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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,”

In the GI tract, microbes outnumber host cells by 10-fold.  We have 1 trillion human cells, but 100 trillium microbial cells.  Thus, we are 90% bacteria, or 10% human, on a cellular level.  On a gene level, we have only 20,000 human genes.  But, our microbial genes, range from 2 to 20 million; we carry around mostly microbial genes! Dr. Rob Knight, “How microbes could cure disease: Rob Knight at TED2014″  

“The microbiome keeps us healthy. It breaks down some of our food into digestible molecules, it detoxifies poisons, it serves as a shield on our skin and internal linings to keep out pathogens, and it nurtures our immune systems, instructing them in the proper balance between vigilance and tolerance”  – Carl Zimmer, “When You Swallow A Grenade,” National Geographic, Dec 2012.

“For the most part, the microbes inhabiting our bodies are either beneficial ones or unobtrusive freeloaders.  They help us digest our food and absorb nutrients.  The manufacture vital vitamins and anti-inflammatory proteins that our own genes cannot produce, and they train our immune systems to combat infectious intruders.  Resident bacteria on our skin secrete a sort of natural moisturizer, preventing cracks that could allow pathogens to penetrate.  We get our first dose of these microbial co-conspriators as we pass through our mother’s vaginal canal, where the bacterial population changes dramatically during pregnancy.”  – Nathan Wolfe, “Small, Small World.”

Indeed, “It is precisely due to our microbiome, and the micobiota that it contains, that we are able to even live as they give us all the genes and proteins our human genome does not encode.  You can think of it as:  humans are actually the bystanders; it is the microbiota that does all of the work.”– ” Animated Life: Seeing the Invisible.”

The host gains products from microbial fermentation conversion of host indigestible components (dietary fibres) into short-chain fatty acids (SCFA; mainly acetate, propionate and butyrate) contributing to an estimated 10% of our energy requirement [4], vitamin K and B12 production [5, 6], and protection against potential pathogens through competitive exclusion [7, 8].  ~ “The first thousand days – intestinal microbiology of early life: establishing a symbiosis,” June 2014

“You can think of it as:  humans are actually the bystanders; it is the microbiota that does all of the work.”  ~‘Animated Life: Seeing the Invisible’

The microbiome is determined at birth and differs not only in total diversity but also in altered prevalence of particular bacterial species depending on:  mode of delivery (vaginal or C-Section), how the newborn is fed (breast-milk or not), and even how long the newborn is breast-fed.  See the post “NEWBORN GUT MICROBIOME BEGINS DURING BIRTH”  for details.

Our individual microbiome regions are virtually changing.  Only in 2012 did we learn that the vaginal microbiome alters throughout pregnancy ultimately becoming much less diverse and increasing tremendously in certain specific bacterial species.  See this study or this study or the post,   Microbiome Rules, What Is It?”

The Western gut has a very different microbiome from that of non-Westerners as detailed in this study, out of Drs. Rob Knight, Jeffery Gordon and Janet K. Jansson’s labs, “Diversity, stability and resilience of the human gut microbiota.”  Many diseases are now known to have altered microbiomes.   “Disruptions to the normal balance between the gut microbiota and the host have been associated with obesity6, 7,  malnutrition8, inflammatory bowel disease (IBD)9, 10, neurological disorders11 and cancer12.”  Most of these diseases are considered to be a Western epidemic: 

Disease Epidemic_PNG file
Slide source:

 The study, “Diversity, stability and resilience of the human gut microbiota,” notes “Disruptions to the normal balance between the gut microbiota and the host have been associated with obesity6, 7,  malnutrition8, inflammatory bowel disease (IBD)9, 10, neurological disorders11 and cancer12.”

The paper, “Gut Microbiota in Health and Disease,”  lists disorders of the microbiome as: IBD, gastrointestinal malignancies, gallstones, and cirrhosis of the liver, as well as complex diseases residing in organs outside (and far from) the gut such as: obesity, allergy, Type1 Diabetes, Familial Mediterranean fever, autism, and bacterial translocation for SIBO and pancreatitis, and ‘leaky gut’ for Type2 Diabetes, atherosclerosis, and systemic inflammatory response syndrome.  Associated study citations are included in this paper.

Distal Organs Related to Gut Microbioata
“Gut Microbiota in Health and Disease,”

Regarding the disease and associated altered microbiome link, the paper, “Diversity, stability and resilience of the human gut microbiota,” notes still unknown is “whether generally opportunistic members of the gut microbiota have a selective advantage during early succession [remember the microbiome is established at birth and differs both by mode of delivery and feeding] or disruption caused by disease, and therefore whether they are the side effects of disease rather than causal agents.”  An example of altered microbiome related to disease is:  The microbiota of individuals with ileal Crohn’s disease can resemble that of infants: both have increased levels of Ruminococcus gnavusand Enterobacteriaceae in their stools, and an under-representation of the genera that are prevalent in healthy adults, including Faecalibacterium and Roseburia51. 


Less diversity can result in increased bacterial strains that cause inflammation representative of obesity, Type2 Diabetes and cardiovascular disease:

The Danish study, “Richness of human gut microbiome correlates with metabolic markers,”  (or read the University of Copenhagen scientific article “One in four has alarmingly few intestinal bacteria” showed thatone in four had 40% less gut bacteria than average. “This is a representative study sample, and the study results can therefore be generalized to people in the Western world,“ says Oluf Pedersen, Professor and Scientific Director at the Faculty of Health and Medical Sciences, University of Copenhagen. This population had reduced bacterial diversity and harbored more bacteria that caused low-grade inflammation of the body that is representative of obesity, Type 2 Diabetes, and some cardiovascular disorders.”

Dr. Maria Gloria Dominguez-Bello estimated that 1/3 of the population has reduced microbiome as seen on this interview for the film “Microbirth.”

Long term therapeutic diets can alter the microbiome: 

“Understanding the resilience of the gut microbiota is crucial for determining the efficacy of therapeutic diets. Consuming a carbohydrate- or fat-restricted low-calorie diet for a year6, or a high-fat and a low-fibre, or low-fat and high-fibre diet for 10 days32 can induce statistically significant changes in the gut microbiota. However, these changes in species and gene content are small compared with the baseline variations that occur between individuals. Long-term dietary surveys and cross-cultural comparisons suggest that changes to diet might lead to regime changes over longer periods of time4, 32, perhaps by eroding the landscape of alternative stable states to allow changes that short-term ‘nudges’ cannot.” -“Diversity, stability and resilience of the human gut microbiota.”

This post does detail the healing affects of long term dietary protocols that achieved remission or management of chronic disease and identifies the state of the art studies of such with a focus on autism and IBD, most likely due to changing up the microbiome which altered health. -“FOOD MANAGING IBD & AUTISM: THE STUDIES” and this post “MICROBIOME DIET MECHANISMS PREVENT OR MANAGE DISEASE (FOCUS: SCD & IBD)” details mechanisms behind “Why” the healing diets might work for healing the gut.  This post “FEED YOUR MICROBIOME TO MANAGE AUTISM” notes trials now extending SCD dietary protocols for autism and discusses skewed autistic microbiome findings.

The Advances in Inflammatory Bowel Disease’s Annual Meeting

Clearly, the microbiome is beginning to pick up clinical integration concerns as the current Scientific Agenda for the December 4-6, 2014 Advances in Inflammatory Bowel Diseases (Annual meeting) notes What’s New? Pretty Much Everything.”  Specific to the microbiome:

  1. Basic Science Track:
    • Roundtable Discussion of New Approaches in IBD Research which includes “Novel approaches for studying the role of the microbiome in IBD,”
    • Integrating Microbiome Discovery “Advances in understanding the role of the microbiome in IBD” and “What is the role of microbial metabolism in homeostasis and IBD,” 
    • Advances in Understanding the Pathogenesis of IBD “Evaluating human gut microbiota and microbe-host phenotype relationships,” and “How can diet effect the human intestinal microbiota,
    • Future Research Challenges in IBD “Understanding the next steps in determining the role of the genome in IBD,” and “What new strategies are needed to allow us to better understand the role of the microbiome,”
  2. Pediatric Track Agenda:  Non-Immunosuppressive management of Pediatric IBD “Can nutritional therapy be used on a practical basis for maintenance,” and “Probiotics, special diets, and complementary therapies: WE KNOW THE PATIENTS WANT THEM, SO WHAT DO WE TELL THEM?”
You can DNA sequence your microbiome

DNA sequence your microbiome at “The American Gut Project“, “Ubiome“, and/or “23AndMe“;  you can pay these centers to have your own or your children’s microbiome sequenced. here and here to learn what your microbiome looks like.  Putting my lawyer hat on… think thoroughly before doing such.  Just some of the issues that come to mind are:  privacy and protecting your identity, sequencing accuracy,  dual-use research which might have both benevolent and harmful applications, you will pay a fee for participation making withdrawal of consent somewhat more difficulty (most research participation can be easily withdrawn since it isn’t tied to your wallet), your children can be sequenced with unknowns for use of their data and identity protection, how will you react and what will you do should you receive results that correlate your DNA to others resembling disease predisposition, etc…)  Just saying… do your own research and think through all ramifications if you decide to sequence.

Some anecdotal microbiome stories:
  1. I know of one mom whose child had chronic ear infections in one ear.  She actually transferred the ear wax from the healthy ear into the chronically infected ear and that stopped all further ear infections for her child.  This article, printed February 2013 in the Pittsburgh Post Gazette, “Bacteria inside us studied as key to health” likewise discussed resolution of an ear infection  occurring in only one ear of a middle aged man:  “I figured, I have one ear that’s bad and one ear that’s good, and whatever’s in my good ear I want to get over to my bad ear, so I just took some wax from my good ear and put it in my bad ear and within a couple days, I was fine.”  “We just assumed that one of our myriad drop regimens had finally hit its mark and wiped out the guy’s bacteria,” said Dr. Goldberg, who now oversees sinus surgery at the University of California at San Francisco Medical Center.  Dr. Goldberg just laughed uncomfortably at the man’s explanation back then. But today, he believes the patient was right: By putting earwax from one ear into the other, he was also transferring the bacterial colonies from the healthy ear into the sick one, and that probably cured his persistent infections.”
    "Bacteria inside us studied as key to health,"
    “Bacteria inside us studied as key to health,”

    PG graphic: The Human Microbiome
    (Click image for larger version)

  2. I know of several women who have stopped using estrogen type vaginal prescriptions for bacterial vaginosis (BV).  As long as they daily ingest about a forkful or two of active live sauerkraut, they have no symptoms of BV.  They also eat a pretty clean, whole foods, anti-inflammatory, nutrient rich diet.  Lastly, they went through the change of life with absolutely NO symptoms.
  3. I know of some women that don’t eat a “clean” diet that successfully used the Jarrow Formulas “Femdophilus” to manage BV without estrogen medication.  Others have used “Rephresh” to adjust the ph and thus the microbiome of the vagina to successfully manage BV without estrogen medication.
  4. I know some managing autoimmune remission and chronic disease such that medications are eliminated or reduced.  I know some that have turned around metabolic syndrome and lost weight in doing so, and it is sustainable.
Some reasons why you want the correct balance of microbes:
    1. Keeps potential pathogens in check (so that the mucosal gut layer is not pierced) and regulates our immune system.  Disturbed mucous layers that line the intestinal cell wall and concomitant inflammation are seen in individuals with IBD, coeliac disease, HIV enteropathy, acute diarrhoea, diverticulosis, carcinoma and IBS52 ,
    2. Keeps zonulin protein functioning correctly so that the gut wall tight junctions operate correctly and “leaky gut” does not occur (see below slide),  Leaky gut can progress to an allergy, chronic disease, and autoimmune disease.  Gluten consumption always stimulates zonulin production and opens the gut’s wall for a limited time. Ordinarily, a normal functioning immune system would successfully deal with crossover substrate during zonulin stimulation.  However, excessive consumption of gluten keeps the gut wall opened excessively and challenges even the best immune system if chronically stimulated. 
    3. Digests food properly as improper digestion can be food for species which flourish at the expense of beneficial species thereby altering the optimal microbiome balance, gut wall integrity, and immunity,
    4. Synthesizes vitamins, makes antibiotics and anti-inflammatory proteins that our own genes cannot produce, and they train our immune systems to combat infectious intruders (see citations noted at the top of this post).
    5. Permits the body to detox properly (this includes toxins that are ingested as well as those toxins already on-board and in the bloodstream and tissues that return to the gut for elimination).

      Ballantyne: What Exactly is A Leaky Gut?
      Snippet from Sarah Ballantyne site at:
    • MICRONUTRIENT DEFICIENT DIET due to anti-nutrients and inherent in our food system (grains, nuts, seeds, and legumes that are not properly prepared) and insufficient macronutrient (fat/carbohydrate/protein) consumption.
    • Compounds that the gut sees that damages the mucosa:  food intolerances and/or food allergies, gut irritating compounds in foods (such as prolamins, agglutinins, saponins that damage enterocytes), food compounds that open tight junctions such as: gliaden (gluten protein), alcohol, agglutinins, sugar alcohols, cortisol, some RXXs, some infections, insufficient live pre- and probiotics, chronic very low carbohydrate diets if not needed for specific aliment management (MS, obesity or other).
    • LIFESTYLE FACTORS such as stress, insufficient sleep, and sedentary lifestyle.
    • TOXINS:  (air, water, topicals, food). See the post “TOTAL BODY BURDEN AND DETOX” for associated implications.
    • DETOX IMPAIRED (Lung, bowel, skin, kidney, liver, and/or digestive disorders).  See the post “TOTAL BODY BURDEN AND DETOX” for implications.
    • ANTIBIOTICS (your past usage, your parents usage preconception, those now in our water, those now in meats, even those now in organic apples).  See the post “NEWBORN GUT MICROBIOME BEGINS DURING BIRTH” in the section titled MICROBIOME IMPACT DUE TO ANTIBIOTIC EXPOSURE.”  Also see the post “DIET AND OTHER THINGS DETERMINES OUR MICROBIOME” in the section titled “ANTIBIOTICS ALTERS THE MICROBIOME.”  Also see “Diversity, stability and resilience of the human gut microbiota.” 
    • MEDICATIONS (your RXXs, and those found in your water).
    • ANTIBACTERIAL PRODUCTS (topical hand sanitizers, topical soaps, household products such as dish cleaners, etc).  See the post “ANTIBACTERIALS: DEMO SAFETY OR REMOVE PER FDA” which discusses microbiome implications of antibacterials.
    • TRAVEL (especially international (may be good for increased microbiome diversity, may be bad if pick up pathogen or bacterial species that compromises your unique biome.)  See the post “MICROBIOME CHANGES FR DIET & ENVIRO AFFECTING HEALTH; ALM” showing that simply walking off a plane and inhaling air overseas practically  instantaneously  changed up the microbiome.
What Optimizes and Most Affects the gut microbiome? 

Dr. Rob Knight just gave a talk, October 18, 2014, that explained what the American Gut project has shown to date, as most affecting the microbiome.  You can catch  details at my post, “Optimal Microbiome Diet From American Gut Data.”   You’ll want to understand the Eleven Factors that Dr. Knight relayed as it is  FOOD FOR THOUGHT most definitely:

  • Eat lots of  plants:  5 to 30 different varieties each week preferably.  See MY NOTES below for more explanation.  
  • Aging increases microbiome diversity:  Microbiomes are more diverse at age 50 to 60 then populations in their twenties  (see below slides).
  • Having an IBD diagnosis means your microbiome is altered.  NOTE:  Many chronic and autoimmune diseases are also following suit.
  • The time of year alters the microbiome with a more diverse microbiome being with sun and outdoor exposure.
  • Antibiotics wipe the microbiome with some folks recovering relatively soon whereas others do not recover the pre-antibiotic microbiome even one year later.
  • Males vs females:  The sex for a  given microbiome can now be accurately predicted.
  • Sleep 8 hours for a more diverse microbiome.  Less than 6 hours yields a less diverse microbiome.
  • BMI but it only subtly affects the microbiome.
  • Plants: eating 6 to 10 each week is good, but eating 30 plus different varieties is best.  (See further discussion below.)
  • Alcohol: one drink is helpful, more than one reduces diversity.
  • Frequent exercisers have a more diverse microbiome and it is best if exercise is outdoors rather than indoors.

“Microbes may be the missing piece of the puzzle that makes personalized medicine work, “ says Dr. Rob Knight, Knight labs UColorado Boulder, describing how the effects of drugs, including toxicity and efficacy, can depend on what microbes you have. “Optimizing the microbes you have may be even more important than optimizing your lifestyle – although in many cases you may be able to optimize your microbes by optimizing your lifestyle.”

Among the interesting patterns emerging from the data:

  • How much of their microbial diversity participants shared with others depended greatly on how recently they had taken antibiotics. Those participants who had taken antibiotics within the last year tended to have less shared diversity.
  • Alcohol imbibers tended to have greater microbial diversity than those that don’t drink alcohol at all.
  • Spikes in microbiome populations seem to occur around holidays: in July, and in November through January.
  • There is no single organism that is found in every person, but some are more common across the population than others.
  • People who sleep more, and who exercise outdoors, have more diverse microbiomes.
  • As seen in other studies, the elderly resemble infants in certain respects of their microbiomes.

You can also check out the post “What Whole Foods Look Like” for what an anti-inflammatory, micronutrient dense, and low toxin diet looks like that presumably would also be microbiome protective as this is the diet many use to heal chronic disease (PALEO, modified PALEO, SCD, GAPS…).

How do you optimize your microbiome? 

You can start implementing some strategies discussed above by addressing the factors listed above that disrupt the microbiome!  Pick what you are comfortable with as every (even small) change is a big plus for the trillions of beasties living in and on you.

Slide source

Last updated: November 3, 2017 at 8:33 am for SEO Optimization.
In good health, wellness and awareness,




  1. From Questioning Answers blog: “Autoantibodies by the way, refers to antibodies against self tissue as per what has been noted in various autoimmune conditions/diseases,” and Paul Whiteley cites to: Plasma Autoantibodies (Disease Associations) located at:

    There is also the work of Dr. Yehuda Shoenfeld, MD, “The Mosaic of Autoimmunity: Prediction, Autoantibodies, and Therapy
    in Autoimmune Diseases – 2008” located at paper (from the Gluten Summit) and which is already cited on some of my tagged “microbiome” posts and the most recent “ALZHEIMER’S, DIET-MICROBIOME, & BIO-MARKER PREDICTORS” posting,

Now I'd like to hear your thoughts... comments are always welcome!