RT Journal Article
SR Electronic
T1 RefSoil: A reference database of soil microbial genomes
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 053397
DO 10.1101/053397
A1 Jinlyung Choi
A1 Fan Yang
A1 Ramunas Stepanauskas
A1 Erick Cardenas
A1 Aaron Garoutte
A1 Ryan Williams
A1 Jared Flater
A1 James M Tiedje
A1 Kirsten S. Hofmockel
A1 Brian Gelder
A1 Adina Howe
YR 2016
UL http://biorxiv.org/content/early/2016/05/14/053397.abstract
AB A database of curated genomes is needed to better assess soil microbial communities and their processes associated with differing land management and environmental impacts. Interpreting soil metagenomic datasets with existing sequence databases is challenging because these datasets are biased towards medical and biotechnology research and can result in misleading annotations. We have curated a database of 922 genomes of soil-associated organisms (888 bacteria and 34 archaea). Using this database, we evaluated phyla and functions that are enriched in soils as well as those that may be underrepresented in RefSoil. Our comparison of RefSoil to soil amplicon datasets allowed us to identify targets that if cultured or sequenced would significantly increase the biodiversity represented within RefSoil. To demonstrate the opportunities to access these underrepresented targets, we employed single cell genomics in a pilot experiment to sequence 14 genomes. This effort demonstrates the value of RefSoil in the guidance of future research efforts and the capability of single cell genomics as a practical means to fill the existing genomic data gaps.