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“Your microbiome is essentially another organ in your body,” says Shayne Morris, PhD, a molecular biologist at Systemic Formulas in Ogden, Utah.  “It helps you digest foods, create nutrients (such as vitamin K), combat pathogens (which can cause illness) and plays a critical role in the development of your immune system.”

That’s just the tip of the iceberg, though. Mounting evidence suggests your microbiome may play an important role in everything from autoimmune diseases to obesity. Scientists are continually uncovering new things about the microbiome and what it does.

In 2007, the National Institutes of Health announced the Human Microbiome Project, which collected and analyzed microbiome samples from healthy U.S. adults in an effort to determine what a “normal” human microbiome looks like. Since then, there’s been a whirlwind of activity.

“The microbiome is the new black,” says Jeff Leach, PhD, a microbiome researcher, founder of the Human Food Project, co-founder of American Gut, and author of Rewild (CreateSpace, 2015). “Everybody’s talking about the human microbiome because we now have the technology and computing power needed to better explore who’s in there and what they might be doing.”

The bugs inside you

“Not long ago, it was thought that everybody had different microbiomes, with each one of us being different, like a snowflake,” Leach says. “Now we know that when you gather microbiome data of several thousand people, as the American Gut Project has, you start to see some people with pretty similar microbiomes.”

To understand the variance from person to person, it’s helpful to understand a little bit about how bacteria are named. Bacteria, such as the ones you get in a probiotic supplement, are identified by their genus, species and strain, such as Lactobacillus (genus) acidophilus(species) LaVK2 (strain). Within each species, there are many different strains, which may have different benefits.

“In terms of bacteria genus, you are quite similar to those around you. However, when you look at abundance and narrow the microbiota to particular species and strains of bacteria, only about 15 percent will overlap with your neighbor’s,” Morris says. You would see even greater differences in microbiomes if you compared yourself to people in another country, due to differences in diet, lifestyle, environment and other factors.


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Nurturing your microbiome

Your microbiome started developing while you were in your mother’s womb. “We no longer believe fetuses are sterile,” Morris says. “After you’re born, your microbiome changes dramatically until about age 3 as you go from breastfeeding to solid foods, then it starts to stabilize.”

“I highly recommend breastfeeding because there are more than 300 different polysaccharides (fermentable carbohydrates) in breast milk whose purpose is to directly nourish the microbiota, not to directly nourish the infant,” Morris says.

Antibiotics can disrupt the microbiome considerably. What you eat (or don’t eat) affects it a lot, too. In fact, so far studies show that diet, in comparison to other environmental factors, has the largest known impact on gut bacteria.

“Dietary fiber is food for microbes,” Leach says. “The human body cannot break down and digest dietary fiber, so it passes on to the colon where the bacteria harbor the genes that enable them to break down the fiber and turn it into energy.”

Feed them and they will come

Gut Health | NJ

Based on findings of the American Gut Project, Leach says people who eat a wide variety of plant foods have a greater diversity of bacteria in their gut than people who eat just a few plant species a week. The fiber in bell peppers is different from the fiber in baby spinach and different from the fiber in onions. That dietary fiber diversity is important to the health of your microbiome.

“Lactobacillus bacteria may prefer one type of fiber, but Bacteroides may prefer fiber from a different food,” Morris says. “As you diversify your diet with different plant foods, you diversify the bacteria that are now happy to stay with you. The diverse bacteria in turn help feed other bacteria. There’s this interplay between bacteria. If you omit certain foods and are no longer feeding the bacteria, they will eventually die off,” Morris says.

Unfortunately, diversity is one of the things we’ve lost in our Western lifestyle. “When we look at hunter-gatherers in East Africa, we find that they contain almost twice as much diversity in bacterial species as people in the United States,” Leach says.

Your bugs and your health

“Although the press has overhyped the microbiome as the new panacea that is going to save us all, there is pretty solid data that suggests microbes could play a potential causal role in a large number of ailments,” Leach says. “It could take years or decades to figure it all out though.”

Studies have associated disruptions in normal gut bacteria (dysbiosis) with obesity, diabetes, various inflammatory bowel diseases and autoimmune conditions, such as rheumatoid arthritis and type 1 diabetes.

When microbes munch on fermentable carbohydrates, including fiber and resistant starch, in your gut, they produce short chain fatty acids, primarily acetate, propionate, and butyrate, which may have far-reaching effects.

“Butyrate is very nourishing to the cells in your gut wall,” says Raphael Kellman, MD, author of The Microbiome Diet (De Capo Lifelong Books, 2015). Studies also suggest butyrate may help improve insulin sensitivity and blood sugar regulation. A significant amount of research (primarily from animals) also suggests short chain fatty acids may help in appetite control and managing your weight, such as by turning on the genes that drive fat breakdown.

A healthy microbiome also may help your memory, improve brain clarity, reduce your response to stress and improve your mood, Kellman says. Scientists are still uncovering how the microbiome could do all of this, such as by decreasing inflammation and supporting the production of brain chemicals including serotonin, a feel-good chemical.

About 90 percent of our serotonin is made in the gut, so if you have a healthy microbiome driving a healthy gut, you’re more likely to produce this important brain chemical.

Looking ahead: The next 5-10 years

Labs around the world are working on the microbiome’s link to specific diseases of interest, such as Alzheimer’s disease, autism, irritable bowel disease, heart disease and so forth. “The overarching theme that I think all of the data is going to point to is, in general, our drop in diversity in microbes. Just like in any ecosystem that loses diversity, the less diverse our microbiome, the more susceptible to disease we may be. But these are early days,” Leach says.

Five to 10 years from now, Leach predicts public health experts are going to be advising us to improve the diversity of microbes in our body by improving the quantity and diversity of fiber we consume, as well as to get outside and expose ourselves to the microbial world around us.

Leach also predicts we’ll see more specialized probiotics, perhaps made with hundreds of strains of bacteria.

In the future, analysis of a person’s microbiome also could help predict which medications a person may need to avoid, Morris says. Bacterial action on certain drugs, such as antidepressants, could cause them to be reabsorbed rather than excreted, potentially causing serious side effects.

What you can do now

For years we’ve been told to consume probiotics, such as in yogurt, kefir, sauerkraut and other fermented foods, which can directly supply beneficial bacteria.

Gut Healthy Foods | Probiotic Foods | NJ

There also are many plant-based foods you can eat to encourage the growth of a healthy microbiome. Such foods may be called prebiotics. “When you modify your diet, changes in your microbiome happen very quickly—within a few days,” Kellman says.

Leach advises us to keep track of all the different kinds of plant foods we eat in a week, and aim for 25 to 35 species. “That’s probably going to do more for you than a gym membership,” Leach says.

A large number of different plant foods are as close as your local natural market. “There are anywhere from 50 to 300 different species of plants in the produce section of stores,” Leach says.

“Unfortunately, the average American eats less than five species of plants a week.”


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If you can, shop at a local market that supplies local, organic produce or grow some of your own, too. The soil that clings to garden-fresh food is teeming with beneficial microbes. Rinse, rather than rigorously scrub, produce to retain some of these beneficial soil-based organisms.

"Exercising on a regular basis, sleeping at least seven hours a night, and spending time outdoors in nature also promote a more diverse microbiome," Leach says.

Ultimately, in order to take care of your microbiome, you have to take care of the planet. “We need to take care of the ocean, the lakes, the soil and the atmosphere because they’re all interconnected,” Morris says. “Soil needs to be healthy in order for your food to be healthy. That circle goes on and on.”

Feeding your microbiome

The following are top foods Kellman and others recommend to nourish your microbiome through their rich supply of fiber and resistant starch. But don’t limit yourself to this list. It appears to be best to eat a wide range of different plant foods. Branch out beyond your familiar favorites.

  • Asparagus

  • Bananas (slightly green)*

  • Bell peppers

  • Berries

  • Broccoli

  • Brown rice (cooked, then chilled)*

  • Brussels sprouts

  • Cauliflower

  • Chickpeas

  • Garlic

  • Jerusalem artichoke

  • Jicama

  • Kiwi

  • Leeks

  • Lentils

  • Onions

  • Pears

  • Potatoes (cooked, then chilled)*

  • Radishes

  • Spinach

  • Tomatoes

  • Turmeric

*To increase resistant starch content.

The pH test for poo

As bacteria ferment dietary fiber and produce short chain fatty acids, your colon (large intestine) becomes more acidic and less hospitable to pathogens—so the more acidic your stool, the better, Leach says.

To measure your stool acidity, buy pH test strips at your local pharmacy and stick a test strip in your poo on toilet tissue. If your stool is consistently an 8 or 9 on the pH scale, for example, you’re likely not eating enough plant foods, but if it’s in the range of 2 to 5 (the lower the number, the more acidic), you’re likely doing a better job of getting a greater amount and variety of plants in your diet.

Using this method, you can track the effects of different dietary changes and watch your pH change over a few days’ time as you modify what you eat.

Microbiome 101: Science, history and stats: what have scientists been up to?

Human Microbiome Project

  • 1680s: Antonie van Leeuwenhoek compares the bugs in his mouth and stool

  • 2001: Joshua Lederberg, an American molecular biologist, coins the term “human microbiome”

  • 2007: NIH Human Microbiome Project (HMP) launched

  • 2012: Two landmark papers on HMP are published in Nature

  • 2013: Crowd-funded American Gut Project launched and is ongoing

  • 2014: Second phase NIH Integrative Human Microbiome Project (iHMP) launched

  • 2016: National Microbiome Initiative launched to coordinate study of microbiomes across different ecosystems

Did you know?

  • A normal human microbiome includes around 1,000 different species.

  • The human microbiome contributes 360 times more bacterial genes than you have human genes.

  • 2–3% of your body weight is microbes.

  • If collected together, your microbiome would occupy about 3 pints.

  • The human genome has fewer than 20 carbohydrate-digesting enzymes; the genome of just one gut bacterium—Bacteroides thetaiotaomicron—has over 260 such enzymes.

  • 95% of your bacteria are located in your gastrointestinal tract (gut)

  • The surface of your skin harbors 200–300 bacterial species.

Want to learn even more about gut health? Watch this presentation:  This article was originally published by Delicious Living.