Catch Today, 1-4pm, Dr. Rob Knight Microbiome Talk

UPDATE:  You’ve missed the talk but can definitely catch the synopsis at “Optimal Microbiome Diet From American Gut Data.  Dr. Knight gave an “Eleven Point” punch list of factors that hugely affect the microbiome.  Totally intriguing and insightful data is now being generated!


Hey! I am copying yesterday’s Facebook post that shouted out today’s unique opportunity for all to hear FREE Dr. Rob Knight (bio is at end of post) speak on the human microbiome and diet implications.  Sorry for the late notice but I received the invitation email only yesterday.

Anyway, it is a great opportunity to hear one of the most leading edge microbiome researchers that I know.  You can catch it live free (this is a continuing education course) if you live near University of Colorado Boulder, and if not, you can catch a live stream online,, and possibly throughout the weekend.  I encourage all to take advantage of hearing Rob… he is amazing! If the links don’t work.. email me and I’ll forward the letter. Have a great weekend!

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Jaminet & Bailor on “Perfect Health Diet”

There’s a fellow health researcher that I respect;  his name is Paul Jaminet, creator and blogger over at “The Perfect Health Diet” site.  Jaminet has no hidden agenda.   He had a health problem, and used his science background to research.  What he found is nearly in line with everything that I speak of, which is SCD/GAPS/PALEO/ MEDITERANEAN… and so many other wonderful healing diets:

When you’re doing things the right way, usually you see results very quickly, so it’s well worth taking a little bit of time to read and think about these things and to do a personal experiment and see how they affect you.

When you’re doing it correctly, you should see results and you should feel good.”

To me, Paul is the epitome of: Here’s what the science and here’s what the research shows, and I hope it will help you.”   Paul has absolutely, no hidden agenda.

I’d be remiss to not mention Paul’s wife, Shou-Ching Shih, a coauthor of the book “Perfect Health Diet.”  This couple is beyond brains:  Paul was an astrophysicist at the Harvard-Smithsonian Center for Astrophysics, became a software entrepreneur during the Internet boom, and now provides strategic advice to entrepreneurial companies while pursuing research in economics.  Shou-Ching is a molecular biologist and cancer researcher at Beth Israel Deaconess Medical Center and Harvard Medical School, and Director of BIDMC’s Multi-Gene Transcriptional Profiling Core. Nuff said.

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Delivery & BreastFeed Studies & Newborn Microbiome Manipulation

Summary: Newborn microbiome differs by mode of delivery and feeding.  Newborn C-section microbiome:  Swabbing C-section babies partially restores the newborn microbiome.
First, a quick refresher of “How we acquire our gut microbiome.

Our gut microbiome is acquired at birth, though this is by no means a simple answer.  The post “Newborn Gut Microbiome Begins at Birth”  details many differences between the newborn gut microbiome  due to mode of delivery (vaginal versus C-Section) as well as feeding (breast-fed versus formula-fed).  The figure below extends this and shows the recent findings that the developing microbiome is shaped not only by delivery and feeding mode, but that antibiotics, probiotics, and environmental exposures also interact and develops the newborn’s microbiome and resultant immune system.

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SUMMARY:   We now understand that disease management requires understanding of:  what is the microbiome, what disrupts it, and what positively affects it.  This post discusses: What is the microbiome, implications of reduced diversity, long term therapeutic diet impact on microbiome, the IBD annual meeting is starting to consider the microbiome, some anecdotal microbiome stories, and why you want microbiome balance & diversity.
FIRST A RECAP (if you already are versed on this information, skip right on down to the Microbiome, What Disrupts It and How to Optimize sections of this post):  
What is the Microbiome?

It is estimated that the human microbiota contains as many as 1014 bacterial cells, a number that is 10 times greater than the number of human cells present in our bodies.  It is more accurate to say we are hosts of our microbiome rather then that we are human.  The human body is permanently colonized by microbial organisms on virtually every surface that is exposed to the external environment and each such surface has a different microbiome:  skin, mouth, genitalia, genitourinary, respiratory tracts, and the largest colonize, the gut (aka gastrointestinal).  The trillions of organisms live on and in us are collectively called the microbiome: a balanced ecosystem. “Gut Microbiota in Health and Disease,”

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Food Managing IBD & AUTISM: The Studies

SUMMARY:  Anytime food choices turns around chronic disease with studies that prove such, that should be an eye opener!  Implementing principles of such diets should be considered for anyone wanting to prevent or manage chronic disease.  This post presents studies for Food Managing IBD & AUTISM, where dietary protocols achieved remission and management (with reduction, if not elimination of medication) for autoimmune IBD , or positively altered the course of autism.

HOW?  Diet can optimize (or modulate) the gut microbiome which is the source of 80 – 85 percent of our immunity:  

The “1st International Symposium on the Microbiome in Health and Disease with a Special Focus on Autism,” July 2014: “the microbiome refers to the constellation of enteric bacteria that create an organ system that makes up 80% of our immune system...

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Testing if calories trigger hormones that regulate fat cell behavior

Summary:  NUSI is now testing if calories trigger hormones that regulate fat cell behavior.  This will help answer the question of  which camp we should we be in, namely:  the sugar is  bad/saturated fat is the good camp versus the whole grain/low fat is the good camp. 

Enter NUSI →   Seems bad science got us into the mess and state of confusion and ignorance.  So Gary Tuabes has aligned with Dr. Peter Attia, MD to do good science and answer the age old question:  Do we get fat because we eat too much and especially too much fat OR is it the food we eat, especially the increased consumption of table sugar and other refined carbohydrates the likely explanation for our current chronic disease epidemic including obesity?  There’s a real difference there, honest!

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Microbiome DIET Mechanisms Prevent or Manage Disease (Focus: SCD & IBD)

Summary: Watch the short video to learn why most of your immunity resides in your gut. Then read about predictive autoimmunity in preventative medicine; the role of gut permeability, and disease, as well as how autoimmunity may contribute to cardiovascular disease risk, and the role of antibodies in unexplained miscarriages. The pearl is have a healthy gut which is your first-line immune defense. To that end, learn what the microbiome diet mechanisms are that prevent or manage disease with a focus on SCD and IBD.

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Antibacterials and microbiome: SHOW SAFETY or REMOVE per FDA

Antibacterials and microbiome — real cause for concern:

FINALLY, the FDA has given soap manufacturers one year to demonstrate that antibacterial additives are safe or to take them out of the products altogether.  This is great considering it has been found in the urine of 3/4 of Americans, and it is detected in 97% of breast-milk tested.  The FDA issued the proposed rule on Dec. 16, 2013 requiring manufacturers to provide more “substantial data” to demonstrate the safety and effectiveness of antibacterial soaps. The proposed rule is limited however and covers only those consumer antibacterial soaps and body washes that are used with water

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Recipe: CLA Grassfed SCD Yogurt Benefits, CYTOKINE STUDIES

SUMMARYSCD yogurt is lactose-free due to its processing.  It can be grassfed if you choose to make it using grassfed milk.  You can also use a milk from A2 casein cows to make the casein less inflammatory.  Some use a milk alternative such as goat, coconut, or almond milk.  Last, there is growing concerns about the MAP suriviving dairy processing.  [Grant et al 2017] is study that published Dec, 2017 that raises growing concerns about MAP and  the safety of dairy products.  To ensure 100% kill of MAP, heat the milk to 194F (90C) for 60 seconds according to the author of the study.  The classic SCD yogurt recipe required heating to 180F with a two minute hold.  I’ve revised the recipe to require heating to 194F for two minutes to ensure MAP and other bacteria are killed.  Below the recipe find details for:  MAP implications for SCD yogurt processing temperature, What is the probiotic load of SCD yogurt, what probiotics can be in the starter and Lets talk about milk options, can I reuse my SCD yogurt as starter for another batch, and RECENT STUDIES FINDING PROBIOTIC YOGURT BENEFITS AND IT’S ANTI-INFLAMMATORY IMMUNE MODULATING PROPERTIES!  It is no wonder that SCD yogurt is the foundation of the healing diets: SCD/GAPS and some PALEO camps, if tolerated.

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How and When does the newborn gut microbiome begin?  What constitutes an “ideal” microbiome is not yet clear: it is not simply a matter of diversity, stability or even function.  This summary report (dated Sept 2013 and written by the Program Director of the Human Microbiome Project (HMP)), Lita M. Proctor, describes that the microbiome is:

    • Dynamic over lifetime changing with respect to both the numbers of microbes and their membership (see below slide),
    • Composed of a collection of bacteria/fungi/viruses unique to each individual,
    • Unique at each region of our body as it has its own distinct community of microbes living on or in it,
    • Impacted by our daily activities (bathing/washing hands/eating probiotics),
    • Susceptible to disturbances resulting from use of antibiotics at sublethal dosages.
    AgeChangesGutMicrobiome Slide:

    Studies have shown that our microbiota can be modified — perhaps irreversibly in some instances — by medical, dietary and hygienic practices.  Infant microbial colonization is affected by delivery mode, dietary exposures, antibiotic exposure, and environmental toxicants many of which can be eliminated or moderated.

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