The Gut Microbiome in Health and in Disease

Andrew B. Shreiner; John Y. Kao; Vincent B. Young


Curr Opin Gastroenterol. 2015;31(1):69-75. 

In This Article

Abstract and Introduction


Purpose of review Recent technological advancements and expanded efforts have led to a tremendous growth in the collective knowledge of the human microbiome. This review will highlight some of the important recent findings in this area of research.

Recent findings Studies have described the structure and functional capacity of the bacterial microbiome in the healthy state and in a variety of disease states. Downstream analyses of the functional interactions between the host and its microbiome are starting to provide mechanistic insights into these interactions. These data are anticipated to lead to new opportunities for diagnosis, prognosis, and treatment of a variety of human diseases.

Summary There is a fast growing collection of data describing the structure and functional capacity of the microbiome in a variety of conditions available to the research community for consideration and further exploration. Ongoing efforts to further characterize the functions of the microbiome and the mechanisms underlying host–microbe interactions will provide a better understanding of the role of the microbiome in health and disease.


The human microbiome is composed of bacteria, archaea, viruses, and eukaryotic microbes that reside in and on our bodies. These microbes have tremendous potential to impact our physiology, both in health and in disease. They contribute metabolic functions, protect against pathogens, educate the immune system, and, through these basic functions, affect directly or indirectly most of our physiologic functions.

The study of the human microbiome has been furthered by technological advancements for performing culture-independent analyses.[1] In most studies, the bacterial constituents of a microbial population are identified by sequencing of the 16S rRNA-encoding gene (hereafter, 16S) followed by comparison to known bacterial sequence databases. Metagenomic analysis by sequencing all microbial DNA in a complex community has the additional advantage of assessing the genetic potential of the microbial population. Other methodologies to analyze the microbial transcriptome, proteome, and metabolome provide additional information at successive levels of microbial physiology.[2] We will not go into further detail on specific technical considerations in this space, but interested readers are referred to recent review articles.[3–5]

Great progress in characterizing the structure of the microbiome recently has paved the way for ongoing and future studies on the functional interactions between the microbiota and the host. Studies on the function of the microbiota will be critical to understanding the role of the microbiota in human homeostasis and disease pathogenesis. In this review, we will discuss recent advancements in our understanding of the structure and function of the microbiome associated with the healthy state and with specific diseased states.