RBUD: A New Functional Potential Analysis Approach for Whole Microbial Genome Shotgun Sequencing

Abstract

Whole metagenome shotgun sequencing is a powerful approach to detect the functional potential of microbial communities. Currently, the read-based metagenomics profiling for established database (RBED) method is one of the two kinds of conventional methods for species and functional annotations. However, the databases, which are established based on test samples or specific reference genomes or protein sequences, limit the coverage of global microbial diversity. The other assembly-based metagenomics profiling for unestablished database (ABUD) method has a low utilization rate of reads, resulting in a lot of biological information loss. In this study, we proposed a new method, read-based metagenomics profiling for unestablished database (RBUD), based on Metagenome Database of Global Microorganisms (MDGM), to solve the above problems. To evaluate the accuracy and effectiveness of our method, the intestinal bacterial composition and function analyses were performed in both avian colibacillosis chicken cases and type 2 diabetes mellitus patients. Comparing to the existing methods, RBUD is superior in detecting proteins, percentage of reads mapping and ontological similarity of intestinal microbes. The results of RBUD are in better agreement with the classical functional studies on these two diseases. RBUD also has the advantages of fast analysis speed and is not limited by the sample size.

Maternal High-Fat Diet Programs White and Brown Adipose Tissues In Vivo in Mice, with Different Metabolic and Microbiota Patterns in Obesity-Susceptible or Obesity-Resistant Offspring

“…In KEGG pathway analysis, only the bacteria secretion system was associated with BAT and SAT outcomes after FDR adjustment in our study. Interestingly, this system regulates nutrient acquisition and is overexpressed in relation to metabolic diseases, such as type 2 diabetes [32].…”