Helping Beneficial Bacteria Survive in the Human Gut


Scientists at Yale report that they have uncovered a novel mechanism by which “good” bacteria colonize the gut. The microbes that inhabit the gut are critical for human health, and understanding the factors that encourage the growth of beneficial bacterial species in the gut may enable medical interventions that promote gut and overall human health.

Specifically, the Yale team discovered that one of the most abundant beneficial species found in the human gut showed an increase in colonization potential when experiencing carbon limitation—a finding that could yield novel clinical interventions to support a healthy gut.

The study “Bacteria require phase separation for fitness in the mammalian gut” appears in Science.

“Therapeutic manipulation of the gut microbiota holds great potential for human health. The mechanisms bacteria use to colonize the gut therefore present valuable targets for clinical intervention. We now report that bacteria use phase separation to enhance fitness in the mammalian gut,” write the investigators.

“We establish that the intrinsically disordered region (IDR) of the broadly and highly conserved transcription termination factor Rho is necessary and sufficient for phase separation in vivo and in vitro in the human commensal Bacteroides thetaiotaomicron. Phase separation increases transcription termination by Rho in an IDR-dependent manner. Moreover, the IDR is critical for gene regulation in the gut. Our findings expose phase separation as vital for host-commensal bacteria interactions and relevant for novel clinical applications.”

The Yale team, based in the lab of geneticist Eduardo Groisman, the Waldemar Von Zedtwitz, PhD, professor of microbial pathogenesis, found that the beneficial gut bacterium Bacteroides thetaiotaomicron responded to starvation for carbon by sequestering a portion of the molecules for an essential transcription factor within a membrane-less compartment.

Important role for a transcription factor

The team established that sequestration of the transcription factor increased its activity, which modified the expression of hundreds of bacterial genes, including several that promote gut colonization and control central metabolic pathways in the bacterium. These findings reveal that “good” bacteria use sequestration of molecules into membrane-less compartments as a vital strategy to colonize the mammalian gut.

Bacteroides thetaiotaomicron and other bacteria residing in the mammalian gut have access to nutrients ingested by the host animal. However, there are also long periods of time when the host organism does not eat. Deprivation of nutrients, including carbon, elicits the production of colonization factors in beneficial gut bacteria, the researchers found.

“One of the things that emerged is that when an organism is starved for carbon, that is the signal that helps produce properties that are good for surviving in the gut,” said Aimilia Krypotou, PhD, a postdoctoral fellow in Groisman’s lab and lead author of the study.

The findings could help spur the development of new probiotic therapies for gut health, noted Krypotou, adding that “most studies just look at abundance of bacterium. If we don’t understand what’s happening at the molecular level, we don’t know if it would help.”

Turning to Bacteria to Fight the Effects of Climate Change


Recently the United Nations warned that the world could suffer a 40 percent shortfall in water by 2030 unless countries dramatically cut consumption. Since 70 percent of the world’s fresh water goes to agriculture, this means changing the way people farm.  The need is ubiquitous. In California’s Central Valley, farmers drilling for water are now tapping stores 30,000 years old. In Kenya, which is facing the worst drought since 2000, farmers are hand-digging wells to reach the receding water table, even as one-in-ten Kenyans are hungry.

But in both regions, a game-changing solution could come from an overlooked resource: billions of beneficial bacteria that teem in the soil near the roots of plants. Such bacteria are found in soil everywhere: from the hard-hit Kenyan coast, where my family grows tomato, peppers and watermelon, to the experimental greenhouses in Alabama where I now work to unearth the secrets of these soil microbiomes.

Indeed, scientists across five continents are digging in to generate evidence of the beneficial associations among microbes and crops such as corn, cotton, tomato and peppers. Plants normally exude a carbon-rich liquid that feeds the microbes. They also exude various chemicals in response to a range of stressors, including insect attacks and water stress. Soil bacteria sense these messages, and secrete chemicals of their own that can activate complex plant defenses.

For example, studies have shown that a combination of beneficial microbes applied directly to seeds is as effective as commercial pesticides in combatting the rice leaf-folder, which wraps itself in and then eats the leaves of young plants. Other studies demonstrate that some soil microbes significantly increase growth and yield of important crops. In Germany, a 10-year field study showed that beneficial microbes increase maize plant growth and the availability of phosphorous—and essential plant nutrient—in the soil. In Colombia, microbiologists have mass-produced bacteria that colonize cassava plants and increase yield by 20 percent.

For farmers struggling to adapt to climate change, especially small-scale farmers with limited resources, an increase in yield can open fresh opportunities for the simple reason that crop sales generate cash, including money that can be invested in a range of “climate-smart” farming techniques that further conserve water and soil, and sustainably increase production on small plots of land.

Most recently, studies point to a direct role for soil bacteria in shielding crops from drought; improving their growth and ability to absorb nutrients; and enhancing their tolerance of flooding, high temperatures, low temperatures and many other challenges of a changing global climate.

In one study, scientists reported that peppers cultivated in arid desert-like conditions act as “resource islands” attracting bacteria that sustain plant development when water is scarce. Another study identified soil bacteria that prompt plants to temporarily close the pores on their leaves. This not only prevents disease-causing bacteria from entering the plant, but also prevents the escape of moisture, preserving the plant’s water.

I can see this in my research labs, where several running experiments dramatically illustrate the role of soil microbes in protecting against water stress. Cotton, corn and tomato plants grown in soil that is infused with certain bacteria have root sizes that are triple the size of plants grown in untreated soil after water has been withheld for just five days. The treated plants stand tall and robust; the untreated wilt and wither. The difference is tremendous.

Although companies such as Nozozymes, Monsanto and Bayer Crop Sciences are exploring the potential commercialization of soil bacteria, and several start-up companies are working around the clock to commercialize microbial cocktails, overall, research into this area has barely begun.

The United Nations designated 2015 as the International Year of Soil, and governments, funders and researchers are taking a hard look at the role of healthy soil in achieving food security as population grows and climate change lowers yields of important food crops. But rarely do their initiatives consider the potential of the communities of beneficial bacteria, billions strong, and adapted through millennia to aid plants in their battle for survival.

Of course, the use of soil microbes is just one part of the complex and interlocking changes needed to ensure the sustainability of our natural resources and the productivity of our food systems. But they could provide novel solutions that are of central significance in contemporary plant science as it addresses the challenges of climate change.

We must invest in understanding and harnessing this resource, which works with nature, not against it. As concerns about food security increase with the global temperatures, soil bacteria could be the next key tool for food security, helping farmers around the world conserve water, increase yields and improve nutrition under the changing climate.

Top 10 Probiotic Foods to Add to Your Diet.


Probiotics are beneficial forms of gut bacteria that help stimulate the natural digestive juices and enzymes that keep our digestive organs functioning properly. In addition to taking a probiotic supplement, you can also support your probiotic intake through eating foods that are hosts to these live bacterium.

We all know of the great health benefits of probiotics, however, not all of us know how to take advantage of these health benefits. Below is a list I put together to outline the best probiotic foods for you to add to your diet. I would also recommend buying the organic version of all these probiotic foods.

Probiotic Article1 300x225 Top 10 Probiotic Foods to Add to Your Diet

1. Yogurt

One of the best probiotic foods is live-cultured yogurt, especially handmade. Look for brands made from goat milk that has been infused with extra forms of probiotics like lactobacillus or acidophilus. Goat’s milk and cheese are particularly high in probiotics like thermophillus, bifudus, bulgaricus and acidophilus. Be sure to read the ingredients list, as not all yogurts are made equally. Many popular brands are filled with High Fructose Corn Syrup, artificial sweeteners and artifical flavors.

2. Kefir

Similar to yogurt, this fermented dairy product is a unique combination of goat milk and fermented kefir grains. High in lactobacilli and bifidus bacteria, kefir is also rich in antioxidants. Look for a good, organic version at your local health food shop.

3. Sauerkraut

Made from fermented cabbage (as well as other vegetables), sauerkraut is not only extremely rich in healthy live cultures, but also aids in reducing allergy symptoms. Sauerkraut is also rich in vitamins B, A, E and C.

4. Dark Chocolate

Probiotics can be added to high-quality dark chocolate, up to four times the amount of probiotics as many forms of dairy. This is only one of the health benefits of chocolate.

5. Microalgae

This refers to super-food ocean-based plants such as spirulina, chorella, and blue-green algae. These probiotic foods have been shown to increase the amount of both Lactobacillus and bifidobacteria in the digestive tract. They also offer the most amount of energetic return, per ounce, for the human system.

6. Miso Soup

Miso is one the main-stays of Japanese traditional medicine, and is commonly used in macrobiotic cooking as a digestive regulator. Made from fermented rye, beans, rice or barley, adding a tablespoon of miso to some hot water makes an excellent, quick, probiotic-rich soup, full of lactobacilli and bifidus bacteria.

Beyond its important live cultures, miso is extremely nutrient-dense and is believed to help neutralize the effects of environmental pollution, alkalinize the body and stop the effects of carcinogens in the system.

7. Pickles

Believe it or not, the common green pickle is an excellent food source of probiotics. Try making your own home-made pickles in the sun. Here’s a great set of instructions for making your own probiotic-rich dill pickles.

8. Tempeh

A great substitute for meat or tofu, tempeh is a fermented, probiotic-rich grain made from soy beans. A great source of vitamin B12, this vegetarian food can be sautéed, baked or eaten crumbled on salads. If prepared correctly, tempeh is also very low in salt, which makes it an ideal choice for those on a low-sodium diet.

9. Kimchi

An Asian form of pickled sauerkraut, kimchi is an extremely spicy and sour fermented cabbage, typically served alongside most meals in Korea. Besides from beneficial bacteria, Kimchi is also a great source of beta-carotene, calcium, iron and vitamins A, C, B1 & B2. Kimchi is one of the best probiotic foods you can add to your diet, assuming you can handle the spice, of course.

10. Kombucha Tea

This is a form of fermented tea high in healthy gut bacteria. This probiotic drink has been used for centuries and is believed to help increase your energy, enhance your wellbeing and maybe even help you lose weight. However, kombucha tea may not be the best fit for everyone, especially those that already have a problem with candida.

Do you have any favorite foods with probiotics that I may have missed? Let me know in the comments below!

Other Sources of Probiotics

Besides from the list of probiotic foods above, you can also get plenty of beneficial bacteria by taking a probiotic supplement. I personally would recommend taking Latero-Flora, but Garden of Lifes Primal Defense Ultra is also a great option.