Skip to Main Content


The term “normal microbial flora” denotes the population of microorganisms that inhabit the skin and mucous membranes of healthy normal persons. Previous estimates suggested that the microorganisms that live inside and on humans (now referred to as the normal microbiota) outnumber human somatic and germ cells by a factor of 10. More recent estimates indicate the ratio is much closer to 1:1. The genomes of these microbial symbionts are collectively defined as the microbiome. Research has shown that the “normal microbiota” provides a first line of defense against microbial pathogens, assists in digestion, plays a role in toxin degradation, and contributes to maturation of the immune system. Shifts in the normal microbiota or stimulation of inflammation by these commensals may cause diseases such as bacterial vaginosis, periodontitis, and inflammatory bowel disease.


In a broad attempt to understand the role played by resident microbial ecosystems in human health and disease, the National Institutes of Health Common Fund supported the Human Microbiome Project (HMP; One of the main goals of this project was to understand the range of human genetic and physiologic diversity, the microbiome, and the factors that influence the distribution and evolution of the constituent microorganisms. One aspect of this project involved having several research groups simultaneous embark upon surveying the microbial communities on human skin and in mucosal areas, such as the mouth, esophagus, stomach, colon, and vagina using small-subunit (16S) ribosomal RNA gene sequencing. Among the questions that have been addressed by the HMP are: How stable and resilient is an individual’s microbiota throughout one day and during his or her life span? How similar are the microbiomes between members of a family or members of a community or across communities in different environments? Do all humans have an identifiable “core” microbiome, and if so, how is it acquired and transmitted? What affects the genetic diversity of the microbiome, and how does this diversity affect adaptation by the microorganisms and the host to markedly different lifestyles and to various physiological or pathophysiological states?

Since 2017, HMP investigators have published over 650 studies that have been cited over 70,000 times. Readers should be aware that this field is rapidly evolving, and our understanding of the human microbiota will necessarily change as more information about resident microbial communities becomes available through the HMP.


The human body harbors a variety of microorganisms that can be arranged into two groups: (1) the resident microbiota consists of relatively fixed types of microorganisms regularly found in a given area at a given age; if disturbed, it promptly reestablishes itself; and (2) the transient microbiota consists of nonpathogenic or potentially pathogenic microorganisms that inhabit body sites for hours, days, or weeks. The transient microbiota is derived from the environment, does not produce disease, ...

Pop-up div Successfully Displayed

This div only appears when the trigger link is hovered over. Otherwise it is hidden from view.