Rye Is Healthy, Thanks to an Interplay of Microbes

Eating rye comes with a variety of health benefits. A new study from the University of Eastern Finland now shows that both lactic acid bacteria and gut bacteria contribute to the health benefits of rye. Published in Microbiome, the study used a metabolomics approach to analyse metabolites found in food and the human body.

Rye sourdough used for the baking of rye bread is rich in lactic acid bacteria. In addition to fermenting the dough, these bacteria also modify bioactive compounds found in rye. They produce branched-chain amino acids and amino acid-containing small peptides, which are known to have an impact on insulin metabolism, among other things.

Many of the compounds found in rye are processed by gut bacteria before getting absorbed into the body. The study found that gut microbes and microbes found in sourdough produce compounds that are partially the same. However, gut microbes also produce derivatives of trimethylglycine, also known as betaine, contained in rye. An earlier study by the research group has shown that at least one of these derivatives reduces the need for oxygen in heart muscle cells, which may protect the heart from ischemia or possibly even enhance its performance. The findings can explain some of the health benefits of rye, including better blood sugar levels and a lower risk of cardiovascular diseases.

The study used metabolomics as the primary method to carry out an extensive analysis of metabolites found in food and the human body. The effects of gut microbes were studied in mice and in an in vitro gastrointestinal model, mimicking the function of the human gut. Using these two models, the researchers were able to eliminate naturally occurring differences in the gut microbiome between different individuals, making it easier to detect metabolites actually originating from rye.

Rye can be traced back to what is now known as present-day eastern Turkey, from where it has spread to many cuisines across the world. In Finland, for example, rye has been consumed for thousands of years, and it was recently selected as the country’s national food.

Although the health benefits of rye are long known, the underlying mechanisms are still poorly understood. For instance, the so-called Rye Factor refers to the lower insulin response caused by rye than, for example, wheat bread. Eating rye makes blood sugar levels fall slower, which leads to beneficial effects on the health – for a reason that remains unknown.

A significant factor contributing to the health benefits of rye are its bioactive compounds, or phytochemicals, which serve as antioxidants. In addition, gut microbes seem to play an important role in turning these compounds into a format that can be easily absorbed by the body, making it possible for them to have a greater effect.

“The major role played by gut microbes in human health has become more and more evident over the past decades, and this is why gut microbes should be taken very good care of. It’s a good idea to avoid unnecessary antibiotics and feed gut microbes with optimal food – such as rye,” Researcher Ville Koistinen from the University of Eastern Finland notes.

Source: University of Eastern Finland

How Foods Can Help The Microbes Inside Us Thrive

Jonathan Lambert wrote . . . . . . . . .

Katherine Harmon Courage wants us to think about digestion as a collaborative journey between us and our microbes. In her new book, Cultured: How Ancient Foods Can Feed Our Microbiome, she envisions digestion not as a simple food-in, excrement-out process, but as a series of encounters with varying microbial players that takes place along the winding 30-foot tunnel of our gastrointestinal tract. Along the way, microbes digest the food we can’t, and in return we give them a warm, well-stocked place to live.

But a surge in microbiome research over the past two decades has revealed they do much more than simply digest food. They can mediate weight gain, fight off infection, and even alter our mood. Scientists still have much to learn about the identity of these microbes, which are important, and how the beneficial ones work their magic.

Incomplete understanding hasn’t stopped the burgeoning probiotic industry, which argues that we can improve our gut health by taking a pill stuffed with billions of beneficial strains of bacteria, or eating a probiotic-infused yogurt with breakfast. The thinking goes that we just need to eat the right microbes to construct a healthier gut.

Courage believes this focus on the microbes themselves is myopic. She views the process of digestion as collaborative because the food we put into our bodies affects the kinds of bacteria that live and thrive there. In her book, she explores the science behind how what we feed our microbes affects our health.

She thinks we can learn how to better work together with our microbial partners by looking to the past. From Greenland to Greece, Courage explores the ancient gut-friendly foods that have become integral parts of many food cultures, and offers suggestions on how to diversify the kinds of foods we feed our microbiome.

We spoke with Courage about the science behind pro- and prebiotics, and what she learned exploring fermented staples across the world. The interview has been edited for brevity and clarity.

A lot of the buzz around the microbiome has been about the microbes themselves, and what they do for us. You focus much of your book on what they eat, the ” prebiotics” we feed them. Why?

It may be less interesting to talk about fiber than about all these new species we’re learning about and infusing into foods, but what we feed our microbes is just as important as what microbes are there.

I think that, from our human perspective, it’s helpful to think about microbes in two broad categories. There are microbes that we have in our guts throughout our lives that are adapted for living there, and then there are the microbes we get from food or supplements. Those latter ones just kind of pass through. They can survive the journey, and can certainly provide benefits along the way, but they aren’t long-term residents of the gut, and they’re not going to have the long-term health impacts that more-permanent residents might have.

We’re starting to learn more about how we can create the conditions for those resident microbes to thrive and potentially benefit us, and a large part of that is what we feed them. And much of what we feed them is fiber.

What happens if we don’t feed our microbes?

So then they start to eat us — our lower intestine, which is only a single human cell thick, which helps us absorb as much as we can from our digested food before we expel it. But it also makes it easy for things to escape.

When our microbes don’t get enough fiber, they can start eating away the mucus lining protecting this thin layer, and sometimes the lining can break, which can lead, literally, to leaky gut syndrome, which is associated with many poor health outcomes.

When I think of fiber, I think processed, cardboard-like breakfast cereal. Is fiber more diverse than that? How important is having a diverse diet of fiber to cultivating a healthy microbiome?

Prebiotic fiber is just any kind of carbohydrate that we can’t digest ourselves that instead passes through out digestive system as food for microbes. There are many different types of fiber that get broken down by different microbes at different stages of digestion. That’s why it’s a good idea to eat a wide variety of foods, and not just focus on a particular supplement here and there. Lots of different kinds of fibers help lots of different microbes thrive and create different beneficial compounds for us. Which is good because we’re learning that generally, a more diverse microbiome is an indicator of health. If you look at people’s guts around the world — and even in the same society — people with more diverse microbiomes tend to be healthier overall.

What are some examples of different types of fiber and the foods that carry them?

One kind of fiber that’s gotten a lot of focus is inulin. We’ve actually been adding it to foods for longer than we’ve been looking closely at it, but it’s commonly found in foods like chicory root or sunchokes. It’s a very long carbohydrate chain, which means it takes a bit longer to pass through our system and get broken down by microbes. Research shows that it encourages growth of bifidobacteria, lactobacteria [two strains of bacteria commonly associated with health benefits].

Another big one comes from fruits and veggies, called Fructo-oligosaccharides. It’s shorter than inulin and adding it to your diet has been shown to reduce markers of inflammation.

Galacto-oligosaccharides are another form of fiber found in milk, and are broken down in the colon.

I was really surprised to learn about resistant starch as another form of fiber. It comes from more simple carbohydrates that have been cooked and then cooled; think of cold potato or pasta salad. So once those starches are crystallized, they become the type of resistant starch that our bodies can’t break down anymore [but our microbes can]. Even cold pasta, which you don’t necessarily think of as being healthy, can be a great source of resistant starch.

Do other aspects of our diet besides fiber affect the microbiome?

Almost everything we eat has some kind of impact on our microbes. One example I talk about in the book is meat. Really kind of fatty meats like pork can have a negative health impact on us via our microbes, because they produce a metabolite called TMAO, which has been linked to negative health outcomes. But fish oil has been shown to be beneficial — the microbes of mice fed fish oil instead of pork lard produced much fewer TMAOs.

Another exciting area of research is looking at how gene expression in the same microbial strains can change, based on what they’re being fed. Different metabolites get produced not by different microbes, but by the same microbes being fed differently.

You looked at a lot of research comparing Western diets to more traditional, hunter-gatherer diets. How did their diets and microbiomes differ?

Researchers look to hunter-gatherer societies to try to understand what our ancestral diets looked like, before the advent of agriculture. This can give us clues potentially to the kinds of diets humans are adapted for.

These studies find that we eat a lot less fiber than we probably used to.

The FDA recommends something like 30 grams of fiber a day, but most Americans don’t even get that. Traditional hunter-gatherer cultures, like the Hadza group in Africa, eat 100-plus grams of fiber a day.

So people eating modern, Western diets are getting maybe 15 to 30 grams of fiber a day, when our bodies may be adapted to expect over 100. This lack of fiber seems to be making a big impact on the diversity of our microbiome. These traditional, high-fiber dieters have a much more diverse microbiome than [people eating] more modern diets, [and the former] is often linked to better health outcomes. It’s hard to draw hard conclusions about cause and effect here, because there are so many other lifestyle factors at play, but it certainly seems that our low-fiber diet is not great for our health.

In reporting your book, you go on a culinary quest exploring all these different fermented and microbial foods. What was the most surprising food you encountered?

By far it was Kiviak, which is a traditional Inuit food from Greenland. Kiviak is birds, specifically Auks, fermented inside a seal skin. So when Auks are in season they capture the birds and stuff [up to 500] in the seal skin, sew it up and leave it underground to ferment for a year, and then dig it up and eat it.

It’s important to remember that fermentation didn’t necessarily come about because people were thinking about the health benefits. It was a way to preserve foods and make it through a harsh Greenland winter.

A lot of these foods are not seen as individual things to be eaten for a specific benefit, but rich, integral parts of food culture. How does culture shape how we feed our microbiome?

There’s really not a culture out there that doesn’t incorporate some kind of fermented food, and many have a rich diversity of different kinds of fermented foods.

We think about things like kimchi as being the Korean fermented food, and it is actually their national food, but they have so many other kinds of fermented foods that they infuse throughout the whole cuisine.

These foods aren’t really viewed as this separate thing. You’re not eating kimchi as a little healthful snack for your microbes and then going back to your normal diet. These fermented foods are incorporated into the food culture — they’re condiments, sides, flavorings. A meal seems incomplete or unbalanced without them.

And that kind of consistency is a healthier, more sustainable way to feed our microbiome?

Yes. Generally, the kind of wild fermented foods — like kimchi, sauerkraut, or pickles — tend to have a higher diversity of microbes than your store-bought, probiotic-infused yogurts. Whether each individual strain in these foods is good for us is still unknown, but again, higher diversity tends to be associated with better health.

What advice do you have for those wanting to boost the health of their microbiome?

It’s really about creating the right environment for our native microbes, and the best way to do that is by eating a lot of diverse types of fiber for them. I don’t think probiotics or seeking out specific fermented foods is bad, of course, but focusing on fiber is a good first step.

Source: npr

The Key to Our Humanity Isn’t Genetic, It’s Microbial

Ian Myles wrote . . . . . . . . .

What if the key to perfecting the human species were actually … yogurt?

The fantasy of trying to perfect humanity through genetics was recently reignited by the announcement of the Chinese scientist claiming to have made the first “CRISPR babies,” which were named for the technique used to edit the DNA of the embryos. While major ethical and regulatory concerns are present, fears that CRISPR will lead us into the dystopian world depicted in the movie “Gattaca” are unfounded. In fact, if the movie were remade today it would likely be a story about the government mandating probiotics and healthy eating.

Eugenics is the belief that humanity can be perfected through genetic manipulation. Past eugenic policies placed restrictions on marriage and immigration, justified slavery and forced sterilizations, and ultimately culminated in the Holocaust. I am a physician-scientist specializing in allergies who became interested in eugenics not in relation to skin color, but skin rashes. Most prominent researchers who study a a skin rash called eczema were convinced that the vast majority of the disease is determined by fixed genetic sequences. Many still are. However, just like the studies of intelligence and criminal behavior that came before it, research into the genetics of eczema has fallen well short of what the 15th-century techniques had predicted.

To be fair, the public’s fascination with this subject is understandable. Commercial breaks are filled with pseudoscientific claims that your DNA can reveal, for example, that you are 12.4 percent Italian, 3.1 percent Neanderthal, and 1/512th Native American. Spoiler alert: It can’t. Prominent magazines, podcasts and newspapers have pushed the debunked claim that intelligence is genetically encoded. In reality, genetic studies that were supposed to explain at least 80 percent of being a genius have explained only 5 percent. This means your genes, at best, have less impact on your IQ score than a good night’s sleep. However, modern misunderstanding of how complex traits are passed down isn’t just burdening society with hucksters and racists. Ignorance is causing us to overlook opportunities for improving health and treating disease.

Where did ideas like a ‘gene for IQ’ come from?

Most of the ideas of “genes for” complex traits come from twin studies that assumed that identical twins and fraternal twins would differ only by the amount of shared DNA. What twin researchers either didn’t realize, or willfully ignored, is that the influence of the environment is also stronger for identical twins. Because identical twins are more likely to be dressed alike and confused for one another, they form more of a shared identity.

Thus, identical twins are more likely to share the same hobbies, eat the same foods, and run in the same social circles than fraternal twins. Modern research shows these differences are more psychology than biology. Furthermore, since identical twins share the same embryonic sac in the womb, their environmental exposures are also more biologically similar than fraternal twins. As such, researchers claiming that twin study data is indicative of genetics are, at best, ill-informed.

What is the modern understanding of heritable traits?

It may seem counterintuitive, but just because one change can worsen a gene’s function, that doesn’t mean that a different change can enhance it. When scientists say a gene “contributes to intelligence” they are referring to situations in which mutations in the gene cause a loss of intelligence or delay in cognitive development. They are not implying that a special version of the gene can guarantee a college degree.

Enhancing the functions of genes is most often accomplished via epigenetic modifications – chemical tags that are attached to the DNA but do not alter the genetic code. If genes are words, sentences and paragraphs, then epigenetics is the cadence, emphasis and diction. This is akin to having Hamlet performed by Gilbert Gottfried versus Benedict Cumberbatch. While epigenetic changes can be passed on from parents to children, they can also be altered by stress, diet, environment and behavior. Therefore, I believe that environmental modification, not CRISPR, would be needed to enhance the vast majority of genetic functions.

Another way to inherit traits

A more recently appreciated influencer of heritable traits is the microbiome, the term for all of the microorganisms (bacteria, fungi and viruses) that peacefully co-exist with humans.

From a genetic standpoint, your human genes are probably outnumbered over 100 to 1 by microbial genes. Modern research suggests that the microbiome may be directly involved in diseases ranging from autism to obesity. The microbial influence can be passed from mother to child during and possibly before birth, but remains partially sensitive to diet and environment into adulthood.

The microbiome can even influence your epigenetics. Researchers are just beginning to tap into the potential of microbial treatments for diseases. Similar to our lab’s experimental treatment for eczema, live bacterial therapies for food allergies, depression and anxiety, heart disease and select cancers are in development. As scientists clarify which strains of microbes are most helpful, these treatments are expected to become even more powerful.

Think of it this way: The current and former U.S. presidents share 99.9 percent of their genetic sequence, despite being slightly more than 0.1 percent different. As such, modern scientists do not hide from eugenics-based ideas because they are controversial; they dismiss them because both “Gattaca” and The Bell Curve are to genetics what Flat Earthers are to astrophysics.

While properly conducted gene therapy does offer real hope for curing rare genetic diseases, its limitations stop well short of sci-fi. As just one example, feeding mice one specific type of bacteria significantly enhanced their memory, whereas genomics has failed to find any genes that could do the same. Ancestry charlatans and neo-eugenicists may deny the fact that people are more a product of their experiences than their genetic heritage, but perhaps their mothers just didn’t breastfeed them long enough.

Source : The Conversation

Today’s Comic

What Are Microbes?

Enlarge image . . . . .

Micro-organisms (or microbes for short) play a very important role in our lives. Some microbes cause disease but the majority are completely harmless. In fact we couldn’t live without them, but they could live without us.

These microscopic organisms play a key role in maintaining life on earth, fixing gases and breaking down dead plant and animal matter into simpler substances that are used at the beginning of the food chain. Biotechnologists can also exploit the activities of microbes to benefit humans, such as in the production of medicines, enzymes and food. They are also used to breakdown sewage and other toxic wastes into safe matter. This process is called bioremediation.

Microbes are very small living organisms, so small that most of them are invisible. The majority can only be seen with a microscope, which magnifies their image so we can see them. In fact microbes are so tiny you would find over a million in a teaspoon of soil. They make up more than 60 % of the Earth’s living matter and scientists estimate that 2-3 billion species share the planet with us.


Microbes – bacteria, archaea, fungi, algae, protozoa and viruses – have been around for at least 3,500 million years and were the only life forms on Earth for most of that time. As the Earth cooled, liquid water formed and the first microbial life appeared. The conditions on Earth in the beginning were very hostile so the first microbes probably resembled the archaea, as they were able to live in the extreme environments such as the high temperature found on the cooling planet.

Around 2,800 million years ago, cyanobacteria, the largest and most diverse group of photosynthetic bacteria, probably appeared. This was an important development as these were the first organisms able to carry out aerobic photosynthesis. It is thought that cyanobacteria were responsible for raising the level of oxygen in the Earth’s atmosphere from less than 1 % to the 21 % of today. The presence of oxygen in the atmosphere allowed the evolution of new aerobic (oxygen using) species of microbes, which began to colonize every habitat on the planet.

Different species of cyanobacteria formed complex microbial communities with other types of microbes as they evolved, and these communities have left an extensive fossil record. They are fossilized in structures called stromatolites, dome-shaped mounds formed by the merger of mineral sediments into microbial mats.

Mammals and flowering plants are relative newcomers and only appeared around 100 million years ago.

Microbes affect every aspect of life on earth. They have an amazing variety of shapes and sizes and can exist in a wide range of habitats from hot springs to the icy wastes of Antarctica and inside the bodies of animals and plants.

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Read more at Microbiology Society . . . . .

Read also:

Microbes: Our tiny, crucial allies . . . . .