Studies now show that the community of bacteria (along with gut infections, viruses, fungi, and parasites) that occupies the ecosystem of the gut microbiome affects: inflammation, chronic disease, allergies, arthritis, skin disorders including acne, psoriasis and eczema, autism, insulin resistance, overall adiposity, dyslipidemia, gastrointestinal and digestive disorders, autoimmunity, gut-brain interactions such as mood, depression, dementia, eating disorders, obesity, cancer, and more (the list literally grows daily).  This makes sense since  70 to 80 percent of our immune cells cells reside here.  We’ve only recently learned that this virtual organ even exists due to new gene sequencing technology.  The slew of disorders is epidemic for Western culture.  This study, out of  Dr. Rob Knight’s lab, “Diversity, stability and resilience of the human gut microbiota,” summarizes how different the Western gut microbiome is from that of non-Westerners and links to many diseases now known to have altered microbiomes.  Matter of fact, Dr. Knight just gave a talk, October 18, 2014, that detailed what the American Gut findings to date reveal which included diet as it affects the microbiome, the synopsis of which you can catch at my post, “Optimal Microbiome Diet From American Gut Data.”   He relayed Eleven Factors that hugely alter the microbiome that you’ll want to understand.  FOOD FOR THOUGHT most definitely!

Many of these diseases are seemingly unrelated but are actually caused by gut microbiome community problems called dysbiois (inbalance of the community).  If you want to fix your health and emotional and mental wellbeing, you must start in your gut.  Gut health literally affects your entire body.

Microbes may be the missing piece of the puzzle that makes personalized medicine work..  [The microbiome] patterns are certainly interesting, and we are hoping that the American Gut data provides other researchers a foundation to further study the effects of diet and lifestyle on the human microbiome...  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.”Dr. Rob Knight

The gut microbiome begins at the beginning with the birthing process:  Vaginal or C-Section.

A vaginal delivery inoculates the baby with a gut microbiome that studies today indicate set a life trajectory for immunity and health.  C-Section delivery on the other hand, yields a gut flora that more closely resembles oral flora.  Matter of fact, read the post,  “Delivery & Breastfeed Studies & Microbiome Manipulation,” to learn of current studies where Cesarean newborns are being swabbed with gauze inserted into the mother one hour prior to delivery to attempt to achieve a microbiome that is more like that of a vaginal delivery. This study and more are detailed on the post, “MICROBIRTH” EVERY PARENT NEEDS TO VIEW, which actually is a film, Microbirth,  that details links between C-section and disease, and which has a cast of characters (researchers) that reads like a who’s who list.  You are familiar with most if you read my work.  Not to be missed is the Downloads section of the  Microbirth website as it contains FAQ, which I excerpted in the post  “MICROBIRTH” EVERY PARENT NEEDS TO VIEW In summary:

Recent population studies have shown babies born by Caesarean Section have approximately:
  • 20% increased risk of developing asthma,
  • 20% increased risk of developing type 1 diabetes,
  • 20% increased risk of obesity,
  • slightly smaller increases with gastro-intestinal conditions like Crohn’s disease or coeliac disease, and
  • These conditions are all linked to the immune system.

In 27 months, a vaginally delivered baby’s gut “matures” to that of adulthood.  Check it out at: “The Assembly of an Infant Gut Microbiome Framed Against Healthy Human Adults”, University of Colorado Boulder, 2:45 minute YouTube. 

The assembly of an infant gut microbiome framed against healthy human adults,

Though we don’t know yet what the C-Section gut looks like at 27 months, we do know that the C-Section infant microbiome at four months is much less bacterial diverse, even if breastfed:

“infants born by cesarean delivery were lacking a specific group of bacteria found in infants delivered vaginally, even if they were breastfed. Infants strictly formula-fed, compared with babies that were exclusively or partially breastfed, also had significant differences in their gut bacteria.

“We want parents (and physicians) to realize that their decisions regarding c-section and breastfeeding can impact their infant’s gut microbiome, and this can have potentially lifelong effects on the child’s health.”

“The Human Microbiome, Diet, and Health: Workshop Summary  book by the Institute of Medicine (US) Food Forum, Washington (DC) 2013 shows some incredible research focusing on the newborn microbiome due to varying situations.  I also suggest you check out the post “Newborn Gut Microbiome Begins at Birth”  that describes some of these finding so that you can begin to fathom the ramifications of delivery and feeding relative to you and your families current and long term health implications.

Why do Westerners have epidemic chronic disease?

 Increased microbiome diversity means stronger immunity.
Less diversity can result in increased bacterial strains that cause inflammation representative of obesity, Type2 Diabetes and cardiovascular disease. 

This Danish study (read the scientific article here) showed that one 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.”

The study, “Diversity, stability and resilience of the human gut microbiota,” noted some dire consequences and ramifications of the altered and depleted microbiome status:

“High-throughput sequencing of samples suggests that the microbiota of each person has some resistance to perturbation, but that this resistance can be overcome by diet, drugs, prebiotics or probiotics. Dietary changes may alter the regime in the gut over long time periods. The surprising success of whole community transplants in healthy rats and in humans with CDAD shows that exogenous microbes can colonize the gut even with resistance from an entrenched microbiota. However, which microbes will be the best colonizers is unknown; neither do we know how a particular microbial configuration and its functional attributes change in response to dietary components or exogenous microbes. We need to learn what conditions promote the health of desired species and exclude the undesirable ones, just as a gardener would exclude weeds…

…How resilient the microbiota is to diet, disturbance by antibiotics and challenge by exogenous microbes will have important implications for health care. The degree to which repeated applications of broad-spectrum antibiotics degrade the microbiota and its ability to function as a healthy system would need to be studied, especially in children, in whom the development of interactions between the microbiota and host is crucial5

…Individuals whose microbiota has been degraded by long-term consumption of a high-fat and high-sugar diet may need long-term dietary changes to restore their microbiota to a healthy state

…changes to the stable equilibrium of the gut microbiota through long-term changes, such as inflammation, diet or repeated antibiotic administration, could make new states reachable with smaller perturbations.. .Individuals whose microbiota has been degraded by long-term consumption of a high-fat and high-sugar diet may need long-term dietary changes to restore their microbiota to a healthy state.”

“The lower taxonomic diversity in individuals from Western cultures who have a high-fat and high-sugar diet raises the concern that global trends in diet could result in important microbial symbionts being lost from the broader population, possibly leading to the extinction of bacterial species that can provide important health benefits. Maintaining a collection of cultures from individuals in the developing world, and specifically from agrarian cultures, could help to preserve potentially important components of the microbiota.”

And this is where the role of:  diet, medicines (antibiotics and others), and environmental toxin exposures (included here are the antibacterial products such as hand soap you use, the chemicals in your topicals, the gases emitted from your furnishings – home, school, and office in addition to that in your food – plastics BPA.BPS, teflon and ceramic dyes, lead, water containing flouride/chloride/drugs and antibiotics, arsenic, cadmium, GMOs, etc…)  all play a role in affecting the gut microbiome (see below slides) which constantly changes and adjusts, regardless of age.

Gut MicrobiomeFactors.1
Slide source:
So, how skewed are our Western microbiomes?

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 study, “Gut Microbiota in Health and Disease,” discusses the association of microbiota with diseases outside of the gastrointestinal tract:  “The intestinal microbiota has been linked to a number of diseases that are associated with remote organ systems. Solid arrows indicate the organ systems affected by the diseases indicated. Obesity is indicated by a dashed black line, and fibromyalgia is illustrated by the characteristic pressure points typically used to diagnose the disease (white dots)…Gut microbiota now appears to influence the host at nearly every level and in every organ system, highlighting our interdependence and coevolution. Its adaptation to our changing life-styles (such as diet- and ethnicity-associated differences in gut microbiota composition) is astounding, highlighting that the consequences of our behaviors affect not only the environment without, but also that within us.”   Included with citations are:  IBD, 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.

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

This study compared the gut microbiota of children aged 1–6 years living in a village of rural Africa in an environment that still resembles that of Neolithic subsistence farmers with that of western European children of the same age, eating the diet and living in an environment typical of the developed world.”  Researchers were looking at why westerners have such an increase in allergic, autoimmune disorders, and inflammatory bowel disease (IBD).  It is hypothesized that improvements in hygiene together with decreased microbial exposure in childhood are considered responsible for this increase (7). The GI microflora imbalance plays a crucial role in the pathogenesis of IBD (8), and  obesity (9, 10). These two childhood populations provide an attractive model for assessing the impact of many environmental variables [including food] on the gut microbiota.”  

The conclusion:  Significant microbiome changes occur; the reduction of Short Chain Fatty Acids produced by certain bacteria for Westerners is significant since these species are precursors for gluconeogenesis, liponeogenesis, and protein and  cholesterol synthesis… all huge anti-inflammatory immune modulators. “Our results suggest that diet has a dominant role over other possible variables such as ethnicity, sanitation, hygiene, geography, and climate, in shaping the gut microbiota. We can hypothesize that the reduction in richness we observe in EU compared with BF children, could indicate how the consumption of sugar [think grains here too as they metabolize to sugar], animal fat [think GMO fed CAFO antibiotic and hormone injected animals], and calorie-dense foods in industrialized countries is rapidly limiting the adaptive potential of the microbiota.”  Please realize that when they say ‘sugar’, they aren’t only speaking to simple table sugar… rather, all carbohydrates metabolize as such and this, surprising to many, includes all of the high grain carbohydrates so prevalent in the Western diet.

 Dr. Kathryn Dewey of the University of California, Davis, [Video]  notes: “I don’t want to give the impression that [the BF] is a better diet in any way,.. we could not argue that Burkinabe children were protected against these microbes, because diarrheal diseases are very, very common there.”

BF, Africa Diet Rural Microbiome Compared To Europe Western Diet
Slide source

 So what does a gut microbiome protective diet look like for Westerners?

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.

And from the BioFrontiers Institute, UColorado news site:  “Microbes may be the missing piece of the puzzle that makes personalized medicine work, “ according to Dr. Rob Knight 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.
There are a lot of healing diets (SCD, GAPS, PALEO, AIP, WAHLs, Mediterranean…) that break down to common tenets.

Finding out and eliminating what the individual can not tolerate (common intolerances are grains, dairy, eggs, nuts, nightshades…), AND eliminating foods that down-out harms the microbiome (like emulsifers — see this post for the whys), AND eating foods supporting the microbiome diversity and richness (lots of diverse forms of fiber, prebiotics, and probiotics) is a protective microbiome  diet.

 Actually, the goal of the healing diets, which are nutrient dense, low-toxin, and anti-inflammatory, is to achieve resiliency in a gut microbiome that supports healthy immune function. When the diet and lifestyle is properly individualized, the resultant microbiome immune status often resolves and manages chronic conditions including autoimmunes.”  -A great listen is Dr. Amy Shah, double board certified in Internal Medicine and Immunology/Allergy.

For Healing Diet RECIPES posted on the website,

Go to the “The Science Behind Food and Disease” section located in the right sidebar.  It is circled below!  Use the drop down menu and scroll down to the R’s, for RECIPES!  Select beverages, breads/crackers, poultry, fish, nuts, quinoa, and so much more…!  You can also link to my Pinterest, for even morefamily/friend tested great Whole Foods/SCD/PALEO/… recipes!

You can also check out the posts  Recipes & What Whole Foods Look Like” and “A FEW INDEX CARD RECIPES FOR WHOLE FOODSfor a few recipe cards to learn what a nutrient dense, anti-inflammatory, low toxin diet looks like for a microbiome protective diet.   The post, What’s in a Practical Whole Foods PALEO, SCD, GAPS Healing Fridge? is another good read and it includes practical tips for transitioning & quality food sourcing links.

Another incredible read where you can begin to grasp the mind boggling microbiome, and say, “Hello” to the 100 trillion bacteria that make-up your microbiome is:  NY Times article, “Some of My Best Friends Are Germs”,  Michael Pollan,  May, 2013.

Disease is rooted in our DNA expression which is hugely influenced by diet, environment, stress (all aspects such as physical, mental, physical ongoing inflammation and disease, and emotional), sleep, toxins exposure, sun exposure, and exercise.  The process whereby these factors influence gene expression is called Epigenetics.”
Your genes are not your destiny.  Epigenetics triggers disease in those predisposed.  Check out the video:  What is Epigenetics?  An entertaining and educational primer”, GreenmedTV, April 2013:  
Epigentics is at the heart of microbiome manipulation and management of chronic disease.  Even though one might be “predisposed” to disease, we can stop the epigenetic changes that trigger disease by implementing lifestyle and diet changes.  That is the mission of Biome Onboard Awareness, LLC:  to make you aware of  Whole Health Pillars so that you can optimize your gut microbiome to preclude triggering disease or if already triggered, to manage chronic disease often with reduction or elimination of medications.  How empowering!  

Our microbiome, manipulable through diet and lifestyle, affects gene expression.  Despite our genome being more or less fixed, our microbiota affects our epigenome.  One such example is DNA methylation and histone modification mechanisms regulating gene expression, which we are only now beginning to understand.  This is called epigenetics.  ~ “The first thousand days – intestinal microbiology of early life: establishing a symbiosis,” June 2014

The below Drew Berry, “Animations of Unseeable Biology,” incredibly shows the biology of cell regeneration and split which happens now, billions of times within you.

Some highlights of the DNA split animation are:

And relevant slides from Biome Onboard Awareness, LLC, of ramifications to DNA altered ramifications are:

This post, Diet and Other Things Determine the Microbiome,  as well as the post “WHAT DISRUPTS THE MICROBIOME?”   further details the many factors that affect the microbiome.


To hammer home the significance of the preceding paragraph I will mention the blogster work of Paul Whiteley,  autism researcher, ScansBrit collaborator, Works at ESPA Research, author of Autism: Exploring the Benefits of a Gluten- and Casein-Free Diet: A practical guide for families and professionals, April 2014.

He writes on Questioning Answers, The epigenetics of Chronic Fatigue Syndrome?” Sept 2014  concerning the deVega paper and is enthusiastic to note the “fact that someone has actually started to apply the science of epigenetics to Chronic Fatigue Syndrome: “1,192 CpG sites were identified as differentially methylated between CFS patients and healthy control subjects, corresponding to 826 genes.”  When it came to where in the genome differences were found and what functions might be impacted, well among other things, there was “an overrepresentation of terms related to immune cell regulation“. With particular regard for gene regulatory elements, and bearing in mind: “Differential methylation of gene regulatory elements is classically associated with alterations in gene expression“, the authors reported “a number” of differentially methylated CpGs in such elements related to the immune response.”

What all that means in Questioning Answers simpleton is that  “genes and gene expression are likely to be only one part of the spectrum of presentations which fall under the CFS banner; not forgetting important areas such as the viral link to cases (see here), the growing emphasis on mitochondrial issues (see here) and even some potential role for those trillions of beasties which call our darkest recesses home (see here).”  And that would be the gut microbiome.

What follows for the balance of this post is the biology relevant to genetic predispositon.  If you are not into technicalities, move on to the post “Microbiome Rules, What Is it?”
Otherwise, enjoy the “Genetics Home Reference, Your Guide to Understanding Genetic Conditions” which succinctly summarizes relevant details:
What does it mean to have a genetic predisposition to a disease?

“A genetic predisposition (sometimes also called genetic susceptibility) is an increased likelihood of developing a particular disease based on a person’s genetic makeup. A genetic predisposition results from specific genetic variations that are often inherited from a parent. These genetic changes contribute to the development of a disease but do not directly cause it. Some people with a predisposing genetic variation will never get the disease while others will, even within the same family.

Current research is focused on identifying genetic changes that have a small effect on disease risk but are common in the general population. Although each of these variations only slightly increases a person’s risk, having changes in several different genes may combine to increase disease risk significantly. Changes in many genes, each with a small effect, may underlie susceptibility to many common diseases, including cancer, obesity, diabetes, heart disease, and mental illness.

In people with a genetic predisposition, the risk of disease can depend on multiple factors in addition to an identified genetic change. These include other genetic factors (sometimes called modifiers) as well as lifestyle and environmental factors. Diseases that are caused by a combination of factors are described as multifactorial. Although a person’s genetic makeup cannot be altered, some lifestyle and environmental modifications… may be able to reduce disease risk in people with a genetic predisposition.”

What Is DNA? Effects of Variation on Human Life.  


“To function correctly, each cell depends on thousands of proteins to do their jobs in the right places at the right times. Sometimes, gene mutations prevent one or more of these proteins from working properly. By changing a gene’s instructions for making a protein, a mutation can cause the protein to malfunction or to be missing entirely. When a mutation alters a protein that plays a critical role in the body, it can disrupt normal development or cause a medical condition.

“Only a small percentage of mutations cause genetic disorders—most have no impact on health or development. For example, some mutations alter a gene’s DNA sequence but do not change the function of the protein made by the gene.

Often, gene mutations that could cause a genetic disorder are repaired by certain enzymes before the gene is expressed and an altered protein is produced. Each cell has a number of pathways through which enzymes recognize and repair mistakes in DNA. Because DNA can be damaged or mutated in many ways, DNA repair is an important process by which the body protects itself from disease.

A very small percentage of all mutations actually have a positive effect. These mutations lead to new versions of proteins that help an individual better adapt to changes in his or her environment.”

“People have two copies of most genes, one copy inherited from each parent. In some cases, however, the number of copies varies—meaning that a person can be born with one, three, or more copies of particular genes. Less commonly, one or more genes may be entirely missing. This type of genetic difference is known as copy number variation (CNV).”

“Researchers were surprised to learn that copy number variation accounts for a significant amount of genetic difference between people. More than 10 percent of human DNA appears to contain these differences in gene copy number. While much of this variation does not affect health or development, some differences likely influence a person’s risk of disease and response to certain drugs. Future research will focus on the consequences of copy number variation in different parts of the genome and study the contribution of these variations to many types of disease.”                                                   Gene Mutations and Health

Can changes in mitochondrial DNA affect health and development?


“Mitochondria (illustration) are structures within cells that convert the energy from food into a form that cells can use. Although most DNA is packaged in chromosomes within the nucleus, mitochondria also have a small amount of their own DNA (known as mitochondrial DNA or mtDNA). In some cases, inherited changes in mitochondrial DNA can cause problems with growth, development, and function of the body’s systems. These mutations disrupt the mitochondria’s ability to generate energy efficiently for the cell.

Conditions caused by mutations in mitochondrial DNA often involve multiple organ systems. The effects of these conditions are most pronounced in organs and tissues that require a lot of energy (such as the heart, brain, and muscles). Although the health consequences of inherited mitochondrial DNA mutations vary widely, frequently observed features include muscle weakness and wasting, problems with movement, diabetes, kidney failure, heart disease, loss of intellectual functions (dementia), hearing loss, and abnormalities involving the eyes and vision.

Mitochondrial DNA is also prone to somatic mutations, which are not inherited. Somatic mutations occur in the DNA of certain cells during a person’s lifetime and typically are not passed to future generations. Because mitochondrial DNA has a limited ability to repair itself when it is damaged, these mutations tend to build up over time. A buildup of somatic mutations in mitochondrial DNA has been associated with some forms of cancer and an increased risk of certain age-related disorders such as heart disease,Alzheimer disease, and Parkinson disease. Additionally, research suggests that the progressive accumulation of these mutations over a person’s lifetime may play a role in the normal process of aging.”

“The Science Behind Food and Disease” section located in the upper right sidebar contains unique Blogs that focus on specific concerns (Specific Diseases such as Autism, Diabetes, Alzheimer’s, Rheumatoid Arthritis, Lupus etc), Digestion, Whole Food,  Microbiome, Toxins, Clinical Trials: Diet/Environment/Disease, Resources, etc ).  The unique Blogs offer current science as it relates to microbiome, health and wellness for these specific concerns.

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Hoping the tools on my website help you find empowerment in realizing and implementing “food can be thy medicine”.

In good health through increased awareness,





  Last updated: February 19, 2017 at 6:29 am  to add in recipe links.  Prior update March 26, 2016 was for SEO optimization.


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

    This Danish study, “Richness of human gut microbiome correlates with metabolic markers,” at (or read the University of Copenhagen scientific article “One in four has alarmingly few intestinal bacteria” at: ) showed that one 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”:

    The study, “Diversity, stability and resilience of the human gut microbiota,” at: noted some dire consequences and ramifications of the altered and depleted microbiome status such as being associated with obesity6,7, malnutrition8, inflammatory bowel diseases (IBD) 9,10, neurological disorders11, and cancer12. (see article for interacting links).

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