Sunday, April 08, 2012

Crowdsourcing some facts for my upcoming #Tedmed talk on #microbes on #humans

OK all I am looking for some help here is finding out some latest pieces of information about the microbes that live in and on people for my Tedmed talk next week Some things I could use


  • 1. What is the number of species of microbes found on one person across their entire body (gut, skin, mouth, etc)? 

  •  2. What is the number of species of known human pathogens (that are microbes) 

  •  3. What human ailments are now thought to be possibly caused by disturbances in the microbiome? 

  •  4. How many viruses (kinds and numbers) are found in the human microbiome? 



  •  5. What is a good source of open (e.g., creative commons) images of the microbes found in / on people? 


 I am going to post these each as a comment below so people can respond to each one ... Thanks
UPDATE 6/4/2012 - Embedding the talk I gave for TEDMED




19 comments:

  1. What is the number of species of microbes found on one person across their entire body (gut, skin, mouth, etc)?

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    1. I have found one recent paper with Ley, Knight, Hugenholtz, etc where there were at least 7000 OTUs from humans.

      See http://www.nature.com/ismej/journal/v6/n1/fig_tab/ismej201182f2.html#figure-title

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  2. What is the number of species of known human pathogens (that are microbes)

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    1. I don't have this number, but I would mine Patric for that. And they have some presentations they've given--you can see if they provide those kinds of stats. http://www.patricbrc.org

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  3. What human ailments are now thought to be possibly caused by disturbances in the microbiome?

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    1. Everything but Housemaid's Knee (bonus points if you get the reference).

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    2. ok i don't get reference in any deep way ... but I should rephrase ... what ailments HAVE BEEN SHOWN TO BE CAUSED BY ...

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    3. "Three Men in a Boat" / Jerome K Jerome. (Chapter 1).
      More to the point: there are many associations of perturbed microbiota with diseases, but cause-and-effect are hard to establish. Those include: periodontal disease, colorectal cancer, IBDs (inc. Crohn's), Obesity, Celiac, Psoriasis, Acne, even Autism. Probably the most immediate Cause-and-effect are gut colonization with C. difficile following aggressive systemic antibiotics, which causes inflammation. That's where you can gross your audience out with the fecal transplant story. Does wonders for my teaching evaluations when I get to that :)Source "Metagenomics of the HUman Body", Ed. K. Nelson, Chapter 1: badger, Pauline Ng. & JC Venter.

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    4. I don't know anything about this study, but heart attacks :

      http://www.fasebj.org/content/26/4/1727

      No cause-effect link, but correlated with onset of type 1 diabetes :

      http://www.ncbi.nlm.nih.gov/pubmed/20613793

      Not an ailment, but mate-selection in fruit flies :

      http://www.scientificamerican.com/article.cfm?id=backseat-drivers

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    5. There seem to be correlations between microbiota diversity and almost every disease, even those caused by the kitchen sink. Hyperbole aside, correlations abound. But as you note above, correlation isn't causation.

      Most evidence for cause and effect is obtained through the use of antibiotics, microbiota transplantation (e.g., fecal bowel transplants, probiotics), or the study of monoassociated mouse models. The effect of the microbiome on disease state has not been thoroughly investigated for most diseases (e.g., phase 3 clinical trials), so some of the claims of cause and effect remain somewhat tenuous. Additionally, it's not clear how other factors, such as host genotype and environmental conditions, contribute to the microbiota-disease relationship.

      That said, there is evidence that the microbiota influences at least the following phenotypes: Clostridium difficile-associated diarrhea (http://www.ncbi.nlm.nih.gov/pubmed/22468996), Chron's disease and other inflammatory bowel diseases (e.g., http://www.ncbi.nlm.nih.gov/pubmed/22014016, note this is somewhat controversial), intestinal inflammation and insulin resistance (http://www.ncbi.nlm.nih.gov/pubmed/19901833), and behavioral conditions (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3139398/?tool=pubmed).

      The above list is certainly incomplete and focuses specifically on the microbiota of the gut, which is the best studied body site regarding this subject. There are, of course, skin diseases (e.g., acne and warts), oral diseases (e.g., gingivitis and dental plaque), and ocular diseases (e.g., conjunctivitis) that are caused (or at least contributed to) by commensals.

      A fascinating subject.

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  4. How many viruses (kinds and numbers) are found in the human microbiome?

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    1. There's a Mya Breitbart paper on that, 2005(?) I believe?

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    2. Yes, though that is SEVEN YEARS OLD ...

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    3. 7-10 phages per microbial cell means 10^15 phages. But estimates based on epifluoroescent microscopy places it at 10^12. 1500 estimated viral genotypes in healthy human body (1kg of marine sediment >=10,000 genotypes). Species are unevenly distributed in a log-oddish histogram.
      Eukaryotic viruses: low (not counting integrated viruse, which, depending on definition can be > 30% of human genome). 20 genotypes or so.
      Source: "Metagenomics of the Human Body" (Springer 2011) , Chapter 4 (Matthew Haynes & Forest Rowher) , Ed. Karen Nelson DOI 10.1007/978-1-14419-7089-4_4

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  5. What is a good source of open (e.g., creative commons) images of the microbes found in / on people?

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    1. There are a few images at NIH, but this is probably a better collection: http://phil.cdc.gov/phil/home.asp

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    2. Last time I checked I didn't find what I needed, but this is a big collection of images (with varying openness). Searching "bacteria" and "microbes" a few cool images were found.

      http://www.nsf.gov/news/mmg/index.cfm

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    3. WikiMedia Commons has a ton of great stuff, if you search for specific things. For example, malaria :

      http://commons.wikimedia.org/wiki/File:Malaria.jpg

      Tuberculosis :

      http://commons.wikimedia.org/wiki/File:Mycobacterium_tuberculosis_8438_lores.jpg

      MRSA :

      http://commons.wikimedia.org/wiki/File:CDC-10046-MRSA.jpg

      Staphylococcus epidermidis :

      http://commons.wikimedia.org/wiki/File:Staphylococcus_epidermidis_lores.jpg

      Micrococcus luteus :

      http://commons.wikimedia.org/wiki/File:Micrococcus_luteus_9759.jpeg

      et cetera.

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