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Rainforests are not just places you visit!


When it comes to gut flora, the more research I do on this subject, the more clear it becomes that we have just scratched the surface of understanding what this organ does for us. And no, the word “organ” is not a typo.

If we define an organ as a body structure that contributes to, and affects various bodily functions, and whose dysfunction results in ill health, then our micoflora certainly meets the definition. In fact, one of my favorite scientific papers is titled The Gut Flora as a Forgotten Organ and is well worth a read if you have the time.

However, as with many things in this fast-moving world of research, there is a glaring error in that paper when the authors restate the dogma that babies only acquire their gut flora after birth. This is not true as explained here.

Such accepted beliefs are continually being challenged by new findings about this amazingly complex ecosystem. However, one hypothesis that is gaining foundational stability in the shifting sands of microbiome science is the discovery that the more diverse your gut flora, the better your health is apt to be.

This brings me to a recently published paper. (1) These researchers analyzed the gut microbial composition of 123 non-obese, and 169 obese, Danish citizens to evaluate what differences, if any, existed between them.

What they discovered was that persons with less bacterial diversity were far more prone to gaining weight, developing type-2 diabetes, having abnormal cholesterol values and exhibiting increased inflammatory markers in contrast to those with a more diverse gut flora. The characterization of low versus high bacterial diversity was made by assessing the relative abundance of genetic material from gut microbes contained in stool samples.

Now, in the past I’ve criticized some research findings that relied solely on stool samples to diagnose conditions that may be affecting health. What appears in feces is most likely to reflect what exists in the lumen of the digestive tract, and not necessarily what is attached to the gut wall. This is doubly true if what is causing mayhem at the level of the enterocytes is encased in a biofilm.

However, when it comes to assessing overall bacterial diversity, I have no reason to doubt the findings of this study. Various disease states have been consistently associated with low bacterial diversity. (2) (3) (4) (5)

Nevertheless, keep in mind that failure to biopsy the gut wall at various locations likely left these researchers with a less than complete picture of the microbial populations inhabiting these people. A further limitation is that even it they had biopsied, many bacterial species that exist in our gut cannot be cultured or identified.

Nor does it seem that any effort was made to catalog diversity in native fungal or viral constituents. While many of you are aware that fungi naturally inhabit the gut, native viruses are also present and are collectively termed the gut virome. (6) As I said at the top of this post, this is a very complex organ.

Returning to the study, after genetic sampling individuals with fewer than 480,000 bacterial genes were classified as having a low gene count (LGC), and consequently described as having a less diverse gut flora. Those with higher counts were classified as high gene count (HGC) individuals and having a more diverse gut flora.

Distinct differences in bacterial composition were noted between groups. In the LGC group, the following genera of bacteria were most commonly found:

  • Bacteroides
  • Parabacteroides
  • Ruminococcus
  • Campylobacter
  • Dialister
  • Porphyromonas
  • Staphylococcus
  • Anaerostipes

In the HGC group, the following bacteria were most abundant:

  • Faecalibacterium
  • Bifidobacterium
  • Lactobacillus
  • Butyrivibrio
  • Alistipes
  • Akkermansia
  • Coprococcus
  • Methanobrevibacter

I’m sure some of you are familiar with a few names on this list, namely Bifidobacterium, Lactobacillus and Akkermansia.

On a species level, Clostridium bolteae, Clostridium symbiosum, Clostridium clostridioforme, Clostridium ramosum and Ruminococcus gnavus were most prevalent in the LGC group. In contrast, Faecalibacterium prausnitizii, Roseburia inulinivorans, Corprococcus eutactus and Methanobrevibacter smithii were most abundant in the HGC group.

The low gene count group were also found to have higher levels of certain metabolites indicative of inflammation and oxidative stress. This makes sense as gut dysbiosis is synonymous with inflammation.

The high gene count group had low inflammatory markers. They also produced more short-chain fatty acids, i.e. lactate, propionate and butyrate. You know, the substances produced by bifidobacteria when fermenting prebiotics. They also exhibited higher hydrogen gas production than the LGC group.

Putting a number of observations together, these researchers noted that those with less diverse gut flora were more prone to:

  • gaining weight
  • having gut flora less capable of producing butyrate, a short-chain fatty acid absolutely vital for nourishing gut epithelial cells and maintaining gut-wall integrity
  • having increased degradation of the protective mucus layer lining the gut wall, along with lower quantities of the bacteria Akkermansia muciniphila
  • having reduced hydrogen and methane production, yet increased production of hydrogen sulphide, a broad-spectrum poison
  • having an increased abundance of both Campylobacter and Shigella, two types of gram-negative gut pathogens rich in inflammation-provoking lipopolysaccharides
  • having higher levels of oxidative stress brought about by inflammation

Apart from difficulty maintaining a healthy weight, the LGC individuals also exhibited higher leptin levels, decreased adiponectin, insulin resistance, high fasting glucose, high levels of triglycerides and free fatty acids, decreased HDL cholesterol, increased C-reactive protein and higher white blood cell counts. As these researchers concluded:

“Together, these analyses suggest that the LGC individuals are featured by metabolic disturbances known to bring them at increased risk of pre-diabetes, type-2 diabetes and ischaemic cardiovascular disorders. We propose that an imbalance of potentially pro- and anti-inflammatory bacterial species triggers low-grade inflammation and insulin resistance.”


Courtesy: Richness of human gut microbiome correlates with metabolic markers

Courtesy: Richness of human gut microbiome correlates with metabolic markers


This graphic encapsulates the findings for those most likely to develop metabolic syndrome. Items outlined in red show increases in specific bacterial groups as well as physiologic effects unique to this cohort. Those in green show decreases in these same characteristics. Potential causes or drivers of metabolic dysfunction are outlined in yellow.

As for the drivers of these effects, I want to highlight three: repeated antibiotic (AB) treatment, diet and our old friend, endotoxemia.

Antibiotic use has saved an untold number of lives and much of modern medicine, including surgery, would be impossible without these wonder drugs. The medical community is now grappling with an unsettling future where more and more bacterial pathogens have developed resistance to the current crop of antibiotics. This is a crises that will affect all of us.

However, apart from encouraging the development of antibiotic-resistant strains through evolutionary adaptation, a less often recognized side effect of antibiotic use has been their potentially devastating impact on native gut flora, particularly when these drugs are taken over extended time periods. There is no doubt in my mind that the multi-decade overuse of antibiotics has devastated the gut flora of millions, especially those in the developed world.

And this devastation is not confined to the current generation. Newborns acquire their gut flora from their mothers both before and after they are born. Sadly, many children are paying the price for the indiscriminate use of these agents both at an early age and as a consequence of overuse in their mothers before conception. While I reject any monocausal explanation for gut dysbiosis, the overuse of antibiotics is certainly a major contributing factor that needs to be addressed.

The two other elephants in the room are of course diet and endotoxemia. Neither can be separated from the other. Clearly, a diet devoid or nearly devoid of the prebiotic fibers beneficial organisms thrive on is highly likely to increase the risk of gut pathogens colonizing sections of the gut wall. And a diet lacking fermented foods rich in beneficial organisms that can help replenish and strengthen existing gut flora colonies is also one that would encourage the development of dysbiosis over time.

Confirmation on the importance of diet in shaping gut flora was the discovery in this study that the gut bacteria most likely to be found in lean, healthy Danes were all butyrate producers. Bifidobacteria are especially prolific at producing butyrate.

As I’ve said, the more butyrate your bacteria produce as a result of fermenting prebiotics, the healthier the cells lining your digestive tract are going to be. And the healthier these cells, the less likely your body’s immune and hormonal systems will have to grapple with inflammatory cascades caused by increased intestinal permeability.

Before I wrap this post up, I have to say I was especially happy to read the following qualification that rarely, if ever, makes it into an American research paper about obesity:

“Contemporary lifestyle is associated with a tide of metabolic abnormalities characterized by a core of excessive body fat accumulation. However, obesity is not just obesity. Some obese individuals seem to have a benign prognosis, whereas others progress to co-morbidities such as type-2 diabetes, ischaemic cardio- and cerebrovascular disorders, and non-alcoholic liver disorders. [emphasis mine] It is also recognized that human obesity in the context of pathogenesis, pathophysiology and therapeutic responsiveness is a heterogeneous condition. The present report provides evidence that studies of alterations in our other genome— the microbial gut metagenome—may define subsets of adult individuals with different metabolic risk profiles and thereby contribute to resolve some of the heterogeneity associated with adiposity-related phenotypes.”

Well said. I can’t emphasize enough that what a person weighs is but one factor among many that need to be looked at when evaluating health. Many mistakenly assume that the normal weight are immune to the health-robbing effects of gut dysbiosis. Far from it. Any thin person who has grappled with celiac disease, irritable bowel syndrome, small intestinal bacterial overgrowth, ulcerative colitis, Crohn’s disease, insomnia, anxiety or depression knows that leanness is no defense against ill health.

The take-home message here remains the same. Cultivate the microbial “garden” hidden within you to stay healthy. Include prebiotic fibers from your diet and/or supplements to “fertilize” them and keep them happy. Introduce new probiotic organisms to your digestive tract daily via supplementation and/or the inclusion of fermented foods.

This advice is especially important for those already dealing with metabolic derangement. Yes, a healthy weight and exercising are good. Nevertheless, given how sadly common it is for many to re-gain the weight they just lost, concentrating solely on weight management is likely to prove insufficient if you don’t also address underlying dysbiosis. And even if the weight remains off, this is still no guarantee that any gut flora imbalances are resolved if doing so results in little to no improvement in health.

And please try as best you can to avoid decimating beneficial gut bacteria unnecessarily. If your doctor tells you you have a viral infection, don’t insist that they prescribe a useless antibiotic “just in case.” Trust me, you are not doing yourself any favors. And stay far, far away from physicians who write scripts for antibiotics without first confirming the presence of a treatable infection.

The same holds true for undergoing unnecessary surgery. This recent Bloomberg piece on cardiac stent surgery is chilling in its own right. The fact that antibiotics were prescribed after these procedures to prevent post-operative infections, decimating beneficial gut flora in the process, adds another layer of insult to injury that the authors of this article fail to even acknowledge.

We can never be healthy unless our beneficial gut bacteria is thriving. Period. Once again, anyone who claims otherwise is delusional.

The findings of this study reinforce the existing hypothesis that a healthy gut flora resembles a rainforest. So do yourself a big favor and slip on those imaginary gardening shoes, gloves, apron and floppy hat and get cultivating so you too can harvest the most important crop of all: good health.


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