there is a lot left to do

This week marks the tenth anniversary of the first major study of microbial diversity in the human body, published in Nature of the Human Microbiome Project (HMP) Consortium, of which I was a member.

Before then, microbiologists knew that the body hosted a large mass of microorganisms – an intoxicating mixture of bacteria, along with archaea, fungi and viruses, spread over the skin, in the mouth and in the intestine – collectively called the microbiome. But until 2012, we lacked an inventory of them.

In fact, this stock – an index of 10 trillion cells belonging to thousands of species, weighing a total of 200 grams in each person – is still incomplete. It is time to build on this early work (Human Microbiome Project Consortium) Nature 486, 207–214; 2012), and renews the project to represent humanity in all its complexity.

It took a long time to start the early work, and the pace of change over the last ten years has been fantastic. Only when high-throughput gene sequencing technologies – first developed to examine the human genome – became cheap and easy to use could HMP begin.

Following its launch in 2007, the consortium sequenced DNA from microbes found in and on 242 individuals from 2 U.S. cities – Boston, Massachusetts and Houston, Texas, selected for their proximity to the then two prominent sequencing centers, the Broad Institute of MIT and Harvard near Boston, and Baylor College of Medicine in Houston. Our activities were funded by the US National Institutes of Health’s Common Fund, and the project involved academic microbiome bioinformatics to work on the data after we generated it.

The result was the first comprehensive catalog of a healthy American human microbiome: a complete list of genes in the gut microbes. HMP showed that the intestinal cellular organisms consist of thousands of species, with a genetic footprint that is 150 times as large as the human genome. Eventually, this abundance led biologists to view the microbiome as an environmentally acquired “second genome”, hidden in the human host.

Ten years later we know much more. The microbiome is essential for the proper functioning of our body, the key to digesting food and averting pathogens. Experiments with mice have shown that microbiome compositions affect levels of social engagement and anxiety. Common diseases such as cardiovascular disease and obesity are linked to distinct microbiomes. How babies acquire their microbiomes – and what affects the development of microbiomes – also becomes clearer.

(Given how basic microbes are to our health, I still find it amazing that we outsource so many functions to countless organisms that we pick up from our environment, from birth.)

We also have many unanswered academic questions. Where did the microbiome first come from in human evolution? How are human microbiomes different from those of other primates, mammals or animals more generally? How do microbiomes move from person to person? And what does changing diets and cleansing lifestyles mean for the long-term health of the microbiome?

The first analysis ten years ago, which recruited people from just two American cities, failed to capture the true diversity of the human microbiome. We now know that people living in Europe and North America have less diverse microbiomes than people living in less industrialized regions – but too little is known about differences between groups of people.

And even less is known about the amount of other animals that themselves contain amounts. We know that the microbiomes of captive animals are different from those of wild animals, much in the same way that industrialized human microbiomes differ from non-industrialized ones. But most of what we know about animal microbes comes from studies of animals in captivity. As we lose the animal diversity to rapid global change, we also lose the microbiome diversity.

Learning more will require a new consortium, testing thousands of people and animals. We need wildlife biologists and microbiome scientists working side by side with crews around the world. Ten years ago, analysis was so new and difficult that we spared little on the idea of ​​sample collection. Now, sample collection from sources globally should lead the process.

Some may ask why we need a new, magnificent, expensive consortium when data is already trickling in – one study at a time, conducted by laboratories working alone. But industrialization is rapid, and modern economic forces have the power to wipe out microbial diversity faster than can be observed.

A new consortium will enable researchers to finally complete the microbiome map. It’s like a census: you’re not waiting for some cities to report their population; you make a single overall effort to do it consistently and quickly, before it changes.

An enormous new diversity analysis of humanity’s microbiome, and of the broader vertebrate microbiome, will finally put our own species’ data in the context of the tree of life. Only then can we really extend the label “human” to the microbiome.

Competing interests

The author declares no competing interests.