Abstract:
:Microbial functional diversification is driven by environmental factors, i.e. microorganisms inhabiting the same environmental niche tend to be more functionally similar than those from different environments. In some cases, even closely phylogenetically related microbes differ more across environments than across taxa. While microbial similarities are often reported in terms of taxonomic relationships, no existing databases directly link microbial functions to the environment. We previously developed a method for comparing microbial functional similarities on the basis of proteins translated from their sequenced genomes. Here, we describe fusionDB, a novel database that uses our functional data to represent 1374 taxonomically distinct bacteria annotated with available metadata: habitat/niche, preferred temperature, and oxygen use. Each microbe is encoded as a set of functions represented by its proteome and individual microbes are connected via common functions. Users can search fusionDB via combinations of organism names and metadata. Moreover, the web interface allows mapping new microbial genomes to the functional spectrum of reference bacteria, rendering interactive similarity networks that highlight shared functionality. fusionDB provides a fast means of comparing microbes, identifying potential horizontal gene transfer events, and highlighting key environment-specific functionality.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Zhu C,Mahlich Y,Miller M,Bromberg Ydoi
10.1093/nar/gkx1060subject
Has Abstractpub_date
2018-01-04 00:00:00pages
D535-D541issue
D1eissn
0305-1048issn
1362-4962pii
4588109journal_volume
46pub_type
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