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home:publications:marshall_dnaday2011 [06.22.2011]
paulalbert
home:publications:marshall_dnaday2011 [01.03.2012] (current)
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 This slide was presented by Claire Fraser-Liggett,​ University of Maryland, at the Human Microbiome Conference just last month. And it results from a study of Amish families that she did, a very concentrated,​ isolated community in America. And she was looking at lean, overweight, obese benign, and obese with metabolic syndrome. And when you look at it in terms of family, whether it's Rhuminococcaceae,​ Bacteroidaceae or whatever the family is, you can see that there is more variation from person to person – each vertical bar here is an individual person within the cohort – there is more variation from person to person than there is from phenotype to phenotype or disease to disease state. And, it doesn'​t matter, you can look at it by phylum and you see exactly the same result. No statistically determinant characteristics like we found in the mouse, or like Washington U. found in the mouse. Which is unfortunate. This slide was presented by Claire Fraser-Liggett,​ University of Maryland, at the Human Microbiome Conference just last month. And it results from a study of Amish families that she did, a very concentrated,​ isolated community in America. And she was looking at lean, overweight, obese benign, and obese with metabolic syndrome. And when you look at it in terms of family, whether it's Rhuminococcaceae,​ Bacteroidaceae or whatever the family is, you can see that there is more variation from person to person – each vertical bar here is an individual person within the cohort – there is more variation from person to person than there is from phenotype to phenotype or disease to disease state. And, it doesn'​t matter, you can look at it by phylum and you see exactly the same result. No statistically determinant characteristics like we found in the mouse, or like Washington U. found in the mouse. Which is unfortunate.
  
-Now EMBL in Europe has, is just in the middle of a big study, and they'​ve gone even further. They have some Japanese human samples, some American human samples. This was published by Arumugam in Bioinformatics and you can see that if you look at the various phyla across here – the Japanese samples firstly are different from each other in the propensities,​ but also they are very different from the American samples. So there is intra-individual variation, which is quite high; and there is intra-regional variation, which is quite high. And it's at the level of the species, at the level of identifying the microbes that are present, really, at this point, human metagenomics has hit a brick wall. At this point the human microbiome project ​knows what's there. Pretty well they know what's there, certainly on all the externally facing tissues. The next phase is to figure out what is it doing. And clearly they can't figure out what is this doing based just on the species. We have to figure out other ways of analysis.+Now EMBL in Europe has, is just in the middle of a big study, and they'​ve gone even further. They have some Japanese human samples, some American human samples. This was published by Arumugam in Bioinformatics and you can see that if you look at the various phyla across here – the Japanese samples firstly are different from each other in the propensities,​ but also they are very different from the American samples. So there is intra-individual variation, which is quite high; and there is intra-regional variation, which is quite high. And it's at the level of the species, at the level of identifying the microbes that are present, really, at this point, human metagenomics has hit a brick wall. At this point the Human Microbiome Project ​knows what's there. Pretty well they know what's there, certainly on all the externally facing tissues. The next phase is to figure out what is it doing. And clearly they can't figure out what is this doing based just on the species. We have to figure out other ways of analysis.
  
 Now this is also from Claire Fraser-Liggett'​s group at University of Maryland. This is a Manhattan Plot of the homology between the Fusobacter genome and the Human genome. And for more information on what we're talking about here, just read our chapter in the Metagenomics of the Human Body book because we point out the homology between genes in the microbiota and human genes is actually quite high. You can see some of the points in the Manhattan Plot here go well above the seven and a half line that Claire chose as being quite deterministic. You've got your chromosomes across the bottom obviously and log p up the left. Now this is also from Claire Fraser-Liggett'​s group at University of Maryland. This is a Manhattan Plot of the homology between the Fusobacter genome and the Human genome. And for more information on what we're talking about here, just read our chapter in the Metagenomics of the Human Body book because we point out the homology between genes in the microbiota and human genes is actually quite high. You can see some of the points in the Manhattan Plot here go well above the seven and a half line that Claire chose as being quite deterministic. You've got your chromosomes across the bottom obviously and log p up the left.
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 Q: What is the mass of the microbiome in a typical human being? ​ Q: What is the mass of the microbiome in a typical human being? ​
  
-A: Well that too was discussed in Vancouver. And the original NIH estimate was 90% of human cells are likely bacterial cells. The current estimate is 99%. So even that is a moving target at this point as discovery continues forward. There'​s more money that the human microbiome project ​is basically looking at all the external cavities and documenting exactly what's there, multiple centers, but at this point it's far more than anybody ever imagined.+A: Well that too was discussed in Vancouver. And the original NIH estimate was 90% of human cells are likely bacterial cells. The current estimate is 99%. So even that is a moving target at this point as discovery continues forward. There'​s more money that the Human Microbiome Project ​is basically looking at all the external cavities and documenting exactly what's there, multiple centers, but at this point it's far more than anybody ever imagined.
  
 Q: How much of it gets into the blood, I mean do these peptides, proteins that you mentioned.... Q: How much of it gets into the blood, I mean do these peptides, proteins that you mentioned....
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