Bacterial Dominance Shift Long Term Diet

Preserve & Restore Loss of Microbiome Diversity is Aggressive Preventative Medicine

SUMMARY:  Aggressive Preventative Medicine means preserving the microbiome you have and restoring any loss incurred.  See how far that thought goes with your doctor!  Diet really does work to alter the microbiome and can help to restore loss of microbiome; for example, fermented kimchi actually positively impacted metabolic syndrome factors including systolic and diastolic blood pressures, percent body fat, fasting glucose, and total cholesterol.  

⇒⇒  This post teaches how to reduce the loss of microbiome diversity and restore such – crowding out concept.

⇒⇒  How much microbiome abundance and diversity we have lost with references to citations for such loss for asthma, diabetes, metabolic syndrome, obesity, and IBD but drop down the menu over on the right sidebar for microbiome impact for other diseases.  Americans tend to have far less microbial diversity in their guts, which raises their risk of obesity, metabolic dysfunction, and all sorts of inflammatory disease.

⇒⇒  Includes a small FMT discussion.  FMT transplants a new microbiome.  CDiff cure is over 90%, and Crohn’s disease (small cohort study) showed remission.

2 prongs for Aggressive Preventative Medicine:  preserve and restore loss of microbiome:
  1. Preserve the microbiome you have: Common muggers include infant mode of feeding (breast or formula), and infant mode of birth (vaginal or C-section), medications (“microbes can activate or inactivate drugs, generate toxic byproducts of drug metabolism, and alter drug metabolism by human cells in both direct and indirect ways”; do your research), chlorinated water, and antibiotics:

    Additional Muggers include those shown on the below slides. Lastly, CDC recent investigations reveal that the source for deadly gut antibiotic resistant CDiff infections (these result in disrupted microbiomes where fecal microbiota transplantation   is >90 percent cure) as not just hospital acquired, rather medical offices including dental may be infection sites, see CDC investigates deadly bacteria’s link to doctors’ offices: a 2013 study, researchers found C. diff present in six out of seven outpatient clinics tested in Ohio, including on patients’ chairs and examining tables... patients should wash their hands after visiting the doctor’s office — with soap and water, because alcohol-based gels don’t get rid of C.diff.”

2.  Restore the microbiome eating a whole foods diet which increases fiber to nudge favorable bacteroides, prevotella to fermicutes ratios and competitively crowd out and secure beneficial microbiota using pre- and probiotics in live whole fermented foods.  This post shows what is in a healing nutrient dense whole foods fridge.

How powerful is diet and disease?  

This review addresses four factors that may be involved in IBS which exceeds 70 percent successful management when eating a whole foods FODMAP type diet:

» Gut microbiota composition,
» Increased intestinal permeability,
» Imbalance in the enteroendocrine system, and
» Perturbed immune system in the gut.

Gut healing diets include SCD, GAPS, AIP, FODMAP, and PALEO, and these seem to work by nudging the microbiome.  For example:

The success of SCD (a whole foods type diet) is partially explained by the competitive crowding out mechanism

The study, Diet and Inflammatory Bowel Disease, Review of Patient-Targeted Recommendations, evaluated the role of popular diets for IBD (SCD, FODMAP, PALEO) and concluded that patient success can be enhanced using a food/symptom type journal to learn food intolerance for IBD. 

In particular, eating SCD for 30 days (at about 80% compliance) caused Faecalibacterium prausnitzii increase for IBD-Crohn’s. IBD CROHN’S: SCD INCREASED MICROBIOME DIVERSITY BUT LOW RESIDUAL DIET REDUCED DIVERSITY SCD, see allowed foods here, is a grain-free, lactose-free, and  sucrose-free diet. It is almost a paleolithic diet when you look at the components; that is, there’s meat, fish, poultry,  fruit, vegetables, nuts. seeds, and some honey.  Aged lactose-free cheeses, yogurt, and fermented vegetables, all of which teem with live diverse probiotics, are included. This post details what’s in SCD yogurt and sauerkraut, and see here to learn that cheese is created by orderly successions of microbial communities that produce compounds responsible for cheese flavor… Each piece [of cheese] contains as many as 10,000,000,000 or 10 billion microbes.  Further details are below in the section titled How to practically “see” your gut microbiome? See the microbiome of the cheese you eat for an example.”

Eating SCD results in competitive crowding out to occur in the gut resulting in F. prausnitzii bloom which happens to be a major player in gut health as it protects against pathogen invasion, modulates the immune system, is an acetate consumer, and is a producer of substantial quantities of butyrate as well as high amounts of antioxidant compounds. Details are in posts: NICE, SCD INCREASED F. PRAUSNITZII… HUGH?!? and IBD CROHN’S: SCD INCREASED MICROBIOME DIVERSITY BUT LOW RESIDUAL DIET REDUCED DIVERSITY.  Even the IBD medical community finally has acknowledged diet impact in it’s last annual Dec. 2014  Advances in IBD conference, IBD CAM “Probiotics, Special Diets [SCD], and Complementary Therapies:  We Know Patients Want Them, So What Do We Tell Them?The presentation by Dr. Sandra Kim, MD, noted, “SO CERTAINLY THERE IS SOME PROMISE IN AT LEAST THINKING ABOUT THIS.” 

embellishment7Bottom line:  There really is disease activity indices improvement and mucosal healing taking place with these modalities.embellishment7

This microbiome skew due to diet finding is rather amazing but makes sense now that you understand that the gut is an ecosystem which will adjust based on what it is fed. Actually, SCD/GAPS/FODMAP/PALEO all have crossover foods and one can start using any of the diets and tweak them for your individual tolerances once gut healing occurs. So a PALEO eater might actually learn that they can add in yogurt (as does Mark Sisson) or a SCD eater might find that they can add in sweet potatoes (a PALEO allowed food) or sprouted quinoa (sprouting is a Westin A. Price Foundation tenet increasing digestibility and nutrient absorption, see WAPF Pinterest Board.)  Also tweak the Whole Health Pillars to improve immunity and gut health (see below slide.) Consider using a food journal to discover your intolerance(s) (input foods and reactions), which looks like this:

embellishment7A word of caution:  I don’t want you to think the solution is to eat a whole lot of something to bloom a particular microbe.  It’s all about diversity and balance, not a few ideal microbiota. embellishment7No cocktail multi strain probiotic someone invents can ever reproduce and replicate the human microbiome diversity. Instead try live fermented foods which contain multi strain bacteria (but note: yogurt typically only contains a few strains whereas fermented vegetables contains many… see the section, “What’s in that SCD yogurt and sauerkraut anyway… bacteria wise???”)   Also worth noting, if it is truly a live probiotic rich food, a serving size is only a condiment size (or forkful) once to several times each day.  What does that say about your ordinary off the shelf 8 oz commercial yogurt?embellishment7 Whole Foods sourced Probiotic bacteria:  Do they colonize the gut or are they transient?  

Honestly, the science does not yet know how long probiotics remain in the gut. Probiotics seem to competitively crowd out and balance the microbiome. In other words, they don’t repopulate the gut so consumption should be long term.  Anecdotal, it seems that 2 or 3 days beneficial effects are realized by a host regularly consuming such once they stop ingestion. For many, regular consumption means daily, though frequency is to be tweaked as well.

Dr. Rob Knight’s Microbiome Reddit explains transiency of yogurt based probiotic bacteria:

[–]Dr_Onion_Rings :  We’ve all heard about the benefits of live active culture foods like yogurt. When I consume a cup of yogurt, do its microbial denizens actually take up residence in my guts for any significant amount of time, or are their beneficial functions carried out as they are “just passing through?”

[–]DrRobKnight[S]:  It depends on the yogurt. Many of them have strains that are specifically selected not to establish in the gut (for regulatory reasons, and/or because they want to keep selling you the yogurt). However, even bacteria that don’t establish in the gut may have a beneficial effect on their gut bacteria while passing through.

Do your homework for which probiotic to use.  

For IBD, Dr. Leo Galland noted in the Autoimmune Summit that he almost never give[s] lactobacilli [SCD yogurt] to patients with Crohn’s disease. Bifidobacteria may be a bit different, because they’re more anti-inflammatory than lactobacilli, so I’ll occasionally use them.  But the probiotic that has the best track record in IBD, especially in Crohn’s, is actually, strangely enough, a yeast: saccharomyces boulardii, which the French call “yeast against yeast”. Saccharomyces boulardii has some very profound immune-stimulating activity. But it has very profound anti-inflammatory effects in the gut. So I especially like it for people with diarrhea.”  I suspect similar preference of probiotic strain variances hold true for other autoimmunes and chronic disease.  Additionally, note that Bifidus (contained in most commercial yogurt) is not legal for SCD/GAPS due to propensity of overgrowth in IBD compromised gut ecosystems.

embellishment7In conclusion, tweak and individualize probiotic, type (dairy and vegetables), dosing, and frequency.embellishment7Tip: you can travel (including TSA board) with a probiotic needing refrigerated with a doctor’s script; I use frozen squash soup in a 4 cup  Ziploc container (see Pinterest Soup Board) as ice keeping all cold for full day east to west coast travel.

Transient Probiotics Chart

How Probiotics Modulate the Gut; much yet to be learned

A metagenomics focus: When a probiotic is introduced into the gut, the precise mechanism(s) of action of probiotics has not thus far been clarified. Potential mechanisms to consider include: (1) modulation of GI immunity by altering inflammatory cytokine profiles and downregulating proinflammatory cascades or inducing regulatory mechanisms in a strain-specific manner; (2) displacement of gas-producing, bile salt-deconjugating bacterial species and thus possibly inhibiting pathogenic bacterial adherence; (3) alteration of bacterial flora by acidification of the colon by nutrient fermentation; (4) enhancement of epithelial barrier function; (5) induction of µ-opioid and cannabinoid receptors in intestinal epithelial cells; (6) reduction of visceral hypersensitivity, spinal afferent traffic, and stress response. [Borchers et al. 2009; Lin et al. 2008; Vanderpool et al. 2008; Lawton et al. 2007; Quigley and Flourie, 2007; Rousseaux et al. 2007; Yan et al. 2007; Focareta et al. 2006; Makras et al. 2006; Roselliet al. 2006; Candela et al. 2005; Collado et al. 2005, 2007; Cotter et al. 2005; Matsumoto et al. 2005; Patonet al. 2005; Sherman et al. 2005; Smits et al. 2005; Sturm et al. 2005; Hart et al. 2004; Mukai et al. 2004;Pathmakanthan et al. 2004; Servin, 2004; McCarthy et al. 2003; Pena and Versalovic, 2003; Borruel et al.2002].

embellishment7This complexity is why I always prefer a whole foods diet and live probiotic whole foods such as SCD lactose free yogurt and vegetable ferments for optimizing the microbiome.   Note:  This is not a quick fix; long term diet is needed to overcome microbiome resilience and optimize the microbiome.
How Much Diversity Have We Lost?

The average American has lost 1/3 of their diversity.  Another study estimates 1 in 4 have 40% less bacteria.

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.

Estimates in the US report even greater loss of diversity:  “We estimate we [US] have lost about a third of the diversity of our microbes,” said Maria Gloria Dominguez-Bello, associate professor of medicine at NYU. –Can we save our body’s ecosystem from extinction?  and Microbirth Documentary.  Incredibly, the C-Section microbiome is less diverse and differs from vaginal birth with long term health implications, see “MICROBIRTH” EVERY PARENT NEEDS TO VIEW:

Babies born by Caesarean Section have a microbiome that differs from vaginal birth and 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.

How to practically “see” your gut microbiome? See the microbiome of the cheese you eat for an example.

Cheese is created by orderly successions of microbial communities that produce compounds responsible for cheese flavor… Each piece of cheese contains as many as 10,000,000,000 or 10 billion microbes… The added starter cultures dominate the cheese microbiota, establishing conditions that select for the next microorganisms that will be capable of thriving in the changing cheese matrix. The starter culture changes the cheese microenvironment, affecting a variety of factors, including pH, redox potential, levels of organic acids such as lactate and acetate, and other nutrients. As some of the lactic acid bacteria (LAB) within the starter culture begin to die, the cells release enzymes that further break down milk proteins, mainly casein, to small peptides and amino acids. In fact, these dead starter culture cells and debris are an important food source for subsequent generations of microbes, referred to as non-starter lactic acid bacteria (NSLAB). If the starter culture is not dying, then the cheese is not growing. Precisely which organisms will comprise the second and future microbial ecologies (this process is called microbial succession) will depend on conditions such as salt concentration and nutrients present, and which microorganisms are present (either intentionally added or contaminants) in the evolving cheese matrix...

  • The smell of a cheese depends on microbial and enzymatic activities changing the casein and fats in milk and also on the microbiota associated with a cheese variety further refining those aromas as the cheese ripens. In general, the more extensively the casein and milk fat are broken down, the stronger the aroma of the final cheese product… the distinctive aroma of Cheddar cheese is due to more than 500 different compounds produced by the microbes that are used in producing this cheese.
  • The occurrence of pathogens in cheese that cause disease in humans is very rare; some cheeses such as Parmigiano-Reggiano, English Cheddar, and Gruyère, that do not support the growth of pathogens if correctly manufactured. These cheeses are dry, acidic (low pH), and have a high salt content, all traits that inhibit pathogen growth.
  • The FDA has regulatory jurisdiction over cheese and stipulates that cheese be made in one of two ways: 1. Use milk that is pasteurized to FDA standards. 2. If made from raw (unpasteurized) milk, cheese must be aged for a minimum of 60 days at a temperature no less than 35°F.  Microbes Make the Cheese, A Report from the American Academy for Microbiology

Questions still unanswered for fermented cheese microbiome:

  1. What are the pre- and probiotic properties, if any, of the microorganisms in cheese?
  2. How do the microbes within cheese interact with the natural microbiota of the human gut and can cheese be used to assist in maintaining a healthy gut microbiota?
Loss of microbiome diversity means bad things can happen: Microbiome skew for Asthma, Diabetes, Metabolic Syndrome, Obesity, and IBD

That the subglottic airways are not sterile, as was once believed, but are populated by a distinct “bronchial microbiome,” is now accepted. Also accepted is the concept that asthma is associated with differences in the composition of this microbiome. What is not clear is whether the differences in microbial community composition themselves mediate pathologic changes in the airways or whether they reflect differences in systemic immune function driven by differences in the development of the gastrointestinal microbiome in early life, when the immune system is most malleable. The respiratory microbiome and innate immunity in asthma (delayed release till January, 2016), and The microbiome in asthma.


In the US, by 2050, one in three will have Diabetes.  That Data Dude created this interactive map showing the percent of the current population that has been diagnosed with diabetes, according to the U.S. Centers for Disease Control and Prevention.

The paper, Before the onset of type 1 diabetes, gut community diversity plummets and markers of inflammation increase, is insightful as it showed that before the onset of Type 1 Diabetes, gut community diversity plummets and markers of inflammation increase:

Gut diversity plummets before T1D diagnosis
source: The Dynamics of the Human Infant Gut Microbiome in Development and in Progression toward Type 1 Diabetes,
Metabolic syndrome and obese microbiome:  Resultant physiological factors is positively impacted by increasing probiotics (whole foods live fermented Kimchi):

Accumulating evidence suggests relationship of compositional changes of gut microbiota with onset of metabolic disorders and obesity:

Conclusions of 2011 study: Ingestion of fermented kimchi had positive effects on various factors associated with metabolic syndrome, including systolic and diastolic blood pressures, percent body fat, fasting glucose, and total cholesterol, compared with the fresh kimchi. These results suggest that the maturity of kimchi (fresh vs fermented) may affect obesity, lipid metabolism, and inflammatory processes..

…significant decreases in body weight, body mass index, and body fat in both groups, and the fermented kimchi group showed a significant decrease in the waist-hip ratio and fasting blood glucose. Net differences in the systolic blood pressure, diastolic blood pressure, percent body fat, fasting glucose, and total cholesterol in the fermented kimchi group were significantly greater than those in the fresh kimchi group. There was also a tendency for a decrease in fasting insulin after consumption of fermented kimchi. -Fermented kimchi reduces body weight and improves metabolic parameters in overweight and obese patients.

Conclusions of 2015 study: Twenty four obese women were randomly assigned to either fresh or fermented kimchi group for eight weeks of kimchi intervention. Pyrosequencing of fecal microbiota and microarray analyses of blood samples revealed that fresh and fermented kimchi interventions exerted differential effects on the obesity-related clinical parameters. Correlations of these effects with changes in blood gene expression and gut microbial population were more evident in the fermented kimchi group than the fresh kimchi group. Contrasting effects of fresh and fermented kimchi consumption on gut microbiota composition and gene expression related to metabolic syndrome in obese Korean women.

Summary of IBD microbiome research

Kristina Campbell, a science writer specializing in microbiota who writes regularly for Gut Microbiota for Health and blogs at The Intestinal Gardener, summarizes the latest IBD microbiome research here: 

The exact role of the microbiota is still unclear.  Are IBDs:

  • caused by having a disrupted microbiota,
  • the result of some ‘perfect storm’ of genes & microbiota, or
  • do the microbiota have no causal role to play, simply changing in response to the onset of an IBD?

Some studies have found differences in microbiota composition between those with IBD and healthy controls – that is, certain bacteria are over-represented or missing in the IBD cohort. But these say nothing about causality (let alone accounting for variability of each person’s microbiota over time), so they’re only the beginning of the story.

Furthermore, geography seems important.   The study, Geographical patterns of the standing and active human gut microbiome in health and IBD examined those with IBD across European (Germany, Lithuania) and South Asia (India) countries and found distinct patterns of microbes in IBD sufferers from each location, but also some microbial biomarkers for IBD that held across all geographic locations (a decrease of Faecalibacterium).

Another avenue of research is examines the interplay between genes and microbiota in IBD. Complex host genetics influence the microbiome in inflammatory bowel disease looked at genetic data and microbiome data from those with IBD and found that they weren’t completely independent: genes and bacteria interacted in complex ways, and both are potentially involved in causing IBDs.IBD_Host factors associated with the IBD microbiome, GenomeMed. 2014; 6(12);107

One more factor may be important in the IBD story: what products the microbes make. As microbes go about their metabolic activities in the gut, certain byproducts may have an effect on health outcomes. Some new research, Jonathan Braun on metabotypes and IBD,  posited that everyone falls into one of two modes of metabolic activity, or ‘metabotypes’, and almost without exception, those with Crohn’s disease have metabotype two.

Since the microbiota are somehow involved in IBDs, FMT has emerged as a possible way to ‘reboot’ the microbiota and possibly quell symptoms. Some, as described in this article, have already been regularly self-administering FMT with good results. The scientific literature, though, has been slow in coming.  This pilot study was recently published in which Chinese doctors treated patients with refractory Crohn’s disease with a single FMT treatment and followed up for a minimum of six months. The immediate effects and high success rate of the treatment should encourage more research studies on the topic.

FMT:  No cocktail probiotic multi strain someone invents can ever reproduce and replicate the human microbiome diversity. Enter FMT and Public Policy Concerns:

Scientists still don’t yet really know exactly what’s in feces since in addition to bacteria there are viruses and phages and friendly parasites that haven’t even been identified yet. This is why some view FMT from a healthy donor (no antibiotic 3 or 6 months prior [this number constantly is questioned as we learn there is long term impact of antibiotics on microbiome for some, if not many], mood swings, depression, overweight, disease, allergies, no constipation or diarrhea… the list goes on and pre-requisite criteria is quite incredible) as the best since no cocktail probiotic multi strain someone invents can ever reproduce and replicate the human microbiome diversity. The very complex microbiome is additionally individualized depending on your birth, environment, type of food you eat, antibiotic history. drug interaction, in utero nutrition and toxin exposure...  

Fecal microbiota transplantation has >90 percent cure for antibiotic resistant CDiff.  FMT recently was proven effective with Crohn’s clinical trial –see Seattle child study discussed below. Despite this, FMT is approved in US only for CDiff that fails many antibiotic treatments, thus the microbiome is decimated by lots of antibiotics.

A clear example where microbiota collapse is the underlying cause of disease: Clostridium difficile infection (CDI). The circumstances that give rise to CDI usually reflect collateral damage on the gut microbiota brought about by incidental antibiotic use, which allows C. difficile to proliferate and thrive without a healthy microbiota to regulate its expansion.11 Because the treatment for CDI is further antimicrobial therapy with either oral vancomycin or metronidazole, it is not surprising that the infection can recur, and a vicious cycle of pathogen expansion followed by antimicrobial suppression (but not clearance) can ensue.11 The ability of FMT to rapidly and effectively clear infection and cure disease, even in recalcitrant cases,12 is a clear indication of the power of the microbiome in the restoration of health.The microbiome: what it means for medicine, British Journal of Medical Practice, Dr. Emma Allen-Vercoe,, Editorial.

Crohn’s clinical trial –see Seattle child study

Not withstanding complexities, in March 2015, Seattle Children’s Hospital reported that nine teenagers with mild to moderate Crohn’s were given FMT using as donor, their parent who did not have CD.  7 of the 9 teenagers went into remission;  5 children still in remission 12 weeks after the treatment.  Crohn’s and Colitis Foundation reported on this study,  Fecal Microbial Transplant Effect on Clinical Outcomes and Fecal Microbiome in Active Crohn’s Disease, also see here, which was published in Inflammatory Bowel Diseases: March 2015 – Volume 21 – Issue 3 – p 556–563.   

Limited US regulations restrict FMT only for CDiff after multiple antibiotic treatments fail — in essence the microbiome is nuked not to mention the years of agony endured.  Thus many resort to DIY FMT for: C. diff, obesity, Crohn’s disease, ulcerative colitis, autism, diabetes, depression and multiple sclerosis.  It is estimated that in 2014, well over 10,000 were performed compared to 1,500-2,000 FMT procedures following lawful regulations. DIY instructions are available online on websites such as The Power of Poop.  Some US citizens choosing FMT for conditions other than CDiff, fly to the UK, Argentina & Australia to undertake FMT.  Some reference interviews with researchers overseas performing FMT for non-CDiff purposes:

  1. Interview with Dr Silvio Najt — Treats IBD and IBS using FMT. Lots of details… he advocates not nuking gut pre-treatment.
  2. London Letter: Clinic pioneers treatment for gut illness — Discusses Taymount Clinic in Hitchin, a commuter town in Hertfordshire, outside London, is moving home to Letchworth shortly, due to an increase in demand from patients.

Whatever the risks of medically supervised FMT, arguably they seem comparable, if not less, than the drugs being prescribed by doctors for these conditions (anti-TNF, biologics…) Conflicting opinions range from this Gastroenterology & Endoscopy comment, Science Should Steward Fecal Transplants (advocates that clinics support DIY FMT using as precedent the model of clinics set up to supervise heroin injections,) to industry position, Mark Smith founder of OpenBiome, emphasizing the need for evidence based clinical trials for non-CDiff use. 

What do I conclude for Aggressive Preventative Medicine, meaning preserve the microbiome you have and restore any loss incurred?  
For Plan A:  JUST EAT REAL WHOLE FOOD, SOME HAVING LIVING REAL PRE and PROBIOTICS and take action to preserve the microbiome you have.

Last updated: July 3, 2016 at 12:05 pm for SEO optimization.

In health through awareness,