Efforts to Link Ecological Metadata with Bacterial Gene Sequences at the Sapelo Island Microbial Observatory

摘要

The existence of public databases for archiving genetic sequence data, such as GenBank and the Ribosomal Database Project, coupled with the availability of standardized sequence alignment and comparison tools has led to rapid advances in the field of bacterial genetics and systematics. Many microbial ecologists now routinely submit gene sequences obtained from environmental isolates, clones, and bands excised from electrophoretic gels to public sequence databases. As the amount of environmental sequence data in these systems has increased, ecologists have begun using sequence databases for broader classes of studies, such as biogeography and community ecology. Unfortunately, the general lack of documentation and data quality control standards has resulted in many sequences being entered without appropriate metadata, effectively orphaning records from their ecological context information and making comparisons impossible. In order to address the shortcomings of public sequence databases, an independent 16S rRNA sequence database was recently developed at the Sapelo Island Microbial Observatory (SIMO) in Georgia, USA. The database was created to store complete information from all SIMO research reflect the actual flow of information from sample collection through final publication. By incorporating key fields from external databases, such as GenBank, the SIMO database is able to serve both as an independent research tool for SIMO scientists and as a reference source for SIMO data stored in other databases.