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Category: human microbiome

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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.

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I keep overhearing misguided statements like these all the time: that somehow any and all probiotic (beneficial) bacteria offered for sale, whether in foods such as yogurt, or in probiotic capsules, are wonderful and beneficial, and will reseed your gut as well as do all sorts of miraculous things for your health. And while in reality, there are many, many bacterial species living in a healthy person's gut, it's the same few species that seem to be offered everywhere.

But if you look at the scientific research for even a few minutes, you realize that NO, we actually know very little about the health benefits of these bacteria species now in stores, and that all the claims out there don't have evidence backing them up. Perhaps taking megadoses of certain bacteria even has some negative effects. Yes, Lactobacillus species are generally considered beneficial by scientists. But even in the Lactobacillus family, there are many more types than the few now available in stores. For example. I can not find Lactobacillus sakei (which is found in kimchi and we use to successfully treat sinusitis - see Sinusitis Treatment link) in any store at this time.

Another problem is that sometimes you don't even get the desired bacteria that has been added to the food or cosmetic. For example, this occurs when some Lactobacillus or other bacteria are added to yogurt or some other food, but then the food is pasteurized, which kills off the bacteria. Duh...This is why I liked the following  opinion piece by Julianne Wyrick. From Scientific American:

Are probiotics helping you?

Consuming probiotics – also know as “good” bacteria – via supplements or yogurt has been popularized as a way to maintain gut health. While taking a daily dose of probiotics may not be harming you, it also may not be helping. The idea that every probiotic is good for every disease or condition is oversimplified, according to Catherine Lozupone, an assistant professor of medicine at the University of Colorado School of Medicine.

Lozupone spoke on a panel about the human microbiome, or the bacteria that reside in and on our bodies, that I attended at the Association of Health Care Journalists Conference last month. The panel touched on misconceptions related to probiotics, so I gave Lozupone a call post-conference to learn more.

One misconception Lozupone brought up was the idea that probiotic supplements should be used for “reseeding the good bacteria” missing in a person’s gut. Probiotic supplements often only contain a few species of bacteria, whereas a healthy gut generally has hundreds of species. In addition, the microbes that are abundant in a healthy gut are often different than those found in many supplements. A healthy gut is mostly composed of bacterial species that fall within a two different groups of bacteria: the phyla Bacteroidetes and Firmicutes. One group of bacteria commonly found in probiotics is known as Lactobacillus. While Lactobacillus is a type of Firmicute, it isn’t a type of Firmicute that is typically found in great abundance in a healthy adult gut, according to Lozupone. While Lactobacillus may be helpful for some people in some situations, the idea that everyone needs to repopulate their gut with this “good” bacteria is an overgeneralization.

“I think probiotics have a ton of potential, but different bacteria are going to do different things in different contexts,” Lozupone said. “This notion [of] ‘oh just reseed the good bacteria … they’re good for you’ is definitely very oversimplified.”

But while some general probiotic health claims are ahead of the research, studies do suggest that particular types of probiotic bacteria have potential for specific uses.

For example, Lozupone noted some rodent studies suggest certain microbes might mitigate certain effects of a high-fat diet, which could be helpful to treating obesity and associated health problems.

“There’s just lots of different contexts where the microbiome has been shown to be important,” Lozupone said. Going forward, researchers hope to not only find microbes that have health effects, but also understand why they have these effects. If you’re interested in keeping track of the current research into our body’s bacteria, keep your eye on the NIH’s Human Microbiome Project, an international effort to study the role of the body’s bacteria in our health.

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A topic that is rarely mentioned is the human virome (the collection of resident viruses in the human body). We all have many viruses, but almost nothing is known about them.This is an introductory article about the human virome. From the January 11, 2014 Science News:

The vast virome

 The microbiome — what scientists refer to as the collection of bacteria, fungi and other single-celled organisms that live in and on the body — has been a hot research topic for more than a decade. But bacteria aren’t the only microbes with which we humans share space.

The most abundant inhabitants of what many researchers are calling “the human ecosystem” are the viruses. Viruses are deceptively simple organisms consisting of genetic material packed in a protein shell. They are tiny and can’t replicate on their own, relying on human or other cells to reproduce.

And yet, scientists estimate that 10 quintillion virus particles populate the planet. That’s a one followed by 31 zeros. They outnumber bacteria 10-to-1 in most ecosystems. And they’re ubiquitous in and on humans.

Pérez-Brocal and others are learning that viruses, once seen only as foreign invaders that make people sick, are an integral part of human biology. Some cause major diseases, including influenza, AIDS and some cancers. Others, conversely, may promote health. Some may even help us gauge how well the human immune system works.

The study of people’s resident viruses, known collectively as the human virome, is “a whole new frontier in the understanding of humans,” and could become important for the future of medicine, says Forest Rohwer, an environmental microbiologist at San Diego State University.

Rohwer’s research indicates that viruses are part of the human defense system. Mucus studded with bacteria-infecting viruses called bacteriophage, or phage, may help protect host cells from invasive microbes, he and his colleagues reported June 25 in the Proceedings of the National Academy of Sciences. 

“We know a lot about the bacteria that inhabit humans,” says David Pride, an infectious disease doctor at the University of California, San Diego. In comparison, “we know absolutely nothing about the viruses.” Not that scientists haven’t been interested in viruses. Until recently there was just no good way to identify them, an important first step toward understanding the biology of health and disease. As a consequence, virome research is in its infancy.

Researchers have gotten a head start on cataloging bacterial denizens of the body because all bacterial cells contain a version of the 16S ribosomal RNA gene. Virus hunters aren’t so lucky. There is no analogous virus-identification tag. Instead, to look for viruses, researchers must sequence hundreds of thousands of bits of DNA from a sample — skin swabs, saliva, feces or mucus, for example. Scientists have gotten really good at generating these DNA sequences; the trick is figuring out what they are.

Every time Frederic Bushman samples a new person’s virome, he says, he finds new viruses. A microbiologist at the University of Pennsylvania Perelman School of Medicine in Philadelphia, Bushman has shown that no two people’s gut viruses are exactly alike. But once a person has picked up a community of bacteria-infecting phage, it tends to stick around. Fully 80 percent of the viruses present when the researchers first started tracking one man’s virome were still there more than two years later.

Maybe researchers can use bacteriophage to shape the human microbiome in healthier ways. Using phage to control bacteria is a resurgence of an old idea. In the 1920s, doctors in the former Soviet Union and other Eastern European countries began using phage to treat specific bacterial infections. Unlike antibiotics, which kill bacteria indiscriminately, phage target only certain microbes for destruction.

“Healthy subjects are just loaded with viruses,” Wylie says. Even viruses known to cause diseases such as the common cold were found in healthy kids. That makes it difficult to determine whether a particular virus is really making someone sick.

Some viruses previously thought innocent may cause harm. To figure out which viruses are friends, foes or neutral passengers on the human body, scientists first need to identify them. Researchers still aren’t very good at recognizing new viruses, says Brian Jones, a molecular biologist at the University of Brighton in England. 

Based on what researchers have learned so far about the virome, Jones is convinced that viruses and other microbes “should be viewed as a part of us rather than something that lives in or on us.” They are part of the puzzle, the intricate ecosystem composed of human and microbial cells, all pushing and pulling at one another and subject to local conditions, such as diet and environment.

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This article summarizes some of the same things I've been posting here. From NY Times:

We Are Our Bacteria

We may think of ourselves as just human, but we’re really a mass of microorganisms housed in a human shell. Every person alive is host to about 100 trillion bacteria cells. They outnumber human cells 10 to one and account for 99.9 percent of the unique genes in the body.

Our collection of microbiota, known as the microbiome, is the human equivalent of an environmental ecosystem. Although the bacteria together weigh a mere three pounds, their composition determines much about how the body functions and, alas, sometimes malfunctions. Like ecosystems the world over, the human microbiome is losing its diversity, to the potential detriment of the health of those it inhabits.

Dr. Martin J. Blaser, a specialist in infectious diseases at the New York University School of Medicine and the director of the Human Microbiome Program, has studied the role of bacteria in disease for more than three decades. In his new book, “Missing Microbes,"Dr. Blaser links the declining variety within the microbiome to our increased susceptibility to serious, often chronic conditions,  from allergies and celiac disease to Type 1 diabetes and obesity. He and others primarily blame antibiotics for the connection.

The damaging effect of antibiotics on microbial diversity starts early, Dr. Blaser said. The average American child is given nearly three courses of antibiotics in the first two years of life, and eight more  during the next eight years. Even a short course of antibiotics like the widely prescribed  Z-pack (azithromycin, taken for five days), can result in long-term shifts in the body’s microbial environment.

But antibiotics are not the only way the balance within us can be disrupted. Cesarean deliveries, which  have soared  in recent decades, encourage the growth of microbes from the mother’s skin, instead of from the birth canal, in the baby’s gut, Dr. Blaser said in an interview.

This change in microbiota can reshape an infant’s metabolism and immune system. A recent review of 15 studies involving 163,796 births found that, compared with  babies delivered vaginally, those born by cesarean section were 26 percent more likely to be overweight and 22 percent more likely to be obese as adults. 

The placenta has a microbiome of its own, researchers have discovered, which may also contribute to the infant’s gut health and help mitigate the microbial losses caused by cesarean sections.

Further evidence of a link to obesity comes from farm animals. About three-fourths of the antibiotics sold in the United States are used  in  livestock. These  antibiotics change the animals’ microbiota, hastening their growth. When mice are given the same  antibiotics used on livestock, the metabolism of their liver changes, stimulating an increase in body fat, Dr. Blaser said.

Even more serious is  the increasing number of serious disorders now linked to a distortion in the microbial balance in the human gut. They include several that are becoming more common in developed countries: gastrointestinal ailments like Crohn’s disease, ulcerative colitis and celiac disease; cardiovascular disease; nonalcoholic fatty liver disease; digestive disorders like chronic reflux; autoimmune diseases like multiple sclerosis and rheumatoid arthritis; and asthma and allergies.

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Study after study is suggesting that exposure to lots of diverse bacteria and microorganisms (think farms with animals) is healthy for the developing immune system. From Science Daily:

Growing up on livestock farm halves risk of inflammatory bowel diseases

New research conducted at Aarhus University has revealed that people who have grown up on a farm with livestock are only half as likely as their urban counterparts to develop the most common inflammatory bowel diseases: ulcerative colitis and Crohn's disease. 

"It is extremely exciting that we can now see that not only allergic diseases, but also more classic inflammatory diseases appear to depend on the environment we are exposed to early in our lives," relates Vivi Schlünssen, Associate Professor in Public Health at Aarhus University.

"We know that development of the immune system is finalized in the first years of our lives, and we suspect that environmental influences may have a crucial effect on this development. The place where you grow up may therefore influence your risk of developing an inflammatory bowel disease later in life."

However, the researchers have a theory that the body may be dependent on exposure to a wide variety of microorganisms to develop a healthy immune system -- in the same way as has been established in studies on allergies and asthma.

"We know that the difference in the microbial environment between city and country has increased over the past century, and that we are exposed to far fewer different bacteria in urban environments today than we were previously. This may in part explain our findings," says Signe Timm.

Over the past 40-50 years, incidence of the diseases has sky-rocketed in Northern Europe -- including Denmark -- as well as in Canada and the United States, although they are still relatively rare in developing countries.

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Even though this study was done in a laboratory, it gives further support for the treatment of sinusitis with bacteria and other microbes. And it could help explain why repeated courses of antibiotics don't "cure"  many chronic infections - because biofilms filled with pathogenic bacteria are signs of microbial communities out-of-whack. Which is why my family's successful chronic sinusitis treatment with kimchi (juice) containing Lactobacillus sakei is all the more impressive. From Science Daily:

Link between antibiotics, bacterial biofilms and chronic infections found

The link between antibiotics and bacterial biofilm formation leading to chronic lung, sinus and ear infections has been found, researchers report. The study results illustrate how bacterial biofilms can actually thrive, rather than decrease, when given low doses of antibiotics. Results of this study may lead to new approach for chronic ear infections in children.

This research addresses the long standing issues surrounding chronic ear infections and why some children experience repeated ear infections even after antibiotic treatment," said Paul Webster, PhD, lead author, senior staff scientist at USC and senior faculty at the Oak Crest Institute of Science. "Once the biofilm forms, it becomes stronger with each treatment of antibiotics."

During the study, non-typeable Haemophilus influenzae (NTHi) bacteria a common pathogen of humans was exposed to non-lethal doses of ampicillin, a class of antibiotics commonly used to treat respiratory, sinus and ear infections, or other beta-lactam antibiotics. The dose of the antibiotic was not enough to kill the bacteria which allowed the bacteria to react to the antibiotic by producing glycogen, a complex sugar often used by bacteria as a food source, to produce stronger biofilms when grown in the laboratory.

Biofilms are highly structured communities of microorganisms that attach to one another and to surfaces. The microorganisms group together and form a slimy, polysaccharide cover. This layer is highly protective for the organisms within it, and when new bacteria are produced they stay within the slimy layer. With the introduction of antibiotic-produced glycogen, the biofilms have an almost endless food source that can be used once antibiotic exposure has ended.

There are currently no approved treatments for biofilm-related infections. Therefore, bacteria forced into forming stronger biofilms will become more difficult to treat and will cause more severe chronic infections. Adults will suffer protracted lung infections as the bacteria hunker down into their protective slime, and children will have repeated ear infections. What may appear to be antibiotic resistance when an infection does not clear up may actually be biofilms at work.

Webster believes modern medicine needs to find ways of detecting and treating biofilm infections before the bacteria are able to form these protective structures. The difficulties of treating biofilm infections, which can be up to 1,000 times more resistant to antibiotics,have prompted some physicians to propose a gradual move away from traditional antibiotic treatments and toward non-antibiotic therapies.

The bacteria called Haemophilus influenzae are a common cause of upper respiratory tract infection. By attaching to surfaces in the body the bacteria form a biofilm. When the bacteria encounter non-lethal amounts of specific antibiotics they are stimulated to form a biofilm, a structure that causes chronic infection and which can be highly resistant to antibiotics. Credit: Paul Webster, Ph.D

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Here are some more articles that I found regarding psychobiotics or the use of probiotics to affect behavior and treat psychiatric disorders.  A probiotic is a microorganism introduced into the body for its beneficial properties. Even though the articles are from 2013, they all give slightly different information about this emerging and exciting new field. Please note that psychotropic means having an effect on how the mind works (and it usually refers to drugs that affect a person's mental state). Remember that this area of research and terminology used is in its infancy. From Medscape (November 2013):

Probiotics a Potential Treatment for Mental Illness

Probiotics, which are live bacteria that help maintain a healthy digestive system, are now often promoted as an important part of dietary supplements and natural food products. "Many of the numerous health-improvement claims have yet to be supported scientifically..."

They note that the term "psychobiotic" was created as recent studies have begun to explore a possible link between probiotics and behavior.  "As a class of probiotic, these bacteria are capable of producing and delivering neuroactive substances such as gamma-aminobutyric acid [GABA] and serotonin, which act on the brain-gut axis," they write.

For this review, the investigators sought to examine studies that assessed whether ingesting these bacteria "in adequate amounts" could potentially lead to an effective treatment for depression and other stress-related disorders. In 1 of the preclinical studies examined, mice that ingested L rhamnosus showed reduced anxiety scores and "altered central expression" on both the GABA type A and type B receptors.

And a study of human patients with chronic fatigue syndrome showed that those who consumed an active strain of L casei 3 times a day had significantly higher improvement scores on anxiety measures than did those who received matching placebo. This provides "further support for the view that a probiotic may have psychotropic effects," write the researchers.

Still, Dr. Dinan called for caution. "What is clear at this point is that, of the large number of putative probiotics, only a small percentage have an impact on behavior and may qualify as psychobiotics," said Dr. Dinan. He added that for now, the field needs to wait for large-scale, placebo-controlled trials to provide definitive evidence of benefit and to detect which probiotics have psychobiotic potential.

Dr. Camille Zenobia wrote this in August 2013. From Real Clear Science:

Can 'Psychobiotic' Bacteria Affect Our Mood?

But what about your brain? Apparently, bacteria influence what’s going on up there, too. Within the last several years, a blossoming field of study called “microbial endocrinology” has provided some provocative insights about the relationship between our GI microbiota and our mood and behavior.

Studies in the field of microbial endocrinology have implicated GI microbes as a factor that can regulate the endocrine system. This could have both good and bad effects since the endocrine system is responsible for the production of hormones and coordinates metabolism, respiration, excretion, reproduction, sensory perception and immune function.

From Nov. 2013 Popular Science:

Forget Prozac, Psychobiotics Are The Future Of Psychiatry

The answer lies in the fact that many psychiatric illnesses are immunological in nature through chronic low level inflammation. There is a plethora of evidence showing the link between gut microbiota and inflammation and studies on probiotic strains have revealed their ability to modulate inflammation and bring back a healthy immunological function.  In this regard, by controlling inflammation through probiotic administration, there should be an effect of improved psychiatric disposition.

The authors bring up another reason why psychobiotics are so unique in comparison to most probiotics.  These strains have another incredible ability to modulate the function of the adrenal cortex, which is responsible for controlling anxiety and stress response. Probiotic strains, such as Lactobacillus helveticus and Bifdobacterium longum have shown to reduce levels of stress hormones and maintain a calmer, peaceful state.  There may be a host of other probiotic bacteria with the same ability although testing has been scant at best.

Finally, the last point in support of psychobiotics is the fact that certain strains of bacteria actually produce the chemicals necessary for a happy self.  But as these chemicals cannot find their way into the brain, another route has been found to explain why they work so well.  They stimulate cells in the gut that have the ability to signal the vagus nerve that good chemicals are in the body.  The vagus nerve then submits this information to the brain, which then acts as if the chemicals were there.  

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Lately some articles have been mentioning the amazing possibility of new treatments for psychiatric disorders using bacteria as psychobiotics. Think of probiotics (microorganisms that have beneficial effects when consumed) that affect the brain. Researchers promoting the use of this term define a psychobiotic as "a live organism that, when ingested in adequate amounts, produces a health benefit in patients suffering from psychiatric illness". This new emerging field is just in its infancy. Lots of speculation and anecdotal evidence, and a few tantalizing studies.

I think the following article is a good introduction to this research area of the gut and mind/brain interaction, even though it was published in late 2013. Or you could order the newly published scholarly book "Microbial Endocrinology: The Microbiota-Gut-Brain Axis in Health and Disease" (Editors M.Lyte and J.F.Cryan) with a $189. purchase price (!).  From November 2103 NPR:

Gut Bacteria Might Guide The Workings Of Our Minds

Could the microbes that inhabit our guts help explain that old idea of "gut feelings?" There's growing evidence that gut bacteria really might influence our minds. 

"I'm always by profession a skeptic," says Dr. Emeran Mayer, a professor of medicine and psychiatry at the University of California, Los Angeles. "But I do believe that our gut microbes affect what goes on in our brains." Mayer thinks the bacteria in our digestive systems may help mold brain structure as we're growing up, and possibly influence our moods, behavior and feelings when we're adults. "It opens up a completely new way of looking at brain function and health and disease," he says.

So Mayer is working on just that, doing MRI scans to look at the brains of thousands of volunteers and then comparing brain structure to the types of bacteria in their guts. He thinks he already has the first clues of a connection, from an analysis of about 60 volunteers. Mayer found that the connections between brain regions differed depending on which species of bacteria dominated a person's gut. 

But other researchers have been trying to figure out a possible connection by looking at gut microbes in mice. There they've found changes in both brain chemistry and behavior. One experiment involved replacing the gut bacteria of anxious mice with bacteria from fearless mice. "The mice became less anxious, more gregarious," says Stephen Collins of McMaster University in Hamilton, Ontario, who led a team that conducted the research. It worked the other way around, too — bold mice became timid when they got the microbes of anxious ones. And aggressive mice calmed down when the scientists altered their microbes by changing their diet, feeding them probiotics or dosing them with antibiotics. 

Scientists also have been working on a really obvious question — how the gut microbes could talk to the brain. A big nerve known as the vagus nerve, which runs all the way from the brain to the abdomen, was a prime suspect. And when researchers in Ireland cut the vagus nerve in mice, they no longer saw the brain respond to changes in the gut. "The vagus nerve is the highway of communication between what's going on in the gut and what's going on in the brain," says John Cryan of the University College Cork in Ireland, who has collaborated with Collins.

Gut microbes may also communicate with the brain in other ways, scientists say, by modulating the immune system or by producing their own versions of neurotransmitters. "I'm actually seeing new neurochemicals that have not been described before being produced by certain bacteria," says Mark Lyte of the Texas Tech University Health Sciences Center in Abilene, who studies how microbes affect the endocrine system. "These bacteria are, in effect, mind-altering microorganisms."

This research raises the possibility that scientists could someday create drugs that mimic the signals being sent from the gut to the brain, or just give people the good bacteria — probiotics — to prevent or treat problems involving the brain. Experiments to test whether changing gut microbes in humans could affect the brain are only just beginning. 

One team of researchers in Baltimore is testing a probiotic to see if it can help prevent relapses of mania among patients suffering from bipolar disorder."The idea is that these probiotic treatments may alter what we call the microbiome and then may contribute to an improvement of psychiatric symptoms," says Faith Dickerson, director of psychology at the Sheppard Pratt Health System.

Mayer also has been studying the effects of probiotics on the brain in humans. Along with his colleague Kirsten Tillisch, Mayer gave healthy women yogurt containing a probiotic and then scanned their brains. He found subtle signs that the brain circuits involved in anxiety were less reactive, according to a paper published in the journal Gastroenterology.

But Mayer and others stress that a lot more work will be needed to know whether that probiotic — or any others — really could help people feel less anxious or help solve other problems involving the brain. He says, "We're really in the early stages."