Alkek Center for Metagenomics and Microbiome Research

The Human Microbiome

Alkek Center for Metagenomics and Microbiome Research

Within the body of a healthy adult, microbial cells are estimated to outnumber human cells by a factor of ten to one. The total number of genes in the human microbiome may exceed the total number of human genes by approximately a factor of 100 to 1. These microbial communities comprise what is known as the ‘human microbiome’.  Until recent years, the human microbiome has been largely unstudied, leaving its influence upon human health largely unknown.  Traditional microbiology has focused on the study of individual isolated species, with most organisms (>80%) having never been successfully cultured.  However, advances in DNA sequencing technologies have created the ability to examine microbial communities, including uncultivable organisms, both in terms of the organisms present and the genetic functions these organisms encode. These advances have led to ‘metagenomic’ approaches that allow the analysis of genetic material derived from complete microbial communities harvested from natural environments thereby providing a largely unbiased view of the human microbiome as well as the microbiomes of other animals and environmental niches.  These metagenomic approaches have resulted in the identification of microbes and microbial functions that are associated with various stages of health and a variety of diseases.  In turn, these discoveries have launched thousands of subsequent projects seeking to understand how the microbiome impacts health and disease in humans and their environment. These studies cross nearly all fields of biological science and represent an exciting component of our understanding of the human existence.  The ultimate goal for us and many others is to understand how the microbiome impacts human health and to translate this knowledge into new diagnostics and therapeutics.

The Alkek Center for Metagenomics and Microbiome Research

The Alkek Center for Metagenomics and Microbiome Research (CMMR) was established in 2011 by Dr. Joseph Petrosino in the Department of Molecular Virology and Microbiology at Baylor College of Medicine. The Mission of the CMMR is to serve as an international hub for the development and implementation of advanced technologies for the understanding of how the microbiome impacts health and disease, and for the translation of this knowledge into microbiome based therapeutics and diagnostics. The Vision for how we plan to structure a fully translational microbiome research center is highlighted in the figure below.

Human Microbiome Project

The human microbiome is defined as the microbes (bacteria, single-cell eukaryotes, and viruses) that colonize the body, while metagenomics refers to culture independent, genomic analyses of the DNA and RNA recovered from these microbial communities. We are particularly interested in identifying the organisms that impact human health and disease, and how these microbes interact with the host and each other in the diverse environments found in the human body.

CMMR researchers are developing molecular and informatic tools and resources to advance numerous clinical and basic research projects pertaining to the organisms that comprise the microbiome, the genetic makeup of these bacteria, viruses and eukaryotes, and how these commensal microorganisms interact with human cells and tissues during the course of life. The intent is for these projects to lead to the development of new treatments and diagnostics for a variety of heritable and infectious diseases as well as the development of additional reagents having other biotech applications.

Specific Services

We provide a variety of metagenomic services in the lab, including 16S rRNA gene sequencing, qPCR, 18S rRNA gene sequencing / ITS sequencing, metagenomic whole genome shotgun sequencing, microbial RNA/transcriptome sequencing, and viral metagenomic sequencing.

CMMR Equipment and Resources

The Alkek Center for Metagenomics and Microbiome Research (CMMR) at Baylor College of Medicine is located in a newly renovated 6,000 sq. ft laboratory. In the lab, we operate automated platforms for sample processing, library preparation, and quality control. These include 2 Hamilton STARlet systems (96-well channel motor head) dedicated to sample processing, 2 Hamilton STAR systems (96-well channel motor head) for library preparation, and 1 Beckman NXP (Span8) dedicated to quality control.  Our sequencing platforms include Illumina MiSeq and HiSeq. The CMMR also maintains a high performance computing cluster (HPCC) to address the emerging computational analysis goals of the center. 

Goals of CMMR

  • Support existing metagenomic research programs that are ongoing at Baylor College of Medicine and affiliated institutions
  • Provide support for investigators/clinical collaborators who have ideal model systems for metagenomics but need additional guidance for conducting such studies
  • Expand metagenomic research into animal and molecular model systems so that hypothesis-driven research can be initiated and supported
  • Provide a critical mass in bioinformatics expertise for analyzing and providing statistical support for metagenomic data
  • Translate novel discoveries from microbiome studies to effective clinical therapeutics and diagnostics