Human Microbiome 101


I’ve been tracking the Human Microbiome Project for a few years now. I was going to blog about it, and then the New York Times published articles about it, and I assumed that meant I didn’t need to say anything. Last week I was talking with a few friends about the human microbiome, and absolutely blasted their minds into outer space. Not only had they not heard about it, the very idea was hard for them to wrap their minds around. So, here is a very brief intro, grabbing wonderful pieces from other folk. Brief take-aways.

1. Most of our body, say roughly 99% (by cell count), is comprised of critters that don’t have any human DNA. Surprise!
2. The groups of critters, a.k.a. microbes, that make up most of our bodies are surprisingly different from person to person.
3. The whole idea of antibiotics might turn out to be one of those really really bad social experiments, in that while killing the “bad” microbes, the antibiotics are also killing our good ones, the ones that we need to live and be healthy.
4. The research into what microbes make up part of different people, and how this impacts on physical and mental health, is provocative, potentially quite valuable, and extremely complicated.
5. This area of research brings up yet more challenges to the ideas of personal privacy and transparency in healthcare.

Brief video explanation (about 3 minutes).


Human Microbiome Project: Analyzing microbes that play a role in health and disease http://www.youtube.com/watch?v=axB_8O4WHYg

Excellent longer video introduction (about ten minutes).

Human Microbiome Research: An Introduction http://www.youtube.com/watch?v=DNZ2e8O7svs

Slides to go into a little more depth and context.


Jonathan Eisen: Human Microbiome 101, Future of Genomic Medicine Meeting #FOGM13, http://www.slideshare.net/phylogenomics/jonathan-eisen-talk-at-fogm13

HUMAN MICROBIOME PROJECT (HMP)

Broad Institute: http://www.broadinstitute.org/scientific-community/science/projects/microbiome-projects/hmp/human-microbiome-project

J. Craig Venter Institute: http://hmp.jcvi.org/

NIH Common Fund Human Microbiome Project (HMP) http://commonfund.nih.gov/hmp/

NIH Human Microbiome Project: http://www.hmpdacc.org/

RESEARCH BASICS

Peter J. Turnbaugh, Ruth E. Ley, Micah Hamady, Claire M. Fraser-Liggett, Rob Knight, Jeffrey I. Gordon. The Human Microbiome Project. Nature 449:18 October 2007
http://obs.rc.fas.harvard.edu/turnbaugh/Papers/Turnbaugh_HMP.pdf

“Before the Human Genome Project was completed, some researchers predicted that ~100,000 genes would be found. So, many were surprised and perhaps humbled by the announcement that the human genome contains only ~20,000 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 own. 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 ‘supraorganism’.”

Elizabeth K. Costello, Christian L. Lauber, Micah Hamady, Noah Fierer, Jeffrey I. Gordon, Rob Knight. Bacterial Community Variation in Human Body Habitats Across Space and Time. Science (18 December 2009) 326(5960):1694-1697. http://www.sciencemag.org/content/326/5960/1694.abstract

“Elucidating the biogeography of bacterial communities on the human body is critical for establishing healthy baselines from which to detect differences associated with diseases. … Within habitats, interpersonal variability was high, whereas individuals exhibited minimal temporal variability. Several skin locations harbored more diverse communities than the gut and mouth, and skin locations differed in their community assembly patterns. These results indicate that our microbiota, although personalized, varies systematically across body habitats and time; such trends may ultimately reveal how microbiome changes cause or prevent disease.”

Chris S. Smillie, Mark B. Smith, Jonathan Friedman, Otto X. Cordero, Lawrence A. David, Eric J. Alm. Ecology drives a global network of gene exchange connecting the human microbiome. Nature 480:241–244 (08 December 2011).
http://www.nature.com/nature/journal/v480/n7376/full/nature10571.html

“Horizontal gene transfer (HGT), the acquisition of genetic material from non-parental lineages, is known to be important in bacterial evolution1, 2. In particular, HGT provides rapid access to genetic innovations, allowing traits such as virulence3, antibiotic resistance4 and xenobiotic metabolism5 to spread through the human microbiome. Recent anecdotal studies providing snapshots of active gene flow on the human body have highlighted the need to determine the frequency of such recent transfers and the forces that govern these events4, 5. … We show that within the human microbiome this ecological architecture continues across multiple spatial scales, functional classes and ecological niches with transfer further enriched among bacteria that inhabit the same body site, have the same oxygen tolerance or have the same ability to cause disease. This structure offers a window into the molecular traits that define ecological niches, insight that we use to uncover sources of antibiotic resistance and identify genes associated with the pathology of meningitis and other diseases.”

Kjersti Aagaard, Joseph Petrosino, Wendy Keitel, Mark Watson, James Katancik, Nathalia Garcia, Shital Patel, Mary Cutting, Tessa Madden, Holli Hamilton, Emily Harris, Dirk Gevers, Gina Simone, Pamela McInnes, James Versalovic. The Human Microbiome Project strategy for comprehensive sampling of the human microbiome and why it matters. FASEB Journal March 2013 27(3):1012-1022.
http://www.fasebj.org/content/27/3/1012.abstract

“In the future, human microbiomes will be defined at many body sites and during different periods in the human life span. A metagenomic survey alone can describe the microbial communities present, but clinical data are required to understand the factors that affect community composition. Studies must consider the role of sex, diet, race/ethnicity, age, residence location, use of medications, dietary supplements, and hygiene products, and many other factors that shape and cause fluctuations in individual microbiomes. Current NIH-funded demonstration projects are exploring differences in microbial communities and whole metagenomes in disease states.”

PLoS Collections: Table of Contents: The Human Microbiome Project Collection: http://www.ploscollections.org/article/browseIssue.action?issue=info:doi/10.1371/issue.pcol.v01.i13

ABOUT THE HMP

Becker, Kate. Less Than One Percent Human. Inside NOVA (PBS) February 18, 2011 1:53 PM. http://www.pbs.org/wgbh/nova/insidenova/2011/02/less-than-one-percent-human.html

Gonzalez, Robert T. 10 Ways the Human Microbiome Project Could Change the Future of Science and Medicine. io9. 6/25/12 10:28am.
http://io9.com/5920874/10-ways-the-human-microbiome-project-could-change-the-future-of-science-and-medicine

Kolata, Gina. In Good Health? Thank Your 100 Trillion Bacteria. New York Times June 13, 2012. http://www.nytimes.com/2012/06/14/health/human-microbiome-project-decodes-our-100-trillion-good-bacteria.html?pagewanted=all

Yong, Ed. The bacterial zoo living on your skin. Discover Magazine May 28, 2009. http://scienceblogs.com/notrocketscience/2009/05/28/the-bacterial-zoo-living-on-your-skin/

Yong, Ed. I, Microbes – my Radio 4 talk on the hordes of microbes inside us. Discover Magazine October 19, 2011 4:35 pm. http://blogs.discovermagazine.com/notrocketscience/2011/10/19/i-microbes-my-radio-4-talk-on-the-hordes-of-microbes-inside-us/

Yong, Ed. Microbial Menagerie: A massive study catalogues the microbes in the healthy human body, uncovering an unexpected level of individual variation in microbial makeup, among other surprises.
The Scientist June 13, 2012. http://www.the-scientist.com/?articles.view/articleNo/32215/title/Microbial-Menagerie-/

Yong, Ed. Our bodies are a global marketplace where bacteria trade genes. Discover Magazine October 31, 2011 9:00 am. http://blogs.discovermagazine.com/notrocketscience/2011/10/31/our-bodies-are-a-global-marketplace-where-bacteria-trade-genes/

Zimmer, Carl. How Microbes Defend and Define Us. New York Times July 12, 2010. http://www.nytimes.com/2010/07/13/science/13micro.html

Zimmer, Carl. Our Microbiomes, Ourselves. New York Times December 3, 2011. http://www.nytimes.com/2011/12/04/opinion/sunday/our-microbiomes-ourselves.html

Zimmer, Carl. Tending the Body’s Microbial Garden. New York Times June 18, 2012
http://www.nytimes.com/2012/06/19/science/studies-of-human-microbiome-yield-new-insights.html

DIY “MICROBIOMICS” – CITIZEN SCIENCE

American Gut: http://www.indiegogo.com/projects/american-gut

uBiome: http://www.indiegogo.com/projects/ubiome-sequencing-your-microbiome?website_name=ubiome

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3 responses to “Human Microbiome 101

  1. Pingback: At the Movies: Microbiomes | Emerging Technologies Librarian

  2. Pingback: Dynamics of the Microbiome | THL News Blog

  3. Pingback: Dynamics of the Microbiome | Emerging Technologies Librarian

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