BDdb: a comprehensive platform for exploration and utilization of birth defect multi-omics data.

BACKGROUND: Birth defects pose a major challenge to infant health. Thus far, however, the causes of most birth defects remain cryptic. Over the past few decades, considerable effort has been expended on disclosing the underlying mechanisms related to birth defects, yielding myriad treatises and data. To meet the increasing requirements for data resources, we developed a freely accessible birth defect multi-omics database (BDdb, http://t21omics.cngb.org ) consisting of multi-omics data and potential disease biomarkers. RESULTS: In total, omics datasets from 136 Gene Expression Omnibus (GEO) Series records, including 5245 samples, as well as 869 biomarkers of 22 birth defects in six different species, were integrated into the BDdb. The database provides a user-friendly interface for searching, browsing, and downloading data of interest. The BDdb also enables users to explore the correlations among different sequencing methods, such as chromatin immunoprecipitation sequencing (ChIP-Seq) and RNA sequencing (RNA-Seq) from different studies, to obtain the information on gene expression patterns from diverse aspects. CONCLUSION: To the best of our knowledge, the BDdb is the first comprehensive database associated with birth defects, which should benefit the diagnosis and prevention of birth defects.

Drought changed soil organic carbon composition and bacterial carbon metabolizing patterns in a subtropical evergreen forest.

Subtropical forests are considerable carbon sinks in the northern hemisphere, yet are increasingly suffering from the impact of extreme drought. To better understand the dynamics and kinetics of forest soil carbon storage under long-term drought, a rainfall-reduction experiment was established in a subtropical evergreen forest of eastern China. Soil organic carbon (SOC) composition, microbial carbon metabolism and the interactions with soil microbial community structure were investigated across different soil aggregate size fractions. After five years' treatment of rainfall reduction, a significant loss of large macroaggregates, as well as an increase of microaggregates by over 100% was observed. Meanwhile, drought changed the composition of SOC, reducing the non-hydrolyzed carbon and humin contents in large- to medium-size macroaggregates. Microbial metabolizing capacity of polymeric compounds was also reduced especially in the above aggregate fractions, whereas the utilization of small-molecular compounds was more impacted in small macroaggregates and microaggregates. The changes in carbon metabolizing patterns were further associated with the abundance changes of specific microbial taxa, revealing the microbially mediated mechanism of soil carbon metabolism under long-term drought. In addition, carbon metabolism in microaggregates was particularly sensitive to the changes of soil moisture, suggesting long-term drought may continually influence the functional resistance of the microbial communities. Taken together, our results provide insights into how biotic and abiotic processes together influence the SOC metabolizing processes, continued monitoring and investigation of which shall contribute to better understanding of the dynamics and kinetics of SOC storage under the impact of long-term drought.