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Category: microbes

Published on Leave a comment on Urinary Tract Infections and D-Mannose

Image result for pills wikipedia My last post was about a recent Medscape article discussing whether probiotics can be used to treat urinary tract infections (UTIs) (answer: probiotics are promising, but too little is known right now to recommend any). Two alternative treatments that the article did not discuss were drinking cranberry juice or taking cranberry supplements (studies are currently mixed regarding their effectiveness in UTIs - possibly due to varying cranberry products and doses used) and taking D-mannose supplements (whether as a powder or pill).

D-mannose is recommended on alternative medical sites as an effective treatment for UTIs caused by E.coli, including recurrent UTIs. Studies show that up to 90% of UTIs are caused by E. coli.The majority of both males and females writing comments about UTI treatments on these sites and for D-mannose product reviews (on Amazon) rave about D-mannose as the only treatment that worked for them after suffering from recurrent UTIs (antibiotics typically did not work well for them).

D-mannose is a naturally occurring sugar found in a number of fruits, especially cranberries and blueberries. D-mannose is effective because it attaches to E. coli bacteria, and prevents them from attaching to the walls of the urinary tract. (Researchers write that D-mannose "inhibits bacterial adhesion to uroepithelial cells.") Persons taking D-mannose are also advised to drink plenty of water, which then flushes out the bacteria.

The typical dose of D-mannose for UTI treatment is 500 mg, in capsule or powder form, taken in a glass of water or juice, every few hours for five days (perhaps 5 or 6 tablets a day). Then continue taking for a few days after all symptoms go away to make sure all the bacteria are flushed out of the urinary tract.

Many long-term recurrent UTI sufferers continue taking D-mannose at lower doses to prevent the UTIs from recurring. There are no known side-effects. D-mannose is easily found at grocery stores, health food stores, and online.

After doing a D-mannose and urinary tract infection search using PubMed (from Medline, the National Institute of Health), I found that currently there is only one published study looking at the use of D-Mannose in urinary tract infections.

The 2014 study by B. Kranjcec, D. Papes, and S. Altarac looked at the effectiveness of D-mannose powder for recurring urinary tract infections in women. 308 women with a history of recurrent UTIs were first treated with an antibiotic (ciprofloxacin) for an UTI, and then were randomly assigned to one of 3 groups for 6 months. The 3 groups were: D-mannose (2 g of D-mannose in 200 ml water daily), or prophylactic antibiotics (50 mg Nitrofurantoin daily) or a control group that didn't take anything (no prophylaxis).

Results were that 98 patients (31.8%) had a recurrent UTI. Of those 98, 14.6% (15 women) were in the D-mannose group, 20.4% (21 women) in the Nitrofurantoin antibiotic group, and 60.8%  (62 women) in the no treatment (no prophylaxis) group. In other words, the D-mannose group did the best in preventing recurrences, even better than the antibiotic. 

From World Journal of Urology: D-mannose powder for prophylaxis of recurrent urinary tract infections in women: a randomized clinical trial.

Overall 98 patients (31.8%) had recurrent UTI: 15 (14.6) in the D-mannose group, 21 (20.4) in Nitrofurantoin group, and 62 (60.8) in no prophylaxis group, with the rate significantly higher in no prophylaxis group compared to active groups (P < 0.001). Patients in D-mannose group and Nitrofurantoin group had a significantly lower risk of recurrent UTI episode during prophylactic therapy compared to patients in no prophylaxis group (RR 0.239 and 0.335, P < 0.0001). In active groups, 17.9% of patients reported side effects but they were mild and did not require stopping the prophylaxis. Patients in D-mannose group had a significantly lower risk of side effects compared to patients in Nitrofurantoin group (RR 0.276, P < 0.0001), but the clinical importance of this finding is low because Nitrofurantoin was well tolerated.

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Amusing but also scary. The negative effects on the gut microbes of one person consuming an all fast food diet for 10 days occurred very quickly, and his gut microbes did not recover even 2 weeks after the fast food diet ended. Biggest problem seemed to be loss of gut diversity - about 40% of his gut bacterial species. Loss of gut diversity is considered a sign of ill health. Written by Tim Spector, with Tom Spector's assistance, from The Conversation:

Your gut bacteria don’t like junk food – even if you do

When Morgan Spurlock famously spent a month eating large portions of McDonalds for the purposes of his documentary Supersize Me, he gained weight, damaged his liver and claimed to have suffered addictive withdrawal symptoms. This was popularly attributed to the toxic mix of carbs and fat plus the added chemicals and preservatives in junk foods. But could there be another explanation?

We may have forgotten others who really don’t enjoy fast food. These are the poor creatures that live in the dark in our guts. These are the hundred trillion microbes that outnumber our total human cells ten to one and digest our food, provide many vitamins and nutrients and keep us healthy. 

For the sake of science and research for my book The Diet Myth, I have been experimenting with several unusual diets and recorded their effects on my gut microbes...My son Tom, a final year student of genetics at the University of Aberystwyth suggested an additional crucial experiment: to track the microbes as they changed from an average western diet to an intensive fast food diet for over a week.

I wasn’t the ideal subject since I was no longer on an average diet, but Tom, who like most students enjoyed his fast food, was. So he agreed to be the guinea pig on the basis that I paid for all his meals and he could analyse and write up his results for his dissertation. The plan was to eat all his meals at the local McDonalds for ten days. He was able to eat either a Big Mac or Chicken nuggets, plus fries and Coke. For extra vitamins he was allowed beer and crisps in the evening. He would collect poo samples before, during and after his diet and send them to three different labs to check consistency.

While it was clear the intensive diet had made him feel temporarily unwell, we had to wait a few months for the results to arrive back....They all told the same story: Tom’s community of gut microbes (called a microbiome) had been devastated.

Tom’s gut had seen massive shifts in his common microbe groups for reasons that are still unclear. Firmicutes were replaced with Bacteroidetes as the dominant type, while friendly bifidobacteria that suppress inflammation halved. However the clearest marker of an unhealthy gut is losing species diversity and after just a few days Tom had lost an estimated 1,400 species – nearly 40% of his total. The changes persisted and even two weeks after the diet his microbes had not recovered. Loss of diversity is a universal signal of ill health in the guts of obese and diabetic people and triggers a range of immunity problems in lab mice.

That junk food is bad for you is not news, but knowing that they decimate our gut microbes to such an extent and so quickly is worrying...We rely on our bacteria to produce much of our essential nutrients and vitamins while they rely on us eating plants and fruits to provide them with energy and to produce healthy chemicals which keep our immune system working normally.

We are unlikely to stop people eating fast food, but the devastating effects on our microbes and our long term health could possibly be mitigated if we also eat foods which our microbes love like probiotics (yogurts), root vegetables, nuts, olives and high-fibre foods. What they seem to crave, above all else, is food diversity and a slice of gherkin in the burger just isn’t enough.

Tom Spector. Credit: Tim Spector

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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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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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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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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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There has been a lot of discussion in the last few years of our gut bacteria (hundreds of species), the microbiome (the community of microbes living within and on a person (gut, nasal cavities, mouth, sinuses, etc.), probiotics, the finding of a link between bacteria and some chronic diseases, and how the modern lifestyle and antibiotics are wiping out our beneficial gut microbes. I am frequently asked how one can improve or nurture the beneficial bacteria in our bodies.

While no one knows what exactly is the "best" or "healthiest" microbial composition of the gut, it does look like a diversity of bacteria is best (may make you healthier and more able to resist diseases). Research also suggests that the diversity and balance of bacteria living in the body can be changed and improved, and changes can occur very quickly. And that the microbial communities fluctuate for various reasons (illness, diet,etc.). Diet seems to be key to the health of your gut microbial community. Prebiotics feed the beneficial bacteria in the gut, probiotics are live beneficial bacteria, and synbiotics are a combination of prebiotics and probiotics. But don't despair - you can improve your gut microbial community starting now. The following are some practical tips, based on what scientific research currently knows.

SOME STEPS TO FEED AND NURTURE YOUR GUT MICROBES:

Eat a wide variety of foods, especially whole foods that are unprocessed or as minimally processed as possible. Eat everything in moderation.

Eat a lot of plant based foods: fruits, vegetables, whole grains, seeds, nuts, and legumes. Think of Michael Pollan's advice: "Eat food. Not too much. Mostly plants."

Eat more washed and raw fruits and vegetables (lots of bacteria and fiber to feed and nurture the bacteria). Some every day would be good.

Eat more soluble and insoluble types of fiber, and increase how many servings you eat every day. A variety of  fiber foods every day, and several servings at each meal, is best. Think fruits, vegetables, whole grains, legumes, nuts, seeds. (See How Much Dietary Fiber Should We Eat? - also has a chart with high fiber foods, and Recent Studies Show Benefits of Dietary Fiber)

Eat as many organic foods as possible. There is much we don't yet know, and pesticides are like antibiotics - they kill off microbes, both good and bad. Somehow I think that lowering the levels in your body of pesticides (as measured in blood and urine) can only be beneficial. Also, organic foods don't contain added antibiotics and hormones. (Eat Organic Foods to Lower Pesticide Exposures).  But even if you can't or won't eat organic foods, it is still better to eat non-organic fruits, vegetables, and whole grains than to not eat them.

Eat some fermented foods such as kimchi and sauerkraut (they contain live bacteria), kefir, and yogurts with live bacteria. Eat other bacteria containing foods such as cheeses, and again a variety is best (different cheeses have different bacteria).

Try to avoid or eat less of mass-produced highly processed foods, fast-foods, preservatives, colors and dyes, additives, partially hydrogenated oils, and high-fructose corn syrup. Read all ingredient lists on labels, and even try to avoid as much as possible "natural flavors" (these are chemicals concocted in a lab and unnecessary). Even emulsifiers (which are very hard to avoid) are linked to inflammation and effects on gut bacteria.

Avoid the use of triclosan or other "sanitizers" in soaps and personal care products (e.g., deodorants). Triclosan promotes antibiotic resistance and also kills off beneficial bacteria. Wash with ordinary soap and water.

Avoid unnecessary antibiotics (antibiotics kill off bacteria, including beneficial bacteria).

Vaginal births are best - microbes from the birth canal populate the baby as it is being born. If one has a cesarean section, then one can immediately take a swab of microbes from the mother's vagina (e.g., using sterile gauze cloth) and swab it over the newborn baby. (See post discussing this research by Maria Gloria Dominguez Bello )

Breastfeeding is best - breastfeeding provides lots of beneficial microbes and oligosaccharides that appear to enrich good bacteria in the baby’s gut.

Live on a farm, or try to have a pet or two. Having pets, especially in the first year of life,  ups exposure to bacteria to help develop and strengthen the immune system, and prevent allergies. Pets such as dogs and cat expose humans to lots of bacteria.

Get regular exercise or physical activity. Professional athletes have more diverse gut bacterial community (considered beneficial) than sedentary people.

Can consider taking probiotics - whether in foods or supplements. They are generally considered beneficial, but not well studied, so much is unknown. The supplements are unregulated, and the ones available in stores may not be those that are most commonly found in healthy individuals. Research the specific bacteria before taking any supplements. Researchers themselves tend to stay away from probiotic supplements and focus on eating a variety of all the foods mentioned above (fruits, vegetables, whole grains, seeds, nuts, legumes, fermented foods) to feed and nurture beneficial bacteria.

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The science world has recently been abuzz with the results finding that an isolated American Indian group (the Yanomami) in the Venezuelan  Amazon have the most diverse microbiome (microbial community) ever discovered in humans.About double those found in humans living in the U.S. The scientists suggest that our Western lifestyle with processed foods, antibiotic use, sanitation, use of antibacterials, Cesarean sections, bottle-feeding (instead of breastfeeding) all have reduced microbial diversity in humans living in developed countries such as the United States. It is currently thought that reduced diversity is linked to some chronic diseases and even some cancers.From Nature:

Bacteria bonanza found in remote Amazon village

An isolated American Indian group in the Venezuelan Amazon hosts the most-diverse constellation of microbes ever discovered in humans, researchers reported on 17 April in Science Advances1.Surprisingly, the group's microbiome includes bacteria with genes that confer antibiotic resistance — even though its members, part of the Yanomami tribe, are not thought to have been exposed to the drugs.

But scientists still do not understand all the factors that determine the make-up of a person's microbiome. “We do know that food, environment and chemicals play the big roles,” says Sarkis Mazmanian, a microbiologist at the California Institute of Technology in Pasadena. The wide adoption of antibiotics, rigorous hygiene and processed diets is thought to have have cut down the genetic diversity of microbiomes in the developed world.

This makes the microbiomes of individual Yanomami particularly interesting, Dominguez-Bello says. The researchers took oral, faecal and skin samples from 34 people in a small Yanomami community that was unknown to the Western world until 2008, when it was spotted by helicopter....When researchers analysed the microbial DNA in those samples, they found that the average Yanomami's microbiota had twice as many genes as that of the average US person. More surprisingly, the Yanomami microbiome was even more diverse than those reported for other indigenous groups in South America and in Africa.

From New Scientist: Is super-diverse Amazon microbiome something to strive for?

The Yanomami people in the Venezuelan rainforest have the most diverse population of gut microbes ever seen, far more varied than Western guts. Does it matter?

Hunter-gathering in the rainforests and mountains of northern Brazil and southern Venezuela, the Yanomami eat a high-fibre diet based largely on cassava. For thousands of years, some groups have lived without contact with the rest of the world and are thought to be some of the few remaining communities never to have been exposed to antibiotics, which can wipe out the microbes in your gut.Sequencing the genes in the faecal samples revealed that the Yanomami carried nearly double the diversity of microbial species in their intestines compared with people living in the US. They also had about 30 to 40 per cent more diversity than a less isolated group of Venezuelan hunter-gatherers that has largely maintained its traditional lifestyle but has occasionally used antibiotics and eaten processed foods.

"Our results suggest that Westernisation leads to the reduction of diversity, to different microbiota compositions," Maria Dominguez-Bello of the New York University School of Medicine, who led the research, told a teleconference on Wednesday. Her colleague Jose Clemente of the Icahn School of Medicine at Mount Sinai in New York, said the results suggest that even minimal exposure to modern lifestyle practices such as using antibacterial soaps and cleansers, taking antibiotics and having Caesarean sections, which mean babies don't pass through their mother's birth canal and pick up her microbes, can result in a dramatic loss of microbial biodiversity.

So does a more diverse microbiome make for a healthier person? Possibly. Healthier people do seem to host a more diverse array of microbes but it's hard to know whether one causes the other. There is some evidence that losing certain microbial species is linked to some cancers, plus giving mice antibiotics can make them gain weight, so perhaps a good mix of microbes in your gut can keep you from piling on the pounds.

Walter doesn't recommend striving drastically to make the paltry Western gut look more Yanomamian. Poor sanitation is probably one factor contributing to the Papua New Guinean's high microbial diversity, but they have high levels of infectious diarrhoea as a result – not a situation that Western urbanised nations would want to return to.