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Human Microbes

Story at-a-glance -

  • What you eat influences the microbes your body contains, and an improved diet may increase the number and integrity of your microbes
  • Ingesting plenty of fiber is an example of how you can improve your microbiome integrity, and pregnant mothers who eat a diet high in healthy fats may prevent asthma in their offspring later on
  • Scientists are exploring the communication pathways between the nervous and digestive systems, the “gut-brain axis,” to treat metabolic disorders

How Microbes Moved From Villain to Hero

August 22, 2016 | 29,244 views

By Dr. Mercola

Microbes live inside all of us. The idea of a "microscopic menagerie" teeming and thriving in your cells, your intestines and your brain might make you a little uncomfortable, but this is good news, according to the latest science.

U.K.-based science writer Ed Yong's new book, "I Contain Multitudes: The Microbes Within Us and a Grander View of Life," says microbiomes — the fungi, bacteria, viruses and other minuscule critters — are necessary "partners" for the betterment of our immune systems.

Your microbiomes change constantly, and what you eat makes a big difference in the kind of microbes your body contains. When people begin improving their diets, the number and integrity of their microbes improve. In fact, through your diet, you can, to a degree, switch them out, Yong asserted:

"It seems that dietary fiber is a really important driver of microbial diversity in our bodies. Fiber consists of large numbers of different carbohydrates — many we can't digest, but our bacteria in our guts can. If we eat low-fiber diets, we narrow the range of our microbial partners.

Simple measures like probiotics — adding a few strains of microbes in the hope that they will take hold and remedy health problems — have been largely unsuccessful. It will take more

… If we want to add microbes to our bodies, we'll need to think about whether we need to eat certain foods to nourish the microbes we're taking."1

Human gut bacteria may have existed for millions of years, maybe before the evolution of people.

A recent study asserts that three types of gut bacteria affected intestinal development, fought off germs and may have influenced mood and behavior and were reportedly present in African great apes that lived more than 10 million years ago.

Scientists believe the bacteria "evolved into distinct strains as humans and great apes went their separate evolutionary ways." Study authors hope similar gut microbes can be eventually traced past amphibians and even vertebrates.2

How Science Approaches 'Fixing' Broken Microbiome Function

While microbiome science is still in the early stages, scientists have explored why certain foods are good for us and others aren't. The connection between food, microbes and health are all inextricably intertwined, and unraveling the mysteries may shed light on how they affect our metabolism.

Fiber, for instance, is good for many of our gut bacteria, so eating more veggies certainly won't hurt. Microbiome researcher Jeff Leach told NPR3 that too little might starve the good bacteria, and "when we starve our bacteria they eat us. They eat the mucus lining — the mucin in our large intestine."

Fiber feeds your bacteria and gives off nourishing nutrients for your gut lining. Veggies are high-fiber foods, so eating a variety and as much of the whole thing as possible is recommended.

Garlic and onions also have antimicrobial properties; garlic impairs some of the undesirable bacteria but leaves the good ones. As Leach explained:

"Those vegetables contain high levels of a type of fiber called inulin, which feeds actinobacteria in our guts. In fact, inulin is considered a probiotic, since it feeds the good bacteria, or probiotics, that live inside us."

He added that slight or short-term diet tweaks may not make much of a difference in gut health, but moving from ingesting 10 to 15 grams of fiber a day to more like 40 or 50, "you may see some changes."

The Gut-Brain Axis: How Your Brain Influences Hunger

Scientists at Rockefeller University used magnetic stimulation in the ventromedial hypothalamus part of the brains of genetically engineered mice to "switch on" neurons to see how the brain might influence appetite. According to Scientific American, they found that the procedure:

"Increased the rodents' blood sugar levels and decreased levels of the hormone insulin. Turning on the neurons also caused the mice to eat more than their control counterparts …

They inhibited these neurons and saw the opposite effects: it drove blood sugar down, elevated insulin levels and suppressed the animals' urge to consume their chow."4

Scientists have been aware for over a century that the brain "talks to the mind" through nerve connections, as well as biochemical signals such as hormones, to affect metabolism in a connection called the "gut-brain axis."

Studies have concentrated on the communication pathways between the nervous and digestive systems to treat metabolic disorders, especially since obesity and metabolic disease is increasing steadily worldwide.

Four in 10 women in the U.S. are considered obese5 and diabetes prevalence has almost quadrupled since 1980, so scientists and pharmaceutical companies are working on the gut-brain link with increased urgency to devise drugs, surgery, devices and probiotic approaches.

In 2011, Dr. Serguei Fetissov from Rouen University in France started his company TargEDys to develop treatment programs for metabolic disorders and conducted mice studies using Escherichia coli (E. coli) intestinal bacteria to reduce their appetite. Scientific American reported:

"Fetissov is trying to replicate these effects in the rodents by using a probiotic to hasten the proliferation of E. coli and boost production of appetite-reducing proteins, rather than by administering injections of the bacterial protein products."6

Early in 2016, TargEDys announced plans for clinical trials using freeze-dried probiotic bacteria in capsule form to use on humans and hoping to replicate the appetite-suppressing effects seen in the mice trials. Similarly, a potential therapy for anorexia patients or elderly involves bacteria to stimulate hunger.

The More (Good) Fat a Pregnant Mom Eats, the Better Her Baby's Gut Health

Unborn babies have microbes, too, and scientists believe the mother's fat intake may affect how healthy the mix of those microbes is, another study revealed.

More than 150 women participated, recording what they ate during their pregnancy. Researchers said their diets contained an average of 33 percent fat, which they considered good since the optimal amount is 20 percent to 35 percent.

However, the levels ranged between 14 percent and 55 percent, so some were inordinately low and others, high by conventional standards. Emerging evidence actually suggests your dietshould be at least half healthy fat and possibly as high as 70 percent.

Gut microbiomes of the babies born to moms who ate a higher-fat diet had fewer Bacteroide microbes at birth and weeks afterward, positively affecting immune system development and energy extraction from food.

Finding the link between fewer Bacteroides and the moms' high-fat diet during pregnancy was a surprise to the researchers, including Dr. Kjersti Aagaard, senior study author and associate professor of obstetrics and gynecology at Baylor College of Medicine and Texas Children's Hospital in Houston. According to Medicine Net:

"Diet is very amenable to change, and women are highly motivated to make healthy changes during pregnancy. Traditionally, dietary interventions during pregnancy have focused on micronutrients, such as iron and folic acid.

We speculate that there may be a sound argument to also discuss and estimate fat intake."7

Getting the Right Microbes Early May Ward Off Certain Diseases

The make-up of babies' digestive tract microbes might have something to do with whether or not they develop asthma later in life, scientists reported.

In fact, their study on 319 babies revealed that low levels of four specific bacteria — Rothia, Lachnospira, Veillonella and Faecalibacterium — indicated a higher risk of the breathing disorder by age 3.8 Conversely, when the babies' intestines revealed higher levels of the microbes, their chances of asthma were much greater.

Brett Finlay, Ph.D., a University of British Columbia microbiologist, said asthma, which is becoming increasingly common, is really an immune allergic-type reaction in the lungs. Several factors raise or lower the risk, Finlay told NPR:

"There's all these smoking guns like, for example, if you breast-feed versus bottle feed you have less asthma. If you're born by C-section instead of vaginal birth you have a 20 percent higher rate of asthma. If you get antibiotics in the first year of life you have more asthma."9

Further: "The microbiomes of kids who aren't breast-fed and are born by cesarean section may miss out on getting helpful bugs. Antibiotics can kill off the good bacteria that seem important for the development of healthy immune systems."

Mice studies indicated that those microbes influence how peoples' immune systems develop later in life. Although the researchers aren't sure how, a possible link might be the fact that babies with low levels of the four microbes were also low in acetate, which may be tied to immune system regulation. Though it is likely years away, confirming their supposition may lead to the next step in scientists' studies: Seeing if the missing microbes might be replenished. In the meantime, NPR reported:

"More breast feeding, fewer C-sections and more careful use of antibiotics could go a long way toward nurturing the microbes babies need to avoid asthma and other diseases."10

Review: 'Bacteroides: the Good, the Bad, and the Nitty-Gritty'

A Clinical Microbiology review titled "Bacteroides: the Good, the Bad, and the Nitty-Gritty,"11 noted that Bacteroides contain "the most antibiotic resistance mechanisms and the highest resistance rates of all anaerobic pathogens." They have a symbiotic relationship with the host unless they escape to other areas of the body, causing harm.

"By a variety of measures, the species Homo sapiens is more microbial than human. Microorganisms comprise only a small, albeit significant, percentage of the body weight (between 2 and 5 pounds of live bacteria). However, in terms of cell numbers, we are about 10 [percent] human and 90 [percent] bacterial!

Consequently, bacteria play a major role in bodily functions, including immunity, digestion and protection against disease. Colonization of the human body by microorganisms occurs at the very beginning of human life, and many of these organisms become truly indigenous to the host."

A subspecies of bacteria called B. infantis feeds on sugars in breast milk, known as human milk oligosaccharides. Because babies can't digest the sugars, they're food for the microbes rather than the babies. According to Yong:

"These sugars are sort of a way of setting up a baby's first microbiome, ensuring that the right species set up shop rather than those that are likely to cause disease. And it's fascinating to me to think of this very common act, breastfeeding, through this new microbial lens."12

Incidentally, more than one scientist has lamented the fact that the microbiomes humans have maintained in their systems for millennia are declining due in part to germ phobia in Western society, such as the prevalence of antibiotics and hand sanitizers.

Fighting Poop With Poop, or The Great Poop Exchange

Clostridium difficile, commonly known as C. diff., is a "hardy bacterium" that instigates stubborn, recurring diarrhea. It may seem contradictory to treat such a condition with a microbe transplant — aka fecal transplant — but it's a treatment that's becoming more common. According to Yong:

"Fecal transplants have been used to treat this condition many times over in many countries. It's been tested in randomized controlled studies, which is the gold standard. The first trial had to be stopped early because [the transplants were so successful that] it seemed unethical to not put all of the patients on this treatment."13

C. diff is an invasive microbe, unlike irritable bowel or inflammatory bowel disease, because as it's zapped by a plethora of antibiotics, necessary microbes "collapse," opening the door, so to speak, for the microbes in a donor stool to invade. Yong told NPR:

"It might just be that C. diff. was the low hanging fruit. That said, fecal transplants are arguably our most successful microbiome-based therapy. They show some important principles that we might like to take heed of like the fact that [the treatment] is a community-based approach."14

At Brown University, where another program focuses on digestive system microbes such as bacteria, fungi and viruses (human microbiomes), scientists say problems with C. diff. started when antibiotics prescribed for another condition altogether disturbed what, again, may have been perfectly functioning, benign gut organisms. Colleen Kelly, a doctor in the program, said microbe transplants are being tested for other conditions as well, including Crohn's disease, colitis and diabetes — even obesity.

"We're at a really interesting point in medicine where we've come to appreciate the microbiome and that [these organisms] have really integral roles in ... energy metabolism, and immune function, and all of these other things."15

The Food and Drug Administration (FDA) is said to have "big concerns" over microbiome transplants, comparing them to snake oil. As such, the FDA restricts doctors' use of the procedure for anything other than C. diff. unless they get FDA approval.

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