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, D.C., 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% were Clostridia, 19% were Bacterioidia, 17% were Bifidobacteriales, 14% were Enterobacterales and from the phylum Firmicutes 20% were Clostridia and 14% 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.

The research was supported by grants from the National Science Foundation, the Clinical and Translational Science Awards Program at the National Center for Advancing Translational Sciences, the McCormick Genomic and Proteomic Center, and the Clinical Translational Science Institute (CTSI) at GW and Children’s National in Washington, D.C. Raw sequence data was generated at KamTek, Inc. with subsidized pricing using MiSeq Illumina instruments at Montgomery College in Rockville, Maryland.

“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.

“Uncovering the complex metabolic exchanges between gut microbial species and their human hosts has tremendous implications for a wide variety of health conditions, possibly even our moods. Can the microbiome be ‘tuned’ to increase beneficial bacterial populations? How does our diet affect this tuning? We are excited this knowledgebase will let us quantify these shifts and relate them to human health,” said Hiroki Morizono, PhD, informatics co-lead on the CTSI grant, co-author, director of biomedical informatics at Children’s National and associate research professor of genomics and precision medicine and pediatrics at the GW School of Medicine and Health Sciences.

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In addition to Mazumder, Crandall, and Morizono, authors of the study include Charles Hadley King, Krista Smith, Hiral Desai, Yao Ren, Shant Ayanyan, Naila Gulzar, Vahan Simonyan, Brian C. Fochtman, Lusine Gasparyan, Lopa Mishra, Michael D. Yao, and Shuyun Rao from the GW School of Medicine and Health Sciences; Allison C. Sylvetsky and Najy Issa from Milken Institute School of Public Health at GW; Jonathan LoTempio from Children’s National; and Sharan VedBrat and Paul Howell at KamTek, Inc.

All data used in this research is freely available at hive.biochemistry.gwu.edu/gfkb.