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Health Protocols

Maintaining a Healthy Microbiome

The human body exists in a dynamic and interdependent relationship with microbes. The skin, digestive tract, airways, vagina, eyes, and ears each have unique microbial ecosystems (Sender 2016; Proctor 2017; Thursby 2017; Huang 2011; Martin 2012; Dibb 1990; Lu, Liu 2016). There is even evidence that regions of the body long thought to be sterile, such as the placenta, urinary tract, uterus, lungs, blood, and even the brain, can harbor communities of microbes (Falana 2015; Potgieter 2015; Branton 2013; Whiteside 2015; O'Dwyer 2016; Chen 2017; Thomas-White 2016). In healthy humans, these complex ecosystems include a range of microorganisms, from bacteria and viruses to fungi and eukaryotes (Lloyd-Price 2016). Rather than being viewed solely as a reservoir for infection, these communities of microorganisms are now recognized as essential to our health as individuals and as a species (Davenport 2017; Turnbaugh 2007).

Historically, the term microbiome has been used to refer to the genetic material of the microbes, while microbiota refers to a community of microbial species (Knight 2017; D'Argenio 2015). These terms have come to be used interchangeably. In this protocol, microbiome will be used to refer to both groups of microorganisms and to their combined genetic material.

The number of microbial cells we harbor is estimated to be at least equivalent to the number of human cells in the body (Sender 2016; Knight 2017). The gut microbiome, which is the largest subset of the human microbiome, includes over 1,000 different bacterial species (across individuals) (Koboziev 2014; Lloyd-Price 2016) and accounts for about 2‒4 pounds of body weight per person (D'Argenio 2015). Furthermore, about 5 million microbial genes have been found in the gut, which is vastly more than the approximately 22,000 protein-encoding genes in the entire human genome (Ursell 2012; D'Argenio 2015). Only recently have we begun to understand and appreciate the significance of our evolutionary relationship with our microbial ecosystems (Davenport 2017).

This protocol describes the microbiome as a whole and its regional subsets. It presents a brief summary of what scientists know about how the microbiome interacts with our own cells and influences our health. This protocol also summarizes how the microbiome is shaped and maintained, and presents dietary and lifestyle strategies for supporting healthy microbial communities, as well as novel and emerging technologies for manipulating the microbiome: fecal microbiota transplant and phage therapy. Finally, this protocol details current and emerging research about the use of probiotics—living beneficial microorganisms—to prevent and treat disease.

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