The Human Microbiome Project

Port Meadow horse

The average human being is a collection of about ten trillion eukaryotic cells: each with a nucleus, 23 chromosomes of nucleic DNA, and a collection of membrane-bound organelles including mitochondria with genetic material of their own. Less obviously, each person is also carrying around one hundred trillion prokaryotic cells, belonging to thousands of different species of bacteria. The implications of that are pretty staggering. Many of those bacteria play critical roles in biological processes that sustain human life, such as digestion. Others may be the benign residents of niches where more harmful microorganisms might otherwise live.

Following up on the Human Genome Project – which sought to decode the three billion nucleotides in the human genome – the Human Microbiome Project seeks to map the genetic sequences of those legions of bacteria. Already, it has been theorized that these bacteria play important roles in maintaining human health, and that their composition and relationship with human cells has an impact on diseases including diabetes, autism, cancer, and cardiovascular disease. Collectively, these bacterial species are thought to have 100 times more genetic material than the colony of human cells they inhabit.

The project is not unrelated to the Global Ocean Sampling Expedition, discussed here earlier, in that it is delving into the complexities of microscopic ecosystems. In so doing, it might serve both the practical function of helping to better understand and treat human disease and the more esoteric one of refining our understanding of what it means to be a human being, biochemically at least.

PS. The DVDs for the BBC’s Planet Earth series, discussed earlier, are now available in North American format. I will definitely buy a copy when I return to Canada. For those who haven’t seen any of the footage, it is absolutely awe inspiring.

Author: Milan

In the spring of 2005, I graduated from the University of British Columbia with a degree in International Relations and a general focus in the area of environmental politics. In the fall of 2005, I began reading for an M.Phil in IR at Wadham College, Oxford. Outside school, I am very interested in photography, writing, and the outdoors. I am writing this blog to keep in touch with friends and family around the world, provide a more personal view of graduate student life in Oxford, and pass on some lessons I've learned here.

13 thoughts on “The Human Microbiome Project”

  1. When I read about this the other week the article said that at least some of the bacterial population on an individual may well be unique to them, or the combination unique to them. This might play a role in how we react to others body odours, attractiveness etc. It posited that there may be a forensic fingerprinting future for such studies.
    It will be interesting to find out what havoc antibiotics, antibacterial washes etc play with an individual’s innate fauna.

  2. Insight

    Nature 449, 804-810 (18 October 2007) | doi:10.1038/nature06244; Published online 17 October 2007

    The Human Microbiome Project

    A strategy to understand the microbial components of the human genetic and metabolic landscape and how they contribute to normal physiology and predisposition to disease.

    Before the Human Genome Project was completed, some researchers predicted that approx100,000 genes would be found. So, many were surprised and perhaps humbled by the announcement that the human genome contains only approx20,000 protein-coding genes, not much different from the fruitfly genome. However, if the view of what constitutes a human is extended, then it is clear that 100,000 genes is probably an underestimate. The microorganisms that live inside and on humans (known as the microbiota) are estimated to outnumber human somatic and germ cells by a factor of ten. Together, the genomes of these microbial symbionts (collectively defined as the microbiome) provide traits that humans did not need to evolve on their own1. If humans are thought of as a composite of microbial and human cells, the human genetic landscape as an aggregate of the genes in the human genome and the microbiome, and human metabolic features as a blend of human and microbial traits, then the picture that emerges is one of a human ‘supra-organism’.

  3. “The HMP is a logical conceptual and experimental extension of the Human Genome Project. The HMP is not a single project. It is an interdisciplinary effort consisting of multiple projects, which are now being launched concurrently worldwide, including in the United States (as part of the next phase of the National Institutes of Health’s Roadmap for Medical Research), Europe and Asia. The advent of highly parallel DNA sequencers and high-throughput mass spectrometers with remarkable mass accuracy and sensitivity is propelling microbiology into a new era, extending its focus from the properties of single organism types in isolation to the operations of whole communities. The new field of metagenomics involves the characterization of the genomes in these communities, as well as their corresponding messenger RNA, protein and metabolic products.”

  4. “Many outcomes of the HMP can be predicted: for example, new diagnostic biomarkers of health, a twenty-first century pharmacopoeia that includes members of the human microbiota and the chemical messengers they produce, and industrial applications based on enzymes that are produced by the human microbiota and can process particular substrates. One important outcome is anticipated to be a deeper understanding of the nutritional requirements of humans. This, in turn, could result in new recommendations for food production, distribution and consumption that are formulated based on knowledge of the microbiome.”

  5. Carolyn Bohach, a microbiologist at the University of Idaho claims that our bodies contain 10 times more bacterial cells than human ones (bacterial cells are a lot smaller and thus occupy less volume). Human genome researchers believe that at least 40 of our genes are bacterial in origin. Let the compulsive washing begin!

    All the bacteria living inside you would fill a half-gallon jug; there are 10 times more bacterial cells in your body than human cells, according to Carolyn Bohach, a microbiologist at the University of Idaho (U.I.), along with other estimates from scientific studies. (Despite their vast numbers, bacteria don’t take up that much space because bacteria are far smaller than human cells.) Although that sounds pretty gross, it’s actually a very good thing.

    The infestation begins at birth: Babies ingest mouthfuls of bacteria during birthing and pick up plenty more from their mother’s skin and milk—during breast-feeding, the mammary glands become colonized with bacteria. “Our interaction with our mother is the biggest burst of microbes that we get,” says Gary Huffnagle, a microbiologist and internist at the University of Michigan at Ann Arbor. And that’s just for starters: Throughout our lives, we consume bacteria in our food and water “and who knows where else,” Huffnagle says.

  6. Commensal (non-pathogenic) bacteria fill niches in our body and use resources that would otherwise be available to other pathogenic microorganisms. For instance, our skin and oral cavity are covered with bacteria, most of which will never harm us, as they live in a delicate balance with our immune system.

  7. Modern medicine
    Microbes maketh man
    People are not just people. They are an awful lot of microbes, too

    Aug 18th 2012 | from the print edition

    The human microbiome
    Me, myself, us
    Looking at human beings as ecosystems that contain many collaborating and competing species could change the practice of medicine

    Aug 18th 2012 | from the print edition

  8. Added together, the genes in these bugs’ genomes amount to perhaps 150 times the number in the human genome alone. If the bacteria in question were doing little more than swimming around digesting lettuce, this would be of small consequence. But they are doing much more than that.

    The members of the microbiome, as this community is known, are, to a surprising extent, partners of humanity. And when that partnership goes wrong, the results can be dreadful. Inflammatory bowel disease, autism, multiple sclerosis, obesity, diabetes and chronic-fatigue syndrome all seem to have links with dysbiosis, as an imbalance in the microbiome is known. Only this month, there was news that human gut microbes influence the way patients respond to a popular new type of cancer treatment called immunotherapy. Certain sorts of bacteria are abundant in patients who respond well. Antibiotics that kill these bacteria render immunotherapy less effective.

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