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Category: microbes

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The following is from a presentation from The American Association of Diabetes Educators Annual Meeting August 6-9, 2014 by M.Jardin and C.Kafity. But the coffee and tea statement is different from what I've read elsewhere, specifically that coffee is beneficial, is a source of soluble fiber, and may keep pathogenic bacteria in check. From Endocrinology Today:

Plant-based diet helps grow healthy microbiota, halt diabetes disease process

With research mounting on the onslaught the body’s microbiota take from human eating patterns and the environment, making choices to maintain inner ecosystem health is essential, according to presenters at the American Association of Diabetes Educators Annual Meeting. Choosing a plant-based diet is one way people can increase the diversity of bacteria in their biome, reduce inflammation and begin to reverse the diseases processes involved in obesity and diabetes — often in just a few days.

“We know obesity and diabetes have increased tremendously in the last 20 years and we know that our genes haven’t changed, so that can’t account for the change,” Meghan Jardine, MS, MBA, RD, LD, CDE, RDN, of Parkland Health and Hospital System, said during a presentation. “Many scientists believe the changes in our diet and physical activity can’t really account for the change either, that there’s something else at work here.”

Weighing at least two kilograms in all and accounting for more than 3 times the amount of the body’s human cells, gut bacteria is colonized after birth, stabilized by age 3 years but influenced by a number of external factors, Jardine explained. Areas of influence include nutrition and immune function, both priorities in treating obesity and diabetes.

“Microbiota releases enzymes that digest food so we can absorb nutrients, produces vitamins, combats opportunistic infections and works with the immune system,” Jardine said. “About 70% of our immune systems are in our gut.”

People who consume plant-based diets have “healthy” gut microbiota in terms of global parameters and functional and compositional features, Christina Kafity, RN, BSN,CHC... “Children and elderly individuals who consumed more plant carbohydrates versus the typical standard American diet had rapid, reproducible alterations of the gut microbiota for the better, and this happened within 24 hours to a week,” Kafity said.

Growing good bacteria depends on creating an environment in which they can thrive, Kafity explained, including choosing foods that contain certain fibers intact in plants and probiotics; among them are soluble, insoluble and functional fibers as well as psyllium and inulin.

Intake of cruciferous vegetables including Brussels sprouts, kale and cabbage can help boost healthy microbes and, further, provide glucosinolates to help to reduce inflammation, Kafity said. Yogurt, kefir and probiotics also promote the growth of good bacteria, Kafity noted, while some popular beverages may not be much help. “We’re considering that coffee and teas may actually sterilize the bacteria.”

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I'm glad that there is interest in therapeutic possibilities of bacteria, but I'm worried (a lot) about the possibility of companies claiming rights to naturally occurring bacteria. The article simply said: "...intellectual-property rights for naturally occurring bacteria, may complicate the path of products to market."  From Scientific American:

Drugs to Be Derived from Insights into Body-Dwelling Bacteria

The human body teems with trillions of microorganisms — a microbial landscape that has attracted roughly $500 million in research spending since 2008. Yet with a few exceptions, such as the use of fecal transplants for treating life- threatening gut infections or inflammatory bowel disease, research on the human microbiome has produced few therapies.

That is poised to change as large pharmaceutical companies eye the medical potential of manipulating interactions between humans and the bacteria that live in or on the body.

On 2 May, drug giant Pfizer announced plans to partner with Second Genome, a biotechnology firm in South San Francisco, California, to study the microbiomes of around 900 people, including those with metabolic disorders and a control group.A day earlier, Paris-based Enterome revealed that it had raised €10 million ($13.8 million) in venture capital to develop tests that use the composition of gut bacteria to diagnose inflammatory and liver diseases.

Experts predict that the next few months will see a boom in such partnerships and investments, and that new microbiome-derived drugs and therapies will come to market within a few years.

Probiotics, or beneficial gut bacteria, have become a popular therapy in recent years. Television advertisements feature celebrities touting Bifidobacterium-laced yogurt, and consumers flock to buy pills that contain Lactobacillus to quell their gut disturbances and other ailments. But many physicians and scientists doubt the effectiveness of such remedies. 

But as scientists come to understand the mechanisms by which specific bacteria affect the body, many think that they can pinpoint the right combination of microbes to treat different conditions. Others aim to develop molecules that mimic a beneficial bacterium–host interaction, or block a harmful one. “Undoubtedly, the microbiome is a  little drug factory in our intestine,” says Justin Sonnenburg, a microbiologist at Stanford University in Palo Alto, California.

Changing the balance of ‘good’ and ‘bad’ bacteria in the gut microbiome can also influence health — inflammation, for example, or even depression and anxiety. 

Getting microbiome-inspired therapies to market presents a number of challenges, however. Small molecules such as those developed by Microbiome Therapeutics may be able to go through the normal drug regulatory pathway. But there may be a different or new set of regulatory hurdles for genetically modified bacteria — for example, those in development by Ghent-based ActoGeniX in Belgium and ViThera Pharmaceuticals in Cambridge, Massachusetts — that deliver anti-inflammatory agents to the gut. Other issues, including intellectual-property rights for naturally occurring bacteria, may complicate the path of products to market.

Pierre Belichard, Enterome’s chief executive, says that such investment has been a long time coming — but companies are now flocking to microbiome research.

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This was done in mice, so much more needs to be done. But...if it holds true for humans, probiotics (with IPA-producing bacteria) can be used as therapies for all sorts of diseases. From Medical Xpress:

'Normal' bacteria vital for keeping intestinal lining intact

Scientists at Albert Einstein College of Medicine of Yeshiva University have found that bacteria that aid in digestion help keep the intestinal lining intact. The findings, reported online in the journal Immunity, could yield new therapies for inflammatory bowel disease (IBD) and a wide range of other disorders.

The research involved the intestinal microbiome, which contains some 100 trillion . The role of these microorganisms in promoting or preventing disease is a major emerging field of study. Einstein scientists found that absorption of a specific bacterial byproduct is crucial for maintaining the integrity of the intestinal epithelium —the single-cell layer responsible for keeping intestinal bacteria  and their toxins inside the gut and away from the rest of the body. Breaching of the intact intestinal epithelium is associated with a number of diseases.

"Intestinal bacteria secrete a wide variety of chemicals known as metabolites," said Sridhar Mani, M.D., co-corresponding author of the paper. Dr. Mani and his colleagues suspected that bacterial metabolites exert their influence by binding to and activating a protein in the nuclei of intestinal epithelial cells called the pregnane X receptor (PXR). PXR was known to be activated by chemicals within the body (such as bile acids) as well as by drugs including steroids and antibiotics.

In a series of mouse studies, the researchers found that a metabolite called indole 3-propionicacid (IPA)—produced exclusively by so-called commensal bacteria, which aid in digestion—both strengthens the intestinal epithelium's barrier function and prevents its inflammation by activating PXR. More specifically, PXR activation suppresses production of an inflammatory protein called tumor necrosis factor alpha (TNF-α) while increasing levels of a protein that strengthens the junctions between adjacent intestinal epithelial cells. 

"By adding probiotics in the form of IPA-producing bacteria to the intestine or by administering IPA directly, we may be able to prevent or treat IBD and other inflammatory disorders that occur when the intestinal epithelium has been compromised," said Dr. Mani. "Such a strategy could also be tried for other health problems that may occur when the intestinal epithelium breaks down, including certain forms of liver disease, diabetes, asthma, allergies, obesity and heart disease."

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Two related articles, the first from a month ago, but both discuss eating fresh foods of summer and the effect on the microbiota. From Gut Microbiota Worldwatch:

Seasonal diet changes affect the composition of our gut microbiota

The mix of bacteria that live in our gut changes throughout the year, to match the food we eat in every specific season. For example, bacteria that process fresh fruit and vegetables are more abundant in the summer, and those that process fats are mode abundant in winter times. A group of scientists at the University of Chicago has found evidence of this seasonal shift in the gut flora, by studying the remote Hutterite population, in North America. The traditional diet and common meals of this community have allowed researchers to study the effect of one common diet in a large population over a long period of time.

Hutterites live in communal farms (colonies) and eat meals in common dining rooms, using traditional recipes that have been relatively stable over time and between colonies. They have little contact with the world outside their colonies, which translates into a very homogeneous genetic pool. Sixty Hutterites from six colonies answered questionnaires about what they ate over the course of a year. During the same period, scientists sampled their stool periodically, to find the genetic sequences of bacteria contained in their gut.

The Hutterites’ diet is relatively stable, except that in summer they eat more fresh fruit and vegetables, and in winter they eat less, and turn to frozen or canned food. Remarkably, their gut flora responded to these changes with massive modification in the abundance of certain bacteria. For example, during summer Bacteroidetes were more abundant: this group of bacteria contain complex carbohydrate digesters, which may be at work in processing fresh fruit and vegetables.

On the other hand Actinobacteria increased in winter: these microbes are associated with processing fat, and with a decreased content of fibre in food. Researchers also found seasonal shifts in other types of bacteria, whose associations with food are still unknown. Notably, the trends were almost identical in all six colonies, possibly a result of a very homogenous lifestyle carried on in a very similar environment.

Although Hutterites live in a relatively isolated way, they use technology and medicine, which makes their lifestyle closer to the general population than that of other more traditional communities. That is why the authors believe that these results may be extended to the general population.

This healthy living article promotes eating fresh fruits and vegetables (tomatoes, blueberries, asparagus, and leeks) as good for the gut microbiome. From Huffington Post:

4 Summer Foods That Can Help Trim Your Waist

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Future microbiome research and therapy will have to take into account that diet affects the gut microbes of men and women differently. From Science Daily:

Diet affects males' and females' gut microbes differently

The microbes living in the guts of males and females react differently to diet, even when the diets are identical, according to a new study. These results suggest that therapies designed to improve human health and treat diseases through nutrition might need to be tailored for each sex.

The researchers studied the gut microbes in two species of fish and in mice, and also conducted an in-depth analysis of data that other researchers collected on humans. They found that in fish and humans diet affected the microbiota of males and females differently. In some cases, different species of microbes would dominate, while in others, the diversity of bacteria would be higher in one sex than the other.

These results suggest that any therapies designed to improve human health through diet should take into account whether the patient is male or female.

Genetics and diet can affect the variety and number of these microbes in the human gut, which can in turn have a profound influence on human health. Obesity, diabetes, and inflammatory bowel disease have all been linked to low diversity of bacteria in the human gut.

Why men and women would react differently to changes in diet is unclear, but there are a couple of possibilities. The hormones associated with each sex could potentially influence gut microbes, favoring one strain over another. Also, the sexes often differ in how their immune systems function, which could affect which microbes live and die in the microbiome.

One notable exception in Bolnick's results was in the mice. Although there was a tiny difference between male and female mice, for the most part the microbiota of each sex reacted to diet in the same manner. Because most dietary studies are conducted on mice, this result could have a huge effect on such research, and it raises questions about how well studies of gut microbes in lab mice can be generalized to other species, particularly humans.

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The study was needed, but my first thought was "Duh! Of course." From Science Daily:

Fist bumping beats germ-spreading handshake

“Fist bumping” transmits significantly fewer bacteria than either handshaking or high-fiving, while still addressing the cultural expectation of hand-to-hand contact between patients and clinicians, according to a study published in the August issue of the American Journal of Infection Control...

In this study from the Institute of Biological, Environmental, and Rural Sciences at Aberystwyth University in the United Kingdom, researchers performed trials to determine if alternative greetings would transmit fewer germs than the traditional handshake. In this experiment, a greeter immersed a sterile-gloved hand into a container of germs. Once the glove was dry, the greeter exchanged a handshake, fist bump, or high-five with a sterile-gloved recipient. Exchanges randomly varied in duration and intensity of contact.

After the exchange, the receiving gloves were immersed in a solution to count the number of bacteria transferred during contact. Nearly twice as many bacteria were transferred during a handshake compared to the high-five, and significantly fewer bacteria were transferred during a fist bump than a high-five. In all three forms of greeting, a longer duration of contact and stronger grips were further associated with increased bacterial transmission.

“Adoption of the fist bump as a greeting could substantially reduce the transmission of infectious diseases between individuals,” said corresponding author, David Whitworth, PhD. This study expands on the recent call from the Journal of the American Medical Association (JAMA) to ban handshakes from the hospital environment. Healthcare providers’ hands can spread potentially harmful germs to patients, leading to healthcare-associated infections (HAIs). 

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This research illustrates how little we currently know about gut bacteria.But it did show the importance of diet. From Science Daily:

Monitoring rise and fall of the microbiome

Trillions of bacteria live in each person's digestive tract. Scientists believe that some of these bacteria help digest food and stave off harmful infections, but their role in human health is not well understood.

To help shed light on the role of these bacteria, a team of researchers led by MIT associate professor Eric Alm recently tracked fluctuations in the bacterial populations of two research subjects over a full year. The findings, described in the July 25 issue of the journal Genome Biology, suggest that while these populations are fairly stable, they undergo daily fluctuations in response to changes in diet and other factors...."To a large extent, the main factor we found that explained a lot of that variance was the diet."

There are a few thousand strains of bacteria that can inhabit the human gut, but only a few hundred of those are found in any given individual, Alm says. For one year, the two subjects in the study collected daily stool samples so bacterial populations could be measured. They also used an iPhone app to track lifestyle factors such as diet, sleep, mood, and exercise, generating a huge amount of data.

Analysis of this data revealed that dietary changes could produce daily variations in the populations of different strains of bacteria. For example, an increase in fiber correlated with a boost in the populations of Bifidobacteria, Roseburia, and Eubacterium rectale. Four strains -- including Faecalibacterium prausnitzii, which has been implicated in protecting against inflammatory bowel disease -- were correlated with eating citrus.

During the study, each of the two subjects experienced an event that dramatically altered the gut microbiome. Subject B experienced food poisoning caused by Salmonella, and Subject A traveled to a developing nation, where he experienced diarrheal illness for two weeks.

During Subject B's infection, Salmonella leapt from 10 percent of the gut microbiome to nearly 30 percent. At the same time, populations of bacteria from the phylum Firmicutes, believed to be beneficial to human health, nearly disappeared. After the subject recovered, Firmicutes rebounded to about 40 percent of the total microbiome, but most of the strains were different from those originally present.

Subject A also exhibited severe disruptions to his microbiome during his trip, but once he returned to the United States, it returned to normal. Unlike Subject B's recovery from food poisoning, Subject A's populations returned to their original composition.

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We know so little about the viruses in the human microbiome that a study just reported a newly discovered gut virus found in most of the world's population. From Medical Xpress:

Newly discovered gut virus lives in half the world's population

Odds are, there's a virus living inside your gut that has gone undetected by scientists for decades. A new study led by researchers at San Diego State University has found that more than half the world's population is host to a newly described virus, named crAssphage, which infects one of the most common types of gut bacteria, Bacteroidetes. This phylum of bacteria is thought to be connected with obesity, diabetes and other gut-related diseases.

The fact that it's so widespread indicates that it probably isn't a particularly young virus, either. "We've basically found it in every population we've looked at," Edwards said. "As far as we can tell, it's as old as humans are." He and his team named the virus crAssphage, after the cross-assembly software program used to discover it.

Some of the proteins in crAssphage's DNA are similar to those found in other well-described viruses. That allowed Edwards' team to determine that their novel virus is one known as a bacteriophage, which infects and replicates inside bacteria—and using innovative bioinformatic techniques, they predicted that this particular bacteriophage proliferates by infecting a common phylum of gut bacteria known as Bacteriodetes.

 Further details about crAssphage have been difficult to come by. It's unknown how the virus is transmitted, but the fact that it was not found in very young infants' fecal samples suggests that it is not passed along maternally, but acquired during childhood.

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Even though it looks to be a modest effect, it is still good news. But they should have added kefir to the list of probiotic containing foods. From Science Daily:

Eating probiotics regularly may improve your blood pressure

Eating probiotics regularly may modestly improve your blood pressure, according to new research in the American Heart Association journal  Hypertension. Probiotics are live microorganisms (naturally occurring bacteria in the gut) thought to have beneficial effects; common sources are yogurt or dietary supplements.

"The small collection of studies we looked at suggest regular consumption of probiotics can be part of a healthy lifestyle to help reduce high blood pressure, as well as maintain healthy blood pressure levels," said Jing Sun, Ph.D., lead author and senior lecturer at the Griffith Health Institute and School of Medicine, Griffith University, Gold Coast, Queensland, Australia. "This includes probiotics in yogurt, fermented and sour milk and cheese, and probiotic supplements."

Analyzing results of nine high-quality studies examining blood pressure and probiotic consumption in 543 adults with normal and elevated blood pressure, researchers found:

  • Probiotic consumption lowered systolic blood pressure (the top number) by an average 3.56 millimeters of mercury (mm Hg) and diastolic blood pressure (the lower number) by an average 2.38 mm Hg, compared to adults who didn't consume probiotics.
  • The positive effects from probiotics on diastolic blood pressure were greatest in people whose blood pressure was equal to or greater than 130/85, which is considered elevated.
  • Probiotics with multiple bacteria lowered blood pressure more than those with a single bacteria.

We believe probiotics might help lower blood pressure by having other positive effects on health, including improving total cholesterol and low-density lipoprotein, or LDL, cholesterol; reducing blood glucose and insulin resistance; and by helping to regulate the hormone system that regulates blood pressure and fluid balance," Sun said.

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After posting yesterday "Probiotic Misconceptions", I was pleasantly surprised that today's NY Times had an article (by Jane Brody) raising similar concerns. What was good is that she wrote about supplements not being regulated. She also left out that probiotic beneficial organisms are found in more than the gut. A case in point being the sinuses - because healthy sinuses also have Lactobacillus sakei (according to the Abreu et al study of 2012), and which has been the basis for my family's successful kimchi treatment for sinusitis (see Sinusitis treatment link for the method). From the NY Times:

Probiotic Logic vs. Gut Feelings

The label on my bottle of Nature’s Bounty Advanced Probiotic 10 says it contains 10 probiotic strains and 20 billion live cultures in each two-capsule dose. The supplement provides “advanced support for digestive and intestinal health” and “healthy immune function.” I have no way to know if any of this is true. Like all over-the-counter dietary supplements, probiotics undergo no premarket screening for safety, effectiveness or even truth in packaging. 

To be sure, lay and scientific literature are filled with probiotic promise, and I am hardly the only consumer who has opted to hedge her bets. The global market for probiotic supplements and foods is expected to reach $32.6 billion this year,with a projected annual growth of 20 percent or more.

 Beneficial micro-organisms have since been shown to inhabit three main locations in the digestive tract: the stomach, the lower part of the small intestine and the large intestine. To better understand the current enthusiasm for enhancing the body’s supply of these micro-organisms, some definitions are needed.

■ Prebiotics are nondigestible carbohydrates that stimulate the growth and activity of beneficial micro-organisms (that is, probiotics) in the gut. They are found naturally in oats, wheat, some fruits and vegetables (bananas, onions, garlic, leeks, asparagus, soybeans, honey and artichokes), and in breast milk, and they are added to some infant formulas.

■ Probiotics are defined by the World Health Organization as “live micro-organisms which when administered in adequate amounts confer a health benefit on the host.” The ailments that probiotics are said to benefit range from infection-caused diarrhea, inflammatory bowel diseases and irritable bowel syndrome to asthma, allergy and Type 1 diabetes.

■ Synbiotics are a combination of prebiotics and probiotics. They are found in so-called functional foods like yogurt and kefir, fermented foods like pickles and some cheeses, and in some supplements.

That probiotic organisms are important to health is not questioned. As researchers at the Institute for Immunology at the University of California,Irvine have written intestinal micro-organisms play “an important role in the development of the gut immune system, digestion of food, production of short-chain fatty acids and essential vitamins, and resistance to colonization from pathogenic microorganisms.”

Dr. Walker has explained that probiotics enhance defensive action by the cells that line the gut. When a person takes antibiotics, especially the broad-spectrum antibiotics most often prescribed, many of these beneficial microbes are destroyed along with the disease-causing bacteria. Patients on antibiotics are often told to consume yogurt with active cultures to replenish the beneficial organisms.

In an extensive review of the evidence published in 2010 in the journal Pediatrics, an expert committee concluded that probiotics might limit the course of virus-caused diarrhea in otherwise healthy infants and children. But the committee said there was not sufficient evidence to justify routine use of probiotics to prevent rotavirus-caused diarrhea in child care centers. Nor did the committee endorse taking probiotics during pregnancy and nursing or giving them to infants to prevent allergic disorders in those at risk.

Only a small percentage of probiotic foods and supplements have the backing of peer-reviewed published research. They include Dannon’s Activia yogurt and DanActive drink and the supplements Culturelle and Align. Although kefir contains even more probiotic strains than yogurt, clinical studies have not shown it to be effective in preventing or treating infectious diarrhea.

The challenge in taking probiotics is to get the microbes past the stomach, where most are killed by gastric acid, said Robert Dunn, a biologist at North Carolina State University. Once in the intestines, they must compete effectively with the microbes already present.

Dr. Dunn, author of "The Wild Life of Our Bodies," says there is good reason to remain skeptical of probiotics. “There are hundreds of kinds of prebiotics and probiotics in stores,” he said. “As a consumer, it’s almost impossible to figure out what is best. What are the specific species in your intestines, and how will what you take compete with them?” Still, he added, taking them doesn’t seem harmful. 

There is growing evidence for the role of the appendix in restoring a healthful balance of microbes in the body. Though long considered an expendable, vestigial organ, the appendix is now being looked at as “a storehouse of good bacteria,” Dr. Dunn said. In a study of recovery rates from Clostridium difficile, which causes a severe form of infectious diarrhea, often following antibiotic therapy, patients whose appendixes had been removed were more likely to have a recurrent infection than those who still had appendixes.