Revealing the Bacterial Butyrate Synthesis Pathways by Analyzing (Meta)genomic Data

Revealing the Bacterial Butyrate Synthesis Pathways by Analyzing (Meta)genomic Data

Butyrate-producing bacteria have recently gained attention, since they are important for a healthy colon and when altered contribute to emerging diseases, such as ulcerative colitis and type II diabetes. This guild is polyphyletic and cannot be accurately detected by 16S rRNA gene sequencing. Consequently, approaches targeting the terminal genes of the main butyrate-producing pathway have been ...

Analyzing metagenomic data with metagenomeSeq

Analyzing Data with Graphs: Metagenomic Data and the Phylogenetic Tree

In biological experiments, researchers often have information in the form of a graph that supplements observed numerical data. Incorporating the knowledge contained in these graphs into an analysis of the numerical data is an important and non trivial task. We look at the example of metagenomic data – data from a genomic survey of the abundence of different species of bacteria in a sample. Here...

Analyzing Metagenomic Data: Inferring Microbial Community Function with Mg-rast

Application of massively parallel throughput DNA sequencing technologies to the generation of metagenomic datasets from environmental samples is presently transforming the field of microbiology. Whereas traditional (Sanger-based) DNA sequencing technology imparted a high economic cost on data generation, the development of “next-generation” technologies now make the large-scale generation of se...

Metagenomic data of free cyanide and thiocyanate degrading bacterial communities

The data presented in this article contains the bacterial community structure of the free cyanide (CN-) and thiocyanate (SCN-) degrading organisms that were isolated from electroplating wastewater and synthetic SCN- containing wastewater. PCR amplification of the 16S rRNA V1-V3 regions was undertaken using the 27F and 518R oligonucleotide primers following the metacommunity DNA extraction proce...