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Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome

Sahar Abubucker, Nicola Segata, Johannes Goll, Alyxandria M. Schubert, Jacques Izard, Brandi L. Cantarel, Beltran Rodriguez-Mueller, Jeremy Zucker, Mathangi Thiagarajan, Bernard Henrissat, Owen White, Scott T. Kelley (+6 others)
2012 PLoS Computational Biology  
Microbial communities carry out the majority of the biochemical activity on the planet, and they play integral roles in processes including metabolism and immune homeostasis in the human microbiome.  ...  Here, we describe an alternative approach to infer the functional and metabolic potential of a microbial community metagenome.  ...  Acknowledgments The authors would like to thank all of the participants in the Human Microbiome Consortium's Metabolic Reconstruction group, including Yuzhen Ye for providing MinPath, Maria Rivera for  ... 
doi:10.1371/journal.pcbi.1002358 pmid:22719234 pmcid:PMC3374609 fatcat:hdm25ej2xjalba2hlkfnxpn2sy

The Microbiome Modeling Toolbox: from microbial interactions to personalized microbial communities [article]

Federico Baldini, Almut Heinken, Laurent Heirendt, Stefania Magnusdottir, Ronan M.T. Fleming, Ines Thiele
2018 bioRxiv   pre-print
reconstructions and metagenomic data.  ...  Motivation: The application of constraint-based modeling to functionally analyze metagenomic data has been limited so far, partially due to the absence of suitable toolboxes.  ...  Moreover, metagenomically-derived data can be integrated with microbial metabolic reconstructions permitting the prediction of altered functional assessment of different microbial communities, e.g., in  ... 
doi:10.1101/318485 fatcat:56d3ulqcnrgs7atztdc3did35a

Using systems biology approaches to elucidate cause and effect in host–microbiome interactions

Elizabeth A. Witherden, David L. Moyes, Kenneth D. Bruce, S. Dusko Ehrlich, Saeed Shoaie
2017 Current Opinion in Systems Biology  
Abstract: The human microbiome is a diverse and complex ecosystem integral for healthy human development.  ...  However, it may be possible to overcome such limitations through the use of novel systems biology thinking and approaches, to integrate and analyse these large 'multi-omics' datasets.  ...  This research did not receive any specific grant from funding agencies in the public, commercial or non-for-profit sectors.  ... 
doi:10.1016/j.coisb.2017.05.003 fatcat:7tcxqtlex5f5dczlfmqveftltm

New insight into the gut microbiome through metagenomics

Jens Nielsen, Boyang Ji
2015 Advances in Genomics and Genetics  
Herein, we describe the metagenomic methods used in human gut microbiome studies and review the roles of gut microbiota as well as the integrative analyses of metagenomic data with other omics data.  ...  Finally, we discuss the application of constraint-based modeling to elucidate the microbemicrobe interaction and host-microbe interaction in the human gut microbiota.  ...  Acknowledgments We gratefully thank Leif Väremo, Manuel Garcia-Albornoz, and Saeed Shoaie for critical review of the manuscript.  ... 
doi:10.2147/agg.s57215 fatcat:mbpttyjl55boblocef4os5hhp4

Computational systems biology and in silico modeling of the human microbiome

E. Borenstein
2012 Briefings in Bioinformatics  
The assembly, ecology and dynamics of the microbiome and its contribution to the development, physiology and nutrition of the host are clearly affected not only by the set of genes or species in the microbiome  ...  for metagenomic-based modeling of the microbiome at the cellular, ecological and supra-organismal level.  ...  Yet, even with these limitations, as shotgun metagenomic data continue to accumulate for both the human microbiome and many other microbiomes of interest, supra-organism models are an increasingly attractive  ... 
doi:10.1093/bib/bbs022 pmid:22589385 fatcat:kc2yb7hi3zbdzahdyumtvv6hki

New insight into the gut microbiome through metagenomics

Ji B, Nielsen J
2015 Advances in Genomics and Genetics  
Herein, we describe the metagenomic methods used in human gut microbiome studies and review the roles of gut microbiota as well as the integrative analyses of metagenomic data with other omics data.  ...  Finally, we discuss the application of constraint-based modeling to elucidate the microbe–microbe interaction and host–microbe interaction in the human gut microbiota.  ...  Metabolic reconstruction for metagenomic data and its application to the human microbiome. PLoS Comput Biol . 2012;8(6):e1002358. 71.  ... 
doaj:becf1dc1b606466d80e46ea29725f989 fatcat:y4uqfliamzd6lbigojimkyksua

Comparative Metagenomics with Metabolic Reconstruction

Nilesh Saratkar
2015 MOJ Proteomics & Bioinformatics  
Abbreviations: KEGG, kyoto encyclopedia of genes and genomes; HMP, human metabiome project; MG-RAST, metagenomics RAST); 3M, metagenomic metabolic manual annotation; DIAG, data intensive academic grid;  ...  HUMAnN, HMP unified metabolic analysis network Comparative metagenomics with metabolic reconstruction Volume 2 Issue 3 -2015  ...  I am also thankful for the DIAG team for making such a great computational resources available for most of the analytical data processing.  ... 
doi:10.15406/mojpb.2015.02.00049 fatcat:dbuoin3ziba7le6vvmlessebgy

From next-generation sequencing to systematic modeling of the gut microbiome

Boyang Ji, Jens Nielsen
2015 Frontiers in Genetics  
Changes in the human gut microbiome are associated with altered human metabolism and health, yet the mechanisms of interactions between microbial species and human metabolism have not been clearly elucidated  ...  The systematic modeling of metabolic interactions could provide a predictive understanding of gut microbiome, and pave the way to synthetic microbiota design and personalized-microbiome medicine and healthcare  ...  Acknowledgments This work was financially supported by the Knut and Alice Wallenberg Foundation, Torsten Söderberska Stiftelse and the EU Framework VII project MetaCardis (grant agreements HEALTH-F4-2012  ... 
doi:10.3389/fgene.2015.00219 pmid:26157455 pmcid:PMC4477173 fatcat:5zmjsbba4rccbbiy2rpnwsksny

mmnet: An R Package for Metagenomics Systems Biology Analysis

Yang Cao, Xiaofei Zheng, Fei Li, Xiaochen Bo
2015 BioMed Research International  
The human microbiome plays important roles in human health and disease.  ...  The result can be represented in an intuitive way and sent to Cytoscape for further exploration.  ...  Introduction The human microbiome has been proved to play a key role in human health and disease.  ... 
doi:10.1155/2015/167249 pmid:26421278 pmcid:PMC4573221 fatcat:im5ilijtifcifab3h53gqbgru4

Mapping the Inner Workings of the Microbiome: Genomic- and Metagenomic-Based Study of Metabolism and Metabolic Interactions in the Human Microbiome

Ohad Manor, Roie Levy, Elhanan Borenstein
2014 Cell Metabolism  
The human gut microbiome is a major contributor to human metabolism and health, yet the metabolic processes that are carried out by various community members, the way these members interact with each other  ...  We will specifically highlight two interrelated lines of work, the first aiming to deconvolve the microbiome and to characterize the metabolic capacity of various microbiome species and the second aiming  ...  This approach was shown to successfully reconstruct species-level gene content of microbiome taxa both in simulated data and in samples from the human microbiome project.  ... 
doi:10.1016/j.cmet.2014.07.021 pmid:25176148 pmcid:PMC4252837 fatcat:2fycfi6z2fen7pbfvoe47iuxje

Advances in constraint-based modelling of microbial communities

Almut Heinken, Arianna Basile, Ines Thiele
2021 Current Opinion in Systems Biology  
of meta-omics data and allows for the mechanistic prediction of metabolic 17 fluxes.  ...  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  ...  To further expand the scope of 197 human microbiome modelling, an organ-resolved whole-body model of human metabolism, 198 which can be contextualised with physiological data and dietary regimes, and  ... 
doi:10.1016/j.coisb.2021.05.007 fatcat:zu4eei6hifdhliigapwkdtsi34

Systems biology of host-microbe metabolomics

Almut Heinken, Ines Thiele
2015 Wiley Interdisciplinary Reviews: Systems Biology and Medicine  
The human gut microbiota performs essential functions for host and well-being, but has also been linked to a variety of disease states, e.g., obesity and type 2 diabetes.  ...  To systematically investigate this complex host-microbial co-metabolism, a systems biology approach integrating high-throughput data and computational network models is required.  ...  The global human reconstruction can be tailored to be both cell-type and individual specific, e.g., by overlaying it with transcriptomic or metabolomic data, 172 and it has been applied successfully  ... 
doi:10.1002/wsbm.1301 pmid:25929487 pmcid:PMC5029777 fatcat:slpvfw5ryfgivks5z7scs6mnxa

Computational Approaches for Integrative Analysis of the Metabolome and Microbiome

Jasmine Chong, Jianguo Xia
2017 Metabolites  
The microbiome contributes functional genes and metabolites, and is an important factor for maintaining health.  ...  analysis to metabolic network-based modeling approaches.  ...  Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/metabo7040062 pmid:29156542 pmcid:PMC5746742 fatcat:j25rzjkxxbgzzkx6dl3t3bqoui

Towards a predictive systems-level model of the human microbiome: progress, challenges, and opportunities

Sharon Greenblum, Hsuan-Chao Chiu, Roie Levy, Rogan Carr, Elhanan Borenstein
2013 Current Opinion in Biotechnology  
The human microbiome represents a vastly complex ecosystem that is tightly linked to our development, physiology, and health.  ...  metabolism, and models of the interaction between the microbiome and the host.  ...  This study introduces the Metagenomic Systems Biology framework, reconstructing and analyzing microbiome-wide metabolic networks based on metagenomic data from 124 human gut microbiome samples.  ... 
doi:10.1016/j.copbio.2013.04.001 pmid:23623295 pmcid:PMC3732493 fatcat:hqtgxtlf5jhsrkqwszeqsx2gye

RevEcoR: an R package for the reverse ecology analysis of microbiomes

Yang Cao, Yuanyuan Wang, Xiaofei Zheng, Fei Li, Xiaochen Bo
2016 BMC Bioinformatics  
This software allows users to obtain large-scale ecological insights into species' ecology directly from high-throughput metagenomic data.  ...  The software has great potential for facilitating the study of microbiomes. Conclusions: RevEcoR is open source software for the study of microbial community ecology.  ...  Acknowledgements We thank all members of the Department of Biotechnology, who helped us improve our software.  ... 
doi:10.1186/s12859-016-1088-4 pmid:27473172 pmcid:PMC4965897 fatcat:x4kifx7mibb2bfprkt6lkpgj2q
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