gfkb

gfkb provides a reference knowledge base that defines baseline human gut microbiota composition in healthy individuals by integrating metagenomic sequencing data and assembled contigs to support comparative and regulatory analyses.

Key Features:

• Baseline Microbiota Profile: A reference list of 157 microbial organisms spanning 8 phyla, 18 classes, 23 orders, 38 families, 59 genera, and 109 species that constitute the baseline gut microbiome in healthy individuals.
• Expandable Database: The reference list can be expanded to include 863 organisms when closely related proteomes are considered.
• Fecal Biome Population Report (FecalBiome): A standardized report format for comparing an individual's microbiome against the established baseline microbiome data.
• Metagenomic Dark Matter Analysis: Assembled contiguous sequences (contigs) from metagenomic dark matter of 10,000 nucleotides or longer provided for primer design and exploration of potential novel organisms.
• Clinical and Regulatory Utility: Provides a benchmark list of organisms from healthy individuals for regulatory assessment of fecal transplant and other microbiome-related products.

Scientific Applications:

• Pre-Clinical and Clinical Studies: Provides baseline data for studies aiming to modify the microbiome for therapeutic purposes.
• Dysbiosis Research: Serves as a control reference for investigations of microbial imbalances.
• Novel Organism Discovery: Supports identification and study of previously unknown organisms via analysis of metagenomic dark matter contigs.

Methodology:

Integration of metagenomic sequencing data, assembly of contigs from unmapped metagenomic reads (metagenomic dark matter) yielding contigs ≥10,000 nucleotides, expansion of the reference list via inclusion of closely related proteomes, and generation of comparative FecalBiome reports.