This week marks the 10th anniversary of the first major study on microbial diversity in the human body, published tempering character from the Human Microbiome Project (HMP) consortium of which I was a member.
Before that, microbiologists had learned that there was a large mass of microorganisms in the body – a intoxicating mixture of bacteria, along with archaea, fungi and viruses that spread through the skin, mouth and intestines – collectively referred to as a microbiome. But until 2012, we lacked their inventory.
In fact, this inventory, which indicates 10 trillion cells belonging to thousands of species and weighing a total of 200 grams per person, is still incomplete. It is time to continue this early work (Consortium of Human Microbiome Projects tempering character 486, 207-214; 2012) and the renewal of the project to represent humanity in all its complexities.
It took a long time to start this early work, and the pace of change over the last 10 years has been astonishing. HMP can only be started when high-throughput genetic sequencing technologies, which were first developed to study the human genome, are cheap and easy enough to use.
Since launching in 2007, the consortium has performed DNA sequencing on 242 people found in 242 people in two American cities, Boston, Massachusetts, and Houston, Texas, selected for proximity to two major sequencing centers at the time, MIT and For Harvard. University near Boston and Baylor Medical College in Houston. Our activities were funded by the Joint Foundation of the U.S. National Institutes of Health, and the project engaged academic bioinformatics experts in the microbiome to work with the data after they were generated.
The result was the first comprehensive intact American microbiome catalog: a complete list of intestinal microbiome genes. The HMP has shown that the cellular organisms in the gut are made up of thousands of species with a genetic footprint 150 times the size of the human genome. Ultimately, this abundance led biologists to consider the microbiome as an ecologically derived “second genome” hidden in the human host.
In ten years, we will know a lot. Microbiome is essential for the proper functioning of our body and is key to digesting food and repelling pathogens. Experiments with mice have shown that the composition of the microbiome affects the level of social involvement and anxiety. Common diseases, such as cardiovascular disease and obesity, are associated with different microbes. It is also becoming clearer how children acquire their own microbiomes and what affects the development of microbiomes.
(Given the importance of microbes to our health, I still find it surprising that we take on so many functions in many organisms that we take in from our environment from birth.)
We also have many unanswered academic questions. Where did the microbiome first appear in human evolution? How are human microbes different from primates, mammals or animals in general? How is a microbiome transferred from one person to another? And what does a sterile diet and lifestyle change mean for a microbiome for long-term health?
The first analysis ten years ago, recruiting people from only two American cities, unfortunately failed to capture the true diversity of the human microbiome. We now know that people in Europe and North America have less diverse microbiomes than people in less industrialized regions, but very little is known about the differences between groups of people.
And even less is known about many other animals that themselves contain masses. We know that the microbes of captive animals are different from those of wild animals, just as industrial microbes are non-industrial. But most of what we know about animal microbes comes from research on captive animals. As we lose animal diversity due to rapid global change, we are also losing microbial diversity.
To learn more, a new consortium will be needed to select thousands of people and animals. We need wildlife biologists and microbiome scientists working side by side with teams around the world. Ten years ago, the analysis was so new and complicated that we didn’t think much about getting samples. This process should now be driven by sampling from global sources.
Some may wonder why we need a large and expensive new consortium while the data is already flowing – one study each by laboratories working on their own. However, industrialization is advancing rapidly and today’s economic forces are able to eradicate microbial diversity faster than can be seen.
A new consortium would allow scientists to finally complete a microbiome map. It’s like a census: don’t wait for individual cities to report their population; You make a concerted effort to do it consistently and quickly before it changes.
Extensive analysis of young human microbiome and wider vertebrate microbiome diversity will finally put our species in the context of the tree of life. Only then can we really apply the term ‘human’ to a microbiome.
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