Probabilistic inference of biochemical reactions in microbial communities from metagenomic sequences.

ABSTRACT: Shotgun metagenomics has been applied to the studies of the functionality of various microbial communities. As a critical analysis step in these studies, biological pathways are reconstructed based on the genes predicted from metagenomic shotgun sequences. Pathway reconstruction provides insights into the functionality of a microbial community and can be used for comparing multiple microbial communities. The utilization of pathway reconstruction, however, can be jeopardized because of imperfect functional annotation of genes, and ambiguity in the assignment of predicted enzymes to biochemical reactions (e.g., some enzymes are involved in multiple biochemical reactions). Considering that metabolic functions in a microbial community are carried out by many enzymes in a collaborative manner,

SUBMITTER: Jiao D 

PROVIDER: S-EPMC3605055 | biostudies-literature | 2013

REPOSITORIES: biostudies-literature