The microbiome has been recognized as an important initiative by the CCTS and by UAB. With institutional support for studying the microbiome in both animal and human models, the CCTS will contribute informatics support and Next-Gen Sequencing analysis. Working collaboratively, these efforts are sufficiently linked to provide a seamless menu of services for clinical and translational investigators. This resource will provide investigators assistance with: 1) experimental design and planning (Microbiome Core), 2) sample collection and preparation (Microbiome Core),
3) sequencing of 16S ribosomal genes, 4) bioinformatic and statistical analysis of the sequence reads (CCTS Informatics), 5) extending the analytical capabilities to provide full metagenomic sequencing of experimental samples, and 6) testing cause-effect hypotheses by utilizing the germ-free animal models (Gnotobiotic Core). These Cores are described further below.
The Microbiome Core is the initial contact point for investigators wishing to use the services of the entire resource. Core personnel are available to meet with researchers for each project, discuss overall goals, provide suggestions regarding experimental design, and provide protocols for sample collection. Once samples are collected, the Microbiome Core will process the samples for PCR amplification using bar-coded primers for the 16S rRNA V4 region,25 purify the PCR product, and transport the library to the Next-Gen Sequencing facility. The Core manages the bar-coding of the samples to allow for efficient use of each DNA flow cell required for sequencing. This allows the sequencing of up to several hundred samples per cell that reduces the cost per microbiome to below $100.
Following completion of the sequencing run, data is placed on the high-capacity storage fabric of the high-performance computing platform maintained by UAB Research Computing and is made available for processing by
CCTS Informatics. To support the analysis of the 16S ribosomal RNA genes, Informatics has established an analytical pipeline similar to that used by Rob Knight from the University of Colorado, and based on the QIIME tool suite. These procedures allow quantitative assessment of the microbiome population down to the genus level. For data collection, analysis, integration, and reporting, Informatics has established an analytical pipeline for routine processing of the 16S sequence reads, along with a website that collects project data, consolidates it into a web-based visualization template, and provides investigator access to the data on our protected intranet site.
Understanding the role of the microbiome in health and disease requires investigation of the interactions among genes of the microbiota and host. Essential to such research is the ability to manipulate and define the microbiota (i.e., develop defined-flora and “humanized” animal models), which requires gnotobiotic technology. The Gnotobiotic Animal Core provides microbiome investigators with the ability to derive lines of germ-free mice with defined genetic characteristics driven by current and anticipated investigator needs. The Core supports the transplantation of archived microbiome samples acquired through UAB studies to the animals that will then be maintained under gnotobiotic conditions. Confirmation of successful engraftment is established through a microbiome analysis of the fecal pellets from the transplanted animals.
For more information, please contact the CCTS Research Commons at
ccts@uab.edu or 934-7442.