Microbial profile to support growing field of human gut research

There are 157 organisms that form the baseline biome of a healthy human gut, according to research published in the journal PLOS ONE by investigators at the George Washington University (GW). The baseline microbial profile, called GutFeelingKB, can be expanded to 863 organisms if closely related proteomes are considered. This information will serve as a reference list for doctors, patients, and researchers, giving them an idea of what a “normal” human microbiome looks like.

“The more we learn about the human microbiome, the more we learn of its importance to our health,” said Raja Mazumder, PhD, co-author and professor of biochemistry and molecular medicine at the GW School of Medicine and Health Sciences. “Knowing what a healthy human gut looks like is critical to research that will inform how to diagnose, treat, and prevent issues with the microbiome.”

This comprehensive knowledge of the types and ratios of microbes that inhabit the healthy human gut is necessary before any kind of pre-clinical or clinical study can be performed. It is also important for researchers looking to find ways to alter the microbiome, treat a condition, or improve a therapy outcome. GutFeelingKB can serve as a healthy control for studies looking at the human microbiome.

To compile their database, the research group genetically sequenced 48 fecal samples from 16 healthy participants recruited in Washington, DC, in addition to using 50 fecal metagenomic samples downloaded from the Human Microbiome Project from individuals also screened as healthy. Of the 157 organisms described in GutFeelingKB, 20 percent were Clostridia, 19 percent were Bacterioidia, 17 percent were Bifidobacteriales, 14 percent were Enterobacterales and from the phylum Firmicutes 20 percent were Clostridia and 14 percent were Lactobacillales — all classes of bacteria found in probiotic foods like yogurt. The research team noted that 84 organisms were common to all the samples, indicating that this group of bacteria may be core species for the human gut.

“This study demonstrates the power of multidisciplinary team science to advance translational research as this team involves colleagues from across multiple institutions, disciplines and schools within GW,” said Keith A. Crandall, PhD, informatics co-lead on the CTSI grant, co-author, and director of the Computational Biology Institute at Milken Institute School of Public Health at GW. “The GutFeelingKB provides a foundational model and initial data to begin to understand the diversity of the healthy gut microbiome, which is a key component of any study trying to detect disease associated with microbiome changes.”

In addition to creating GutFeelingKB, the research group published a novel Fecal Biome Population Report, known as FecalBiome, which has clinical capability. FecalBiome can help physicians compare a patient’s microbiome to the microbiomes of healthy individuals, allowing them to better assess the effectiveness of fecal transplants and other microbiome products. The research team also developed a prototype reporting template for physicians to relay the information to patients.

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