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Full-Text Articles in Genetics and Genomics
Micom: Metagenome-Scale Modeling To Infer Metabolic Interactions In The Gut Microbiota., Christian Diener, Sean M Gibbons, Osbaldo Resendis-Antonio
Micom: Metagenome-Scale Modeling To Infer Metabolic Interactions In The Gut Microbiota., Christian Diener, Sean M Gibbons, Osbaldo Resendis-Antonio
Articles, Abstracts, and Reports
Compositional changes in the gut microbiota have been associated with a variety of medical conditions such as obesity, Crohn's disease, and diabetes. However, connecting microbial community composition to ecosystem function remains a challenge. Here, we introduce MICOM, a customizable metabolic model of the human gut microbiome. By using a heuristic optimization approach based on L2 regularization, we were able to obtain a unique set of realistic growth rates that corresponded well with observed replication rates. We integrated adjustable dietary and taxon abundance constraints to generate personalized metabolic models for individual metagenomic samples. We applied MICOM to a balanced cohort of …
A Pipeline For Creation Of Genome-Scale Metabolic Reconstructions, Shaun W. Norris
A Pipeline For Creation Of Genome-Scale Metabolic Reconstructions, Shaun W. Norris
Theses and Dissertations
The decreasing costs of next generation sequencing technologies and the increasing speeds at which they work have lead to an abundance of 'omic datasets. The need for tools and methods to analyze, annotate, and model these datasets to better understand biological systems is growing. Here we present a novel software pipeline to reconstruct the metabolic model of an organism in silico starting from its genome sequence and a novel compilation of biological databases to better serve the generation of metabolic models. We validate these methods using five Gardnerella vaginalis strains and compare the gene annotation results to NCBI and the …