tag:blogger.com,1999:blog-10781944.post7197085722331318886..comments2024-03-28T00:36:36.460-07:00Comments on The Tree of Life: Crowdsourcing some facts for my upcoming #Tedmed talk on #microbes on #humansJonathan Eisenhttp://www.blogger.com/profile/07953790938128734305noreply@blogger.comBlogger19125tag:blogger.com,1999:blog-10781944.post-55768413848627409962012-04-09T13:13:25.953-07:002012-04-09T13:13:25.953-07:00There seem to be correlations between microbiota d...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. <br /><br />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.<br /><br />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). <br /><br />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.<br /><br />A fascinating subject.Thomas Sharptonhttps://www.blogger.com/profile/14154047498732458281noreply@blogger.comtag:blogger.com,1999:blog-10781944.post-1660792024253633532012-04-09T01:37:43.131-07:002012-04-09T01:37:43.131-07:00WikiMedia Commons has a ton of great stuff, if you...WikiMedia Commons has a ton of great stuff, if you search for specific things. For example, malaria :<br /><br />http://commons.wikimedia.org/wiki/File:Malaria.jpg<br /><br />Tuberculosis : <br /><br />http://commons.wikimedia.org/wiki/File:Mycobacterium_tuberculosis_8438_lores.jpg<br /><br />MRSA :<br /><br />http://commons.wikimedia.org/wiki/File:CDC-10046-MRSA.jpg<br /><br />Staphylococcus epidermidis :<br /><br />http://commons.wikimedia.org/wiki/File:Staphylococcus_epidermidis_lores.jpg<br /><br />Micrococcus luteus :<br /><br />http://commons.wikimedia.org/wiki/File:Micrococcus_luteus_9759.jpeg<br /><br />et cetera.Russell Necheshttps://www.blogger.com/profile/00253304712038983943noreply@blogger.comtag:blogger.com,1999:blog-10781944.post-13202805159215523052012-04-09T01:26:10.575-07:002012-04-09T01:26:10.575-07:00I don't know anything about this study, but he...I don't know anything about this study, but heart attacks :<br /><br />http://www.fasebj.org/content/26/4/1727<br /><br />No cause-effect link, but correlated with onset of type 1 diabetes :<br /><br />http://www.ncbi.nlm.nih.gov/pubmed/20613793<br /><br />Not an ailment, but mate-selection in fruit flies : <br /><br />http://www.scientificamerican.com/article.cfm?id=backseat-driversRussell Necheshttps://www.blogger.com/profile/00253304712038983943noreply@blogger.comtag:blogger.com,1999:blog-10781944.post-7580070354697634842012-04-08T11:58:45.570-07:002012-04-08T11:58:45.570-07:00"Three Men in a Boat" / Jerome K Jerome...."Three Men in a Boat" / Jerome K Jerome. (Chapter 1).<br />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.Iddo Friedberghttps://www.blogger.com/profile/06100900696954623019noreply@blogger.comtag:blogger.com,1999:blog-10781944.post-59549722990074898532012-04-08T11:34:53.345-07:002012-04-08T11:34:53.345-07:00ok i don't get reference in any deep way ... b...ok i don't get reference in any deep way ... but I should rephrase ... what ailments HAVE BEEN SHOWN TO BE CAUSED BY ...Jonathan Eisenhttps://www.blogger.com/profile/07953790938128734305noreply@blogger.comtag:blogger.com,1999:blog-10781944.post-69237558325331396592012-04-08T11:32:17.980-07:002012-04-08T11:32:17.980-07:00Everything but Housemaid's Knee (bonus points ...Everything but Housemaid's Knee (bonus points if you get the reference).Iddo Friedberghttps://www.blogger.com/profile/06100900696954623019noreply@blogger.comtag:blogger.com,1999:blog-10781944.post-78263418899808439942012-04-08T11:28:09.593-07:002012-04-08T11:28:09.593-07:007-10 phages per microbial cell means 10^15 phages....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.<br />Eukaryotic viruses: low (not counting integrated viruse, which, depending on definition can be > 30% of human genome). 20 genotypes or so. <br />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_4Iddo Friedberghttps://www.blogger.com/profile/06100900696954623019noreply@blogger.comtag:blogger.com,1999:blog-10781944.post-90057438429680511792012-04-08T11:27:44.641-07:002012-04-08T11:27:44.641-07:00Yes, though that is SEVEN YEARS OLD ...Yes, though that is SEVEN YEARS OLD ...Jonathan Eisenhttps://www.blogger.com/profile/07953790938128734305noreply@blogger.comtag:blogger.com,1999:blog-10781944.post-79546715794798734522012-04-08T11:15:59.215-07:002012-04-08T11:15:59.215-07:00There's a Mya Breitbart paper on that, 2005(?)...There's a Mya Breitbart paper on that, 2005(?) I believe?Iddo Friedberghttps://www.blogger.com/profile/06100900696954623019noreply@blogger.comtag:blogger.com,1999:blog-10781944.post-7948416563383674112012-04-08T11:15:29.080-07:002012-04-08T11:15:29.080-07:00Last time I checked I didn't find what I neede...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. <br /><br />http://www.nsf.gov/news/mmg/index.cfmMaryhttp://blog.openhelix.comnoreply@blogger.comtag:blogger.com,1999:blog-10781944.post-59331779749894747702012-04-08T10:56:43.585-07:002012-04-08T10:56:43.585-07:00I have found one recent paper with Ley, Knight, Hu...I have found one recent paper with Ley, Knight, Hugenholtz, etc where there were at least 7000 OTUs from humans. <br /><br />See http://www.nature.com/ismej/journal/v6/n1/fig_tab/ismej201182f2.html#figure-titleJonathan Eisenhttps://www.blogger.com/profile/07953790938128734305noreply@blogger.comtag:blogger.com,1999:blog-10781944.post-5273196769418873882012-04-08T10:55:47.704-07:002012-04-08T10:55:47.704-07:00Thanks will look it over.Thanks will look it over.Jonathan Eisenhttps://www.blogger.com/profile/07953790938128734305noreply@blogger.comtag:blogger.com,1999:blog-10781944.post-69402161402754693872012-04-08T10:55:05.131-07:002012-04-08T10:55:05.131-07:00There are a few images at NIH, but this is probabl...There are a few images at NIH, but this is probably a better collection: http://phil.cdc.gov/phil/home.aspMaryhttp://blog.openhelix.comnoreply@blogger.comtag:blogger.com,1999:blog-10781944.post-17498866429346979642012-04-08T10:51:35.471-07:002012-04-08T10:51:35.471-07:00I don't have this number, but I would mine Pat...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.orgMaryhttp://blog.openhelix.comnoreply@blogger.comtag:blogger.com,1999:blog-10781944.post-48627788749410734812012-04-08T10:39:17.404-07:002012-04-08T10:39:17.404-07:00What is a good source of open (e.g., creative comm...What is a good source of open (e.g., creative commons) images of the microbes found in / on people?Jonathan Eisenhttps://www.blogger.com/profile/07953790938128734305noreply@blogger.comtag:blogger.com,1999:blog-10781944.post-5437759571776923692012-04-08T10:38:58.727-07:002012-04-08T10:38:58.727-07:00How many viruses (kinds and numbers) are found in ...How many viruses (kinds and numbers) are found in the human microbiome?Jonathan Eisenhttps://www.blogger.com/profile/07953790938128734305noreply@blogger.comtag:blogger.com,1999:blog-10781944.post-40282970726393342892012-04-08T10:38:44.292-07:002012-04-08T10:38:44.292-07:00What human ailments are now thought to be possibly...What human ailments are now thought to be possibly caused by disturbances in the microbiome?Jonathan Eisenhttps://www.blogger.com/profile/07953790938128734305noreply@blogger.comtag:blogger.com,1999:blog-10781944.post-73244506410531501942012-04-08T10:38:29.469-07:002012-04-08T10:38:29.469-07:00What is the number of species of known human patho...What is the number of species of known human pathogens (that are microbes)Jonathan Eisenhttps://www.blogger.com/profile/07953790938128734305noreply@blogger.comtag:blogger.com,1999:blog-10781944.post-40278401081270630472012-04-08T10:38:11.086-07:002012-04-08T10:38:11.086-07:00What is the number of species of microbes found on...What is the number of species of microbes found on one person across their entire body (gut, skin, mouth, etc)?Jonathan Eisenhttps://www.blogger.com/profile/07953790938128734305noreply@blogger.com