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Author: Sima

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Wondering about microbes found in beards? Recent TV stories made it sound as if they are incredibly filthy and harbor bacteria. Well, the news stories were not good because they asked the wrong question (should have asked: do bearded men have more bacteria on their faces than clean shaven ones? - and a 2014 study found that they don't) and they neglected to say that we are all covered with bacteria, all sorts of bacteria, and this is normal. And the "enteric bacteria" they found? Well, they're all over - the human gut, normal human skin, cheese,etc. Microbiologist David Coil from Slate:

Your Beard Is Covered in Bacteria

The irrational germophobia story of the week is that beards harbor “dangerous germs.” This story hits almost all the sweet spots of the genre: It has no actual data, no controls, nonsensical interpretation of results (such as they are), and a punch line that can be summed up in 140 characters or fewer.

In this “study,” the news station swabbed a few beards, sent them off to a company for analysis, and got back a report that the beards contained “germs,” specifically enteric bacteria, which are part of the human gut microbiome and therefore also found in feces. Voila: “Your beard is as dirty as a toilet,” and “Beards contain poop” sweep the Internet. Let’s take apart each piece of this misleading viral phenomenon.

The original story doesn’t say how many beards were tested … just a “handful.” Let’s be generous and call it 10 beards. Not exactly a great sample size, but not the end of the world. The real problem here is the lack of swabs from clean-shaven men. People are covered, absolutely covered in bacteria. Yes, that means you too … 15 showers a week notwithstanding. Everything is covered in bacteria, most of which are harmless or beneficial. Any story that starts with “we found germs on X” is already pointless unless you’re talking about Mars, the moon, or something that’s supposed to have been sterilized (like surgical equipment). So of course they found bacteria on beards. And I can promise you that if they swabbed any other part of those dudes, they’d also find bacteria. Amazing!

What we’d want to know is whether men with beards harbored more bacteria than men with clean-shaven faces. Which of course they didn’t look at.Fortunately, this question has been addressed in the scientific literature. A recent article titled “Bacterial ecology of hospital workers’ facial hair: a cross-sectional study” concluded that health care workers with and without beards harbored similar numbers of bacteria.

OK, so what about the kinds of bacteria? If we’re concerned about health, then the type of bacteria is far more important that the numbers....The microbiologist in this story says that they found “enteric” bacteria, which were the “kind of things that you’d find in feces.” Well, OK. Many members of the Enterobacteriaceae family are found in the gut (and therefore feces). Some are even pathogens. Most are not; some are beneficial, even essential for human health. Assuming that finding enteric bacteria equates to finding feces is like saying that finding cat hair on your couch means you’re at risk of being eaten by a lion. Members of the Enterobacteriaceae family can also be found on normal human skin, cheese, plants, seeds, water, and soil. I’d be willing to bet that you can find enteric bacteria pretty much everywhere if you look hard enough. And do those present a health risk? Probably not, as even the microbiologist in the original story admits.

IMG_3880Credit:Mara Silgailis at Lacto Bacto

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Get up every hour from your seat and walk a few minutes, and cut your risk of early death by 33% (by 41% in those with chronic kidney disease). Standing won't do it - have to move. Just make sure that little walk is not to the refrigerator. Other studies have found that sitting for long periods may increase the risk for chronic disease and early death. From Scientific American:

A Little Bit of Walking Can Add up to Improve Your Health

Want to reduce your risk of dying at a young age? Try walking casually for as little as 2 minutes per hour.While it is well known that intense exercise can help you get fitter, a new study has found that even a little exercise can still go a long way. Study participants who traded time on the sofa for a total of 30 minutes of walking during the day reduced their risk of dying over a three-year period by 33 percent.

For the participants with chronic kidney disease, the risk of dying was reduced by more than 40 percent, according to the findings, published today (April 30) in the Clinical Journal of the American Society of Nephrology.

The Physical Activity Guidelines for Americans, a complement to the government's diet guidelines, recommend that people do at least 75 minutes of high-intensity aerobic physical activity (such as running, swimming or biking), or 150 minutes of moderate-intensity activity (such as brisk walking) every week to reduce the risk of obesity, diabetes and other chronic diseases. But the researchers on the new study wanted to know what the minimum threshold was—the lowest amount of physical activity that could still provide health benefits, said Dr. Srinivasan Beddhu, a kidney specialist at the University of Utah School of Medicine in Salt Lake City and lead author of the new study. [How Many Calories Am I Burning? (Infographic)]

"This study specifically looked at what intensity of activity should be used to replace sedentary activity.... being sedentary is an active choice to indulge in activities that barely raise the energy expenditure above basal metabolic rate." That threshold of intensity, Beddhu said, appears to be low. The study found that "light-intensity activities," such as casual walking, are beneficial. In contrast, activities that are "low intensity," such as standing or writing at a desk, aren't enough to provide any meaningful health benefits, the study found.

For this study, Beddhu and his colleagues at the University of Utah and the University of Colorado used information from the National Health and Nutrition Examination Survey, which includes data collected from an accelerometer, a device that measures motion. This enabled the researchers to study the activities of more than 3,600 adults representing the general U.S. population, including 383 adults with chronic kidney disease. Over the course of three years, 137 of these participants died as a result of various causes. In general, those who exercised more were less likely to die during the study period.

Positive effects of exercise could be seen down to the level of 30 minutes per day of any kind of light activity....it could be attained merely by getting up to move around a few minutes every hour. The finding could be particularly beneficial for people with kidney disease, who tend to be sedentary and inactive throughout most of the day, Beddhu added.

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Guess what? Our microbiome (the collection of microbes living within and on us) also normally contains fungi. This is our mycobiome.  Very little is known about the mycobiome. (in contrast, much, much more is known about the bacteria within us) The fungi within us may be as low as 0.1% of the total microbiota (all our microbes). But what is known is because advanced genetic analyses have been done (specifically "next-generation” sequencing") or culturing of the fungi.

In some studies of fungi in healthy adults, nothing at all is known about up to 50% of the species found. And each human has a diversity or variety of fungi living within them, and these seem to vary between different parts of the body. What little is known is that fungi that we may have thought of as pathogenic (or no good) and involved in diseases (think Candida and Aspergillus) are also found normally in healthy individuals. For example, Candida were found in the mouth or oral microbiome of healthy adults as well as the gut of many healthy adults (thus part of a healthy microbial ecosystem). Some studies suggest that our diet influences which fungi species are present in the gut.

Fungi are both part of health and disease. They interact with the other microbes within us. Some fungi appear to prevent disease by competing with pathogenic organisms (bad bugs).They have functions in our body that we know very little about. We don't know much about disruptions to the fungi in our bodies or even how fungi come to live within us. The following excerpts are from a scholarly article summarizing what is known about our fungi or mycobiome. Written by Patrick C. Seed, from the Cold Spring Harbor Perspectives in Medicine:

The Human Mycobiome

Fungi are fundamental to the human microbiome, the collection of microbes distributed across and within the body... Here, a comprehensive review of current knowledge about the mycobiome, the collective of fungi within the microbiome, highlights methods for its study, diversity between body sites, and dynamics during human development, health, and disease. Early-stage studies show interactions between the mycobiome and other microbes, with host physiology, and in pathogenic and mutualistic phenotypes. Current research portends a vital role for the mycobiome in human health and disease.

In particular, the diversity and dynamics of the so-called mycobiome, the fungi distributed on and within the body, is poorly understood, particularly in light of the considerable association of fungi with infectious diseases and allergy (Walsh and Dixon 1996). Despite being as low as ≤0.1% of the total microbiota (Qin et al. 2010), the fungal constituents of the microbiome may have key roles in maintaining microbial community structure, metabolic function, and immune-priming frontiers, which remain relatively unexplored. Further questions exist as to how fungi interact cooperatively and noncooperatively with nonfungal constituents of the microbiome.

Fungal colonization of the term infant remains poorly characterized. Although it is known that fungi, such as Candida, are prevalent constituents of the vagina through which most infants are delivered, transmission to the newborn is not well documented, and assembly of additional environmental fungi into the microbiome has not been monitored in the otherwise healthy infant.

Although the microbiome of the healthy term infant remains poorly understood, more effort has been placed on understanding fungal colonization of preterm infants. Infants born 8 or more weeks before term and weighing ≤1500 g at birth are at significantly increased risk for invasive fungal disease, primarily with Candida species (spp.) these infants at risk of Candida colonization and infection.

Based on culture-dependent or genus/species-focused culture-independent methods of identification, the fungi of the oral cavity were previously believed to be few and relatively nondiverse. The genera Candida, Saccharomyces, Penicillium,Aspergillus, Scopulariopsis, and Genotrichum were among those previously reported.... In the oral samples from 20 participants, most had ∼15 fungal genera present...To put this level of diversity into context, prior studies have identified more than 50–100 bacterial genera in the healthy oral microbiome.

Of the oral fungal genera noted among each of the healthy subjects from the Ghannoum study (Ghannoum et al. 2010), Candida and Cladosporium were most common, present in 75% and 65% of participants, respectively. Fungal genera associated with local oral and invasive diseases, including Aspergillus,Cryptococcus, Fusarium, and Alternaria were also identified, indicating that these genera are present in the oral microbiome even during a state of health....The discovery of previously unidentified fungi is a reminder that the oral microbiome remains underexplored.

Although the bacterial constituents of the gut-associated microbiome have been intensely studied, the diversity and function of gut-associated fungi is understudied and lags far behind other aspects of microbiome studies.Only recently have larger studies specifically focused on the gut mycobiome been performed. Hoffmann et al. (2013).... from 98 healthy individuals without known gastrointestinal disease. In total, the researchers identified 66 fungal genera with 13 additional taxa for which a genus-level classification was not possible. An estimated 184 species were present in total. Eighty-nine percent of the samples had Saccharomyces present. Candida and Cladosporium were the second and third most prevalent, present in 57% and 42% of samples, respectively. The research was not able to definitively determine whether certain taxa were resident fungal microbota or transient as part of dietary intake.

Mutualism between fungi and humans is generally not well understood and has not been well studied. However, several examples related to the gut microbiome provide evidence of a beneficial relationship. S. boulardii, closely related to Saccharomyces cerevisiae, has been studied in controlled trials for the prevention and mitigation of antibiotic-associated diarrhea, including diarrhea caused by Clostridium difficile...These studies show the potency of fungi to compete with pathogenic organisms, modify intestinal function, and attenuate inflammation, presumably because of an interaction with the intestinal microbiota....A recent retrospective data review suggested an inverse relationship between Candida and C. difficile, pointing to some common impact of yeast on the gut microbiome and the exclusion of C. difficle outgrowth and/or toxin production (Manian and Bryant 2013).

Humans have a lifelong interaction with complex microbial communities distributed across the body, which fundamentally contributes to the development and physiology of the macro-organism. Only recently has the diversity of fungi within the human microbiome begun to be determined, with early studies showing that, although relatively nonabundant, fungi are diverse within the microbiome as a whole. Although still in the early stage, studies suggest complex interactions between fungal and bacterial constituents of the microbiome.

Microspcopic image of intestinal fungus. Credit: Iliyan Iliev

Published on Leave a comment on Some Childbirth Practices Mess With Needed Microbes

Currently, during birth there are many potential disruptions to the healthy development of the infant's microbial ecosystem. Some practices to be concerned about: the use of antibiotics during pregnancy and during delivery, c-sections, newborns routinely given antibiotics, and then bottle feeding instead of breastfeeding. Sometimes one or more of these practices are medically necessary, but currently they are being done much too frequently and casually. In these ways we are conducting an experiment on every baby's microbial ecosystem with unknown long-term consequences. The following excerpts from Dr.Martin Blaser's popular 2014 book Missing Microbes: How the Overuse of Antibiotics Is Fueling Our Modern Plagues, even though written a year ago, are a nice summary of these issues. From Wired:

The Way You’re Born Can Mess With the Microbes You Need to Survive

THROUGHOUT THE ANIMAL kingdom, mothers transfer microbes to their young while giving birth....And for millennia, mammalian babies have acquired founding populations of microbes by passing through their mothers’ vagina. This microbial handoff is also a critical aspect of infant health in humans. Today it is in peril.

Microbes play a hidden role in the course of every pregnancy. During the first trimester, certain species of bacteria become overrepresented while others become less common. By the third trimester, just before the baby is born, even greater shifts occur. These changes, involving scores of species, are not random. The compositions change in the same direction across the dozens of women who have been studied.... Women of reproductive age carry bacteria, primarily lactobacilli, which make the vaginal canal more acidic. This environment provides a hardy defense against dangerous bacteria that are sensitive to acid. Lactobacilli also have evolved a potent arsenal of molecules that inhibit or kill other bacteria.

Whether the birth is fast or slow, the formerly germ-free baby soon comes into contact with the lactobacilli. The baby’s skin is a sponge, taking up the vaginal microbes rubbing against it. The first fluids the baby sucks in contain mom’s microbes, including some fecal matter.

Once born, the baby instinctively reaches his mouth, now full of lactobacilli, toward his mother’s nipple and begins to suck. The birth process introduces lactobacilli to the first milk that goes into the baby. This interaction could not be more perfect. Lactobacilli and other lactic acid–producing bacteria break down lactose, the major sugar in milk, to make energy. The baby’s first food is a form of milk called colostrum, which contains protective antibodies. The choreography of actions involving vagina, baby, mouth, nipple, and milk ensures that the founding bacteria in the baby’s intestinal tract include species that can digest milk for the baby.

Breast milk, when it comes in a few days later, contains carbohydrates, called oligosaccharides, that babies cannot digest. But specific bacteria such as Bifidobacterium infantis, another foundational species in healthy babies, can eat the oligosaccharides. The breast milk is constituted to give favored bacteria a head start against competing bacteria.

Cesarian delivery is a largely unrecognized threat to the microbial handoff from mother to child. Instead of traveling down the birth canal picking up lactobacilli, the baby is surgically extracted from the womb through an incision in the abdominal wall....For all of these reasons, U.S. C-section rates increased from fewer than one in five births in 1996 to one in three births in 2011—a 50 percent increase.

The founding populations of microbes found on C-section infants are not those selected by hundreds of thousands of years of human evolution. A few years ago in Puerto Ayacucho, Venezuela, my wife, Gloria, conducted the first study of its kind to test whether the microbes found on newborn babies delivered vaginally or by C-section varied in any way....The mouths, skin, and first bowel movements of babies born vaginally were populated by their mother’s vaginal microbes: Lactobacillus, Prevotella, or Sneathia species. Those born by C-section harbored bacterial communities found on skin, dominated by Staphylococcus, Corynebacterium, and Propionibacterium.

In other words, their founding microbes bore no relationship to their mother’s vagina or any vagina. At all the sites—mouth, skin, gut—their microbes resembled the pattern on human skin and organisms floating in the air in the surgery room. They were not colonized by their mother’s lactobacilli. The fancy names of these bacteria don’t matter as much as the notion that the founding populations of microbes found on C-section infants are not those selected by hundreds of thousands of years of human evolution or even longer.

Another threat to a baby’s newly acquired resident microbes involves antibiotics given to the mother. Most doctors consider it safe to prescribe penicillins for all sorts of mild infections in pregnancy—coughs, sore throats, urinary tract infections. Sometimes when doctors think that the mother has a viral infection they also give antibiotics just in case it is actually a bacterial infection.

Then comes the birth itself. Women in labor routinely get antibiotics to ward off infection after a C-section....Antibiotics are broad in their effects, not targeted....The problem, of course, is that we know antibiotics are broad in their effects, not targeted. While the antibiotic kills Group B strep, it also kills other often-friendly bacteria, thus selecting for resistant ones. This practice is altering the composition of the mother’s microbes in all compartments of her body just before the intergenerational transfer is slated to begin.

The baby also is affected in similar unintended ways. Any antibiotic that gets into the bloodstream of the fetus or into the mother’s milk will inevitably influence the composition of the baby’s resident microbes, but we are only beginning to understand what this means.

Finally, the babies are directly exposed. Most parents are not aware that all American-born babies today are given an antibiotic immediately after birth. The reason is that many years ago, before antibiotics, women who unknowingly had gonorrhea would pass the infection to their babies, giving the newborns terrible eye infections that could cause blindness...The dose is low but is likely affecting the composition of the infant’s resident microbes just when the founding populations are developing. We should be able to develop a better way to screen, so we can target those babies at the highest risk, perhaps a few hundred among the millions of births a year.

Although babies are born into a world replete with diverse bacteria, the ones that colonize them are not accidental. These first microbes colonizing the newborn begin a dynamic process. We are born with innate immunity, a collection of proteins, cells, detergents, and junctions that guard our surfaces based on recognition of structures that are widely shared among classes of microbes. In contrast, we must develop adaptive immunity that will clearly distinguish self from non-self. Our early-life microbes are the first teachers in this process, instructing the developing immune system about what is dangerous and what is not.

A newborn infant, seconds after delivery. Amniotic fluid glistens on the child's skin.  Credit: Wikipedia, Ernest F

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Published on 1 Comment on Obesity Markers Found In Urine

You can deceive yourself by calling yourself "big-boned" or "hefty", but your urine doesn't lie! Researchers found 29 biological markers in urine that are associated with body mass. These biological markers in urine are a "metabolic signature" of obesity. Note: Body mass index (BMI) is a measure of body fat based on height and weight that applies to adult men and women. From Medical Xpress:

Urine profiles provide clues to how obesity causes disease

Scientists have identified chemical markers in urine associated with body mass, providing insights into how obesity causes disease. Being overweight or obese is associated with higher risk of heart disease, stroke, diabetes and cancer, but the mechanisms connecting body fat and disease are not well understood.

The new study, led by Imperial College London, shows that obesity has a 'metabolic signature' detectable in urine samples, pointing to processes that could be targeted to mitigate its effects on health. 

Urine contains a variety of chemicals known as metabolites, from a vast range of biochemical processes in the body. Technologies that analyse the metabolic makeup of a sample can therefore offer huge amounts of information that reflects both a person's genetic makeup and lifestyle factors.

The Imperial researchers analysed urine samples from over 2,000 volunteers in the US and the UK. They found 29 different metabolic products whose levels correlated with the person's body mass index, and how they fit together in a complex network that links many different parts of the body.

Some of these metabolites are produced by bacteria that live in the gut, highlighting the potentially important role these organisms play in obesity. Altered patterns of energy-related metabolites produced in the muscles were also identified as being linked to obesity.

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Every time you inhale, you suck in thousands of microbes. And depending on where you live, the microbes will vary. From Wired:

An Atlas of the Bacteria and Fungi We Breathe Every Day

EVERY TIME YOU inhale, you suck in thousands of microbes. (Yes, even right then. And just then, too.) But which microbes? Scientists mostly assumed that the living components of air—at the tiniest scales, anyway—were the same no matter where you went.

And? Not true, it turns out. Thanks to a 14-month citizen-science project that sampled and analyzed airborne dust around the country, researchers have constructed the first atlas of airborne bacteria and fungi across the continental US. And airborne microscopic life is really diverse.

More than 1,400 volunteers swabbed surfaces in 1,200 houses around the country, focusing on the places people don’t usually clean. The dust there passively collects microbes. In the end those swabs revealed about 112,000 bacterial and 57,000 fungal phylotypes (i.e. familial groups).

Most of these little guys were harmless. The few pathogens and allergens ended up being location-specific. Alternaria, a fungal genus that’s also a common allergen, is ubiquitous but concentrates most in the midwest. The fungus Cladosporium has smaller hotspots scattered all over the country east of Texas, most frequently in the South and Mid-Atlantic. Meanwhile, the bacterial genus Cellulomonas, an normally harmless microbe (but an emerging pathogen according to one study), is much more common in the west.

The two biggest factors that shape this airborne environment, according to study author and University of Colorado microbial ecologist Noah Fierer, are the types of soil and plants that are located in the area (affecting the acidity in the environment), and the climate (humidity, temperature, etc.) Cities, for example, tended to be more like other cities than the rural areas nearby, which Fierer attributes to urban areas tending to plant the same types of trees and flowers and playing host to the same types of wildlife (pigeons, rats, etc).

Clasdosporium is a genus of fungi including some of the most common indoor and outdoor molds. Credit: Wikipedia.

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Since so many people are taking Vitamin D supplements because of its supposed health benefits, the question becomes - how much is too much? For those desiring to take vitamin D supplements, what is a good maintenance dosage to take daily? That question has not been answered from the studies I've seen other than 1000 units per day is safe. However, sunlight is the best and safest source of vitamin D (even though that makes dermatologists nuts because of their concern with sunlight leading to skin cancer).From Science Daily:

Vitamin D toxicity rare in people who take supplements, researchers report

Over the last decade, numerous studies have shown that many Americans have low vitamin D levels and as a result, vitamin D supplement use has climbed in recent years. Vitamin D has been shown to boost bone health and it may play a role in preventing diabetes, cancer, cardiovascular disease and other illnesses. In light of the increased use of vitamin D supplements, Mayo Clinic researchers set out to learn more about the health of those with high vitamin D levels. They found that toxic levels are actually rare.

A vitamin D level greater than 50 nanograms per milliliter is considered high. Vitamin D levels are determined by a blood test called a serum 25-hydroxyvitamin D blood test. A normal level is 20-50 ng/mL, and deficiency is considered anything less than 20 ng/mL, according the Institute of Medicine (IOM).

The researchers analyzed data collected between 2002 and 2011 from patients in the Rochester Epidemiology Project...Of 20,308 measurements, 8 percent of the people who had their vitamin D measured had levels greater than 50 ng/mL, and less than 1 percent had levels over 100 ng/mL.

"We found that even in those with high levels of vitamin D over 50 ng/mL, there was not an increased risk of hypercalcemia, or elevated serum calcium, with increasing levels of vitamin D," says study co-author Thomas D. Thacher, M.D., a family medicine expert at Mayo Clinic. Hypercalcemia, or high blood calcium, can occur when there are very high levels of vitamin D in the blood. Too much calcium in the blood can cause weakness, lead to kidney stones, and interfere with the heart and brain, and even be life threatening.

The Mayo researchers also found that women over age 65 were at the highest risk of having vitamin D levels above 50 ng/mL. The result was not surprising because that's a group that often takes vitamin D supplements, Dr. Thacher says. Another notable outcome: The occurrence of high vitamin D levels over 50 ng/mL increased during the 10-year period of the study, from nine per 100,000 people at the start of the study up to 233 per 100,000 by the end.

Only one case over the 10-year study period was identified as true acute vitamin D toxicity; the person's vitamin D level was 364 ng/mL. The individual had been taking 50,000 international units (IU) of vitamin D supplements every day for more than three months, as well as calcium supplements. The IOM-recommended upper limit of vitamin D supplementation for people with low or deficient levels is 4,000 IU a day. 

Some natural sources of vitamin D include oily fish such as mackerel and salmon, fortified milk, and sunlight.

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This nice general summary of what scientists know about the microbial community within us was just published by a division of the NIH (National Institutes of Health). Very simple and basic. From the National Institute of General Medical Sciences (NIGMS):

Facts about our microbial menagerie

Trillions of microorganisms inhabit us -- inside and out. Scientists are surveying these microbial metropolises to learn more about their role in health. Microbiologists Darren Sledjeski of the National Institutes of Health (NIH) and Andrew Goodman of Yale University share a few details of what researchers have learned so far.

1. The majority of the microbes that inhabit us are bacteria. The rest of the microbial menagerie is fungi and viruses, including ones that infect the bacteria! Collectively, our resident microorganisms are referred to as the human microbiota, and their genomes are called the human microbiome.

2. Our bodies harbor more bacterial cells than human ones. Even so, the microbiota accounts for less than 3 percent of a person's body mass. That's because our cells are up to 10,000 times bigger in volume than bacterial cells.

3. Your collection of bacteria has more genes than you do. Scientists estimate that the genomes of gut bacteria contain 100-fold or more genes than our own genomes. For this reason, the human microbiome is sometimes called our second genome.

4. Most of our microbes are harmless, and some are helpful. For example, harmless microbes on the skin keep infectious microbes from occupying that space. Microbes in the colon break down lactose and other complex carbohydrates that our bodies can't naturally digest.

5. Different microbes occupy different parts of the body. Some skin bacteria prefer the oily nooks near the nose, while others like the dry terrain of the forearm. Bacteria don't all fare well in the same environment and have adapted to live in certain niches.

6. Each person's microbiota is unique. The demographics of microbiota differ among individuals. Diet is one reason. Also, while a type of microbe might be part of one person's normal microbial flora, it might not be part of another's, and could potentially make that person sick.

7. Host-microbial interactions are universal. Microbial communities may vary from person to person, but everyone's got them, including other creatures. For this reason, researchers can use model organisms to tease apart the complexities of host-microbial interactions and develop broad principles for understanding them. The mouse is the most widely used animal model for microbiome studies.

8. The role of microbiota in our health isn't entirely clear. While it's now well accepted that the microbial communities that inhabit us are actively involved in a range of conditions -- from asthma to obesity -- research studies have not yet pinpointed why or how. In other words, the results may suggest that the presence of a bacterial community is associated with a disease, but they don't show cause and effect.

9. Most of our microbes have not been grown in the lab. Microbes require a certain mix of nutrients and other microbes to survive, making it challenging to replicate their natural environments in a petri dish. New culturing techniques are enabling scientists to study previously uncultivated microbes.

10. The impact of probiotic and prebiotic products isn't clear. Fundamental knowledge gaps remain regarding how these products may work and what effects they might have on host-microbial interactions. A new NIH effort to stimulate research in this area is under way.

11. There's even more we don't know! Additional areas of research include studying the functions of microbial genes and the effects of gut microbes on medicines. The more we learn from these and other studies, the more we'll understand how our normal microbiota interacts with us and how to apply that knowledge to promote our health.

Lactobacilli. Credit: Wikipedia.

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A recent study confirms all my recent posts on the importance of fiber, fruits, vegetables, whole grains, seeds, nuts, and legumes for beneficial gut bacteria health (have to feed the them!). This study found dramatic changes in the colon (specifically in the colonic mucosa) from dietary changes in as little as 2 weeks.

In the study, for 2 weeks the Americans ate the typical low-fat, high fiber diet of South Africa which included foods such as hi-maize corn fritters, beans, salmon croquettes, spinach, red pepper and onions, homemade tater tots, mango slices,okra, tomatoes, corn muffins, black-eyed peas, catfish nuggets, navy bean soup, banana, lentils, rice, fish taco (tilapia), and pineapple. Meanwhile, people in South Africa ate an “American” high-fat, low-fiber diet. Foods included beef sausage links and pancakes for breakfast; hamburger and French fries for lunch; and meatloaf and rice for dinner. Plus all sorts of American favorites such as macaroni and cheese, steak, beef hot dog and beans.

The African style low fat and high fiber diet contained about 55 grams of fiber per day, and the American diet (low fiber and high fat ) had about 14 grams of fiber per day (which is typical of a Western diet). Bottom line: fiber feeds beneficial microbes in the gut, which results in beneficial changes in the gut (in the mucosa of the colon). From Science Daily:

Diet swap has dramatic effects on colon cancer risk for Americans and Africans

Scientists have found dramatic effects on risk factors for colon cancer when American and African volunteers swapped diets for just two weeks. Western diets, high in protein and fat but low in fibre, are thought to raise colon cancer risk compared with African diets high in fibre and low in fat and protein.The new study, published in Nature Communications today, confirms that a high fibre diet can substantially reduce risk, and shows that bacteria living in the gut play an important role in this effect.

Colon cancer is the fourth commonest cause of death from cancer worldwide, accounting for over 600,000 deaths per year. Colon cancer rates are much higher in the western world than in Africa or the Far East, yet in the United States, African Americans shoulder the greatest burden of the disease.

To investigate the possible roles of diet and gut bacteria, an international team including scientists from the University of Pittsburgh and Imperial College London carried out a study with a group of 20 African American volunteers and another group of 20 participants from rural South Africa. The two groups swapped diets under tightly controlled conditions for two weeks.... At the start, when the groups had been eating their normal diets, almost half of the American subjects had polyps -- abnormal growths in the bowel lining that may be harmless but can progress to cancer. None of the Africans had these abnormalities.

After two weeks on the African diet, the American group had significantly less inflammation in the colon and reduced biomarkers of cancer risk. In the African group, measurements indicating cancer risk dramatically increased after two weeks on the western diet.

"The findings suggest that people can substantially lower their risk of colon cancer by eating more fibre. This is not new in itself but what is really surprising is how quickly and dramatically the risk markers can switch in both groups following diet change. These findings also raise serious concerns that the progressive westernization of African communities may lead to the emergence of colon cancer as a major health issue."

Professor Stephen O'Keefe at the University of Pittsburgh, who directed the study, said: "Studies on Japanese migrants to Hawaii have shown that it takes one generation of westernization to change their low incidence of colon cancer to the high rates observed in native Hawaiians. Our study suggests that westernization of the diet induces changes in biomarkers of colon cancer risk in the colonic mucosa within two weeks. Perhaps even more importantly, a change in diet from a westernized composition to a 'traditional African' high fiber low fat diet reduced these biomarkers of cancer risk within two weeks, indicating that it is likely never too late to change your diet to change your risk of colon cancer."

The study found that a major reason for the changes in cancer risk was the way in which the bacteria in the gut -- known as the microbiome -- altered their metabolism to adapt to the new diet. In the American group, the researchers found that the African diet led to an increase in the production of butyrate, a byproduct of fibre metabolism that has important anti-cancer effects.

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Another study finding negative effects of air pollution - this time high levels of traffic-related air pollution is linked to slower cognitive development among 7 to 10 year old children in Barcelona, Spain. From Science Daily:

Air pollution linked to slower cognitive development in children

Attendance at schools exposed to high levels of traffic-related air pollution is linked to slower cognitive development among 7- to 10-year-old children in Barcelona, according to a new study.

The researchers measured three cognitive outcomes (working memory, superior working memory, and attentiveness) every 3 months over a 12-month period in 2715 primary school children attending 39 schools. By comparing the development of these cognitive outcomes in the children attending schools where exposure to air pollution was high to those children attending a school with a similar socio-economic index where exposure to pollution was low, they found that the increase in cognitive development over time among children attending highly polluted schools was less than among children attending paired lowly polluted schools, even after adjusting for additional factors that affect cognitive development.

Thus, for example, there was an 11.5% 12-month increase in working memory at the lowly polluted schools but only a 7.4% 12-month increase in working memory at the highly polluted schools. These results were confirmed using direct measurements of traffic related pollutants at schools.

The findings suggest that the developing brain may be vulnerable to traffic-related air pollution well into middle childhood, a conclusion that has implications for the design of air pollution regulations and for the location of new schools. While the authors controlled for socioeconomic factors, the accuracy of these findings may be limited by residual confounding, that is, the children attending schools where traffic-related pollution is high might have shared other unknown characteristics that affected their cognitive development.