Metabolic network modeling of microbial communities

Matthew B. Biggs, Gregory L. Medlock, Glynis L. Kolling, Jason A. Papin
2015 Wiley Interdisciplinary Reviews: Systems Biology and Medicine  
Genome-scale metabolic network reconstructions and constraint-based analysis are powerful methods that have the potential to make functional predictions about microbial communities. Current use of genome-scale metabolic networks to characterize the metabolic functions of microbial communities includes species compartmentalization, separating species-level and community-level objectives, dynamic analysis, the "enzyme-soup" approach, multi-scale modeling, and others. There are many challenges
more » ... rent to the field, including a need for tools that accurately assign high-level omics signals to individual community members, new automated reconstruction methods that rival manual curation, and novel algorithms for integrating omics data and engineering communities. As technologies and modeling frameworks improve, we expect that there will be proportional advances in the fields of ecology, health science, and microbial community engineering. Microbial communities represent a gargantuan force of nature that exerts influence on global geochemical cycles 1 , agriculture 2 , human health 3 , food preparation 4 , and a host of relevant aspects of life on earth 5,6 . Traditional microbiology has made great strides over the last century in describing and categorizing these microscopic neighbors. More recently, advances in sequencing technologies have provided the first glimpses at the composition of natural microbial communities, including insights into the physiology of non-culturable microbes 7 . Databases are filling with mountains of genomic fragments, gene and protein expression data, and other such large-scale "-omics" information, all describing the content of diverse microbial communities 8, 9 . Despite the plethora of data, we yet lack true understanding of the mechanisms that cause communities to function and interact with their environments 10 . Considering the importance of microbial communities to many global ecosystems, health, and various industries, there is a great need to move beyond a
doi:10.1002/wsbm.1308 pmid:26109480 pmcid:PMC4575871 fatcat:xy2brs6dzvcupac6ywnipm5fgy