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How Unique is my Microbiome?

It has long been known that fingerprints are like snowflakes--no wo are said to be alike, so your fingerprints remain a prime way to identify you. But that’s all they can do.

Your DNA and your microbiome are just as unique, and can never be replicated exactly. Science moving towards an understanding of how your microbiome and DNA can tell the story of you and what health issues you may face, so they can be prevented—not treated. This is the future of health.

Research into the human genome and DNA is relatively recent; a working draft of the human genome was published in 2001, and completion and publication of the sequencing of the full human genome occurred in April 2003.

Francis Collins, then director of the National Human Genome Research Institute, described the genome as follows: "It's a history book -- a narrative of the journey of our species through time. It's a shop manual, with an incredibly detailed blueprint for building every human cell. And it's a transformative textbook of medicine, with insights that will give health care providers immense new powers to treat, prevent and cure disease."

It took Human Genome project (HGP) scientists up to eight years and approximately $1 billion to sequence the first human genome. By 2016, a human genome (which contains approximately 20,500 genes) was able to be sequenced in one or two days and cost approximately $1000.

This work, for all intents and purposes, began in 1987 with the announcement of the Human Genome Initiative by the Environmental Research Advisory Committee (HERAC).

In his letter to the Assistant Secretary of the Office of Energy Research, Mortimer Mendelsohn, MD, PhD, on behalf of HERAC, envisions “A concerted, broadly based, scientific effort to provide new methods of sufficient power and scale [to] transform this activity from an inefficient one-gene-at-a-time, single laboratory effort into a coordinated, worldwide, comprehensive reading of ‘the book of man.’”

In 2009, the Human Microbiome Project (HMP) was launched. Its goals were to utilize available technology to characterize the human microbiome by studying samples of multiple body sites from 250 healthy volunteers; to reveal potential associations between alterations in the microbiome and health/disease states and to provide a standardized data resource as well as new technological approaches for broad research in the area. The researchers wrote, “The ultimate objective of the HMP is to demonstrate that there are opportunities to improve human health through monitoring or manipulation of the human microbiome.”

In 2015, researchers from the Harvard T.H. Chan School of Public Health used data collected from the Human Microbiome Project and found that identifying people from microbiome data is definitively feasible, due to their unique microbial populations. The authors wrote, “Our results demonstrated that individuals could be uniquely identified among populations of 100s based on their microbiomes alone.”

Another initiative, the American Gut Project, is a crowdsourced global citizen science microbiome research effort launched in 2012.

According to its abstract, as of May 2017, the AGP possessed microbial sequence data from 15,096 samples provided by 11,336 participants, totaling over 467 million 16S rRNA V4 gene fragments, of which were 48,599 unique. They write, “This reference database characterizes the diversity of the industrialized human gut microbiome on an unprecedented scale; reveals novel relationships with health, lifestyle, and dietary factors; and establishes the AGP resource and infrastructure as a living platform for discovery.”

The information collected by the AGP shows several observations, such as the gut microbiomes in those individuals who took antibiotics in the previous month (139) were less diverse than those who had not taken antibiotics in the previous year (117). However, those who recently took antibiotics exhibited more diversity in the chemicals found in their gut samples.

They also found that the number of plant foods a person normally eats impacts the diversity of his/her gut microbiome. Those who ate more than 30 varied plant types per week (41 people) exhibited gut microbiomes that were more diverse than those who ate 10 or fewer (44). Another observation was that individuals who had a mental health disorder had specific bacteria types in common with each other than in those individuals without mental health issues but other corresponding traits (such as age, gender, BMI, etc.).

Interestingly, medical science is now working on the ability to diagnose via microbiome composition testing. One review makes a strong case for exploring this avenue. In their conclusion, the authors write, “the potential utility of microbiome diagnostics has been demonstrated by a rapidly growing body of literature. Although limited replicability may have raised questions, at least some associations have been corroborated in large meta-analyses and studies have begun to reveal mechanisms of interactions between microbiota and host phenotypes (an individual’s composition depicted by observable factors or characteristics).” They also believe that in this new decade there will likely be a much broader adoption of microbiome diagnostics.

In autumn 2019, researchers compiled a database through genetically sequencing fecal samples from 16 individuals in addition to using 50 healthy samples from the Human Microbiome Project. They found 157 organisms that compose what they call the “baseline biome” of a healthy human gut. Dubbed “GutFeelingKB” the foundational profile is said by the authors to provide a base for comparison of microbiome changes to detect disease. Comprehensive understanding and identification of what makes a healthy base microbiome is critical, they said, to undertake research that will more accurately allow for diagnosis, treatment and even prevention of health issues with the microbiome.

And yes, research has begun on microbiome population content and links to health or disease state. For example, a 2020 published study on pulmonary arterial hypertension (PAH) and the gut microbiome showed that the those with PAH had a distinctive gut microbiome. To wit, according to the authors, “Significant taxonomic and functional changes in microbial communities in the PAH cohort were observed.”

Also, in an earlier study, researchers found that “Obesity is associated with different profiles of gut microbiota.”


Today, there are labs that can test your stool sample to provide you with a profile of your unique gut microbiome. They can discern microbes that make you gain weight and fat, lose sleep, and impact mood, among other health issues.

This is wonderful news for the near future: as medical science continues to link the human microbiome with specific health profiles and disease states, there may be more opportunities to help individuals prevent the onset of genetically pre-dispositioned disease onsets, prolonging quality of life with knowledge.

As Sir Francis Bacon said, “Knowledge is power.”

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