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Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome
2012
PLoS Computational Biology
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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]
2018
bioRxiv
pre-print
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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
2017
Current Opinion in Systems Biology
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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
2015
Advances in Genomics and Genetics
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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
2012
Briefings in Bioinformatics
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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
2015
Advances in Genomics and Genetics
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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
2015
MOJ Proteomics & Bioinformatics
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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
2015
Frontiers in Genetics
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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
2015
BioMed Research International
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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
2014
Cell Metabolism
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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
2021
Current Opinion in Systems Biology
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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
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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
2015
Wiley Interdisciplinary Reviews: Systems Biology and Medicine
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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
2017
Metabolites
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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
2013
Current Opinion in Biotechnology
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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
2016
BMC Bioinformatics
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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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