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      Microbial Dark Matter: from Discovery to Applications

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          Abstract

          With the rapid increase of the microbiome samples and sequencing data, more and more knowledge about microbial communities has been gained. However, there is still much more to learn about microbial communities, including billions of novel species and genes, as well as countless spatiotemporal dynamic patterns within the microbial communities, which together form the microbial dark matter. In this work, we summarized the dark matter in microbiome research and reviewed current data mining methods, especially artificial intelligence (AI) methods, for different types of knowledge discovery from microbial dark matter. We also provided case studies on using AI methods for microbiome data mining and knowledge discovery. In summary, we view microbial dark matter not as a problem to be solved but as an opportunity for AI methods to explore, with the goal of advancing our understanding of microbial communities, as well as developing better solutions to global concerns about human health and the environment.

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          Most cited references153

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          Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

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            Metagenomic biomarker discovery and explanation

            This study describes and validates a new method for metagenomic biomarker discovery by way of class comparison, tests of biological consistency and effect size estimation. This addresses the challenge of finding organisms, genes, or pathways that consistently explain the differences between two or more microbial communities, which is a central problem to the study of metagenomics. We extensively validate our method on several microbiomes and a convenient online interface for the method is provided at http://huttenhower.sph.harvard.edu/lefse/.
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              Structure, Function and Diversity of the Healthy Human Microbiome

              Studies of the human microbiome have revealed that even healthy individuals differ remarkably in the microbes that occupy habitats such as the gut, skin, and vagina. Much of this diversity remains unexplained, although diet, environment, host genetics, and early microbial exposure have all been implicated. Accordingly, to characterize the ecology of human-associated microbial communities, the Human Microbiome Project has analyzed the largest cohort and set of distinct, clinically relevant body habitats to date. We found the diversity and abundance of each habitat’s signature microbes to vary widely even among healthy subjects, with strong niche specialization both within and among individuals. The project encountered an estimated 81–99% of the genera, enzyme families, and community configurations occupied by the healthy Western microbiome. Metagenomic carriage of metabolic pathways was stable among individuals despite variation in community structure, and ethnic/racial background proved to be one of the strongest associations of both pathways and microbes with clinical metadata. These results thus delineate the range of structural and functional configurations normal in the microbial communities of a healthy population, enabling future characterization of the epidemiology, ecology, and translational applications of the human microbiome.
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                Author and article information

                Contributors
                Journal
                Genomics Proteomics Bioinformatics
                Genomics Proteomics Bioinformatics
                Genomics, Proteomics & Bioinformatics
                Elsevier
                1672-0229
                2210-3244
                26 April 2022
                October 2022
                26 April 2022
                : 20
                : 5
                : 867-881
                Affiliations
                MOE Key Laboratory of Molecular Biophysics, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center of Artificial Intelligence Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
                Author notes
                [* ]Corresponding author. ningkang@ 123456hust.edu.cn
                [#]

                Equal contribution.

                Article
                S1672-0229(22)00037-7
                10.1016/j.gpb.2022.02.007
                10025686
                35477055
                a3eccd9a-7100-4907-993f-ac412fc228b4
                © 2022 The Authors. Published by Elsevier B.V. and Science Press on behalf of Beijing Institute of Genomics, Chinese Academy of Sciences / China National Center for Bioinformation and Genetics Society of China.

                This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).

                History
                : 6 July 2021
                : 28 September 2021
                : 22 March 2022
                Categories
                Review

                microbiome,dark matter,artificial intelligence,knowledge discovery,application

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