| Título: | Genome-based Modeling and Design of Metabolic Interactions in Microbial Communities |
| Autores: |
Mahadevan, Radhakrishnan; University of Toronto Henson, Michael A |
| Fecha: | 2012-11-11 |
| Publicador: | Computacional and structural biotechnology journal |
| Fuente: |
 |
| Tipo: |
info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion Peer-reviewed Article |
| Tema: | No aplica |
| Descripción: | Biotechnology research is traditionally focused on individual microbial strains that are perceived to have the necessary metabolic functions, or the capability to have these functions introduced, to achieve a particular task. For many important applications, the development of such omnipotent microbes is an extremely challenging if not impossible task. By contrast, nature employs a radically different strategy based on synergistic combinations of different microbial species that collectively achieve the desired task. These natural communities have evolved to exploit the native metabolic capabilities of each species and are highly adaptive to changes in their environments. However, microbial communities have proven difficult to study due to a lack of suitable experimental and computational tools. With the advent of genome sequencing, omics technologies, bioinformatics and genome-scale modeling, researchers now have unprecedented capabilities to analyze and engineer the metabolism of microbial communities. The goal of this review is to summarize recent applications of genome-scale metabolic modeling to microbial communities. A brief introduction to lumped community models is used to motivate the need for genome-level descriptions of individual species and their metabolic interactions. The review of genome-scale models begins with static modeling approaches, which are appropriate for communities where the extracellular environment can be assumed to be time invariant or slowly varying. Dynamic extensions of the static modeling approach are described, and then applications of genome-scale models for design of synthetic microbial communities are reviewed. The review concludes with a summary of metagenomic tools for analyzing community metabolism and an outlook for future research. |
| Idioma: | Inglés |
1 Systems biology and metabolic engineering of Arthrospira cell factories por Klanchui, Amornpan,Vorapreeda, Tayvich,Vongsangnak, Wanwipa,Kannapho, Chiraphan,Cheevadhanarak, Supapon,Meechai, Asawin | 6 The Role of INDY in Metabolic Regulation por Willmes, Diana M; Charité University School of Medicine Berlin,Birkenfeld, Andreas L; Charité University School of Medicine Berlin |
2 Structure-based Methods for Computational Protein Functional Site Prediction por KC, Dukka B; North Carolina A&T State University | 7 The Biochemistry of Vitreoscilla hemoglobin por Stark, Benjamin C.; Illinois Institute of Technology,Dikshit, Kanak L.; Institute of Microbial Technology,Pagilla, Krishna R.; Illinois Institute of Technology |
3 Computer-Aided Protein Directed Evolution: a Review of Web Servers, Databases and other Computational Tools for Protein Engineering por Verma, Rajni; Jacobs University Bremen,Schwaneberg, Ulrich; RWTH Aachen University,Roccatano, Danilo; Jacobs University Bremen | 8 A method to predict edge strands in beta-sheets from protein sequences por Guilloux, Antonin,Caudron, Bernard,Jestin, Jean-Luc |
4 MD simulation studies to investigate iso-energetic conformational behaviour of modified nucleosides m2G and m22G present in tRNA por Bavi, Rohit S,Sambhare, Susmit B,Sonawane, Kailas D; Structural Bioinformatics Unit,
Department of Biochemistry,
Shivaji University, Kolhapur 416 004,
Maharashtra (M.S.), India. | 9 Conformational Sampling in Template-Free Protein Loop Structure Modeling: An Overview por Li, Yaohang; Old Dominion University |
5 Metabolomics in the identification of biomarkers of dietary intake por O’Gorman, Aoife,Gibbons, Helena,Brennan, Lorraine | 10 Development of microorganisms for cellulose-biofuel consolidated bioprocessings: metabolic engineers’ tricks por Mazzoli, Roberto; University of Torino, Italy. |