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Advancing functional and translational microbiome research using meta-omics approaches

Xu Zhang, Leyuan Li, James Butcher, Alain Stintzi, Daniel Figeys
2019 Microbiome  
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.  ...  Lastly, we discuss and exemplify strategies for implementing microbiome-based precision medicines using these meta-omics approaches and high throughput microbiome assays.  ...  Given the high complexity of the human gut microbiota and the challenges in culturing a high proportion of gut microbial species [7] , most microbiome studies employ "meta-omics" approaches, including  ... 
doi:10.1186/s40168-019-0767-6 pmid:31810497 pmcid:PMC6898977 fatcat:iezzv2yfk5bvphgav3osb4qraq

Gut Microbiota Dysbiosis as Risk and Premorbid Factors of IBD and IBS Along the Childhood–Adulthood Transition

Lorenza Putignani, Federica Del Chierico, Pamela Vernocchi, Michele Cicala, Salvatore Cucchiara, Bruno Dallapiccola
2016 Inflammatory Bowel Diseases  
They include (1) high risk or flare-up recurrence -omics-based dysbiosis profiles; (2) microbial and molecular biomarkers of health and disease; (3) -omics-based pipelines for laboratory medicine diagnostics  ...  Gut microbiota has been studied for inflammatory bowel disease (IBD) and irritable bowel syndrome (IBS) in either children or adults, while modifiable gut microbiota features, acting as risk and premorbid  ...  over millions of years of evolution. 55, 56 High-throughput sequencing studies have FIGURE 1 .  ... 
doi:10.1097/mib.0000000000000602 pmid:26588090 fatcat:n2jgz5ya6fakdkt4tzzqexihly

Gut–Brain Axis and Neurodegeneration: State-of-the-Art of Meta-Omics Sciences for Microbiota Characterization

Bruno Tilocca, Luisa Pieroni, Alessio Soggiu, Domenico Britti, Luigi Bonizzi, Paola Roncada, Viviana Greco
2020 International Journal of Molecular Sciences  
In the present review we aim to provide an overview of the state-of-the-art of meta-omics sciences including metagenomics for the study of microbial genomes and taxa strains, metatranscriptomics for gene  ...  Recent advances in the field of meta-omics sciences and related bioinformatics tools have allowed a comprehensive investigation of human-associated microbiota and its contribution to achieving and maintaining  ...  community proteins PD Flores Saiffe Farìas et al., 2018 [41] Metabolomics High-throughput method for the comprehensive study of the metabolite array resulting from the microbiota-host interactions  ... 
doi:10.3390/ijms21114045 pmid:32516966 pmcid:PMC7312636 fatcat:ydhydiidvzebzhdj5zj2r2pbve

Synthetic Gut Microbiome: Advances and Challenges

Humphrey A. Mabwi, Eunjung Kim, Dae-Geun Song, Hyo Shin Yoon, Cheol-Ho Pan, Erick.V.G. Komba, GwangPyo Ko, Kwang Hyun Cha
2020 Computational and Structural Biotechnology Journal  
Here, we provide an overview of the developments and challenges of the synthetic human gut microbiome, and propose the incorporation of multi-omics and mathematical methods in a better synthetic gut ecosystem  ...  design, for easy translation of microbiome information to therapies.  ...  and Innovation Fund of the Partnership for Skills in Applied Sciences, Engineering and Technology (RSIF-PASET).  ... 
doi:10.1016/j.csbj.2020.12.029 pmid:33489006 pmcid:PMC7787941 fatcat:4lh7uourbfbdfa62s5vb2lykde

Multi-Omics Approaches: The Key to Improving Respiratory Health in People With Cystic Fibrosis?

Andrew J. Lee, Gisli G. Einarsson, Deirdre F. Gilpin, Michael M. Tunney
2020 Frontiers in Pharmacology  
The advent of high-throughput multi-omics technologies has underpinned the expansion in lung microbiome research, increasing our understanding of the nature, complexity and significance of the polymicrobial  ...  With further refinement, multi-omics approaches present the opportunity to untangle the complex interplay between microbe-microbe and microbe-host interactions in the lung and the relationship with respiratory  ...  MICROBIOTA DIRECTED THERAPEUTIC APPROACHES If correctly exploited, the information generated by multi-omics investigations of the complete airway biome offers the potential to develop novel methods for  ... 
doi:10.3389/fphar.2020.569821 pmid:33013411 pmcid:PMC7509435 fatcat:bcpzaedi6nbgtfume7dva45lba

Gut microbiota as important modulator of metabolism in health and disease

Xiang-qian Wang, Ai-hua Zhang, Jian-hua Miao, Hui Sun, Guang-li Yan, Fang-fang Wu, Xi-jun Wang
2018 RSC Advances  
The human gastrointestinal tract colonizes a large number of microbial microflora to participate in various metabolic processes in the human body, and plays a major role in the host immune response.  ...  The combined use of multi-omics provides a completely new approach for the study of gut microbiota.  ...  In recent years, metagenomics using high-throughput sequencing technology as an analytical tool has been continuously applied for the study of gut microbiota. 13 Microgenomics, which is based on the microbial  ... 
doi:10.1039/c8ra08094a pmid:35558413 pmcid:PMC9092240 fatcat:7cjhowo565hvlpztv3ffbnwbuu

Meta-omics in Inflammatory Bowel Disease Research: Applications, Challenges, and Guidelines

Mireia Valles-Colomer, Youssef Darzi, Sara Vieira-Silva, Gwen Falony, Jeroen Raes, Marie Joossens
2016 Journal of Crohn's & Colitis  
Meta-omics [metagenomics, metatranscriptomics, and metaproteomics] are rapidly expanding our knowledge of the gut microbiota in health and disease.  ...  Yet, meta-omics data analysis, interpretation, and among-study comparison remain challenging.  ...  Acknowledgments We thank all members of the Raes Laboratory for lively discussions. MVC and YD performed the literature review and drafted the manuscript.  ... 
doi:10.1093/ecco-jcc/jjw024 pmid:26802086 fatcat:dccwiqhofzgvvalmldalbdupym

Integrated Multi-Omics for Novel Aging Biomarkers and Antiaging Targets

Lei Wu, Xinqiang Xie, Tingting Liang, Jun Ma, Lingshuang Yang, Juan Yang, Longyan Li, Yu Xi, Haixin Li, Jumei Zhang, Xuefeng Chen, Yu Ding (+1 others)
2021 Biomolecules  
Advancements in high-throughput technology provide new opportunities for omics research to understand the pathological process of various complex human diseases.  ...  The integration of multi-omics technologies can systematically reveal the interactions among aging molecules from a multidimensional perspective.  ...  Acknowledgments: We sincerely thank those who contributed to this research, without which this study would not have been possible. Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/biom12010039 pmid:35053186 pmcid:PMC8773837 fatcat:v4252oz3drdslihakz42hnzcsi

A comprehensive review of integrative pharmacology-based investigation: A paradigm shift in traditional Chinese medicine

Haiyu Xu, Yanqiong Zhang, Ping Wang, Junhong Zhang, Hong Chen, Luoqi Zhang, Xia Du, Chunhui Zhao, Dan Wu, Feng Liu, Hongjun Yang, Changxiao Liu
2021 Acta Pharmaceutica Sinica B  
Finally, we further discuss the applications of TCMIP for the improvement of TCM quality control, clarification of the molecular mechanisms underlying the actions of TCMs and discovery of potential new  ...  After that, we summarize the existing data resources, computational models and experimental methods of TCMIP and highlight the urgent establishment of mathematical modeling and experimental methods.  ...  Virtual Metabolic Human (VMH) is a metabolic database of human and intestinal flora that can be combined with human and intestinal flora to reconstruct a metabolic model for large-scale, multi-omics research  ... 
doi:10.1016/j.apsb.2021.03.024 fatcat:bdmy3k2skzh5nc7jt4gotx7q6e

"Omic" investigations of protozoa and worms for a deeper understanding of the human gut "parasitome"

Valeria Marzano, Livia Mancinelli, Giorgia Bracaglia, Federica Del Chierico, Pamela Vernocchi, Francesco Di Girolamo, Stefano Garrone, Hyppolite Tchidjou Kuekou, Patrizia D'Argenio, Bruno Dallapiccola, Andrea Urbani, Lorenza Putignani (+1 others)
2017 PLoS Neglected Tropical Diseases  
and particularly on their coexistence and interaction with the intestinal microbiota.  ...  Studies of the gut "parasitome" through "omic" technologies, such as (meta)genomics, transcriptomics, proteomics, and metabolomics, are herein reviewed to better understand their role in the relationships  ...  Acknowledgments We would like to thank the English-speaking experts from BioMed Proofreading LLC for manuscript revision.  ... 
doi:10.1371/journal.pntd.0005916 pmid:29095820 pmcid:PMC5667730 fatcat:l2udkwsiszbi5oxweqeyrrd57i

An Integrated Multi-Disciplinary Perspectivefor Addressing Challenges of the Human Gut Microbiome

Rohan M. Shah, Elizabeth J. McKenzie, Magda T. Rosin, Snehal R. Jadhav, Shakuntla V. Gondalia, Douglas Rosendale, David J. Beale
2020 Metabolites  
In doing so, we contextualize the experimental and technical challenges of undertaking such studies and provide a framework for capitalizing on the breadth of insight such approaches afford.  ...  Furthermore, these studies highlight our need to address the issues of individual variation, and of samples as proxies.  ...  Acknowledgments: The authors would like to acknowledge and thank the contributions and comments of Starin McKeen, Caterina Carco and Shanalee James during the preparation of this manuscript.  ... 
doi:10.3390/metabo10030094 pmid:32155792 pmcid:PMC7143645 fatcat:zyn3vvzg5zahzbo7c5ggzzbzn4

The Integrative Human Microbiome Project: Dynamic Analysis of Microbiome-Host Omics Profiles during Periods of Human Health and Disease

2014 Cell Host and Microbe  
Human subject whole genome sequences Analysis of the sequence of the host genome using high-throughput DNA sequencing.  ...  Create an integrated data repository, the IBDMDB, for standardized community access to multi-omic data, building on existing resources and supporting rapid future algorithm development.  ... 
doi:10.1016/j.chom.2014.08.014 pmid:25211071 pmcid:PMC5109542 fatcat:dvxhnxp56faszijc5izip3ojfq

Network-based drug discovery by integrating systems biology and computational technologies

E. L. Leung, Z.-W. Cao, Z.-H. Jiang, H. Zhou, L. Liu
2012 Briefings in Bioinformatics  
The complex multi-component nature of medicinal herbs may serve as valuable resources for network-based multi-target drug discovery due to its potential treatment effects by synergy.  ...  Further integration across various '-omics' platforms and computational tools would accelerate development of network-based drug discovery and network medicine.  ...  Dalhen for carefully proofreading the manuscript and providing valuable comments.  ... 
doi:10.1093/bib/bbs043 pmid:22877768 pmcid:PMC3713711 fatcat:t3wp24cgyff6zechfsm5hagfji

Applications of Omics Technology for Livestock Selection and Improvement

Dibyendu Chakraborty, Neelesh Sharma, Savleen Kour, Simrinder Singh Sodhi, Mukesh Kumar Gupta, Sung Jin Lee, Young Ok Son
2022 Frontiers in Genetics  
With the advent of high-throughput omics techniques and the availability of multi-omics technologies and sophisticated analytic packages, several promising tools and methods have been developed to estimate  ...  This manuscript provides an overview of various omics technologies and their limitations for animal genetic selection and breeding decisions.  ...  FUNDING This study was supported by the Department of Biotechnology, Government of India (No.  ... 
doi:10.3389/fgene.2022.774113 pmid:35719396 pmcid:PMC9204716 fatcat:57b3w6exvjbtnkok5qpbhwckye

Reconstructing functional networks in the human intestinal tract using synthetic microbiomes

Sudarshan A Shetty, Hauke Smidt, Willem M de Vos
2019 Current Opinion in Biotechnology  
The human intestinal tract harbors one of the most densely populated and open microbial ecosystems.  ...  The application of multi-omics approaches has provided insight into a wide array of complex interactions between the various groups of mainly anaerobic colonic microbes as well as the host-microbe dialogue  ...  Acknowledgements This work was supported by the Soehngen Institute for Anaerobic Microbiology024-002-002 grant to WMdV and the UNLOCK project (NRGWI.obrug.2018.005) of the Netherlands Organisation for  ... 
doi:10.1016/j.copbio.2019.03.009 pmid:30959425 fatcat:4by6wik7dvaonk4ke2xsg7k7wq
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