Microbiome Core

Overview

The Microbiome Core, with the goal of developing the microbiome as a biomarker for precision IBD management and as a point of intervention for new and improved treatments, provides consultation, training, bioinformatics support, and access to methodology in service of cutting-edge IBD and digestive disease microbiome research. The Core strives to meet the demand for bioinformatics support by actively developing new computational methods and pipelines and by providing CSIBD members with training critical for ensuring optimal data analysis and interpretation. The Core also offers access to microbiome isolate collections for Center investigators to leverage toward a better understanding of host-microbe interactions.

Objectives

1. Provide best-in-class resources for comprehensive high-throughput microbial community profiling
2. Facilitate collaboration, knowledge sharing, and consulting for microbiome studies
3. Maintain data resources for CSIBD and related microbial community studies
4. Integrate studies of the IBD microbiome with those of the gut microbiome in related conditions

Services

• Consultation and training. The Core offers individualized, end-to-end support and training activities for microbiome research, with extensive experience in taxonomic and functional profiling from large cohorts, qualitative and quantitative ecology, multi'omics and meta-analysis, microbial systems biology, and human epidemiological analysis. Support begins with experimental design, power calculations, and cost-benefit analysis and extends through to data generation, bioinformatics analysis, statistics, and results interpretation. Consultations are central to all services.
• Microbiome data generation. Services include coordinated sample collection from patients, de-identified receipt, and sample handling; high-throughput DNA/RNA extraction from multiple sample types (bacterial culture, stool, and biopsy); metagenomic, metatranscriptomic, and metabolomic profiling of microbiome samples; high-throughput 16S rRNA sequencing; DNA library construction and deep shotgun sequencing; and RNA and RNAtag-Seq library construction, rRNA depletion, and deep shotgun sequencing. For experimental work, full access is granted to protocols and reagents for microbiome-based approaches.
• Bioinformatics support. The Core provides bioinformatics and computational expertise, capabilities, and consultancy to the CSIBD community and actively develops state-of-the-art computational methods, analytical frameworks, tools, and pipelines available from bioBakery, the Core's comprehensive system for end-to-end microbiome data analysis.
• Biobanking and microbiome isolate collections. The Core offers access to the OpenBiome Microbiome Library (BIO-ML) and Harvard Chan Microbiome Collection Core (HCMCC) to aid mechanistic microbiome research. These collections facilitate functional studies to understand how the microbiome impacts health and disease by providing the capacity for direct hypothesis testing.
• Access to human microbiome data portals. Standardized data resources are essential for advancing microbiome research by ensuring that data are findable, accessible, interoperable, and reusable. By adhering to consistent data formats, storage, and dissemination practices, researchers can more effectively share, compare, and build upon existing datasets; this facilitates meta-analyses, synthesis of results across studies, and testing the reproducibility of individual studies.