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Category: probiotics

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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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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."

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For those who missed it. An amusing and informative personal story (Julia Scott) about trying to cultivate a healthy skin biome. Well worth reading. Excerpts from the May 22, 2014 NY Times:

My No-Soap, No-Shampoo, Bacteria-Rich Hygiene Experiment

For most of my life, if I’ve thought at all about the bacteria living on my skin, it has been while trying to scrub them away. But recently I spent four weeks rubbing them in. I was Subject 26 in testing a living bacterial skin tonic, developed by AOBiome, a biotech start-up in Cambridge, Mass. The tonic looks, feels and tastes like water, but each spray bottle of AO+ Refreshing Cosmetic Mist contains billions of cultivated Nitrosomonas eutropha, an ammonia-oxidizing bacteria (AOB) that is most commonly found in dirt and untreated water. AOBiome scientists hypothesize that it once lived happily on us too — before we started washing it away with soap and shampoo — acting as a built-in cleanser, deodorant, anti-inflammatory and immune booster by feeding on the ammonia in our sweat and converting it into nitrite and nitric oxide.

 Because the N. eutropha are alive, he said, they would need to be kept cold to remain stable. I would be required to mist my face, scalp and body with bacteria twice a day. I would be swabbed every week at a lab, and the samples would be analyzed to detect changes in my invisible microbial community.

While most microbiome studies have focused on the health implications of what’s found deep in the gut, companies like AOBiome are interested in how we can manipulate the hidden universe of organisms (bacteria, viruses and fungi) teeming throughout our glands, hair follicles and epidermis. They see long-term medical possibilities in the idea of adding skin bacteria instead of vanquishing them with antibacterials — the potential to change how we diagnose and treat serious skin ailments. 

For my part in the AO+ study, I wanted to see what the bacteria could do quickly, and I wanted to cut down on variables, so I decided to sacrifice my own soaps, shampoo and deodorant while participating. I was determined to grow a garden of my own. Some skin bacteria species double every 20 minutes; ammonia-oxidizing bacteria are much slower, doubling only every 10 hours. And now the bacteria were on my skin.

I had warned my friends and co-workers about my experiment, and while there were plenty of jokes — someone left a stick of deodorant on my desk; people started referring to me as “Teen Spirit” — when I pressed them to sniff me after a few soap-free days, no one could detect a difference. Aside from my increasingly greasy hair, the real changes were invisible. By the end of the week, Jamas was happy to see test results that showed the N. eutropha had begun to settle in, finding a friendly niche within my biome.

AOBiome is not the first company to try to leverage emerging discoveries about the skin microbiome into topical products. The skin-care aisle at my drugstore had a moisturizer with a “probiotic complex,” which contains an extract of Lactobacillus, species unknown. There is even a “frozen yogurt” body cleanser whose second ingredient is sodium lauryl sulfate, a potent detergent, so you can remove your healthy bacteria just as fast as you can grow them.

Although a few studies have shown that Lactobacillus may reduce symptoms of eczema when taken orally, it does not live on the skin with any abundance, making it “a curious place to start for a skin probiotic,” said Michael Fischbach, a microbiologist at the University of California, San Francisco. Extracts are not alive, so they won’t be colonizing anything.

It doesn’t help that the F.D.A. has no regulatory definition for “probiotic” and has never approved such a product for therapeutic use. “The skin microbiome is the wild frontier,” Fischbach told me. “We know very little about what goes wrong when things go wrong and whether fixing the bacterial community is going to fix any real problems.”

I asked AOBiome which of my products was the biggest threat to the “good” bacteria on my skin. The answer was equivocal: Sodium lauryl sulfate, the first ingredient in many shampoos, may be the deadliest to N. eutropha, but nearly all common liquid cleansers remove at least some of the bacteria. Antibacterial soaps are most likely the worst culprits, but even soaps made with only vegetable oils or animal fats strip the skin of AOB.

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Yesterday I read and reread a very interesting journal review paper from Sept. 2013 that discussed recent studies about probiotics and treatment of respiratory ailments, including sinusitis. Two of the authors are those from the Abreu et al sinusitis study from 2012 (that I've frequently mentioned and that guided our own Sinusitis Treatment) that found that Lactobacillus sakei protects against sinusitis and treats sinusitis. Some of the things this paper discussed are: microbial communities in the airways and sinuses vary between healthy and non-healthy individuals (and each area or niche seems to have distinct communities), that lactic acid bacteria (including Lactobacillus sakei) are generally considered the "good guys" in our sinus microbiomes (the communities of microbes living in our sinuses), and that treatments of the future could consist of "direct localized administration of microbial species" (for example, getting the bacteria directly into the sinuses through the nasal passages with a nasal spray, or dabbing fermented kimchi juice like I did). They also mentioned that maybe one could also get probiotics to the GI tract (e.g., by eating probiotics) and maybe this would have some benefits. So far it seems that administering something containing L.sakei directly (by nasal spray or dabbing kimchi juice - as I did) seems to work best for treating sinusistis.

They also discussed that lactic acid bacteria are found in healthy mucosal surfaces in the respiratory, GI, and vaginal tract. They then proposed that lactic acid bacteria (including L.sakei) act as pioneer, or keystone species, and that they act to shape mucosal ecosystems (the microbiomes), and permit other species to live there that share similar attributes, and so promote "mucosal homeostasis". It appears that having a healthy sinus microbiome protects against pathogenic species.

So yeah - the bottom line is that microbial supplementation of beneficial bacteria seems very promising in the treatment of respiratory ailments. And for long-term successful sinusitis treatment, one would need to improve the entire sinus microbial community (with a "mixed species supplement"), not just one bacteria species. (By the way, maybe that is also why using kimchi in our successful Sinusitis Treatment works - it is an entire microbial community with several lactic acid species, including the all important Lactobacillus sakei. (NOTE: See Sinusitis Treatment Summary page and The One Probiotic That Treats Sinusitis for some easy methods  using various probiotics to treat chronic sinusitis. These articles get updated frequently.) From Trends in Microbiology:

Probiotic strategies for treatment of respiratory diseases.

More recently, Abreu et al. profiled the sinus microbiome of CRS (chronic rhinosinusitis) patients and healthy controls at high resolution [2]. Microbial burden was not significantly different between healthy subject and CRS patient sinuses. Moreover, known bacterial pathogens such as H. influenza, P. aeruginosa, and S. aureus were detected in both healthy and CRS sinuses; however, the sinus microbiome of CRS patients exhibited characteristics of community collapse, in other words many microbial species associated with healthy individuals, in particular lactic acid bacteria, were significantly reduced in relative abundance in CRS patients. In this state of microbiome depletion, the species C. tuberculostearicum was significantly enriched. This indicates that composition of the microbiome is associated with disease status and appears to influence the activity of pathogens within these assemblages.

Although sinusitis patients in the Abreu study exhibited hallmark characteristics of community collapse, the comparator group – healthy individuals – represented an opportunity to mine microbiome data and identify those bacterial species specific to the sinus niche that putatively protect this site. The authors demonstrated that a relatively diverse group of phylogenetically distinct lactic acid bacteria were enriched in the healthy sinus microbiota [2]. As proof of principle that the sinonasal microbiome itself or indeed specific members of these consortia protect the mucosal surface from pathogenic effects, a series of murine studies were undertaken. These demonstrated that a replete, unperturbed sinus microbiome prevented C. tuberculostearicum pathogenesis. Moreover, even in the context of an antimicrobial-depleted microbiome, Lactobacillus sakei when co-instilled with C. tuberculostearicum into the nares of mice afforded complete mucosal protection against the pathogenic species. Although this is encouraging, it is unlikely that a single species can confer long-term protection in a system that is inherently multi-species and constantly exposed to the environment. Indeed, previous studies and ecological theory supports the hypothesis that multi-species consortia represent more robust assemblages, and tend to afford improved efficacy with respect to disease or infection outcomes [44,45]. This study therefore provides a basis for the identification of what may be termed a minimal microbial population (MMP) composed of multiple phylogenetically distinct lactic acid bacteria, including L. sakei. Such a mixed species assemblage would form the foundation of a rationally designed, sinus-specific bacterial supplement to combat established chronic diseases or, indeed, be used prophylactically to protect mucosal surfaces against acute infection.

Therefore, although site-specific diseases such as chronic sinusitis may well be confined to the sinus niche and be resolved simply by localized microbe-restoration approaches, it is also entirely plausible that an adjuvant oral microbe-supplementation strategy and dietary intervention (to sustain colonization by the introduced species) may increase efficacy and ultimately improve long-term patient outcomes. This two-pronged approach may be particularly efficacious for patients who have lost protective GI microbial species due to
administration of multiple courses of oral antimicrobials to manage their sinus disease.

Although it is impossible to define the precise strains or species that will be used in future microbial supplementation strategies to treat chronic inflammatory diseases, there is a convergence of evidence indicating that healthy mucosal surfaces in the respiratory, GI, and vaginal tract are colonized by lactic acid bacteria. We would venture that members of this group act as pioneer, keystone species that, through their multitude of functions (including bacteriocin production, competitive colonization, lactate and fatty acid production), can shape mucosal ecosystems, thereby permitting co-colonization by phylogenetically distinct
species that share functionally similar attributes. Together, these subcommunities promote mucosal homeostasis and represent the most promising species for future microbe-supplementation strategies.

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It is now more than 69 weeks since I first successfully started using kimchi to treat the chronic sinusitis that had plagued me (and my family) for so many years. I originally reported on the Sinusitis Treatment on Dec. 6, 2013 (the method is described there) and followed up on Feb. 21, 2014.

Based on the sinus microbiome research of N. Abreu et al (from Sept. 2012 in Sci.Transl.Med.) that discussed Lactobacillus sakei as a sinusitis treatment, I had looked for a natural source of L.sakei and found it in kimchi. Since dabbing the kimchi juice in our nostrils as needed, all 4 of us are still free of chronic sinusitis and off all antibiotics at close to a year and a half (I'm optimistic). So how is year two shaping up?

Well, it is different and even better than year one. Much of the first year seemed to be about needing to build up our beneficial bacteria sinus community (sinus microbiome) through kimchi treatments, eating fermented foods (such as kimchi, kefir, yogurt), whole grains, vegetables, and fruits. And of course not having to take antibiotics helped our sinus microbial community.

But now in year two we notice that we absolutely don't need or want frequent kimchi treatments - even when sick. Daily kimchi treatments, even during acute sinusitis (after a cold), actually seems to be too much and makes us feel worse (for ex., the throat becomes so dry, almost like a sore throat). But one treatment every 2 or 3 days while sick is good. In fact, this year we have done so few treatments, that even when ill, each time the sick person stopped doing kimchi treatments before he/she was fully recovered, and any sinusitis symptoms kept improving on their own until full recovery! Amazing!

To us, this is a sign that all of us have much improved sinus microbiomes from a year ago. And interestingly, we are getting fewer colds/viruses than ever.  Our guiding principle this year is: "Less is more." In other words, at this point only do a kimchi sinus treatment when absolutely needed, and then only do it sparingly. Looking back, we think we should have adopted the "less is more" last year after the first 6 months of kimchi treatments.

The other thing we've done is cut back on daily saline nasal irrigation, especially when ill and doing kimchi treatments. We've started thinking that the saline irrigation also flushes out beneficial bacteria.

The conclusion is: YES, a person's microbiome can improve, even after years or decades of chronic sinusitis. It is truly amazing and wonderful to not struggle with it, and to feel normal.

(UPDATE: See Sinusitis Treatment Summary page and The Best Probiotic For Sinus Infections for more information, more products one can use, and more L. sakei treatment information. We are using the high quality refrigerated product Lacto Sinus these days.)

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SUMMARY OF TREATMENT METHOD USING KIMCHI

The following is a quick summary of the method we use (see Sinusitis Treatment Summary page).We use live (fermented and not pasteurized) vegan (no seafood added) kimchi. Choosing vegan (no seafood added) kimchi is a personal preference. Lactobacillus sakei is found in meat, seafood, and some vegetables.

Treatment Method: 1) Wash hands, and then use a clean teaspoon to put a little juice from the kimchi jar into a small clean bowl. 2) Dip finger in the kimchi juice and dab it or smear it along the insides of one nostril (about 1/2" into the nostril). 3) Dip finger in kimchi juice again and repeat in other nostril. 4) Do this several times. If I needed to blow my nose at this point I would, and afterwards I would put more kimchi juice up each nostril (again repeating the procedure) and then not blow my nose for at least an hour (or more). 5) Afterwards, any unused kimchi in the little bowl was thrown out and not replaced in the main kimchi jar. (Note: Put the main kimchi jar back in the refrigerator. Also, once opened, take kimchi juice from it for no more than 6 days.)

My rationale was that I was inhaling the bacteria this way and that it would travel up the nasal passages on their own to my sinuses. I did this regimen once or twice a day initially until I started feeling better, then started doing it less frequently, and eventually only as needed.

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I spent time this past week searching the medical literature (US National Library of Medicine - Medline/PubMed) for the latest in sinusitis research. I wish I could tell you that amazing research has been happening recently, especially with the sinus microbiome (which could mean treating sinusitis with microbes), but I was disappointed. Really disappointed.

I did four searches: one for "sinusitis" (looked at 600+ studies dating back to summer 2013), then "chronic sinusitis" (going back to fall 2012), then "sinusitis, probiotics", and finally "sinusitis, microbiome". The "sinusitis, probiotics" search turned up 10 studies dating back to 2002. The "sinusitis, microbiome" search turned up a grand total of 13 studies, with the oldest dating back to 2004. Of course the sinus microbiome research by Abreu et al from September 2012  discussing Lactobacillus sakei and which I based my personal (and successful) kimchi sinusitis treatment was on the list (see my Dec. 5 post for a discussion of their research). But none of the other studies looked at Lactobacillus sakei (which is in kimchi).

Some of the findings among the many chronic sinusitis studies: microbial diversity is lower in antibiotic treated chronic sinusitis sufferers (than in healthy controls) and the microbial communities more uneven (meaning some microbes dominated over others), and greater Staphylococcus aureus populations among those with chronic sinusitis. After antibiotic treatment patients typically became colonized by microbes that are less susceptible to the prescribed antibiotics. One study found that Staphylococcus epidermidis (SE) may have some effectiveness against Staphylococcus aureus (SA) in the sinusitis microbiome in mice. Lactobacillus rhamnosus was not found to be effective against sinusitis. A number of studies reported biofilms in the sinuses which are highly resistant to medicines. Some studies found that smoking or exposure to second-hand smoke is linked to chronic sinusitis. (June 2016 UPDATE: I should have said that Lactobacillus rhamnosus (R0011 strain) was not effective against sinusitis when taken orally (a tablet) twice a day for 4 weeks in the study. There have been no further studies since then looking at L. rhamnosus for sinusitis treatment. It is unknown whether spraying or smearing/dabbing L. rhamnosus directly into the nostrils would have a positive effect)

Everyone agreed that state of the art genetic analyses found many more microbial species than older methods (the least effective was the traditional culture method). Several studies suggested that perhaps chronic sinusitis is due to immunological defects and one suggested that it was due to "immune hyperresponsiveness" to organisms in the sinuses. Surprisingly, some studies reported that there are more microbes or microbial species in chronic sinusitis patients than in control patients and that Staphylococcus aureus may be dominant (NOTE: These results may be due to not having been done with state of the art genetic analyses which would have picked up more microbial diversity. Another issue is where in the respiratory tract the samples were taken from, because it seems that the different areas have different microbial communities).

There was frequent mention that chronic sinusitis affects millions of people each year in the US, that little is known about its exact cause, and that there is controversy over appropriate treatment. Originally doctors thought that healthy sinuses were sterile, and it has taken a while to realize that is untrue. It is clear that researchers are only now trying to discover what microbial communities live in healthy individuals compared to those with chronic sinusitis.

But it appeared to me that the majority of the studies from the last 2 years indicated that treatment of chronic sinusitis is still: first try antibiotics, then antibiotics plus inhaled corticosteroids and perhaps nasal saline irrigation, then followed by endoscopic sinus surgery (or sometimes balloon dilation), then perhaps steroid drip implants (steroid-eluting sinus implants), and then there may be revision surgeries.

So I'm sticking with my easy-to-do, inexpensive, and fantastically successful kimchi (Lactobacillus sakei) sinusitis treatment. Of course! (see my Dec. 6, 2013 and Feb. 21, 2014 posts or click on the Sinusitis Treatment link for further information).

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Another article stating that the future is feces in treating a number of diseases. From Pacific Standard:

Medicine’s Dirty Secret: Fecal Transplants Are the Next Big Thing in Health Care

POO IS A DECIDEDLY IMPERFECT delivery vehicle for a medical therapy. It’s messy. It stinks. It’s inconsistent, not to mention a regulatory nightmare. But it can be incredibly potent. A classic study of nine healthy British volunteers found that bacteria accounted for more than half of the mass of their fecal solids. That astonishing concentration of microorganisms, both living and dead, makes sense when you consider that the microbial colonists inhabiting our gastrointestinal tract outnumber our own cells roughly three to one, on recent estimates.

In the ideal conditions of the human gut, a thriving ecosystem of 1,000 or more bacterial species that rivals the complexity of a rainforest has co-evolved with us. This microscopic jungle is constantly adapting in response to our diet, antibiotic use and other environmental influences. As the science has progressed, researchers are now comparing the entire collection of microbial inhabitants of the human gut, our microbiome, to a “hidden metabolic organ.” Scientists have linked disruptions to this organ, a condition known as dysbiosis, to everything from inflammatory bowel disease and high blood pressure to diabetes and obesity.

Viewed in this light, a fecal microbiota transplant is nothing more than an attempt to reseed an intestinal tract, often after antibiotics have killed off the native flora that might have kept invasive species at bay. No other medical therapy can claim such a high cure rate for the infection widely known as C. diff.

Some doctors have likened the recoveries of desperately ill patients to those seen with anti-HIV protease inhibitors in the mid-1990s. After the Mayo Clinic in Scottsdale, Arizona, performed its first fecal microbiota transplant in 2011, a patient who had been bed-ridden for weeks left the hospital 24 hours later. And in 2013, researchers in the Netherlands halted a landmark C. diff. clinical trial early for ethical reasons when they saw that the overall cure rate of 94 percent with donor feces had far outpaced the 31 percent cured with the antibiotic vancomycin.

Yet few other interventions elicit such disgust, revulsion, and ridicule. Chronicling a potential advance by a team of Canadian scientists, one newspaper account warned readers: “Hold your nose and don’t spit out your coffee.” In 2013, the founder of a patient advocacy blog called The Power of Poop wrote an open letter to 13 gastroenterology associations detailing the story of a Kentucky man who contracted an acute case of C. diff. Despite his family’s pleas, his doctor dismissed the idea of a fecal transplant as “quackery.” The man died the next day.

Although most providers haven’t published their overall success rates, their self-reported results are surprisingly similar, and consistent with what published reports there are. Khoruts says he has achieved a success rate of about 90 percent after one infusion, 99 percent after two. “In medicine, it’s pretty startling to have therapy that’s that effective for the most refractory patients with that condition,” he says. Colleen Kelly, a gastroenterologist with the Women’s Medicine Collaborative in Providence, Rhode Island, has performed the procedure on 130 patients with recurrent C. diff., with a success rate of about 95 percent. Most of the transplants have taken after just one attempt.

For a relatively simple bacterial infection, Petrof says, the potential remedy may be fairly straightforward. “With recurrent C. diff. what you’ve done is you’ve basically torched the forest,” she says. Nearly everything has been killed off by the antibiotics, leaving very low bacterial diversity. “So the C. diff. can just take root and grow.” Adding back almost any other flora—the equivalent of planting seedlings in the dirt—could help the ecosystem keep interloping pathogens at bay.

For more complicated conditions, though, a simple fecal transplant may not be enough, at least with donors from the Western world. One hypothesis suggests that people in lower-income countries might harbor more diverse bacterial populations in their guts than those who have grown up in a more sterile, antibiotic-rich environment. And in fact, a 2012 study found that residents of Venezuela’s Amazonas state and rural Malawi had markedly more diverse gut microbiomes than people living in three U.S. metropolitan areas. Scientists have already raised the idea that a rise in allergies and autoimmunity in industrialized nations may derive from a kind of collective defect of reduced microbial diversity.

“We cannot find people who’ve never been on antibiotics,” Khoruts says of his donors. For complex autoimmune diseases such as ulcerative colitis, fecal transplants may offer only a partial solution. And with some data suggesting that susceptibility may be linked in part to past antibiotic exposure, perhaps no Western donor can provide the microbes needed to fully reseed the gut.

What then? Khoruts says it may be necessary to seek out ancestral microbial communities—the ones all humans hosted before the advent of the antibiotic era—within people in Africa or the Amazon. “It’s just a disappearing resource,” he says.

By the beginning of April 2014, nearly 30 fecal transplant clinical trials were underway around the world. Roughly half were aimed at C. diff., including two testing the therapy in combination with vancomycin, and another multi-center trial evaluating the effectiveness of fresh versus frozen donor poo.

As the therapy becomes more widely established, via something akin to a “poop pill” or “crapsule,” perhaps the infectious pool of C. diff. patients may start to dwindle. More clinicians, then, might feel emboldened to explore how our bowel flora may affect not only the gastrointestinal system but also the immune and neurological systems. At least a dozen trials are now investigating whether fecal transplants can help treat some form of inflammatory bowel disease, be it Crohn’s disease or ulcerative colitis. Another is looking into Type 2 diabetes, and one is even using lean donors to test fecal transplants on patients with metabolic syndrome. Researchers say it won’t be along before they’re joined by studies investigating whether the therapy might aid diseases like multiple sclerosis and autism.

For those who want to know more, another article form The Pacific Standard:

6 Ways to Transplant Fecal Matter, at Home or at the Hospital

And the following two groups:  The Fecal Transplant Foundation

The Power of Poop

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Excerpts from a very interesting NPR interview with Dr. Martin Blaser and his views on the human microbiome. The big take-away: our modern life-style is not good for the gut microbiome. His recently published book is Missing Microbes: How the Overuse of Antibiotics is Fueling Our Modern Plagues.

From NPR News: Modern Medicine May Not Be Doing Your Microbiome Any Favors

There are lots of theories about why food allergies, asthma, celiac disease and intestinal disorders like Crohn's disease have been on the rise. Dr. Martin Blaser speculates that it may be connected to the overuse of antibiotics, which has resulted in killing off strains of bacteria that typically live in the gut.

Blaser is an expert on the human microbiome, which is the collection of bacteria, viruses, fungi and other microbes that live in and on the body. In fact, up to 90 percent of all the cells in the human body aren't human at all — they're micro-organisms. Blaser is the director of NYU's Human Microbiome Program and a former chairman of medicine there. His new book is called Missing Microbes: How the Overuse of Antibiotics Is Fueling Our Modern Plagues.

"Since World War II, we've seen big rises in a number of diseases: asthma, allergies, food allergies, wheat allergy, juvenile diabetes, obesity. ... These are all diseases that have gone up dramatically in the last 50 or 70 years. One of the questions is: Why are they going up? Are they going up for 10 different reasons, or perhaps there is one reason that is fueling all of them."

"My theory is that the one reason is the changing microbiome; that we evolved a certain stable situation with our microbiome and with the modern advances of modern life, including modern medical practices, we have been disrupting the microbiome. And there's evidence for that, especially early in life, and it's changing how our children develop."

"There's a choreography; there's a normal developmental cycle of the microbiome from birth over the first few years of life, especially the first three years, [that] appear[s] to be the most important. And that's how nature has, how we have, evolved together so that we can maximize health and create a new generation, which is nature's great purpose. And because of modern practices, we have disrupted that. And then the question is: Does that have consequence[s]?"

"As far as we know, when the baby is inside the womb it is apparently sterile. ... The big moment of truth is when the membranes rupture, the water breaks, and the baby starts coming out. And that's where they first get exposed to the bacteria of the world, and the first bacteria they're exposed to is their mother's bacteria in the birth canal. So as labor proceeds, the babies are in contact with the microbes lining their mother's vagina and, as they're going out, they're covered by these bacteria. They swallow the bacteria; it's on their skin. ..."

"That's their initial exposure to the world of bacteria. That's how mammals have been doing it for the last 150 million years, whether they're dolphins or elephants or humans. ... And we know a little about what those bacteria are. The most common bacteria are lactobacillus and there's evidence that over the course of pregnancy the microbiome in the vagina changes, just as many other parts of the body are changing. The microbiome is changing in its composition in terms of maximizing lactobacilli, and these are bacteria that eat lactose, which is the main component of milk. So the baby's mouth is filled with lactobacilli. The first thing that happens is they go up against their mom's breast and they inoculate the nipple with lactobacilli and now milk and lactobacilli go into the new baby and that's the foundation for their microbiome and that's how they start their life. ..."

"You could project that if they didn't acquire these organisms or they didn't acquire them normally or at the normal time, then the foundations might be a little shaky."

"Shortly after birth, they compared the microbiomes in the babies that came out. The babies that were born vaginally, their microbiome, not surprisingly, looked like the mom's vagina everywhere in the body — in their GI tract, on their skin, in their mouth. But the babies born by C-section, their microbiome looked like skin and it didn't even necessarily look like the mom's skin, maybe it was somebody else in the operating room. So it's clear that the microbiome is different immediately depending on the kind of birth."

"What I can tell you is that our immune system is quite complex. There are many kinds of immune cells. There are cells that strongly recognize foreign substances, there are ones that try to damp [the immune system] and down-regulate it. There's what we call innate immunity, which is the immunity we're all born with, and then there's adaptive immunity — the immunity that develops when we experience different kinds of exposures. So it's very complex."

"There are many different probiotics.  I think I can say three things: The first is that they're almost completely unregulated; second is that they seem to be generally safe; and third is that they're mostly untested. ... I'm actually a big believer in probiotics; I think that's going to be part of the future of medicine, that we're going to understand the science of the microbiome well enough so that we can look at a sample from a child and say this child is lacking such-and-such an organism and now we're going to take it off the shelf and we're going to give it back to that child. ... "