analyses with a focus on covariate analyses and ecological interpretation. RESULTS Population-level characterization of gut microbiota variation among healthy volunteers has allowed identifying microbiome covariates required for clinical studies. Currently, microbiome research is moving from relative to quantitative approaches that will shed a new light on microbiota-host interactions in health and disease. CONCLUSIONS Covariate characterization and technical advances increase reproducibility of microbiome research. Targeted in vitro/in vivo intervention studies will accelerate clinical implementation of microbiota findings.
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Affiliation(s)
- Gwen Falony
- Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
- Center for Microbiology, VIB, Leuven, Belgium
| | - Doris Vandeputte
- Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
- Center for Microbiology, VIB, Leuven, Belgium
| | - Clara Caenepeel
- Translational Research Center for Gastrointestinal Disorders (TARGID), KU Leuven, Leuven, Belgium
| | - Sara Vieira-Silva
- Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
- Center for Microbiology, VIB, Leuven, Belgium
| | - Tanine Daryoush
- Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
- Center for Microbiology, VIB, Leuven, Belgium
| | - Séverine Vermeire
- Translational Research Center for Gastrointestinal Disorders (TARGID), KU Leuven, Leuven, Belgium
| | - Jeroen Raes
- Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
- Center for Microbiology, VIB, Leuven, Belgium
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19
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Gisbert JP, Chaparro M. Clinical Usefulness of Proteomics in Inflammatory Bowel Disease: A Comprehensive Review. J Crohns Colitis 2019; 13:374-384. [PMID: 30307487 DOI: 10.1093/ecco-jcc/jjy158] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The protein domain is probably the most ubiquitously affected in disease, response and recovery, and therefore proteomics holds special promise for biomarker discovery in general, and particularly in inflammatory bowel disease [IBD], i.e. ulcerative colitis and Crohn's disease. Tremendous progress has been made over the past decade in the development and refinement of proteomics technologies. These advances provide opportunities for a long-anticipated personalized medicine approach to the treatment of IBD. The present review examines the current state of IBD proteomics research and its usefulness in clinical practice. We performed a systematic bibliographic search to identify studies investigating the use of proteomics in patients with IBD, and we then summarized the current 'state of the art' in the applications of proteomic technologies in the study of IBD. In particular, in the present review we provide: [1] a brief introduction to proteomics in health and disease; [2] a review of the different stages from biomarker discovery to clinical application; and [3] a comprehensive review of the clinical usefulness and application of proteomics in IBD, including: [a] screening to differentiate IBD from healthy controls; [b] differentiating Crohn's disease from ulcerative colitis; [c] prediction of the behaviour or the IBD course; [d] prediction of IBD response to biological treatment; and [e] monitoring response to treatment. We also review the importance of the type of sample-blood vs intestinal tissue-for the study of proteomics in IBD patients. Finally, we emphasize the current limitations of proteomic studies in IBD.
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Affiliation(s)
- Javier P Gisbert
- Gastroenterology Unit, Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria Princesa (IIS-IP), Universidad Autónoma de Madrid, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Madrid, Spain
| | - María Chaparro
- Gastroenterology Unit, Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria Princesa (IIS-IP), Universidad Autónoma de Madrid, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Madrid, Spain
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20
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Practical guidelines for gut microbiome analysis in microbiota-gut-brain axis research. Behav Brain Sci 2019. [DOI: 10.1017/s0140525x18002881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
AbstractThe microbiota-gut-brain (MGB) axis field is at an exciting stage, but the most recent developments in microbiota research still have to find their way into MGB studies. Here we outline the standards for microbiome data generation, the appropriate statistical techniques, and the covariates that should be included in MGB studies to optimize discovery and translation to clinical applications.
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Moen AEF, Lindstrøm JC, Tannæs TM, Vatn S, Ricanek P, Vatn MH, Jahnsen J. The prevalence and transcriptional activity of the mucosal microbiota of ulcerative colitis patients. Sci Rep 2018; 8:17278. [PMID: 30467421 PMCID: PMC6250705 DOI: 10.1038/s41598-018-35243-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 11/01/2018] [Indexed: 12/16/2022] Open
Abstract
Active microbes likely have larger impact on gut health status compared to inactive or dormant microbes. We investigate the composition of active and total mucosal microbiota of treatment-naïve ulcerative colitis (UC) patients to determine the microbial picture at the start-up phase of disease, using both a 16S rRNA transcript and gene amplicon sequencing. DNA and RNA were isolated from the same mucosal colonic biopsies. Our aim was to identify active microbial members of the microbiota in early stages of disease and reveal which members are present, but do not act as major players. We demonstrated differences in active and total microbiota of UC patients when comparing inflamed to non-inflamed tissue. Several taxa, among them the Proteobacteria phyla and families therein, revealed lower transcriptional activity despite a high presence. The Bifidobacteriaceae family of the Actinobacteria phylum showed lower abundance in the active microbiota, although no difference in presence was detected. The most abundant microbiota members of the inflamed tissue in UC patients were not the most active. Knowledge of active members of microbiota in UC patients could enhance our understanding of disease etiology. The active microbial community composition did not deviate from the total when comparing UC patients to non-IBD controls.
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Affiliation(s)
- Aina E Fossum Moen
- Department of Clinical Molecular Biology (EpiGen), Division of Medicine, Akershus University Hospital, Lørenskog, and University of Oslo, Oslo, Norway
| | - Jonas Christoffer Lindstrøm
- Health Services Research Unit, Akershus University Hospital, Lørenskog, Norway
- Institute of Clinical Medicine, Campus Ahus, University of Oslo, Oslo, Norway
| | - Tone Møller Tannæs
- Department of Clinical Molecular Biology (EpiGen), Division of Medicine, Akershus University Hospital, Lørenskog, and University of Oslo, Oslo, Norway.
| | - Simen Vatn
- Department of Gastroenterology, Division of Medicine, Akershus University Hospital, Lørenskog, and University of Oslo, Oslo, Norway
| | - Petr Ricanek
- Department of Gastroenterology, Division of Medicine, Akershus University Hospital, Lørenskog, and University of Oslo, Oslo, Norway
| | - Morten H Vatn
- Institute of Clinical Medicine, Campus Ahus, University of Oslo, Oslo, Norway
| | - Jørgen Jahnsen
- Institute of Clinical Medicine, Campus Ahus, University of Oslo, Oslo, Norway
- Department of Gastroenterology, Division of Medicine, Akershus University Hospital, Lørenskog, and University of Oslo, Oslo, Norway
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Reinglas J, Gonczi L, Kurt Z, Bessissow T, Lakatos PL. Positioning of old and new biologicals and small molecules in the treatment of inflammatory bowel diseases. World J Gastroenterol 2018; 24:3567-3582. [PMID: 30166855 PMCID: PMC6113721 DOI: 10.3748/wjg.v24.i32.3567] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 05/09/2018] [Accepted: 06/25/2018] [Indexed: 02/06/2023] Open
Abstract
The past decade has brought substantial advances in the management of inflammatory bowel diseases (IBD). The introduction of tumor necrosis factor (TNF) antagonists, evidence for the value of combination therapy, the recognition of targeting lymphocyte trafficking and activation as a viable treatment, and the need for early treatment of high-risk patients are all fundamental concepts for current modern IBD treatment algorithms. In this article, authors review the existing data on approved biologicals and small molecules as well as provide insight on the current positioning of approved therapies. Patient stratification for the selection of specific therapies, therapeutic targets and patient monitoring will be discussed as well. The therapeutic armamentarium for IBD is expanding as novel and more targeted therapies become available. In the absence of comparative trials, positioning these agents is becoming difficult. Emerging concepts for the future will include an emphasis on the development of algorithms which will facilitate a greater understanding of the positioning of novel biological drugs and small molecules in order to best tailor therapy to the patient. In the interim, anti-TNF therapy remains an important component of IBD therapy with the most real-life evidence and should be considered as first-line therapy in patients with complicated Crohn’s disease and in acute-severe ulcerative colitis. The safety and efficacy of these ‘older’ anti-TNF therapies can be optimized by adhering to therapeutic algorithms which combine clinical and objective markers of disease severity and response to therapy.
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Affiliation(s)
- Jason Reinglas
- Department of Gastroenterology, McGill University Health Center, Montreal, Québec H4A 3J1, Canada
| | - Lorant Gonczi
- First Department of Medicine, Semmelweis University, H-1083, Budapest, Koranyi S. 2A, Hungary
| | - Zsuzsanna Kurt
- First Department of Medicine, Semmelweis University, H-1083, Budapest, Koranyi S. 2A, Hungary
| | - Talat Bessissow
- Department of Gastroenterology, McGill University Health Center, Montreal, Québec H4A 3J1, Canada
| | - Peter L Lakatos
- Department of Gastroenterology, McGill University Health Center, Montreal, Québec H4A 3J1, Canada
- First Department of Medicine, Semmelweis University, H-1083, Budapest, Koranyi S. 2A, Hungary
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D'hoe K, Conterno L, Fava F, Falony G, Vieira-Silva S, Vermeiren J, Tuohy K, Raes J. Prebiotic Wheat Bran Fractions Induce Specific Microbiota Changes. Front Microbiol 2018; 9:31. [PMID: 29416529 PMCID: PMC5787670 DOI: 10.3389/fmicb.2018.00031] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 01/09/2018] [Indexed: 01/08/2023] Open
Abstract
Wheat bran fibers are considered beneficial to human health through their impact on gut microbiota composition and activity. Here, we assessed the prebiotic potential of selected bran fractions by performing a series of fecal slurry anaerobic fermentation experiments using aleurone as well as total, ultrafine, and soluble wheat bran (swb) as carbon sources. By combining amplicon-based community profiling with a fluorescent in situ hybridization (FISH) approach, we found that incubation conditions favor the growth of Proteobacteria such as Escherichia and Bilophila. These effects were countered in all but one [total wheat bran (twb)] fermentation experiments. Growth of Bifidobacterium species was stimulated after fermentation using ultrafine, soluble, and twb, in the latter two as part of a general increase in bacterial load. Both ultrafine and swb fermentation resulted in a trade-off between Bifidobacterium and Bilophila, as previously observed in human dietary supplementation studies looking at the effect of inulin-type fructans on the human gut microbiota. Aleurone selectively stimulated growth of Dorea and butyrate-producing Roseburia. All fermentation experiments induced enhanced gas production; increased butyrate concentrations were only observed following soluble bran incubation. Our results open perspectives for the development of aleurone as a complementary prebiotic selectively targeting colon butyrate producers.
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Affiliation(s)
- Kevin D'hoe
- Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium.,Jeroen Raes Lab, VIB KU Leuven Center for Microbiology, Leuven, Belgium.,Research Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Lorenza Conterno
- Department of Food Quality and Nutrition, Research and Innovation Centre, Fondazione Edmund Mach, Trento, Italy.,Fermentation and Distillation, Laimburg Research Centre, Bolzano, Italy
| | - Francesca Fava
- Department of Food Quality and Nutrition, Research and Innovation Centre, Fondazione Edmund Mach, Trento, Italy
| | - Gwen Falony
- Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium.,Jeroen Raes Lab, VIB KU Leuven Center for Microbiology, Leuven, Belgium
| | - Sara Vieira-Silva
- Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium.,Jeroen Raes Lab, VIB KU Leuven Center for Microbiology, Leuven, Belgium
| | | | - Kieran Tuohy
- Department of Food Quality and Nutrition, Research and Innovation Centre, Fondazione Edmund Mach, Trento, Italy
| | - Jeroen Raes
- Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium.,Jeroen Raes Lab, VIB KU Leuven Center for Microbiology, Leuven, Belgium.,Research Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
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24
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Quantitative microbiome profiling links gut community variation to microbial load. Nature 2017; 551:507-511. [PMID: 29143816 DOI: 10.1038/nature24460] [Citation(s) in RCA: 585] [Impact Index Per Article: 83.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 09/22/2017] [Indexed: 02/08/2023]
Abstract
Current sequencing-based analyses of faecal microbiota quantify microbial taxa and metabolic pathways as fractions of the sample sequence library generated by each analysis. Although these relative approaches permit detection of disease-associated microbiome variation, they are limited in their ability to reveal the interplay between microbiota and host health. Comparative analyses of relative microbiome data cannot provide information about the extent or directionality of changes in taxa abundance or metabolic potential. If microbial load varies substantially between samples, relative profiling will hamper attempts to link microbiome features to quantitative data such as physiological parameters or metabolite concentrations. Saliently, relative approaches ignore the possibility that altered overall microbiota abundance itself could be a key identifier of a disease-associated ecosystem configuration. To enable genuine characterization of host-microbiota interactions, microbiome research must exchange ratios for counts. Here we build a workflow for the quantitative microbiome profiling of faecal material, through parallelization of amplicon sequencing and flow cytometric enumeration of microbial cells. We observe up to tenfold differences in the microbial loads of healthy individuals and relate this variation to enterotype differentiation. We show how microbial abundances underpin both microbiota variation between individuals and covariation with host phenotype. Quantitative profiling bypasses compositionality effects in the reconstruction of gut microbiota interaction networks and reveals that the taxonomic trade-off between Bacteroides and Prevotella is an artefact of relative microbiome analyses. Finally, we identify microbial load as a key driver of observed microbiota alterations in a cohort of patients with Crohn's disease, here associated with a low-cell-count Bacteroides enterotype (as defined through relative profiling).
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Palmieri O, Mazza T, Castellana S, Panza A, Latiano T, Corritore G, Andriulli A, Latiano A. Inflammatory Bowel Disease Meets Systems Biology: A Multi-Omics Challenge and Frontier. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2017; 20:692-698. [PMID: 27930092 DOI: 10.1089/omi.2016.0147] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The inflammatory bowel disease (IBD) is a systemic disease that is characterized by the inflammation of the gastrointestinal tract. It includes ulcerative colitis and the Crohn's disease. Presently, IBD is one of the most investigated common complex human disorders, although its causes remain unclear. Multi-omics mechanisms involving genomic, transcriptomic, proteomic, and epigenomic variations, not to forget the miRNome, together with environmental contributions, result in an impairment of the immune system in persons with IBD. Such interactions at multiple levels of biology and in concert with the environment constitute the actual engine of this complex disease, demanding a multifactorial and multi-omics perspective to better understand the root causes of IBD. This expert analysis reviews and examines the latest literature and underscores, from the perspective of systems biology, the value of multi-omics technologies as opportunities to unravel the "IBD integrome." We anticipate that multi-omics research will accelerate the new discoveries and insights on IBD in the near future. It shall also pave the way for early diagnosis and help clinicians and families with IBD to forecast and make informed decisions about the prognosis and, possibly, personalized therapeutics in the future.
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Affiliation(s)
- Orazio Palmieri
- 1 Division of Gastroenterology, IRCCS "Casa Sollievo della Sofferenza" Hospital , San Giovanni Rotondo, Italy
| | - Tommaso Mazza
- 2 Laboratory of Bioinformatics, IRCCS "Casa Sollievo della Sofferenza" Hospital , San Giovanni Rotondo, Italy
| | - Stefano Castellana
- 2 Laboratory of Bioinformatics, IRCCS "Casa Sollievo della Sofferenza" Hospital , San Giovanni Rotondo, Italy
| | - Anna Panza
- 1 Division of Gastroenterology, IRCCS "Casa Sollievo della Sofferenza" Hospital , San Giovanni Rotondo, Italy
| | - Tiziana Latiano
- 1 Division of Gastroenterology, IRCCS "Casa Sollievo della Sofferenza" Hospital , San Giovanni Rotondo, Italy
| | - Giuseppe Corritore
- 1 Division of Gastroenterology, IRCCS "Casa Sollievo della Sofferenza" Hospital , San Giovanni Rotondo, Italy
| | - Angelo Andriulli
- 1 Division of Gastroenterology, IRCCS "Casa Sollievo della Sofferenza" Hospital , San Giovanni Rotondo, Italy
| | - Anna Latiano
- 1 Division of Gastroenterology, IRCCS "Casa Sollievo della Sofferenza" Hospital , San Giovanni Rotondo, Italy
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A Perspective on Brain-Gut Communication: The American Gastroenterology Association and American Psychosomatic Society Joint Symposium on Brain-Gut Interactions and the Intestinal Microenvironment. Psychosom Med 2017; 79:847-856. [PMID: 27922565 DOI: 10.1097/psy.0000000000000431] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
BACKGROUND Alterations in brain-gut communication and the intestinal microenvironment have been implicated in a variety of medical and neuropsychiatric diseases. Three central areas require basic and clinical research: (1) how the intestinal microenvironment interacts with the host immune system, central nervous system, and enteric nervous system; (2) the role of the intestinal microenvironment in the pathogenesis of medical and neuropsychiatric disease; and (3) the effects of diet, prebiotics, probiotics, and fecal microbiota transplantation on the intestinal microenvironment and the treatment of disease. METHODS This review article is based on a symposium convened by the American Gastroenterology Association and the American Psychosomatic Society to foster interest in the role of the intestinal microenvironment in brain-gut communication and pathogenesis of neuropsychiatric and biopsychosocial disorders. The aims were to define the state of the art of the current scientific knowledge base and to identify guidelines and future directions for new research in this area. RESULTS This review provides a characterization of the intestinal microbial composition and function. We also provide evidence for the interactions between the intestinal microbiome, the host, and the environment. The role of the intestinal microbiome in medical and neuropsychiatric diseases is reviewed as well as the treatment effects of manipulation of the intestinal microbiome. CONCLUSIONS Based on this review, opportunities and challenges for conducting research in the field are described, leading to potential avenues for future research.
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Rojo D, Méndez-García C, Raczkowska BA, Bargiela R, Moya A, Ferrer M, Barbas C. Exploring the human microbiome from multiple perspectives: factors altering its composition and function. FEMS Microbiol Rev 2017; 41:453-478. [PMID: 28333226 PMCID: PMC5812509 DOI: 10.1093/femsre/fuw046] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 12/15/2016] [Indexed: 02/07/2023] Open
Abstract
Our microbiota presents peculiarities and characteristics that may be altered by multiple factors. The degree and consequences of these alterations depend on the nature, strength and duration of the perturbations as well as the structure and stability of each microbiota. The aim of this review is to sketch a very broad picture of the factors commonly influencing different body sites, and which have been associated with alterations in the human microbiota in terms of composition and function. To do so, first, a graphical representation of bacterial, fungal and archaeal genera reveals possible associations among genera affected by different factors. Then, the revision of sequence-based predictions provides associations with functions that become part of the active metabolism. Finally, examination of microbial metabolite contents and fluxes reveals whether metabolic alterations are a reflection of the differences observed at the level of population structure, and in the last step, link microorganisms to functions under perturbations that differ in nature and aetiology. The utilisation of complementary technologies and methods, with a special focus on metabolomics research, is thoroughly discussed to obtain a global picture of microbiota composition and microbiome function and to convey the urgent need for the standardisation of protocols.
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Affiliation(s)
- David Rojo
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad CEU San Pablo, Campus Montepríncipe, 28668 Madrid, Spain
| | | | - Beata Anna Raczkowska
- Department of Endocrinology, Diabetology and Internal Medicine, Medical University of Bialystok, 15-276 Bialystok, Poland
| | - Rafael Bargiela
- Institute of Catalysis, Consejo Superior de Investigaciones Científicas (CSIC), 28049 Madrid, Spain
| | - Andrés Moya
- Foundation for the Promotion of Health and Biomedical Research in the Valencian Community Public Health (FISABIO), 46020 Valencia, Spain
- Network Research Center for Epidemiology and Public Health (CIBER-ESP), 28029 Madrid, Spain
- Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Universidad de Valencia, Paterna, 46980 Valencia, Spain
- These authors contributed equally to this work
| | - Manuel Ferrer
- Institute of Catalysis, Consejo Superior de Investigaciones Científicas (CSIC), 28049 Madrid, Spain
- Corresponding author: Institute of Catalysis, Consejo Superior de Investigaciones Científicas (CSIC), 28049 Madrid, Spain. Tel: (+34) 915854872; E-mail:
| | - Coral Barbas
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad CEU San Pablo, Campus Montepríncipe, 28668 Madrid, Spain
- These authors contributed equally to this work
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Zhang S, Cao X, Huang H. Sampling Strategies for Three-Dimensional Spatial Community Structures in IBD Microbiota Research. Front Cell Infect Microbiol 2017; 7:51. [PMID: 28286741 PMCID: PMC5323387 DOI: 10.3389/fcimb.2017.00051] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Accepted: 02/10/2017] [Indexed: 12/12/2022] Open
Abstract
Identifying intestinal microbiota is arguably an important task that is performed to determine the pathogenesis of inflammatory bowel diseases (IBD); thus, it is crucial to collect and analyze intestinally-associated microbiota. Analyzing a single niche to categorize individuals does not enable researchers to comprehensively study the spatial variations of the microbiota. Therefore, characterizing the spatial community structures of the inflammatory bowel disease microbiome is critical for advancing our understanding of the inflammatory landscape of IBD. However, at present there is no universally accepted consensus regarding the use of specific sampling strategies in different biogeographic locations. In this review, we discuss the spatial distribution when screening sample collections in IBD microbiota research. Here, we propose a novel model, a three-dimensional spatial community structure, which encompasses the x-, y-, and z-axis distributions; it can be used in some sampling sites, such as feces, colonoscopic biopsy, the mucus gel layer, and oral cavity. On the basis of this spatial model, this article also summarizes various sampling and processing strategies prior to and after DNA extraction and recommends guidelines for practical application in future research.
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Affiliation(s)
- Shaocun Zhang
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin UniversityTianjin, China; Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin UniversityTianjin, China; Collaborative Innovation Center of Chemical Science and EngineeringTianjin, China
| | - Xiaocang Cao
- Department of Gastroenterology and Hepatology, Tianjin Medical University General Hospital; Tianjin Medical University Tianjin, China
| | - He Huang
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin UniversityTianjin, China; Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin UniversityTianjin, China; Collaborative Innovation Center of Chemical Science and EngineeringTianjin, China
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29
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Sartor RB, Wu GD. Roles for Intestinal Bacteria, Viruses, and Fungi in Pathogenesis of Inflammatory Bowel Diseases and Therapeutic Approaches. Gastroenterology 2017; 152:327-339.e4. [PMID: 27769810 PMCID: PMC5511756 DOI: 10.1053/j.gastro.2016.10.012] [Citation(s) in RCA: 512] [Impact Index Per Article: 73.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Revised: 10/13/2016] [Accepted: 10/14/2016] [Indexed: 02/08/2023]
Abstract
Intestinal microbiota are involved in the pathogenesis of Crohn's disease, ulcerative colitis, and pouchitis. We review the mechanisms by which these gut bacteria, fungi, and viruses mediate mucosal homeostasis via their composite genes (metagenome) and metabolic products (metabolome). We explain how alterations to their profiles and functions under conditions of dysbiosis contribute to inflammation and effector immune responses that mediate inflammatory bowel diseases (IBD) in humans and enterocolitis in mice. It could be possible to engineer the intestinal environment by modifying the microbiota community structure or function to treat patients with IBD-either with individual agents, via dietary management, or as adjuncts to immunosuppressive drugs. We summarize the latest information on therapeutic use of fecal microbial transplantation and propose improved strategies to selectively normalize the dysbiotic microbiome in personalized approaches to treatment.
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Affiliation(s)
- R Balfour Sartor
- Departments of Medicine, Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.
| | - Gary D Wu
- Division of Gastroenterology, Perelman School of Medicine, the University of Pennsylvania, Philadelphia, Pennsylvania.
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30
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Contreras AV, Cocom-Chan B, Hernandez-Montes G, Portillo-Bobadilla T, Resendis-Antonio O. Host-Microbiome Interaction and Cancer: Potential Application in Precision Medicine. Front Physiol 2016; 7:606. [PMID: 28018236 PMCID: PMC5145879 DOI: 10.3389/fphys.2016.00606] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 11/21/2016] [Indexed: 12/19/2022] Open
Abstract
It has been experimentally shown that host-microbial interaction plays a major role in shaping the wellness or disease of the human body. Microorganisms coexisting in human tissues provide a variety of benefits that contribute to proper functional activity in the host through the modulation of fundamental processes such as signal transduction, immunity and metabolism. The unbalance of this microbial profile, or dysbiosis, has been correlated with the genesis and evolution of complex diseases such as cancer. Although this latter disease has been thoroughly studied using different high-throughput (HT) technologies, its heterogeneous nature makes its understanding and proper treatment in patients a remaining challenge in clinical settings. Notably, given the outstanding role of host-microbiome interactions, the ecological interactions with microorganisms have become a new significant aspect in the systems that can contribute to the diagnosis and potential treatment of solid cancers. As a part of expanding precision medicine in the area of cancer research, efforts aimed at effective treatments for various kinds of cancer based on the knowledge of genetics, biology of the disease and host-microbiome interactions might improve the prediction of disease risk and implement potential microbiota-directed therapeutics. In this review, we present the state of the art of sequencing and metabolome technologies, computational methods and schemes in systems biology that have addressed recent breakthroughs of uncovering relationships or associations between microorganisms and cancer. Together, microbiome studies extend the horizon of new personalized treatments against cancer from the perspective of precision medicine through a synergistic strategy integrating clinical knowledge, HT data, bioinformatics, and systems biology.
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Affiliation(s)
| | - Benjamin Cocom-Chan
- Instituto Nacional de Medicina GenómicaMexico City, Mexico; Human Systems Biology Laboratory, Instituto Nacional de Medicina GenómicaMexico City, Mexico
| | - Georgina Hernandez-Montes
- Coordinación de la Investigación Científica, Red de Apoyo a la Investigación-National Autonomous University of Mexico (UNAM) Mexico City, Mexico
| | - Tobias Portillo-Bobadilla
- Coordinación de la Investigación Científica, Red de Apoyo a la Investigación-National Autonomous University of Mexico (UNAM) Mexico City, Mexico
| | - Osbaldo Resendis-Antonio
- Instituto Nacional de Medicina GenómicaMexico City, Mexico; Human Systems Biology Laboratory, Instituto Nacional de Medicina GenómicaMexico City, Mexico; Coordinación de la Investigación Científica, Red de Apoyo a la Investigación-National Autonomous University of Mexico (UNAM)Mexico City, Mexico
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31
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Schulze S, Schleicher J, Guthke R, Linde J. How to Predict Molecular Interactions between Species? Front Microbiol 2016; 7:442. [PMID: 27065992 PMCID: PMC4814556 DOI: 10.3389/fmicb.2016.00442] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 03/18/2016] [Indexed: 12/21/2022] Open
Abstract
Organisms constantly interact with other species through physical contact which leads to changes on the molecular level, for example the transcriptome. These changes can be monitored for all genes, with the help of high-throughput experiments such as RNA-seq or microarrays. The adaptation of the gene expression to environmental changes within cells is mediated through complex gene regulatory networks. Often, our knowledge of these networks is incomplete. Network inference predicts gene regulatory interactions based on transcriptome data. An emerging application of high-throughput transcriptome studies are dual transcriptomics experiments. Here, the transcriptome of two or more interacting species is measured simultaneously. Based on a dual RNA-seq data set of murine dendritic cells infected with the fungal pathogen Candida albicans, the software tool NetGenerator was applied to predict an inter-species gene regulatory network. To promote further investigations of molecular inter-species interactions, we recently discussed dual RNA-seq experiments for host-pathogen interactions and extended the applied tool NetGenerator (Schulze et al., 2015). The updated version of NetGenerator makes use of measurement variances in the algorithmic procedure and accepts gene expression time series data with missing values. Additionally, we tested multiple modeling scenarios regarding the stimuli functions of the gene regulatory network. Here, we summarize the work by Schulze et al. (2015) and put it into a broader context. We review various studies making use of the dual transcriptomics approach to investigate the molecular basis of interacting species. Besides the application to host-pathogen interactions, dual transcriptomics data are also utilized to study mutualistic and commensalistic interactions. Furthermore, we give a short introduction into additional approaches for the prediction of gene regulatory networks and discuss their application to dual transcriptomics data. We conclude that the application of network inference on dual-transcriptomics data is a promising approach to predict molecular inter-species interactions.
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Affiliation(s)
- Sylvie Schulze
- Research Group Systems Biology and Bioinformatics, Leibniz-Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute Jena, Germany
| | - Jana Schleicher
- Research Group Systems Biology and Bioinformatics, Leibniz-Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute Jena, Germany
| | - Reinhard Guthke
- Research Group Systems Biology and Bioinformatics, Leibniz-Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute Jena, Germany
| | - Jörg Linde
- Research Group Systems Biology and Bioinformatics, Leibniz-Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute Jena, Germany
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