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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.

Keywords: Gut microbiome, microbiota, dysbiosis, health, disease

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INTRODUCTION

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.

Accumulation of data on the human microbiome

The tremendous expansion of information collected on the human microbiome in recent years is highlighted by data generated through several large-scale endeavors to characterize the human microbiome, namely the European Metagenomics of the Human Intestinal Tract (MetaHIT) and the NIH-funded Human Microbiome Project (HMP) (6, 7). In 2010, the initial MetaHIT consortium study reported sequencing 3.3 million non-redundant fecal microbial genes, representing almost 200 times the quantity of microbial DNA sequences reported in all previous studies (7). In July 2014, a combined set of metagonomic sequencing data from 1267 gut metagenomes from 1070 individuals, including 760 European samples from MetaHIT, 139 American samples from HMP and 368 Chinese samples from a large diabetes study, was published with a non-redundant gene catalog of 9.8 million microbial genes (*8). Each sample contained about 750,000 genes or about 30 times the number of genes in the human genome, and less than 300,000 genes were SHARED by greater than 50% of individuals. The majority of the new genes identified in this latest study were relatively rare, found in less than 1% of individuals. This collection is thought to contain nearly a complete set of genes for most human gut bacteria and illustrates the quantity and variability of the human microbiome.

Structure and dynamics of the healthy adult microbiota

Characterization of the microbiome in healthy individuals is an important initial step in understanding the role of the microbiome in CONTRIBUTING to health and disease. Healthy adult humans each typically harbor more than 1000 species of bacteria belonging to a relatively few known bacterial phyla with Bacteroidetes and Firmicutes being the dominant phyla (9).  

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