title: Microbial Community Metabolic Modeling: A Community Data-Driven Network Reconstruction.
abstract: Metabolic network modeling of microbial communities provides an in-depth understanding of community-wide metabolic and regulatory processes. Compared to single organism analyses, community metabolic network modeling is more complex because it needs to account for interspecies interactions. To date, most approaches focus on reconstruction of high-quality individual networks so that, when combined, they can predict community behaviors as a result of interspecies interactions. However, this conventional method becomes ineffective for communities whose members are not well characterized and cannot be experimentally interrogated in isolation. Here, we tested a new approach that uses community-level data as a critical input for the network reconstruction process. This method focuses on directly predicting interspecies metabolic interactions in a community, when axenic information is insufficient. We validated our method through the case study of a bacterial photoautotroph-heterotroph consortium that was used to provide data needed for a community-level metabolic network reconstruction. Resulting simulations provided experimentally validated predictions of how a photoautotrophic cyanobacterium supports the growth of an obligate heterotrophic species by providing organic carbon and nitrogen sources. J. Cell. Physiol. 231: 2339-2345, 2016. © 2016 Wiley Periodicals, Inc.
authors.affiliation: Division of Mathematics and Computer Science, Argonne National Laboratory, Argonne, Illinois.|Computation Institute, University of Chicago, Chicago, Illinois.
authors.forename: Christopher S
authors.initials: CS
authors.lastname: Henry
authors.affiliation: Biodetection Sciences, National Security Directorate, Pacific Northwest National Laboratory, Richland, Washington.|Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington.|The Gene and Linda Voiland School of Chemical Engineering and Bioengineering, Washington State University, Pullman, Washington.
authors.forename: Hans C
authors.initials: HC
authors.lastname: Bernstein
authors.affiliation: Division of Mathematics and Computer Science, Argonne National Laboratory, Argonne, Illinois.|Division of Biosciences, Argonne National Laboratory, Argonne, Illinois.
authors.forename: Pamela
authors.initials: P
authors.lastname: Weisenhorn
authors.affiliation: Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington.
authors.forename: Ronald C
authors.initials: RC
authors.lastname: Taylor
authors.affiliation: Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington.
authors.forename: Joon-Yong
authors.initials: JY
authors.lastname: Lee
authors.affiliation: Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington.
authors.forename: Jeremy
authors.initials: J
authors.lastname: Zucker
authors.affiliation: Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington.
authors.forename: Hyun-Seob
authors.initials: HS
authors.lastname: Song
mesh_terms: D001419:Bacteria / Q000235:genetics / Q000378:metabolism*; D020869:Gene Expression Profiling; D015964:Gene Expression Regulation, Bacterial; D016680:Genome, Bacterial; D053858:Metabolic Networks and Pathways; D059013:Microbial Consortia / Q000235:genetics; D008954:Models, Biological