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Paul McGlothin

Analyzing your microbiome

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Almost everyone agrees that gut health is important. It determines how energetic and happy you feel, and it is foundational to the health of systems throughout the body. It may also determine disease risk and even length of life. So it’s a pity that until now, evaluating gut health has been largely guesswork. Old methods of stool sample analysis provide limited information and more invasive procedures like colonoscopies are also limited in scope.

 

We’re happy to report that the ability to analyze the gut microbiome improves rapidly. In 2009, Dr. Jeffrey Gordon at Washington University led a study that looked at the gut health of calorie restrictors:

 

Diet drives convergence in gut microbiome functions across mammalian phylogeny and within humans.

 

Science. 2011 May 20;332(6032):970-4. doi: 10.1126/science.1198719.

 

Muegge BD, Kuczynski J, Knights D, Clemente JC, González A, Fontana L, Henrissat B, Knight R, Gordon JI.

 

Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63108, USA.

 

 

Abstract

Coevolution of mammals and their gut microbiota has profoundly affected their radiation into myriad habitats. We used shotgun sequencing of microbial community DNA and targeted sequencing of bacterial 16S ribosomal RNA genes to gain an understanding of how microbial communities adapt to extremes of diet. We sampled fecal DNA from 33 mammalian species and 18 humans who kept detailed diet records, and we found that the adaptation of the microbiota to diet is similar across different mammalian lineages.

 

Functional repertoires of microbiome genes, such as those encoding carbohydrate-active enzymes and proteases, can be predicted from bacterial species assemblages. These results illustrate the value of characterizing vertebrate gut microbiomes to understand host evolutionary histories at a supraorganismal level.

 

PMID: 21596990. NIH, NLM, PubMed access to MEDLINE

 

The study by Dr. Gordon and his colleagues is a great start. We would also like to know more about the rest of the body microbiome – skin, ears, mouth, sinuses, and genitals.

 

We plan to include microbiome analysis [the microbiome is the totality of microbes, their genetic elements (genomes), and environmental interactions on and in the human body.] in DNA HACR, DNA Healthy Aging and Calorie Restriction, a new study that the CR Society and LivingTheCRWay.com are collaborating to launch. More details soon)! The trouble is that the field of microbiomics is in its infancy and the major players are still working out the best analytical methods. We’ve heard from one of leaders of the field, Dr. Rob Knight, who gave a great presentation on a CR Way Expert Teleconference, and is a principal scientist behind the American Gut Health Project.

 

Another group that has made quite a splash is μBiome. Currently, they have initiated a citizen science project that competes with the American Gut Health Project. Here’s is where to sign up for the American Gut Health Project and μBiome. American Gut Health Project and μBiome. Hurry! Both of these projects stop their sign-ups within days.

 

Meredith and I have already signed up to participate. While we are excited about the potential, both groups have yet to send out one test. So we are cautious in our recommendations. Still we want to make sure that CR Society members and LivingTheCRWay members take advantage of either or both opportunities.

 

What they are doing is extremely important. Share your experience here and help us decide whether we want to partner with one or both of these organizations and/or scientists on the forthcoming DNA HACR Project.

 

Paul

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