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Computational Modeling of the Human Microbiome

Chowdhury, Fong
2020 Microorganisms  
Here, we focus on the four main anatomical sites of the human microbiome: gut, oral, skin, and vaginal, and provide information on site-specific background, experimental data, and computational modeling  ...  The impact of microorganisms on human health has long been acknowledged and studied, but recent advances in research methodologies have enabled a new systems-level perspective on the collections of microorganisms  ...  Modeling Methodologies A number of different computational modeling approaches have been developed to study the gut microbiome to help analyze and understand its function including aspects of network topology  ... 
doi:10.3390/microorganisms8020197 pmid:32023941 pmcid:PMC7074762 fatcat:2cnuf7tnkjejze6ezqwrnx2ut4

Microbe-set enrichment analysis facilitates functional interpretation of microbiome profiling data

Yan Kou, Xiaomin Xu, Zhengnong Zhu, Lei Dai, Yan Tan
2020 Scientific Reports  
Overall, MSEA is a useful knowledge-based computational approach to interpret the functions of microbes, which can be integrated with microbiome profiling pipelines to help reveal the underlying mechanism  ...  Microbiome profiling followed by differential abundance analysis has been established as an effective approach to study the mechanisms of host-microbiome interactions.  ...  Acknowledgements We gratefully thank Zichen Wang for his assistance in method development; We would like to thank Han Hu for discussion on the study design and interpreting results.  ... 
doi:10.1038/s41598-020-78511-y pmid:33293650 fatcat:tpqxpan4bjesrm22367ul332bq

Metabolic Modeling of Human Gut Microbiota on a Genome Scale: An Overview

Partho Sen, Matej Orešič
2019 Metabolites  
Genome-scale metabolic modeling (GSMM) is an emerging approach that has been increasingly applied to infer diet–microbiome, microbemicrobe and host–microbe interactions under physiological conditions.  ...  Furthermore, we summarize various tools and resources available for metagenomic data processing and GSMM, highlighting the experimental approaches needed to validate the model predictions.  ...  Acknowledgments: We thank to Alex Dickens and Santosh Lamichhane for helpful scientific discussions. We also  ... 
doi:10.3390/metabo9020022 pmid:30695998 pmcid:PMC6410263 fatcat:3xgsy2jrxfe2ld4uhubvpfrefa

The Promise of the Plant's Second Genome

Pradeep Reddy Marri
2015 Journal of Investigative Genomics  
Concerted, collaborative, cross-functional approaches involving scientists from diverse fields including but not limited to genetics, physiology, genomics, chemistry, computer sciences and plant breeding  ...  A few focused studies have shown the utility of plant-microbial association to abiotic and biotic stress tolerance through the modulation of plant exudates to either recruit beneficial microbes or drive  ...  Metagenomics approaches are also helping us to study microbes in their native ecological states, thus unraveling the role of microbiomes in our lives.  ... 
doi:10.15406/jig.2015.02.00031 fatcat:pe56u6xaubhsvdbfkvbphgwb54

A review of 10 years of human microbiome research activities at the US National Institutes of Health, Fiscal Years 2007-2016

2019 Microbiome  
to progress to microbiome-based interventions for treating disease and supporting health.  ...  This analysis closes with a few comments on the technical needs and knowledge gaps which remain for this field to be able to advance over the next decade and for the outcomes of this research to be able  ...  Acknowledgements The NIH Human Microbiome Portfolio Analysis Group would like to thank the Trans-NIH Microbiome Working Group for their continued interest and input into this effort.  ... 
doi:10.1186/s40168-019-0620-y pmid:30808411 pmcid:PMC6391833 fatcat:o7h7j7j5xvh55inygjr7xjn5au

Computational Approaches for Integrative Analysis of the Metabolome and Microbiome

Jasmine Chong, Jianguo Xia
2017 Metabolites  
The study of the microbiome, the totality of all microbes inhabiting the host or an environmental niche, has experienced exponential growth over the past few years.  ...  In this review, we provide an overview of different computational approaches that have been used in recent years for integrative analysis of metabolome and microbiome data, ranging from statistical correlation  ...  The seed set framework has also been applied to predict microbe-microbe interactions by computing competition and mutualism scores based upon the predicted seed set of each microbe-microbe pair at the  ... 
doi:10.3390/metabo7040062 pmid:29156542 pmcid:PMC5746742 fatcat:j25rzjkxxbgzzkx6dl3t3bqoui

Machine Learning as a Tool in Investigating the Possible Role of Microbiome in Development and Treatment of Cancer

Sreehita Hajeebu, Ngonack J Ngembus, Pushyami Satya Bandi, Preetish Kumar Panigrahy, Stacey Heindl
2021 Cureus  
However, it requires adaptive learning techniques and high computational power to bring this research to light empirically.  ...  Microbiome and its composition have been a key area of interest among the scientific community.  ...  FIGURE 1: Traditional approach versus machine learning approach The primary goal is to allow the computer systems to learn automatically without human intervention, continuously facilitate intelligent  ... 
doi:10.7759/cureus.17415 pmid:34589326 pmcid:PMC8459918 fatcat:e4omgtlvqrd6leriarbne3fh3a

The Human Microbiome Project: A Community Resource for the Healthy Human Microbiome

Dirk Gevers, Rob Knight, Joseph F. Petrosino, Katherine Huang, Amy L. McGuire, Bruce W. Birren, Karen E. Nelson, Owen White, Barbara A. Methé, Curtis Huttenhower
2012 PLoS Biology  
Acknowledgments The authors would like to thank Jean McEwen and Lita Proctor for consultation to confirm the accuracy of Human Microbiome Project program elements.  ...  '' [9] both to describe a technological approach-sequencing and analysis of the genes from whole communities rather than from individual genomes-and to emphasize that microbes function within communities  ...  Microbial ecologists, realizing that .99% of environmental microbes could not be easily cultured, developed approaches to study microorganisms in situ [5] , primarily by sequencing the 16S ribosomal RNA  ... 
doi:10.1371/journal.pbio.1001377 pmid:22904687 pmcid:PMC3419203 fatcat:hu3vyz6nbvgt7flkbgnfoc4igu

Challenges and Approaches in Microbiome Research: From Fundamental to Applied

Chrysi Sergaki, Beatriz Lagunas, Ian Lidbury, Miriam L. Gifford, Patrick Schäfer
2018 Frontiers in Plant Science  
Soil microbes harbor enormous potentials to provide sustainable and economically favorable solutions that could introduce novel approaches to improve agricultural practices and, hence, crop productivity  ...  In this review we give an overview regarding the current stateof-the-art of microbiome research by discussing new technologies and approaches.  ...  All these analytical approaches have greatly benefitted from the advancements in computational analyses and machine learning and their significance for the development of microbiome research (Knight et  ... 
doi:10.3389/fpls.2018.01205 pmid:30174681 pmcid:PMC6107787 fatcat:lcbbp7eekrboznefcxirsfqqqa

Systematic interrogation of the distinct metabolic potential in gut microbiomes of inflammatory bowel disease patients with dysbiosis [article]

Almut Heinken, Ines Thiele
2019 bioRxiv   pre-print
Taken together, we presented an efficient, scalable, tractable computational approach to systematically interrogate the metabolic potential of individual microbiomes.  ...  patients with and without dysbiosis, and healthy control children to construct a personalized microbiome model for each sample using the AGORA resource of genome-scale gut microbial reconstructions.  ...  Funding This study was funded by Luxembourg National Research Fund (FNR) through the ATTRACT programme grant (FNR/A12/01) and by the European Research Council (ERC) under the European Union's Horizon 2020  ... 
doi:10.1101/640649 fatcat:hvskpctp2fdjzfi7qej4wftsly

A unified initiative to harness Earth's microbiomes

A. P. Alivisatos, M. J. Blaser, E. L. Brodie, M. Chun, J. L. Dangl, T. J. Donohue, P. C. Dorrestein, J. A. Gilbert, J. L. Green, J. K. Jansson, R. Knight, M. E. Maxon (+5 others)
2015 Science  
However, we lack many tools required to advance beyond descriptive approaches to studies that enable a mechanistic, predictive, and actionable understanding of global microbiome processes.  ...  Adaptive models that capture the complexity of interactions from molecules to microbes, and communities to ecosystems, and new approaches for visualizing complex data sets in multiple dimensions, will  ... 
doi:10.1126/science.aac8480 pmid:26511287 fatcat:nxu66mrt3fgr3m7m5r2at6m4vu

From Microbiome to Traits: Designing Synthetic Microbial Communities for Improved Crop Resiliency

Rafael Soares Correa de Souza, Jaderson Silveira Leite Armanhi, Paulo Arruda
2020 Frontiers in Plant Science  
Computational methods, including machine learning and artificial intelligence, will leverage the approaches of screening and identifying beneficial microbes while improving the process of determining the  ...  A recently introduced approach is the use of synthetic microbial communities (SynComs), which involves applying concepts from both microbial ecology and genetics to design inoculants.  ...  Recent studies have shown that the plant microbiome is composed of a highly diverse and complex community, often sustained by multiple interactions between microbes and their host.  ... 
doi:10.3389/fpls.2020.01179 pmid:32983187 pmcid:PMC7484511 fatcat:5er5m72xszelpkcd6hv6bybkwy

Parasite Microbiome Project: Systematic Investigation of Microbiome Dynamics within and across Parasite-Host Interactions

Nolwenn M. Dheilly, Daniel Bolnick, Seth Bordenstein, Paul J. Brindley, Cédric Figuères, Edward C. Holmes, Joaquín Martínez Martínez, Anna J. Phillips, Robert Poulin, Karyna Rosario
2017 mSystems  
We hereby propose the Parasite Microbiome Project to bring together researchers with complementary expertise and to study the role of microbes in host-parasite interactions.  ...  This is a call to arms to prevent fragmented research endeavors, encourage best practices in experimental approaches, and allow reliable comparative analyses across model systems.  ...  The PMP will trigger and support functional approaches in parasite systems of interest, thereby leading to opportunities for using parasite-associated microbes as an indicator of system health and novel  ... 
doi:10.1128/msystems.00050-17 pmid:28761932 pmcid:PMC5516220 fatcat:rm6n6pvsergxxedvbkfoa26eq4

Advances in constraint-based modelling of microbial communities

Almut Heinken, Arianna Basile, Ines Thiele
2021 Current Opinion in Systems Biology  
We show that constraint-based microbiome modelling can 23 complement experimental approaches and has valuable applications spanning from ecology, 24 human health, industry to environmental conservation  ...  In a follow-up study, the behaviour of a microbe-microbe pair when 132 introducing a third species to the community has been analysed, revealing that adding 133 another mutualist reduced selection for  ...  has been applied to a wide variety of studies simulating microbe-microbe, host-43 microbe, and microbiome interactions.  ... 
doi:10.1016/j.coisb.2021.05.007 fatcat:zu4eei6hifdhliigapwkdtsi34

Mathematical-based microbiome analytics for clinical translation

Jayanth Kumar Narayana, Micheál Mac Aogáin, Wilson Wen Bin Goh, Kelin Xia, Krasimira Tsaneva-Atanasova, Sanjay H. Chotirmall
2021 Computational and Structural Biotechnology Journal  
This is predominantly due to a lack of suitable computational tools to facilitate microbiome analytics.  ...  These approaches primarily view human disease through the lens of a single species and its relevant clinical setting however such approaches fail to account for the surrounding environment and wide microbial  ...  Topological data analysis (TDA), a widely-used dimensionality reduction and featurization approach is used to study the ''shape of data" using models and methods from computational, combinatorial and algebraic  ... 
doi:10.1016/j.csbj.2021.11.029 pmid:34900137 pmcid:PMC8637001 fatcat:hfsip6qw2bftrdrus6ww6nnj3y
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