Initial Steps to Compile a Healthy Human Gut Microbiome Reference Database Underway

Metagenomic analysis pipeline for 3 samples. Step 1: CensuScope is run for each read file against Filtered-nt. Each of the aligned organism approved by manually check is added to the GutFeelingKB and it is versioned. Step 2: For the final analysis the raw read files are mapped against GutFeelingKB organism sequences using HIVE-hexagon. Outputs are tabulated as relative abundance percentages. Unaligned reads from each sample were assembled using IDBA-UD. Contigs that were over 10,000 nucleotides long had their headers modified to include the following: sample ID, numbered according to length (long to short), and additional metadata data about the participant.

An initial baseline healthy gut microbiome database and abundance profile is described in a study published in PLOS ONE by Charles Hadley King of George Washington University Medical Center and colleagues.

Though research interest in the human gut microbiome’s importance to overall health continues to grow, there’s currently no comprehensive gut microbiome reference list available to researchers and patients. In this study, King and colleagues begin to catalog the organismal makeup of healthy human gut microbiomes, and developed a prototype reporting template for clinicians to relay results to patients.

To compile their database, the authors genetically sequenced 48 fecal samples from sixteen healthy participants recruited from George Washington University campus in Washington, D.C., in addition to using 50 fecal metagenomic samples downloaded from the Human Microbiome Project from individuals screened as “healthy”.

Stacked bar plot of phylogenetic composition of all microbiome taxa in this study collapsed at the phyla level in fecal samples. Green bars represent Firmicutes and the blue represent Bacteroidetes, the two most abundant bacterial families. For aesthetic purposes the samples (n = 98, bottom) were sorted according to their composition of Bacteroidetes and Firmicutes to demonstrate how the baseline gut microbiome results from this study could be used in conjunction with results from past studies.

After parsing all samples’ genomic and metagenomic sequences using a novel software-based workflow, King and colleagues compiled an initial database of confirmed microbes and their relative abundance across all samples, the GutFeelingKB, using NCBI’s comprehensive and publicly available genetic information to provide metadata on the organisms described.

The GutFeelingKB describes 157 organisms (155 bacterial and two archaeal organisms) across 60 distinct genera. The largest phylum of bacteria represented was Firmicutes (40 percent of all organisms on the list), which in turn was made up of 20 percent Clostridia, 19 percent Bacterioidia, 17 percent Bifidobacteriales, 14 percent Enterobacterales, and 14 percent Lactobacillales bacteria–classes of bacteria also found in yogurt and other probiotic foods. The authors also note that 84 organisms were common to all of the samples, potentially indicating that these may be core species for the human gut.

This study only recruited sixteen participants, a small sample. But while further studies might continue to identify additional organisms present in healthy guts from around the world, GutFeelingKB is an important first step. The database could act as a starting point for comparative analysis of samples and the development of future patient microbiome treatments.

The authors add “Our goal is to map the healthy gut microbiome so that we and other researchers can use our data to develop disease specific prediction models.”

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