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Try to avoid triclosan. Read labels (especially soaps, personal care, and household cleaning products) and avoid anything that says it contains triclosan, or is anti-bacterial, anti-fungal, anti-microbial, or anti-odor. We easily absorb triclosan into our bodies, and it has been detected in our urine, blood, and breast milk. Among its many negative effects (e.g., here and here) is that it is now linked to disruption of gut bacteria.

The gut microbiome performs vital functions in our bodies. Deviation from the normal microbiome (our microbial communities being out of whack) is known as dysbiosis. Dysbiosis has been associated with human diseases, including diabetes, heart disease, arthritis, and malnutrition. The researchers used zebrafish because they are commonly used to study impacts of various chemicals on gut microbial communities. So yes, the findings are valid and match what other studies have found. So please try to avoid triclosan. From Science Daily:

Common antimicrobial agent rapidly disrupts gut bacteria

A new study suggests that triclosan, an antimicrobial and antifungal agent found in many consumer products ranging from hand soaps to toys and even toothpaste, can rapidly disrupt bacterial communities found in the gut.The research was published in PLOS ONE by scientists from Oregon State University. It was based on findings made with zebrafish, which researchers believe are an important animal model to help determine possible human biological and health impacts of this antimicrobial compound.

Triclosan was first used as a hospital scrub in the 1970s and now is one of the most common antimicrobial agents in the world, found in shampoos, deodorants, toothpastes, mouth washes, kitchen utensils, cutting boards, toys, bedding, socks and trash bags. It continues to be used in medical settings, and can be easily absorbed through the skin.

"However, there's now a growing awareness of the importance of the bacteria in our gut microbiome for human health, and the overuse of antibiotics that can lead to the rise of 'superbugs.' There are consequences to constantly trying to kill the bacteria in the world around us, aspects we're just beginning to understand."

In the new study, researchers found that triclosan exposure caused rapid changes in both the diversity and composition of the microbiome in the laboratory animals. It's not clear what the implication may be for animal or human health, but scientists believe that compromising of the bacteria in the intestinal tract may contribute to the development or severity of disease. Some bacteria were more susceptible to the impact of triclosan than others, such as the family Enterobacteriaceae; and others were more resilient, such as the genus Pseudomonas.

The gut-associated microbiome performs vital functions for human health, prevents colonization with pathogens, stimulates the development of the immune system, and produces micronutrients needed by the host. Dysfunction of this microbiome has been associated with human disease, including diabetes, heart disease, arthritis and malnutrition, the scientists pointed out in their study.

Triclosan has been a concern in part because it is so widely used, and it's also readily absorbed through the skin and gastrointestinal tracts, showing up in urine, feces and breast milk. It also has been associated with endocrine disruption in fish and rats, may act as a liver tumor promoter, and can alter inflammatory responses.

In a newly published study looking at how infant gut microbes change over time, once again babies had differences in gut bacteria depending on whether they were delivered vaginally or by Cesarean section. But what's interesting is that stopping breastfeeding changed their gut bacteria  more (to more adult-like species) than just introducing solid foods. Certain types of bacteria thrive on the nutrients breast milk provides and once these nutrients are no longer available, then other bacteria emerge that are more commonly seen in adults.In other words, stopping breastfeeding seems to drive "maturation" of the gut bacteria. From The Scientist:

Maturation of the Infant Microbiome

Like babies themselves, the intestinal microbiomes of infants start out in an immature state and over time grow into communities similar to those of adults. In a new survey of 98 Swedish babies whose microbiota were sampled several times during their first year of life, researchers found that the microbiomes of breastfed infants persisted in a “younger” state longer than those of non-breastfed babies, even after the introduction of solid foods.

The conclusion that “stopping breastfeeding—rather than introducing solids—drives maturation is a new idea, because we all thought so far that solids introduction was a key factor in changing the microbiota,” said Maria Gloria Dominguez-Bello, a microbiologist at New York University School of Medicine who did not participate in the study.

Researchers from University of Gothenburg in Sweden and their colleagues found more adult-like taxa in the microbiomes of babies who stopped breastfeeding earlier, while the microbiota of babies breastfed for longer were dominated by bacteria present in breastmilk. The results, published today (May 13) in Cell Host & Microbe, are part of an effort to catalog the microbial changes that occur as children age and to note how those changes correlate with health and disease. Fredrik Bäckhed of Gothenburg and his colleagues collected stool samples from 98 moms and their newborns, and again sampled the babies’ stool at four and 12 months.

Confirming previous work, his team’s analysis found that the 15 babies born via cesarean section were colonized by different bacteria—many from oral and skin communities—than babies born vaginally, who shared numerous microbes with those present in their mothers’ stool.

For instance, in the vaginally delivered newborns’ microbiomes, genes that break down sugars in breastmilk were common. As these babies celebrated their first birthdays, the genes in their microbiomes favored the ability to breakdown starches, pectins, and more complex sugars.

“What’s nice about this paper is that they show this maturation [of the microbiome] in normal, healthy kids in a Western population follows this transition based on diet,” said Steven Frese, a postdoc at the University of California, Davis, who penned a commentary accompanying the study with his advisor, David Mills. “Being exposed to new foods promotes the growth of new bacteria that can consume them,” Frese told The Scientist.

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

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.

The researchers think that repeated courses of antibiotics destroy the gut bacteria resulting in gut bacteria imbalance. From Red Orbit:

Antibiotic overuse could up diabetes risk, study says

Repeated use of some antibiotics could increase a person’s risk of developing type 2 diabetes, according to research published online Tuesday in the European Journal of Endocrinology. In the study, scientists from the University of Pennsylvania found that men and women who had ever been prescribed with at least two courses of specific types of antibiotics were more likely to eventually be diagnosed with type 2 diabetes than those who had taken no more than one.

The antibiotics used in the research came from one of four categories, according to LiveScience: penicillins, cephalosporins, quinolones and macrolides. The authors reviewed a database of UK patients, looking at the number of antibiotic prescriptions given to over 200,000 diabetic patients at least one year before those individuals were diagnosed with the condition...They found that the more courses of antibiotics that were prescribed to a person, the greater the risk that he or she would go on to develop the disease.

Patients who had been prescribed between two and five courses of penicillin increased their risk of diabetes by 8 percent, according to the Daily Mail, and the risk increased by 23 percent for those receiving more than five courses of the frequently used antibiotic versus the one- or no-course group.

Those who were given between two and five courses of quinolones, which are used to treat respiratory and urinary tract infections, had an increased diabetes risk of 15 percent, and those receiving more than five courses saw that risk shoot up by 37 percent. 

Those who were given just one course of antibiotics showed no such increase in diabetes risk, the researchers reported. Nor was there any link found between exposure to anti-virals and anti-fungals and diabetes risk. The reason for the association between frequent antibiotic use and the risk of diabetes is not clear, but may be related to a gut bacteria imbalance, they wrote.“Gut bacteria have been suggested to influence the mechanisms behind obesity, insulin resistance and diabetes in both animal and human models. Previous studies have shown that antibiotics can alter the digestive ecosystem,” added lead author Dr. Ben Boursi.

How much fiber is there in the different foods we eat? And how much should we eat? Recent posts (Where Do I Get That Beneficial Gut Bacteria? and A Special Gut Microbe) stressed the importance of eating dietary fiber for various health benefits and to feed the beneficial bacteria (such as Faecalibacterium prausnitzii) in our gut. But how much should we be eating daily? Are there different types of fiber and does it matter?

Currently the average American adult eats about 12 to 18 grams of dietary fiber daily. But the latest advice (from both National Academy of Sciences and Academy of Nutrition and Dietetics) is to eat over 20 grams of dietary fiber daily to about 35 grams daily, depending on weight. So a person eating a 2000 calorie daily diet should have about 25 grams of fiber daily.Their recommendation for children is that intake should equal age in years plus 5 g/day (e.g., a 4 year old should consume 9 g/day). Good fiber foods are: fruits, vegetables, whole grains, legumes (beans), nuts, and seeds. But people eating a typical westernized diet are instead eating a high fat, high meat, highly processed food diet which neglects plant-based foods. Go look at the ingredient labels of favorite American foods and see that many don't have fiber or are low in dietary fiber (e.g., hot dogs, salami, candy, cookies, potato chips).

Dietary fiber or roughage is the indigestible portion of food derived from plants. There are two types of fiber: soluble and insoluble, and both should be eaten for good health because they benefit health in a number of ways. Insoluble fiber doesn't dissolve in water and passes through the intestines (it provides bulking), while soluble fiber dissolves in water, and becomes a gel. Plant foods contain both types of fiber in varying degrees, depending on the plant's characteristics. For example, plums and prunes have a thick skin covering a juicy pulp. The skin is a source of insoluble fiber, whereas soluble fiber is in the pulp. One can also take fiber supplements, but actual real foods have many more benefits to them, and also provide a variety of fiber sources. Eating a variety of whole plant-based foods is beneficial in many ways, including feeding the variety of bacteria species in your gut. Remember that different bacteria need different foods, and so eating a variety of foods is best.

To increase your daily dietary fiber intake, first take a look at the amount of fiber in different foods. And then eat lots of fruits, vegetables, whole grains, legumes (beans), seeds, and nuts. The following tables give approximate fiber amounts in some high fiber foods (NOTE: different sources give slightly different numbers):

Fresh & Dried Fruit  Serving Size Fiber (g)
 Apples with skin  1 medium 5.0
 Apricot  3 medium 1.0
 Apricots, dried  4 pieces 2.9
 Banana  1 medium 3.9
 Blueberries  1 cup 4.2
 Cantaloupe, cubes  1 cup 1.3
 Figs, dried  2 medium 3.7
 Grapefruit  1/2 medium 3.1
 Orange, navel  1 medium 3.4
 Peach  1 medium 2.0
 Peaches, dried  3 pieces 3.2
 Pear  1 medium 5.1
 Plum  1 medium 1.1
 Raisins  1.5 oz box 1.6
 Raspberries  1 cup 8.0
 Strawberries  1 cup 4.4
Grains, Beans (Legumes), Nuts, Seeds  Serving Size Fiber (g)
 Almonds  1 oz 4.2
 Black beans, cooked  1 cup 13.9
 Bran cereal  1 cup 19.9
 Bread, whole wheat  1 slice 2.0
 Brown rice, dry  1 cup 7.9
 Cashews  1 oz 1.0
 Flax seeds  3 Tbsp. 6.9
 Garbanzo beans, cooked  1 cup 5.8
 Kidney beans, cooked  1 cup 11.6
 Lentils, red cooked  1 cup 13.6
 Lima beans, cooked  1 cup 8.6
 Oats, rolled dry  1 cup 12.0
 Quinoa (seeds) dry  1/4 cup 6.2
 Quinoa, cooked  1 cup 8.4
 Pasta, whole wheat  1 cup 6.3
 Peanuts  1 oz 2.3
 Pistachio nuts  1 oz 3.1
 Pumpkin seeds  1/4 cup 4.1
 Soybeans, cooked  1 cup 8.6
 Sunflower seeds  1/4 cup 3.0
 Walnuts  1 cup 5.0
 Vegetables  Serving Size Fiber (g)
 Avocado (fruit)  1 medium 11.8
 Beets, cooked  1 cup 2.8
 Beet greens  1 cup 4.2
 Bok choy, cooked  1 cup 2.8
 Broccoli, cooked  1 cup 4.5
 Brussels sprouts, cooked  1 cup 3.6
 Cabbage, cooked  1 cup 4.2
 Carrot  1 medium 2.6
 Carrot, cooked  1 cup 5.2
 Cauliflower, cooked  1 cup 3.4
 Cole slaw  1 cup 4.0
 Collard greens, cooked  1 cup 2.6
 Corn, sweet  1 cup 4.6
 Green beans  1 cup 4.0
 Celery  1 stalk 1.1
 Kale, cooked  1 cup 7.2
 Onions, raw  1 cup 2.9
 Peas, cooked  1 cup 8.8
 Peppers, sweet  1 cup 2.6
 Pop corn, air-popped  3 cups 3.6
 Potato, baked w/ skin  1 medium 4.8
 Spinach, cooked  1 cup 4.3
 Summer squash, cooked  1 cup 2.5
 Sweet potato, cooked  1 medium 4.9
 Swiss chard, cooked  1 cup 3.7
 Tomato  1 medium 1.5
 Winter squash, cooked  1 cup 6.2
 Zucchini, cooked  1 cup 2.6

The tables were from http://commonsensehealth.com/high-fiber-foods-list-for-a-high-fiber-diet/

Gut bacteria in children varies among different Asian countries. The microbiota profiled for the 303 subjects were classified into two main clusters: driven by Prevotella (P-type) or by Bifidobacterium/Bacteroides (BB-type) The majority of children in China, Japan and Taiwan harbored Bifidobacterium/Bacteroides (BB type),whereas those from Indonesia and Khon Kaen in Thailand mainly harbored Prevotella (P-type).Interesting in that even eating different types of rice result in different gut bacteria.From Asian Scientist:

Diet, Location And Your Kid’s Gut Bacteria

An Asia-wide study of the gut microbiota of primary school children has identified differences linked to diet and geographical location

The human intestinal tract hosts a large and diverse community of microorganisms—predominantly bacteria—which plays an important role in the host’s metabolism and ability to combat disease. In a study recently published in Scientific Reports, an international team of researchers led by Associate Professor Lee Yuan-Kun at the National University of Singapore examined fecal samples from 303 primary school children living in urban and rural cities of China, Japan, Taiwan, Thailand, and Indonesia. Unlike infants, children in the 7-11 age bracket have already developed a gut flora similar to that of adults but, unlike adults, they eat predominantly at home so their diets could be tracked more accurately.

The results show a strong correlation between the children’s gut microbiota and their place of residence and diet. The samples from China, Japan and Indonesia diverged the most, with Taiwan and Thailand filling the gaps in between, reflecting not only location but also patterns of human migration and agricultural exchanges. Bacterial communities in the gut vary widely between individuals, but they can be broadly classified into three types, according to the abundance of either Bacteroides, Prevotella, or Ruminococcus bacteria.The researchers found that Asian children display mainly the P-type (abundant in Prevotellaceae) and the BB-type (abundant in Bacteroidaceae and Bifidobacteriaceae), with the abundance of Bifidobacterium being a distinctive feature of the gut flora of Asian children.

P-type (Prevotella) gut communities are normally found in individuals with a high dietary intake of carbohydrates, while a diet rich in proteins and fats will favor a BB-type (Bifidobacterium/Bacteroides) community. Accordingly, the study revealed that Thai children living in Bangkok and eating a diet low in vegetables and fruit displayed a BB-type gut flora, while those living in Khon Kaen and eating a diet high in fruit and vegetables, displayed the P-type.

Not only was the P-type microbiota positively correlated with rice intake across the samples, but differences in contents of digestion-resistant starch across rice cultivars seemed to make a difference. P-type bacteria thrive in an environment rich in digestion-resistant starch, both because resistant starch is a substrate for bacterial fermentation and because it decreases the concentration of secondary bile acids—harmful to P-type bacteria—in the large intestine. After cooking, long grained Indica rice contains 6.6 percent digestion-resistant starch while short grained Japonica rice contains only 0.7 percent. The researchers suggest that the low content of resistant starch in Japonica rice might be the reason why 13 percent of Japanese children who ate a diet predominantly rice-based, still exhibited a BB-type microbiota. Other foodstuff were seen to be associated with P-type gut flora: soybeans (in the form of tempeh, not tofu) because of a high concentration of fiber; eggs, chicken and sweet potatoes because of their high content of vitamin A, which is thought to be beneficial to the growth of Prevotella bacteria.

The article can be found at: Nakayama et al. (2015) Diversity in Gut Bacterial Community of School-Age Children in Asia. 

Of course! From Science Magazine:

Guts of obese dogs look similar to those of obese people

Obese people have a less diverse array of bacteria living in their guts than do thin people—and the same holds true for dogs. In a new study, researchers fed seven beagles unrestricted amounts of food for 6 months, during which each dog gained an average of 4.93 kilograms—about 67% of their initial average weight of 7.37 kilograms. The investigators fed another seven beagles controlled food portions, and, as expected, this group did not gain weight.

When the researchers examined the fecal samples collected from both groups after 6 months, they found that the guts of obese beagles contained a smaller diversity of bacteria than those of the other dogs. What’s more, microbes from the phylum Firmicutes were the predominant group in the lean dogs, whereas Gram-negative bacteria called Proteobacteria were prevalent in the obese group, the team reported online this month in the Journal of Veterinary Internal Medicine. The researchers speculate that an abundance of Proteobacteria may lead to an increase in lipopolysaccharide, a major component of the cell wall of Gram-negative bacteria, which has been linked to weight gain in mice. More research is needed to examine what role gut bacteria may play in the development of obesity, however, the authors say.

Natural ways that may help GERD symptoms without drugs : eating smaller portions, losing weight, not lying down for 2 hours after eating, and avoiding alcohol, cigarettes, and "trigger" foods.From Health Day News:

Could Popular Heartburn Drugs Upset Your 'Good' Gut Bugs?

Heartburn drugs such as Prilosec and Nexium may disrupt the makeup of bacteria in the digestive system, potentially boosting the risk of infections and other problems, a small new study suggests.

According to Harvard Medical School, billions of dollars are spent annually on antacid drugs in an attempt to combat heartburn, ulcers and gastroesophageal reflux disease, also known as GERD. Old standbys such as Maalox and Mylanta have been supplanted by more effective, more expensive drugs, including proton pump inhibitors. These include Prevacid (lansoprazole) and Protonix (pantoprazole) in addition to Prilosec (omeprazole) and Nexium (esomeprazole).

Long-term use of proton pump inhibitors has been linked to infection with a germ called Clostridium difficile, which causes severe diarrhea, he said. Researchers have also connected the medications to vitamin deficiencies, bone fractures and pneumonia, among other conditions.

In the new study, researchers sought to understand what happens to the trillions of germs in the digestive system when people take omeprazole, the generic name for the drug best known as Prilosec.Ten participants, aged 18 to 57, took 20 or 40 milligrams of the drug a day for 28 days. Researchers analyzed the study participants' stool samples to understand the germs in their guts.

"These microbes have evolved with us to participate in our normal development and metabolism, and perform certain functions that we would not be able to accomplish without their help," DiBaise said. Many scientists believe that people's risk of disease goes up when their normal germ makeup changes, he said.

The researchers found evidence that the medications disrupted the balance of bacteria in the digestive systems of the participants, and the changes lasted for at least a month after they discontinued the drug. It didn't seem to matter whether they took the higher or lower dose, DiBaise said.

DiBaise cautioned that the study doesn't prove that the drug causes users to become more vulnerable to C. difficile infections. However, it shows that the drug "creates a situation in the gut microbial environment that may increase an individual's susceptibility," he said.

What should users do for now? According to DiBaise, proton pump inhibitors are "the most effective medications to treat gastroesophageal reflux disease." If patients don't have the most severe symptoms, he said, other types of heartburn drugs might help. Also recommended: eating smaller portions, losing weight, not lying down for two hours after eating, and avoiding alcohol, cigarettes and "trigger" foods.

Red meat,bacteria, and atherosclerosis.From Medical Xpress:

Why does red meat increase the risk for cardiovascular disease? Blame our gut bacteria

New research provides details on how gut bacteria turn a nutrient found in red meat into metabolites that increase the risk of developing heart disease. Publishing in the November 4th issue of the journal Cell Metabolism, the findings may lead to new strategies for safeguarding individuals' cardiovascular health.

Previous research led by Dr. Stanley Hazen, of Lerner Research Institute and the Miller Family Heart and Vascular Institute at Cleveland Clinic, revealed a pathway by which red meat can promote atherosclerosis, or hardening of the arteries. Essentially, bacteria in the gut convert L-carnitine, a nutrient abundant in red meat, into a compound called trimethylamine, which in turn changes to a metabolite named trimethylamine-N-oxide (TMAO), which promotes atherosclerosis. Now Dr. Hazen and his team extend their earlier research and identify another metabolite, called gamma-butyrobetaine, that is generated to an even greater extent by gut bacteria after L-carnitine is ingested, and it too contributes to atherosclerosis.

The discovery that metabolism of L-carnitine involves two different gut microbial pathways, as well as different types of bacteria, suggests new targets for preventing atherosclerosis—for example, by inhibiting various bacterial enzymes or shifting gut bacterial composition with probiotics and other treatments.