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Category: human microbiome

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Obviously children on farms are exposed to a lot of dirt and animals, both teaming with microorganisms. But I wonder, and it's not discussed, is whether people living on dairy farms are drinking raw milk, which contains lots of microorganisms. After all, the point of milk pasteurization is to kill off bacteria. Will we go back to drinking raw milk to try to prevent allergies? From Science Daily:

Children on dairy farms run one-tenth the risk of developing allergies; Dairy farm exposure also beneficial during pregnancy

Children who live on farms that produce milk run one-tenth the risk of developing allergies as other rural children. According to researchers at The University of Gothenburg in Sweden, pregnant women may benefit from spending time on dairy farms to promote maturation of the fetal and neonatal immune system.

The occurrence of allergic diseases has risen dramatically in Western societies. One frequently cited reason is that children are less exposed to microorganisms and have fewer infections than previous generations, thereby delaying maturation of the immune system.

A study by researchers at Sahlgrenska Academy, University of Gothenburg, monitored children until the age of three to examine maturation of the immune system in relation to allergic disease. All of the children lived in rural areas of the Västra Götaland Region, half of them on farms that produced milk. The study found that children on dairy farms ran a much lower risk of developing allergies than the other children.

"Our study also demonstrated for the first time that delayed maturation of the immune system, specifically B-cells, is a risk factor for development of allergies," says Anna-Carin Lundell, one of the researchers. Children with an allergic disease at the age of 18 and 36 months had a higher percentage of immature B-cells in their blood circulation at birth and during the first month of life. 

"We need to identify the specific factors on dairy farms that strengthen protection against allergies and appear to promote maturation of the immune system as early as the fetal stage," Ms. Lundell says.

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New discoveries of what is going on in our intestines, plus a new vocabulary to understand it all. Yes, it all is amazingly complex. Bottom line: we have complex communities (bacteria, bacterial viruses or bacteriophages, etc.) living and interacting in our intestines. And only with state-of-the-art genetic analysis (DNA sequencing) can we even "see" what is going on. I highlighted really important items in bold type. From Medical Xpress:

Researchers uncover new knowledge about our intestines

Researchers from Technical University of Denmark Systems Biology have mapped 500 previously unknown microorganisms in human intestinal flora as well as 800 also unknown bacterial viruses (also called bacteriophages) which attack intestinal bacteria.

"Using our method, researchers are now able to identify and collect genomes from previously unknown microorganisms in even highly complex microbial societies. This provides us with an overview we have not enjoyed previously," says Professor Søren Brunak who has co-headed the study together with Associate Professor Henrik Bjørn Nielsen.

So far, 200-300 intestinal bacterial species have been mapped. Now, the number will be more than doubled, which could significantly improve our understanding and treatment of a large number of diseases such as type 2 diabetes, asthma and obesity.

The two researchers have also studied the mutual relations between bacteria and viruses. Previously, bacteria were studied individually in the laboratory, but researchers are becoming increasingly aware that in order to understand the intestinal flora, you need to look at the interaction between the many different bacteria found.

And when we know the intestinal bacteria interactions, we can potentially develop a more selective way to treat a number of diseases. "Ideally we will be able to add or remove specific bacteria in the intestinal system and in this way induce a healthier intestinal flora," says Søren Brunak.

From Science Daily:

Revolutionary approach to studying intestinal microbiota

Analyzing the global genome, or the metagenome of the intestinal microbiota, has taken a turn, thanks to a new approach to study developed by an international research team. This method markedly simplifies microbiome analysis and renders it more powerful. The scientists have thus been able to sequence and assemble the complete genome of 238 intestinal bacteria, 75% of which were previously unknown. 

Research carried out in recent years on the intestinal microbiota has completely overturned our vision of the human gut ecosystem. Indeed, from "simple digesters" of food, these bacteria have become major factors in understanding certain diseases such as obesity, type 2 diabetes, or Crohn's disease. Important and direct links have also been demonstrated between these bacteria and the immune system, as well as with the brain. It is estimated that 100,000 billion bacteria populate the gut of each individual (or 10 to 100 times more than the number of cells in the human body), and their diversity is considerable, estimated to around a thousand different bacterial species in the intestinal human metagenome. However, because only 15% of these bacteria were previously isolated and characterized by genome sequencing, an immense number of the microbial genes previously identified still need to be assigned to a given species.

An analysis of 396 stool samples from Danish and Spanish individuals allowed the researchers to cluster these millions of genes into 7381 co-abundance groups of genes. Approximately 10% of these groups (741) corresponded to bacterial species referred to as metagenomic species (MGS); the others corresponded to bacterial viruses (848 bacteriophages were discovered), plasmids (circular, bacterial DNA fragments) or genes which protected bacteria from viral attack (known as CRISPR sequences). 85% of these MGS constituted unknown bacteria species (or ~630 species).

Using this new approach, the researchers succeeded in reconstituting the complete genome of 238 of these unknown species, without prior culture of these bacteria. Living without oxygen, in an environment that is difficult to characterise and reproduce, most of these gut bacteria cannot be cultured in the laboratory. 

The authors also demonstrated more than 800 dependent relationships within the 7381 gene co-abundance groups; this was the case, for example, of phages which require the presence of a bacterium to survive. These dependent relationships thus enable a clearer understanding of the survival mechanisms of a micro-organism in its ecosystem. 

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20131201_101300 Several people have recently written to me about kimchi and asked why I originally chose vegan kimchi over kimchi containing a seafood ingredient (typically fish or shrimp sauce) for sinusitis treatment. I have also been asked whether vegan kimchi has enough Lactobacillus sakei bacteria in it as compared to kimchi made with a seafood seasoning. (see Sinusitis Treatment Summary page and/or Sinusitis posts for in-depth discussions of Lactobacillus sakei in successful sinusitis treatment).

Korean kimchi is a fermented food typically made with cabbage and other vegetables and seasonings, and can contain some seafood (perhaps fish or shrimp sauce) as a seasoning, or just be vegan (no seafood ingredients). It can also be made using a starter culture.

These questions arose because Lactobacillus sakei (L.sakei) is commonly found on meat and fish, and plays a role in the fermentation and preservation of meat. L.sakei "outcompetes other spoilage- or disease-causing microorganisms" and so prevents them from growing. Thus it is considered beneficial and is used commercially in lactic acid starter cultures (for example, in making European salami and sausages).

L. sakei was originally isolated from sake or rice wine (thus plant origin), is found in very low levels in some fermented sauerkraut, and according to the studies I looked at, is found during fermentation in most brands of Korean kimchi.

Currently there are over 230 different strains of L.sakei isolated from meat, seafood, or vegetables from all over the world (from S. Chaillou et al 2013 study looking at population genetics of L.sakei). So this bacteria, which is found by using state of the art genetic analysis, turns out to be quite common.

So why did I only use vegan kimchi and only mention vegan kimchi in our Sinusitis Treatment method?

It's because when I first started dabbing kimchi juice in my nose about 1 1/2 years ago, I was in uncharted territory. I was desperate for something with L.sakei in it, and from my reading I found kimchi. However, putting (by dabbing or smearing) a live fermented product in my nostrils was a big unknown. When I first opened some jars, the kimchi juice would bubble and sometimes overflow and run down the sides of the jar. Would the microbes in kimchi harm or benefit me? Obviously I was conducting an experiment with unknown results.

I settled on vegan (no seafood) kimchi because a totally plant-based product sounded safer to me. I wondered what other microbes are in the kimchi with seafood. Could any of them be harmful?  And my choice of vegan kimchi turned out great.

Our experiences with kimchi are that it works amazingly well in treating sinusitis and causes no harm (as far as we can tell). This is the best I've felt in many, many years - back to normal!

But I don't know if other brands of vegan kimchi, with different recipes and ingredients and thus different microbial communities, would have worked out so well. The levels of L.sakei and other beneficial microbes in the many kimchi brands are unknown.

So now I wonder- if L. sakei is so pervasive on meat and seafood, perhaps kimchi with a seafood ingredient in it would be even better, with consistently higher amounts of L. sakei. Or maybe there is no difference between the two kinds of kimchi. Only the very expensive state-of-art genetic testing would give me the answer to that question.

Based on my successful 1 1/2 years of vegan kimchi experience, I may be willing to experiment further and try non-vegan kimchi. Or maybe not. Perhaps it is better. But I'm very cautious.... 

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Lactobacilli

The human vagina is another microbial community that is nowhere as simple as earlier thought - and it's not just Lactobacillus bacteria.

From The Scientist: Characterizing the “Healthy” Vagina

For years, researchers characterized the microbial community of women’s vaginas as being dominated by Lactobacillus bacteria, which ferment carbohydrates to lactic acid, yielding a low pH that is toxic to many pathogenic microbes. When levels of Lactobacillus drop, the pH becomes more neutral, and the risk of infection rises.

But with research revealing notable variation among women’s vaginal microbiomes, as well as some interesting dynamics of the microbial communities within a single organ, “that dogma is changing a little bit,” said Gregory Buck of the Vaginal Microbiome Consortium at Virginia Commonwealth University (VCU).

The composition and stability of the vaginal microbiome varies by race, age, even within an individual—and it’s quickly become clear that the formula for a “normal,” “healthy” microbial community cannot be computed by ratios of bacterial species. “In the past we’ve made some generalizations about what kinds of bacteria are found in the vagina, what kinds of bacteria are good or healthy or protective,” said microbial ecologist Larry Forney of the University of Idaho. “What the research is showing is there are tremendous differences between women in terms of the kinds of bacteria that are present and the changes in the communities that occur over time.”

In June 2010, Forney, Jacques Ravel of the University of Maryland School of Medicine, and their collaborators published a survey of the vaginal microbiomes of nearly 400 women and found that the majority harbored bacterial communities dominated by one of four Lactobacillus strains. More than a quarter of the women studied, however, did not follow this pattern. Instead, their vaginas had fewer Lactobacillus and greater numbers of other anaerobic bacteria, although the bacterial communities always included members of genera known to produce lactic acid.

In many ways, the microbiome of these women resembled the bacterial communities of women suffering from bacterial vaginosis (BV), an infection characterized by an odorous vaginal discharge, Buck noted. “By looking at the microbial components, you’d say they have BV, but they have no clinical symptoms,” he said. “These people are not unhealthy.”

The researchers also found that the composition of a woman’s vaginal microbiome was linked to her race. Eighty percent of Asian women and nearly 90 percent of white women harbored vaginal microbiomes that were dominated by Lactobacillus, while only about 60 percent of Hispanic and black women did. Moreover, vaginal pH varied with ethnicity as well, with Hispanic and black women averaging 5.0 and 4.7, respectively, and Asian and white women averaging 4.4 and 4.2. 

This raises questions about the role of the commensal bacteria and risk of preterm labor , which has been linked to BV—and to low levels of Lactobacillus in particular—and is one-and-a-half times more common among African American women than Caucasian women.

Meanwhile, the researchers continue to sort through 40,000 swabs from more than 6,000 women to better characterize the bacterial communities living in the vagina. But Fettweis and her colleagues face a common problem in microbiome research. “In many samples, only a fraction of [the genetic sequences] align to anything we have in our databases,” she said. “So I think there’s still a lot of work to be done in terms of actually understanding: What are these organisms?”

Another question facing researchers probing the vaginal microbiome is how it is initially colonized. “Where do [the bacteria] come from?” said Forney.

Many suspect that the process occurs during vaginal childbirth. But the adolescent microbiome does not resemble that of a sexually mature woman, having far less Lactobacillus, leading some to suspect that there may be a second colonization of the vagina later in life. And if the birthing process is important to establish the vaginal microbiome, what happens in the case of C-sections? “We have more questions than answers,” Forney said.

The microbiome is also not stable later in life. It is now well known that the vaginal microbiome changes after menopause, containing fewer Lactobacillus than the vaginas of reproductive-aged women, with the notable exception of women on hormone-replacement therapies.

Moreover, recent research has revealed that the composition of the vaginal microbiome can change in as little as 24 hours.

The temporal dynamics of the vaginal microbiome raise important questions about developing microbiota-based diagnostics and therapeutics, said Forney. “If you perform a diagnostic test, would you get a different result tomorrow or the day after? In some cases, yes. How do you incorporate that into [a] decision about whether some kind of intervention is required?”

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The study talked specifically about 3 types of bacteria that were different among the groups (severely obese, diabetics, healthy) studied: Firmicutes, Bifidobacteria, Clostridium leptum. From Science Daily:

Gut microbe levels are linked to type 2 diabetes and obesity

People with Type 2 diabetes or obesity have changes in the composition of their intestinal micro-organisms -- called the gut microbiota -- that healthy people do not have, researchers from Turkey have found.

The study lends support to other recent reports that have found an association between specific bacterial species in the human digestive system and obesity and diabetes, according to lead investigator Yalcin Basaran, MD, an endocrinologist from Gulhane Military Medical Academy School of Medicine, Ankara, Turkey.

The human digestive system contains an estimated 10 trillion to 100 trillion bacteria and other microscopic organisms, with each person housing at least 160 different species of organisms, according to Basaran. 

Basaran and his fellow researchers sought to identify the relationship between the gut microbe composition and obesity and Type 2 diabetes. Their study included 27 severely obese adults (20 men and seven women) whose body mass index, or BMI, exceeded 35 kg/m2, as well as 26 adults (18 men and eight women) with newly diagnosed Type 2 diabetes and 28 healthy control subjects (22 men and six women). 

Fecal analysis using a molecular biology technique showed that several of the most common types of bacteria in the gut were present at considerably lower levels in the obese and diabetic groups, compared with healthy controls. These reductions ranged from 4.2 to 12.5 percent in the obese patients and 10 to 11.5 percent in the diabetic patients, Basaran reported.

"Manipulation of intestinal bacteria could offer a new approach to manage obesity and Type 2 diabetes."

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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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Interesting to think of bacteria and biofilms (bacterial communities resistant to treatment) involved in stress related heart attacks. From Science Daily:

Bacteria help explain why stress, fear trigger heart attacks

Scientists believe they have an explanation for the axiom that stress, emotional shock, or overexertion may trigger heart attacks in vulnerable people. Hormones released during these events appear to cause bacterial biofilms on arterial walls to disperse, allowing plaque deposits to rupture into the bloodstream, according to research published in published in mBio®, the online open-access journal of the American Society for Microbiology.

"Our hypothesis fitted with the observation that heart attack and stroke often occur following an event where elevated levels of catecholamine hormones are released into the blood and tissues, such as occurs during sudden emotional shock or stress, sudden exertion or over-exertion" said David Davies of Binghamton University, Binghamton, New York, an author on the study.

Davies and his colleagues isolated and cultured different species of bacteria from diseased carotid arteries that had been removed from patients with atherosclerosis. Their results showed multiple bacterial species living as biofilms in the walls of every atherosclerotic (plaque-covered) carotid artery tested.

In normal conditions, biofilms are adherent microbial communities that are resistant to antibiotic treatment and clearance by the immune system. However, upon receiving a molecular signal, biofilms undergo dispersion, releasing enzymes to digest the scaffolding that maintains the bacteria within the biofilm. These enzymes have the potential to digest the nearby tissues that prevent the arterial plaque deposit from rupturing into the bloodstream. According to Davies, this could provide a scientific explanation for the long-held belief that heart attacks can be triggered by a stress, a sudden shock, or overexertion.

To test this theory they added norepinephrine, at a level that would be found in the body following stress or exertion, to biofilms formed on the inner walls of silicone tubing."At least one species of bacteria -- Pseudomonas aeruginosa -- commonly associated with carotid arteries in our studies, was able to undergo a biofilm dispersion response when exposed to norepinephrine, a hormone responsible for the fight-or-flight response in humans," said Davies. Because the biofilms are closely bound to arterial plaques, the dispersal of a biofilm could cause the sudden release of the surrounding arterial plaque, triggering a heart attack.

To their knowledge, this is the first direct observation of biofilm bacteria within a carotid arterial plaque deposit, says Davies. This research suggests that bacteria should be considered to be part of the overall pathology of atherosclerosis and management of bacteria within an arterial plaque lesion may be as important as managing cholesterol.

Note the red biofilm bacterial colonies within the diseased arterial wall:

Bacteria stained with a fluorescent bacterial DNA probe show up as red biofilm microcolonies within the green tissues of a diseased carotid arterial wall.

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A big benefit to exercising - more microbial diversity, which means a healthier gut microbiome, which means better health. From Medscape:

Exercise Linked to More Diverse Intestinal Microbiome

Professional athletes are big winners when it comes to their gut microflora, suggesting a beneficial effect of exercise on gastrointestinal health, investigators report in an article published online June 9 in Gut.

DNA sequencing of fecal samples from players in an international rugby union team showed considerably greater diversity of gut bacteria than samples from people who are more sedentary.

Having a gut populated with myriad species of bacteria is thought by nutritionists and gastroenterologic researchers to be a sign of good health. Conversely, the guts of obese people have consistently been found to contain fewer species of bacteria, note Siobhan F. Clarke, PhD, from the Teagasc Food Research Centre, Moorepark, Fermoy. "Our findings show that a combination of exercise and diet impacts on gut microbial diversity. In particular, the enhanced diversity of the microbiota correlates with exercise and dietary protein consumption in the athlete group," the authors write.

The investigators used 16S ribosomal RNA amplicon sequencing to evaluate stool and blood samples from 40 male elite professional rugby players (mean age, 29 years) and 46 healthy age-matched control participants. 

Relative to control participants with a high BMI, athletes and control participants with a low BMI had improved metabolic markers. In addition, although athletes had significantly increased levels of creatine kinase, they also had overall lower levels of inflammatory markers than either of the control groups.

Athletes were also found to have more diverse gut microbiota than controls, with organisms in approximately 22 different phyla, 68 families, and 113 genera. Participants with a low BMI were colonized by organisms in just 11 phyla, 33 families, and 65 genera, and participants with a high BMI had even fewer organisms in only 9 phyla, 33 families, and 61 genera.

The professional rugby players, as the investigators expected, had significantly higher levels of total energy intake than the control participants, with protein accounting for 22% of their total intake compared with 16% for control participants with a low BMI and 15% for control participants with a high BMI. When the authors looked for correlations between health parameters and diet with various microbes or microbial diversity, they found significant positive association between microbial diversity and protein intake, creatine kinase levels, and urea.

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It seems like the more microbe exposure in the first year of life, the better for the immune system. From Science Daily:

Newborns exposed to dirt, dander, germs may have lower allergy, asthma risk

Infants exposed to rodent and pet dander, roach allergens and a wide variety of household bacteria in the first year of life appear less likely to suffer from allergies, wheezing and asthma, according to results of a study conducted by scientists at the Johns Hopkins Children's Center and other institutions.

Previous research has shown that children who grow up on farms have lower allergy and asthma rates, a phenomenon attributed to their regular exposure to microorganisms present in farm soil. Other studies, however, have found increased asthma risk among inner-city dwellers exposed to high levels of roach and mouse allergens and pollutants. The new study confirms that children who live in such homes do have higher overall allergy and asthma rates but adds a surprising twist: Those who encounter such substances before their first birthdays seem to benefit rather than suffer from them. Importantly, the protective effects of both allergen and bacterial exposure were not seen if a child's first encounter with these substances occurred after age 1, the research found.

"What this tells us is that not only are many of our immune responses shaped in the first year of life, but also that certain bacteria and allergens play an important role in stimulating and training the immune system to behave a certain way."

The study was conducted among 467 inner-city newborns from Baltimore, Boston, New York and St. Louis whose health was tracked over three years.

Infants who grew up in homes with mouse and cat dander and cockroach droppings in the first year of life had lower rates of wheezing at age 3, compared with children not exposed to these allergens soon after birth. The protective effect, moreover, was additive.  In addition, infants in homes with a greater variety of bacteria were less likely to develop environmental allergies and wheezing at age 3.

When researchers studied the effects of cumulative exposure to both bacteria and mouse, cockroach and cat allergens, they noticed another striking difference. Children free of wheezing and allergies at age 3 had grown up with the highest levels of household allergens and were the most likely to live in houses with the richest array of bacterial species. Some 41 percent of allergy-free and wheeze-free children had grown up in such allergen and bacteria-rich homes. By contrast, only 8 percent of children who suffered from both allergy and wheezing had been exposed to these substances in their first year of life.

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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.