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Gut Bacteria

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  • Differences in microbial communities have been detected among obese people and lean people, patients with non-alcoholic fatty liver disease and healthy patients, and much more
  • The same species of bacteria may act differently in different people and may even have a drastically different genetic make up
  • Research suggests it’s not only the species of bacteria that is important but also what each microbe produces that matters
  • Some microbes produce anti-inflammatory molecules or vitamins while others speed the conversion of calories you eat into body fat

You Are What Your Microbes Eat

September 02, 2015 | 80,564 views
| Available in EspañolDisponible en Español

By Dr. Mercola

While it’s long been said that “you are what you eat,” a more accurate description might be “you are what your microbes eat.” There are more bacteria and other microorganisms in your body than there are human cells, and your unique microbial community is constantly changing in response to your environment.

In fact, a new diet can rapidly reshape the microbes in your gut, which has implications not only for your digestive health but far beyond this to your weight, risk of chronic diseases, and more. According to research published in the journal Nature, such changes may occur in as little as one day:1

“… [S]hort-term consumption of diets composed entirely of animal or plant products alters microbial community structure and overwhelms inter-individual differences in microbial gene expression.

The animal-based diet increased the abundance of bile-tolerant microorganisms (Alistipes, Bilophila, and Bacteroides) and decreased the levels of Firmicutes that metabolize dietary plant polysaccharides.”

Gut microbes known as Firmicutes have been detected in higher numbers in obese individuals, who also may have 90 percent less of a bacteria called bacteroidetes than lean people.2

It’s been suggested that altering gut bacteria could therefore play a role in obesity, although a computer analysis led by Katherine Pollard, a biostatistics professor at the University of California, San Francisco suggests it’s much more complex than that.

What Your Microbes Produce Matters…

While it’s becoming increasingly clear that microbes play an integral role in your health, it’s not only the phylum or species of bacteria that matter.

Research by Pollard and colleagues suggests the same species of bacteria may act differently in different people, but most studies don’t get into that fine level of detail.

Pollard’s research suggests it’s not only the species of bacteria that is important but also what each microbe produces that matters.

For instance, some microbes produce anti-inflammatory molecules or vitamins while others speed the conversion of calories you eat into body fat.3 Further, the same species of bacteria may have vast genetic differences. NPRreported:4

“‘Individual microbial species can have widely variable genomes,’ says William Anton Walters, a researcher in molecular biology and genetics at Cornell University. Any given bacterium may share less than half of its genes with another member of the same species.

These genetic differences, rather than phylum or even species designations, Walters says, ‘could explain the differences between the obese and lean gut microbiota.’”

So while there’s clearly a connection between gut bacteria and obesity, researchers are still trying to pin down exactly what that connection is. In the meantime, intriguing studies continue to be published.

Preliminary research from the Netherlands, for instance, has even revealed that transplanting fecal matter from healthy thin people into obese people with metabolic syndrome led to an improvement in insulin sensitivity.5

What is known is that obesity rates have been increasing steadily over the last several decades, and it appears to be a much more complex issue than the simple “calories in, calories out” explanation promoted by the USDA.

Metrocosm’s Max Galka put together a clear example of how obesity rates in the US keep rising, and its pervasiveness suggests a variety of factors, from gut bacteria to environmental chemicals, are likely to blame. Check out the revealing graphic below.6

Liver Disease Linked to Gut Bacteria

While the role of your gut bacteria on your weight continues to be explored, so, too, does its role in other chronic diseases, including liver disease – specifically non-alcoholic fatty liver disease (NAFLD).

Differences in gut microbiota between people with NAFLD and lean individuals have been detected. Those with NAFLD are also more likely to have bacterial overgrowth in the small intestine along with increased intestinal permeability.

In one study by researchers from the National University of Ireland, NAFLD patients were found to have over double the frequency of small intestine bacterial overgrowth compared to the healthy patients.7

Bacterial overgrowth refers to the growth of an excessive amount of pathogenic microbes, which release waste products known as endotoxins (which travel through your intestinal walls and eventually must be filtered by your liver). This becomes an even greater issue if you have increased intestinal permeability, or leaky gut, as it allows more of the waste products to enter your bloodstream.

It makes sense, then, that restoring the health of your gut with probiotics to balance out the bacterial overgrowth would be beneficial to NAFLD patients, and this is what the research suggests. According to the World Journal of Hepatology:8

“… [S]ome data indicate that the immunoregulatory effects of probiotics may be beneficial in NAFLD treatment as they modulate the intestinal microbiota; improve epithelial barrier function and strengthen the intestinal wall decreasing its permeability; reduce bacterial translocation and endotoxemia; improve intestinal inflammation; and reduce oxidative and inflammatory liver damage.”

Further, one of the most severe effects of eating too much sugar is its potential to wreak havoc on your liver, including causing NAFLD. Excess sugar will also upset the balance of bacteria in your gut, making it easier for pathogenic strains to flourish…

Scientists Are Increasingly Studying Microbes to Understand Human Health and Disease

Researchers from MIT are undertaking the so-called “Underworlds” project beginning this year. They intend to test Boston-area sewage for the presence of viruses, bacterial pathogens, and pharmaceutical and illegal drugs. As the Boston Globe reported:9

Data on such substances could predict epidemics or tell when they’re waning. They could also demonstrate the impact of shifts in regulations, such as bans on using trans fat in restaurants.”

The US National Institute of Health’s Human Microbiome Project (HMP) is also underway to “characterize microbial communities found at multiple human body sites and to look for correlations between changes in the microbiome and human health.”

So far, this data gathering has resulted in nearly 200 scientific papers, along with a repository of resources that scientists can access to explore the relationships between human gut bacteria and disease.

The American Gut Project decided to take it a step further by allowing the American public to participate. (I published an invitation to join the project in 2012. Hopefully, some of you decided to join, as I did. If you didn’t, you can still sign up to participate on the Human Food Project’s website.10)

All the gathered information from this project will be made public. It’s an extremely ambitious project seeking to identify the parameters for the ideal gut flora and how diet affects it. According to the American Gut Project:11

“One of the big questions the American Gut scientists hope to figure out is what characterizes healthy and sick guts (or even just healthier and sicker guts) and how one might move from the latter to the former…

Even just beginning to know how many and which species live in our guts will be exciting, particularly since most of these species have never been studied, which is to say there are almost certainly new species inside you, though until you sample yourself… we won't know which ones.”

Optimizing Your Gut Flora for Optimal Health

All of this information should really drive home the point that optimizing your gut flora – living in harmony with your microbiome instead of assaulting it – is of critical importance for disease prevention and optimal health. Reseeding your gut with beneficial bacteria is essential for maintaining proper balance here. In light of this, here are my recommendations for optimizing your gut bacteria.

  • Fermented foods are the best route to optimal digestive health, as long as you eat the traditionally made, unpasteurized versions. Healthy choices include lassi (an Indian yoghurt drink, traditionally enjoyed before dinner), fermented grass-fed organic milk such as kefir, various pickled fermentations of cabbage, turnips, eggplant, cucumbers, onions, squash, and carrots, and natto (fermented soy). 
  • Fermented vegetables are an excellent way to supply beneficial bacteria back into our gut. As an added bonus, they can also a great source of vitamin K2 if you ferment your own using the proper starter culture.

    We had samples of high-quality, fermented organic vegetables made with our specific starter culture tested, and a typical serving (about two to three ounces) contained not only 10 trillion beneficial bacteria, but it also had 500 mcg of vitamin K2, which we now know is a vital co-nutrient to both vitamin D and calcium.

    Most high-quality probiotic supplements will only supply you with a fraction of the beneficial bacteria found in such homemade fermented veggies, so it's your most economical route to optimal gut health as well.

  • Probiotic supplement. Although I'm not a major proponent of taking many supplements (as I believe the majority of your nutrients need to come from food), probiotics is an exception if you don't eat fermented foods on a regular basis.

In addition to knowing what to add to your diet and lifestyle, it's equally important to know what to avoid and these include:

Antibiotics, unless absolutely necessary (and when you do, make sure to reseed your gut with fermented foods and/or a probiotic supplement) Conventionally-raised meats and other animal products, as CAFO animals are routinely fed low-dose antibiotics, plus genetically engineered grains, which have also been implicated in the destruction of gut flora Processed foods (as the excessive sugars, along with otherwise "dead" nutrients, feed pathogenic bacteria)
Chlorinated and/or fluoridated water Antibacterial soap Agricultural chemicals, glyphosate (Roundup) in particular

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