Turnbaugh:Research

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==Key Questions==
==Key Questions==
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#UNDER CONSTRUCTION
 
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==The human gut microbiome==
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==Inactivation of cardiac drug by gut microbes==
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The human ‘metagenome’ is a composite of Homo sapiens genes and genes present in the genomes of the trillions of microbes that colonize our adult bodies (the ‘microbiome’). Our largest collection of microbes resides in the gut, where an estimated 10-100 trillion organisms reside (the gut microbiota). The gut microbiome encodes metabolic capacities that remain largely unexplored but include the degradation of otherwise indigestible components of our diet. Our recent metagenomic analyses of humans and mice have revealed linkages between distal gut microbial ecology, microbial community gene content, and host energy balance. Other studies have also demonstrated links between microbial ecology and human disorders such as Crohn’s disease, ulcerative colitis, and diabetes.
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We are using cell culture, mass spectrometry, and studies in gnotobiotic mice (germ-free and colonized) to determine the mechanism of reduction of digoxin and other cardiac glycosides by members of the gut microbiota, and to determine whether or not it is possible to limit this reaction in vivo.  
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Despite the recent surge in human gut microbiome research NIH HMP, a number of basic questions regarding the assembly, structure, and functional operations of the gut microbiome remain unanswered. Our research involves the development and application of computational and experimental methods for the analysis of community structure, gene content, and function of complex microbial communities. We plan to couple these techniques to additional experimental techniques such as functional metagenomics and in vitro cell culture to study the metabolic functions of the human gut microbiome, with potential implications for human health and nutrition.
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==Single cell methods for analyzing microbial physiology and gene content==
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We are using flow cytometry and microfluidics to analyze complex microbial communities collected from the human gut at single cell resolution. These techniques allow us to determine the baseline physiology, activity, and gene content of gut microbes, and how these factors are shaped by clinically relevant perturbations, i.e. exposure to host-targeted drugs and antibiotics.
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==The role of diet and surgery in shaping the gut microbiome and host metabolic outcomes==
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We are studying how Roux-en-Y gastric bypass surgery re-shapes the gut microbiota, and to what degree these changes contribute to the metabolic outcomes of surgery (in collaboration with Lee Kaplan group at Mass General Hospital). We are also performing experiments on the role of diet in shaping gut microbial ecology.
==Data==
==Data==
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See Gordon lab website [http://gordonlab.wustl.edu/SuppData.html Supplementary Data]
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Data can be analyzed in [http://metagenomics.anl.gov MGRAST]<br>
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<br>New data pending...
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Raw datasets are available from [http://www.ncbi.nlm.nih.gov/geo/ GEO] and [http://www.ncbi.nlm.nih.gov/sra NCBI-SRA]<br>
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See Gordon lab website for previous manuscript supporting information [http://gordonlab.wustl.edu/SuppData.html Supplementary Data]
==Press==
==Press==

Revision as of 09:08, 18 October 2012

the turnbaugh lab

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Contents

Inactivation of cardiac drug by gut microbes

We are using cell culture, mass spectrometry, and studies in gnotobiotic mice (germ-free and colonized) to determine the mechanism of reduction of digoxin and other cardiac glycosides by members of the gut microbiota, and to determine whether or not it is possible to limit this reaction in vivo.

Single cell methods for analyzing microbial physiology and gene content

We are using flow cytometry and microfluidics to analyze complex microbial communities collected from the human gut at single cell resolution. These techniques allow us to determine the baseline physiology, activity, and gene content of gut microbes, and how these factors are shaped by clinically relevant perturbations, i.e. exposure to host-targeted drugs and antibiotics.

The role of diet and surgery in shaping the gut microbiome and host metabolic outcomes

We are studying how Roux-en-Y gastric bypass surgery re-shapes the gut microbiota, and to what degree these changes contribute to the metabolic outcomes of surgery (in collaboration with Lee Kaplan group at Mass General Hospital). We are also performing experiments on the role of diet in shaping gut microbial ecology.

Data

Data can be analyzed in MGRAST
Raw datasets are available from GEO and NCBI-SRA
See Gordon lab website for previous manuscript supporting information Supplementary Data

Press

Biotechniques piece on microfluidics

Harvard Gazette write-up on the Turnbaugh lab

Human Microbiome Project

Systems Biology Paper out in PNAS

Science Podcast on detecting novel associations

Wired Microbiome Atlas

Nature News

National Public Radio spot 2009

Economist

Nature video about obesity

New York Times Fat Factors

Nature News 2006

National Public Radio spot 2006

Nature Podcast transcript 2006

Outreach

Exploring Biodiversity Lecture


Personal tools