human microbiome

 An amazing new study is about to start in Sweden - this study will see if "snot transplants" work for the treatment for chronic sinusitis! Will this turn out to be a permanent treatment? While studies show that probiotic supplements tend not to stick around in the gut (they're gone after about a week), people receiving a fecal microbiota transplant (FMT) find that these microbial communities do stick around (colonize).  So there is something about getting an entire microbial community (bacteria, fungi, viruses) that is more effective than just a few species that are in typical probiotic supplements.

We have found the same problem in sinusitis treatment - the Lactobacillus sakei treatment works to treat sinusitis, but then doesn't stick around - as evidenced by having to treat again after a cold or sore throat.  And so we treat again - and again it's successful. And this happens again and again. Sooo.... it's important to find out if a transplant of the entire microbial community of snot (the sinonasal microbiome) works. And if works, will the treatment be a permanent one? I also wonder.... Several people have mentioned this idea to me, but has anyone with sinusitis tried a "snot transplant" at home? (And yes, this is self-experimentation.)

The description and purpose of the study refer to what this site has discussed for several years: the sinus microbiome is out of whack (dysbiosis) in chronic rhinosinusitis (CRS), whether due to antibiotics or something else (viruses, etc). The study will enroll 30 people, start May 15, 2017, and end December 31, 2018. The purpose of the study is to have patients with chronic rhinosinusits without nasal polyps (CRSsNP) receive microbiome transplants from healthy donors without any sinus problems. They would receive a snot transplant for 5 days in a row. Unfortunately we'll have to wait at least 1 1/2 years for any results. Excerpts from clinical

Sinonasal Microbiome Transplant as a Therapy for Chronic Rhinosinusitis Without Nasal Polyps (CRSsNP)

Purpose: Chronic rhinosinusitis (CRS) is a disease associated with impaired quality of life and substantial societal costs. Though sometimes co-appearing with other conditions, such as asthma, allergy, and nasal polyps, many cases present without co-morbidities. Micro-biological diagnostic procedures are frequently undertaken, but the results are often inconclusive. Nevertheless, antibiotics are usually prescribed, but invariably with limited and temporary success. Accordingly, there is a need for new treatments for CRS.

Recent studies indicate that the sinuses are colonized by a commensal microbiome of bacteria and that damage to this natural microbiome, by pathogens or antibiotics, may cause an imbalance that may promote CRS. Therefore, treatments that restore the commensal microbiome may offer an alternative to current protocols. Arguably, as suggested by studies on patients with intestinal infections (next paragraph), one such possibility may be to transfer a "normal microbiome" to patients with CRS.

A disrupted microbiome is linked to intestinal clostridium difficile infections. Probiotic restitution therapy may be effective even in cases recalcitrant to antibiotic treatment. However, a key to effective probiotic restitution is selecting the bacteria that facilitate regrowth of normal microbiome. As an answer to this, researchers have chosen to simply transplant the entire microbiome from a healthy donor. In the case of clostridium difficile infection in the form of faecal transplants.

In this study, we will examine the possibility to treat patients with chronic rhinosinusitis without polyps (CRSsNP) with complete sinonasal microbiomes obtained from healthy donors. Our analysis will focus on symptoms and signs of disease as well as on nasal inflammatory and microbiological indices.

Detailed DescriptionOver the last few years the theory of a damaged microbiome as a cause or promoting factor behind chronic rhinosinusitis has gained increasing interest from the scientific community. A number of studies aimed at investigating the microbiota of the nose and paranasal sinuses in health and disease has been published with very varying outcomes. Furthermore, other studies have been aimed at probiotic treatment of sinonasal disease either locally or through immunologic manipulation via the gastrointestinal microbiota.

A problem common to all these studies is that studies examining the normal nasal microbiota have identified a great amount of different bacterial species. It is as of today not known which individual species or combinations of species that promotes health

In this study the investigators aim at recruiting patients suffering from chronic rhinosinusitis without polyps (CRSsNP) and healthy participants without any history sinonasal disease. The patients and the healthy participants will be examined for infectious diseases in a manner similar to other medical transplant procedures to minimize the risk for the recipients. The patients will then be treated with antibiotics to reduce the bacterial load of the nose and the paranasal sinuses. After the patient has finished the antibiotic treatment a microbiome transplant will be harvested from the healthy participant as a nasal lavage. The raw lavage fluid will then be used to transplant the microbiome to the patient. The procedure will be repeated for five consecutive days.

The outcome measures analysed will focus on subjective sinonasal health and symptoms of the patients but also include nasal inflammatory and microbiological indices.

 Once again a study looked at biofilms in sinuses - but this time in the sinuses of healthy people and not those with sinusitis. Various different species of bacteria and small size "microcolonies" or biofilms were found in the healthy maxillary sinuses of all 30 people - so yes, it appears that the presence of biofilms in the sinuses is normal in healthy people. And yes, the presence of bacteria (even some low levels of species which are typically associated with sinusitis) are normally found in the sinuses of healthy people.  (Earlier research also found this last finding.)

The researchers state that it is normal for people to have "small size bacterial microcolonies" (of different kinds of bacteria) in the sinuses. The researchers theorized that the biofilms are probably "in equilibrium" under the influence of  "inhibiting defensive factors of the body", but they can become a source of infection if there are favorable conditions (such as illness). In other words, the researchers said that these biofilms are more like "bacteria films" in that they contain bacteria, but they live in small colonies that don't cause an inflammatory response with sinusitis symptoms.

One negative of this study was that advanced genetic sequencing was not done on the samples. Instead all samples taken from the people were cultured, which we now know misses a lot of bacterial and other microbial species (fungi, viruses). They looked at the microcolonies (biofilms) with scanning microscopes. Thus, while they found an assortment of bacteria on the sinuses of each person - they only found a total of 41 bacterial species among 30 persons. This is in contrast to studies using modern genetic sequencing that found hundreds of microbial species in healthy sinus microbiomes (microbial communities).

The other issue is that it is not clear to me if there were biofilms or  microcolonies that contained "beneficial" species in any of the samples. Other research suggests that biofilms of beneficial bacteria are also found in humans, and that this is one way beneficial bacteria that normally can't survive with exposure to oxygen can survive oxygen (the slime coating on the colony protects the bacteria within).

Other studies also stress that in healthy people there is "homeostasis" or "equilibrium" among all the microbes living in the sinuses, - a microbial community (which includes biofilms), and which helps maintain sinus health. See post with discussion of Mackenzie et al 2017 study: "A stable network of microbial interactions, established through processes such as niche competition, nutrient cycling, immune evasion, and biofilm formation help maintain homeostasis during health." But, as has been usual in recent sinus research, the current study also stated that much is unknown, that there are theories which are not yet proven one way or another, and more research needs to be done. Of course.... From  PLoS ONE:

The presence of bacterial microcolonies on the maxillary sinus ciliary epithelium in healthy young individuals

The aim of this cross-sectional in vitro study was to evaluate the mucosal surfaces of healthy maxillary sinuses, explore different forms of bacterial microorganism colonies present on the mucous membrane, and determine a mucosal surface area they occupy. Samples of the maxillary sinus mucosa were collected from 30 healthy patients (M = 11; F = 19). The material was obtained during the Le Fort I osteotomy performed during corrective jaw surgery. The morphological and morphometric analysis of sinus mucosa and bacterial film that was grown on it was performed using scanning electron microscopy (SEM) as well as imaging software.

Scanning electron microscopy analysis showed the presence of different bacterium and bacteria-like structures in all the analyzed samples. In most cases, the bacterial film was mostly composed of diplococci-like and streptococci-like structures on the mucosa of the paranasal sinus. In any case, the mucous layer did not cover the whole lining of the evaluated sample. Each colony consists of more than 20 single bacterial cells, which has grown in aggregates.

Under the conditions of normal homeostasis of the body, the maxillary sinuses present diverse bacterial colonization. The bacteria are dispersed or concentrated in single microcolonies of the biofilm on the border of the mucous covering the ciliary epithelium. There is no uniform layer of the biofilm covering the mucosa of the maxillary sinuses. Because the biofilm is detected on healthy individuals sinus mucosa, the clinical question if it may become pathogenic is unclear and require an explanation.

It should also be noted that pathogenic organisms, such as Pseudomonas aeruginosa, Haemophilus influenzae, Streptococcus pneumoniae, or Staphylococcus aureus can be found in patients without active symptoms of the disease. Usually, colonization is defined as the presence of bacteria on the mucous membrane, and the lack of the inflammatory response distinguishes it from an infection.

However, the bacteria film in contrast to typical biofilm might be defined by the presence of bacteria, that growth in colonies without inducing the inflammatory response. Thus, the aim of the study was to evaluate the mucosal surfaces of the healthy maxillary sinuses (without any history of recent acute sinus inflammations or chronic inflammation in the past), to identify different forms of bacterial microorganisms which could, under certain conditions, become opportunistic or pathogenic and determine a mucosal surface of the area they occupy.

Scanning electron microscope investigations revealed the presence of bacterial film on the surface of maxillary sinus mucosa in 30 patients. Moreover, microbiological examinations of specimens taken from study participants revealed the presence of various types of aerobic and anaerobic bacteria in 28 cases (93.34%) out of 30 studied samples. All samples had mixed flora. In total, 41 different microorganisms were isolated. The most frequently found microorganism was Streptococcus spp. in over 90% of all samples, while Propionibacterium acnes were present in 29,2% of samples, and Staphylococcus spp. was present in 17% of the samples.

Scanning electron microscopy analysis showed that the mucous layer has a thickness of 200 nm (± 40), which is covered up to 5% of the surface of each sample. The analysis showed the presence of bacteria-like microcolony structures in all analyzed samples.....Each colony consisted of more than 20 single bacterial cells, that had grown in aggregates. These clearly indicate the existence of a bacterial-like microcolony on maxillary sinus mucosa.

thumbnailScanning electron microscopy images of biofilms seen on the mucosal surface of the healthy paranasal sinus mucosa. See spherical structures related to Haemophilus influenzae (Fig B and D). Credit: Morawska-Kochman et al 

Mediterranean Diet is Healthy Eating – A Good Option for Seniors An article was just published in a research journal to discuss the fact that humans - in part due to lifestyles which include less dietary fiber (due to eating fewer varieties and amounts of plants) and due to medical practices (such as frequent use of antibiotics) has resulted in gut "bacterial extinctions". In other words, humans (especially those living an urban industrialized Western lifestyle) have fewer gut bacterial species than those living a more traditional lifestyle, and this loss of bacterial species is linked to various diseases. Humans can increase the number of certain bacterial species, but the loss of some bacterial species is forever. 

The researchers discuss that humans have the "lowest level of gut bacterial diversity"  of any hominid and primate. They stated that the shrinking of the variety of microbial species in the human gut (the gut microbiome) began early in human evolution (as humans started eating more meat), but that it has accelerated dramatically within industrialized societies. And that evidence is accumulating that this gut bacterial "depauperation" - the loss of a variety of bacterial species - may predispose humans to a range of diseases.  Some of it is due to evolution (as humans ate more meat), and some to lifestyle changes. A term is used throughout this paper: depauperate - which means lacking in numbers or variety of species in the gut microbiome (the microbial community or ecosystem).

Other research has also shown that eating a highly processed Western diet results in gut microbial changes that are linked to various diseases (here, here, here) - that is, the microbes being fed are those associated with diseases. Also, certain diets encourage certain microbial species to flourish (here, here).  Bottom line: studies find health benefits from higher levels of dietary fiber - from fruits, vegetables, seeds, nuts, whole grains, and legumes (beans). From Current Opinion In Microbiology:

The shrinking human gut microbiome

Highlights: Humans harbor the lowest levels of gut bacterial diversity of any hominid. Humans in industrialized nations harbor fewer gut bacterial taxa than any primate. Medical practices and lack of dietary fiber may drive gut bacterial extinctions. Depauperate microbiotas may predispose entire human populations to certain diseases.

Mammals harbor complex assemblages of gut bacteria that are deeply integrated with their hosts’ digestive, immune, and neuroendocrine systems. Recent work has revealed that there has been a substantial loss of gut bacterial diversity from humans since the divergence of humans and chimpanzees. This bacterial depauperation began in humanity’s ancient evolutionary past and has accelerated in recent years with the advent of modern lifestyles. Today, humans living in industrialized societies harbor the lowest levels of gut bacterial diversity of any primate for which metagenomic data are available, a condition that may increase risk of infections, autoimmune disorders, and metabolic syndrome. Some missing gut bacteria may remain within under-sampled human populations, whereas others may be globally extinct and unrecoverable.

A typical human harbors on the order of 1013 bacterial cells in the large intestine. This gut microbiota, which can contain over a thousand species, is deeply integrated with virtually every tissue and organ system in the body. Gut bacteria process difficult to digest components of the diet, promote angiogenesis in the intestine, train the immune system, regulate metabolism, and even influence moods and behaviors.

In contrast to hunter–gatherer to agricultural transitions, adoptions of industrial and post-industrial lifestyles have led to massive reductions in bacterial richness within human gut microbiotas. Individuals living in urban centers in the United States harbor fewer gut bacterial species on average than do individuals living more traditional lifestyles in Malawi , Venezuela, Peru, and Papua New Guinea.....Industrialized and traditional lifestyles differ in many respects, confounding the identification of the specific practices that have led to decreases in gut bacterial diversity within industrialized societies. One potential cause is the rise of food processing and the corresponding reductions in the intake of dietary fiber in favor of simple sugars. Recently, studies in model systems have indicated that long-term reductions in dietary fiber can lead to the extirpation of gut bacterial taxa from host lineages. 

Other potential causes of reduced gut bacterial diversity within industrialized human populations include certain modern medical practices. For example, longitudinal studies in humans have shown that levels of gut bacterial diversity decrease drastically after antibiotic use. Although bacterial richness may recover after treatment is completed, the timeline and extent of the restoration is highly subject-dependent. The consequences of antibiotic use on gut bacterial diversity may be most severe when treatment is administered during the early years of life, before the adult microbiota has fully formed .

 More research supports that being exposed to pets during pregnancy or in the first months of life changes the gut bacteria, and in a way that is thought to be beneficial. The researchers found that infants exposed to pets prenatally or after birth (or both) had higher levels of two microbes that are associated with a lower risk of allergies and obesity. The two microbes are Ruminococcus and Oscillospira, but in case you're wondering - they are not (yet) available in probiotics.

And these differences in gut bacteria occurred no matter how the infants were born or fed (C-section, vaginal, breastfed, formula fed), or whether they received antibiotics at birth or not  - it was the pet exposure that was most important. The evidence is building that if one wants to avoid allergies in children - to have them exposed to furry pets in the first  year of life, and according to this study - perhaps before birth also. From Science Daily:

Pet exposure may reduce allergy and obesity

A new University of Alberta study showed that babies from families with pets -- 70 per cent of which were dogs -- showed higher levels of two types of microbes associated with lower risks of allergic disease and obesity.

"There's definitely a critical window of time when gut immunity and microbes co-develop, and when disruptions to the process result in changes to gut immunity," said Anita Kozyrskyj, a U of A pediatric epidemiologist....The latest findings from Kozyrskyj and her team's work on fecal samples collected from infants registered in the Canadian Healthy Infant Longitudinal Development study build on two decades of research that show children who grow up with dogs have lower rates of asthma

Her team of 12, including study co-author and U of A post-doctoral fellow Hein Min Tun, take the science one step closer to understanding the connection by identifying that exposure to pets in the womb or up to three months after birth increases the abundance of two bacteria, Ruminococcus and Oscillospira, which have been linked with reduced childhood allergies and obesity, respectively.

"The abundance of these two bacteria were increased twofold when there was a pet in the house," said Kozyrskyj, adding that the pet exposure was shown to affect the gut microbiome indirectly -- from dog to mother to unborn baby -- during pregnancy as well as during the first three months of the baby's life. In other words, even if the dog had been given away for adoption just before the woman gave birth, the healthy microbiome exchange could still take place.

The study also showed that the immunity-boosting exchange occurred even in three birth scenarios known for reducing immunity, as shown in Kozyrskyj's previous work: C-section versus vaginal delivery, antibiotics during birth and lack of breastfeeding. What's more, Kozyrskyj's study suggested that the presence of pets in the house reduced the likelihood of the transmission of vaginal GBS (group B Strep) during birth, which causes pneumonia in newborns and is prevented by giving mothers antibiotics during delivery. [Original study.]

 Nice research that basically says: food is medicine. In other words, eat lots of whole grains and legumes (beans) for gut health - to feed the beneficial microbes in your gut and prevent (hopefully) colon cancer. While the clinical trial studied colorectal cancer survivors and the effects of 4 weeks of adding rice bran or navy beans or placebo (nothing extra) daily to their diet - the positive effects of adding the extra dietary fiber included increased microbiome richness and diversity in the rice bran group (which is good).

And when researchers treated colorectal cancer cells with stool extracts from these groups, they saw reduced cell growth from the groups that had increased rice bran and navy bean consumption. This was an important finding and stresses that adding fiber to the diet is beneficial to gut health, and perhaps may prevent colorectal cancer.

Other studies have also found a diet with lots of legumes (beans), whole grains, vegetables, fruits, nuts, and seeds to be beneficial for gut microbes and gut health. A classic study (from 2015) found dramatic changes in the colon (specifically in the colonic mucosa) from dietary changes in as little as 2 weeks. They compared the typical low-fat, high fiber diet of South Africa with an “American” high-fat, low-fiber diet, and found that after two weeks on the high fiber African diet, there was significantly less inflammation in the colon and reduced biomarkers of cancer risk. On the other hand, measurements indicating cancer risk dramatically increased after two weeks on the western diet. That study found that a major reason for the changes in cancer risk was the way in which the bacteria in the gut (the microbiome) were altered in adapting to the new diet. The researchers suggested trying for at least 50 grams of fiber per day for gut health benefits.

From Medical Xpress: Phase II trial: Rice bran adds microbiome diversity, slows growth of colon cancer cells

Today at the American Association for Cancer Research (AACR) Annual Meeting 2017, University of Colorado Cancer Center researchers at Colorado State University present results of a phase II clinical trial of 29 people exploring the effects of adding rice bran or navy beans to the diets of colorectal cancer survivors. After the 4-week randomized-controlled trial during which people added rice bran, navy bean powder or neither, both the rice bran and navy bean groups showed increased dietary fiber, iron, zinc, thiamin, niacin, vitamin B6, folate, and alpha-tocopherol. The rice bran group also showed increased microbiome richness and diversity. When researchers treated colorectal cancer cells with stool extracts from these groups, they saw reduced cell growth from the groups that had increased rice bran and navy bean consumption.

Previous work shows the ability of these diets to decrease colorectal cancer risk in animal models. The current trial confirms that people can eat enough bean- and rice bran-enhanced foods to promote gut health at levels shown to prevent colorectal cancer in animals. Guidelines from the American Institute for Cancer Research recommend reducing the risk of cancer by eating more vegetables, fruits, whole grains and legumes, such as beans. Ryan has established from these studies that eating a half-cup of beans and 30 grams of rice bran per day is enough to see changes in small molecules that can confer protection against colorectal cancer.

"The simple message is, 'Food is medicine,' and we are looking at how to simplify that and make it apply to our everyday lives," says study co-author Regina Brown, MD, assistant professor at the CU School of Medicine and oncologist for CUHealth...."The evidence is there in animals and we can now study this in people. The question is, what are we doing to achieve adequate levels of intake of these foods?" Ryan said. "It's not enough to say 'I eat them once in a while.' That's not going to work, particularly if you are at higher risk. You have to meet a dose, just like you need a dose of a certain drug, you need to reach intake levels and consume increased amounts of these foods, and that's where people, including me, are challenged. Not everyone wants to open up a can of beans and eat them every day."

Image result for maple tree allergies Could this be true? Probiotics for seasonal allergies? A study by Univ. of Florida researchers reported that taking a combination probiotic of Lactobacillus gasseri, Bifidobacterium bifidum, and Bifidobacterium longum (sold as Kyo-Dophilus) for 8 weeks during spring allergy season resulted in an improvement in seasonal allergy symptoms. It must be noted that the people participating had mild seasonal allergies, not severe allergies. While they reported overall allergy symptom improvement, there was no significant improvement with eye symptoms. Too bad, because for those suffering from itchy eyes, it is a symptom that causes anguish during allergy season.

All participants had their stool (fecal) samples tested (with modern genetic sequencing) and it was found that the group taking the probiotic supplements had a beneficial shift in their overall microorganisms in the gut - with some bacteria such as Escherichia coli decreasing and the very beneficial and anti-inflammatory bacteria Faecalibacterium prausnitzii increasing. (See posts here and here on F. prausnitzii.) What was really good about the study was that it was a "double-blind, randomized clinical trial", meaning that people were randomly  assigned to the probiotic treatment or placebo group, and no one knew who was getting a placebo or the probiotic until the end of the study. The researchers say that why the probiotics improved allergy symptoms is s till not clear, but they have some theories. From Science Daily:

Allergies? Probiotic combination may curb your symptoms, new study finds

As we head into allergy season, you may feel less likely to grab a hanky and sneeze. That's because new University of Florida research shows a probiotic combination might help reduce hay fever symptoms, if it's taken during allergy season. Many published studies have shown a probiotic's ability to regulate the body's immune response to allergies, but not all of the probiotics show a benefit, UF researchers say. Scientists already know that the probiotic combination of lactobacilli and bifidobacteria, sold as Kyo-Dophilus in stores, helps maintain digestive health and parts of the immune system. They suspect that probiotics might work by increasing the human body's percentage of regulatory T-cells, which in turn might increase tolerance to hay fever symptoms.

UF researchers wanted to know if the components in this combination probiotic would help alleviate allergy symptoms. To do that, they enrolled 173 healthy adults who said they suffered seasonal allergies and randomly split them into two groups: Some took the combination probiotic; others took a placebo. Each week during the eight-week experiment, participants responded to an online survey to convey their discomfort level. Scientists also analyzed DNA from participants' stool samples to determine how their bacteria changed, because probiotics aim to deliver good bacteria to the human's intestinal system.

Participants who took the probiotic reported improvements in quality of life, compared to those taking the placebo, the study showed. For example, participants suffered fewer allergy-related nose symptoms, which meant that they were less troubled during daily activities. Researchers note that this study did not include severe allergy sufferers. But the combination of probiotics showed clinical benefit for those with more mild seasonal allergies, Langkamp-Henken said. [Original study.]

  It's now 4 years being free of chronic sinusitis and off all antibiotics! Four amazing years since I (and then the rest of my family) started using easy do-it-yourself sinusitis treatments containing the probiotic (beneficial bacteria) Lactobacillus sakei. My sinuses feel great! And yes, it still feels miraculous.

After reading the original ground-breaking research on sinusitis done by Abreu et al (2012), it led to finding and trying L. sakei as a sinusitis treatment. Of course, there is an entire community of microbes (bacteria, fungi, viruses) that live in healthy sinuses - the sinus microbiome - but L. sakei seems to be a key one for sinus health.

I just updated the post The One Probiotic That Treats Sinusitis (originally posted January 2015) using my family's experiences (lots of self-experimentation!) and all the information that people have sent me. The post has a list of brands and products with L. sakei, treatment results, as well as information about some other promising probiotics (beneficial bacteria). Thank you so much!

Thank you all who have written to me  - whether publicly or privately. Please keep writing and tell me what has worked or hasn't worked for you as a sinusitis treatment. If you find another bacteria or microbe or product that works for you - please let me know. It all adds to the sinusitis treatment knowledge base. I will keep posting updates. 

(NOTE: I wrote our background story - Sinusitis Treatment Story back in December 2013, and there is also a  Sinusitis Treatment Summary page with the various treatment methods quickly discussed. One can also click on SINUSITIS under CATEGORIES to see more posts about what is going on in the world of sinusitis research.)


 People assume that taking probiotics results in the beneficial probiotic bacteria colonizing and living in the gut (or sinuses when using L. sakei). It is common to hear the phrase "take probiotics to repopulate the gut" or "improve the gut microbes". The human gut microbiota (human gut microbiome) refers to all the microbes that reside inside the gut (hundreds of species). Probiotics are live bacteria, that when taken or administered, result in a health benefit. But what does the evidence say?

First, it is important to realize that currently supplements and foods contain only a small variety of probiotic species, with some Lactobacillus and Bifidobacterium species among the most common. But they are not the most common bacteria found in the gut. And very important bacteria such as Faecalibacterium prausnitzii (a reduction of which is associated with a number of diseases) are not available at all in supplements. One problem is the F. prausnitzii are "oxygen sensitive" and they die within minutes upon exposure to air, a big problem when trying to produce supplements.

The evidence from the last 4 years  of L. sakei use for sinusitis treatment is that for some reason, the L. sakei is not sticking around and colonizing in the sinuses. My family's experiences and the experience of other people contacting me is that every time a person becomes sick with a cold or sore throat, it once again results in sinusitis, and then another treatment with a L. sakei product is needed to treat the sinusitis. And of course this has been a surprise and a big disappointment.

The same appears to be true for probiotics (whether added to a food or in a supplement) that are taken for other reasons, including intestinal health. Study after study, and a review article, finds that the beneficial bacteria do not colonize in the gut even if there are health benefits from the probiotics. That is, there may be definite health benefits from the bacteria, but within days of stopping the probiotic (whether in a food or a supplement) it is no longer found in the gut. Researchers know this because they can see what bacteria are in the gut by analyzing (using modern genetic sequencing tests) what is in the fecal matter (the stool).

However, the one exception to all of the above is a fecal microbiota transplant (FMT) - which is transfer of fecal matter from one person to another. There the transplanted microbes of the donor do colonize the recipient's gut, referred to as "engraftment of microbes". Some researchers found that viruses in the fecal matter helped with the engraftment. So it looks like more than just some bacterial strains are involved. Another thing to remember is that study after study finds that dietary changes result in microbial changes in the gut, and these changes can occur very quickly.

From Gut Microbiota News Watch: Learning what happens between a probiotic input and a health output

What scientists know is that probiotics in healthy individuals are associated with a number of benefits. Meta-analyses of randomized, controlled trials show that probiotics help prevent upper respiratory tract infections, urinary tract infections, allergy, and cardiovascular disease risk in adults. But between the input and the output, what happens? A common assumption is that probiotics work by influencing the gut microbe community, leading to an increase in the diversity of bacterial species in the gut ecosystem and measurable excretion in the stool.

But this theory doesn’t seem to be true, according to a recently published systematic review by Kristensen and colleagues in Genome Medicine. Authors of the review analyzed seven studies and found no evidence that probiotics have the ability to change fecal microbiota composition. So even though individuals in the different studies were ingesting live bacterial species, the bacteria didn’t stick around to increase the diversity of the gut fecal microbiota.

Do probiotics alter the fecal composition of healthy adults? The answer seems to be no,” says Dr. Mary Ellen Sanders, Executive Science Officer for the International Scientific Association for Probiotics and Prebiotics (ISAPP)....Dr. Dan Merenstein, Research Division Director and Associate Professor of Family Medicine at Georgetown University Medical Center in Washington, DC (USA), agrees. “Initially when probiotics were studied, some people expected to see permanent colonization. We now realize that is unlikely to occur,” he says. “This study shows that the probiotics tested to date do not result in overarching bacterial community structure changes in healthy subjects. But clinical effects are clearly demonstrated for probiotics, and likely some are mediated by microbiome changes.

At issue, then, is not what probiotics do for healthy individuals, but exactly how they work: the so-called ‘mechanism’. Sanders, who described some alternative mechanisms in her BMC Medicine commentary about the Kristensen review, points out a logical error in news stories worldwide that covered the article: the assumption that if probiotics fail to change the microbiota composition, they fail to have any health effects. Sanders emphasizes that probiotics might work in many possible ways. “Probiotics may act through changing the function of the resident microbes, not their composition. They may interact with host immune cells,” she says. “They may inhibit opportunistic pathogens that are not dominant members of the microbiota. They may promote microbiota stability… .” 

 A new study has summarized what we know about fungi that live in and on babies - and yes, we all have fungi both on and within us. It's called the mycobiome. In healthy individuals all the microbes (bacteria, viruses, fungi, etc) live in balanced microbial communities, but the communities can become "out of whack" (dysbiosis) for various reasons, and microbes that formerly co-existed peacefully can multiply and become problematic. Or other pathogenic microbes can enter the community, and the person becomes ill.

In healthy adults, approximately 0.1% of the microbes in the adult intestine are fungi, from approximately 60 unique species. Most species live peacefully in the body, and some fungi even have health benefits (e.g., Saccharomyces boulardii prevents gastrointestinal disease). Some fungi that many view as no good and involved with diseases (e.g., Candida and Aspergillus) are also found normally in healthy people. Studies show that normally infants also have fungi. Some fungi that live in the baby's gut (thus detected in fecal samples) are Candida (including C. albicans), Saccharomyces, and Cladosporium. The researchers (from the Univ. of Minnesota) point out that the study of fungi in babies has been neglected and much more research needs to be done.

Whether an infant is born vaginally or through cesarean delivery (C-section) affects the composition of the baby's bacterial communities over the first 6 months of life. And similarly, it looks like when the baby passes through the birth canal, the baby is exposed to the mother's mycobiota (fungi), and then these colonize in the infant's gut. Babies born by C-section have some differences in their fungi, such as being colonized by the mother's skin fungi (such as Malassezia fungi). After birth, a parent kissing and touching the baby (skin to skin contact) also transmits microbes, including fungi, to the baby.

Whether a baby drinks breast milk or formula strongly affects the infant's bacteria within the GI tract. For example, breast-fed infants have more Bifidobacteria and Labctobacilli in their gut compared to formula-fed infants. One study found about 700 species of bacteria in breast milk. Thus, scientists think that human breast milk also influences the infant gut mycobiota (fungi), although this research still needs to be done.

Whether a baby is born prematurely or at term (gestational age) is important. For infants born prematurely, intestinal fungi can cause big problems, such as an overgrowth in the gut. For example, 10% of premature babies get invasive, systemic Candidiasis, and about 20% die. Some factors leading to this are: a naïve immune system, bacterial communities out of whack (dysbiosis) due to antibiotic exposure, and use of parenteral nutrition (because this doesn't contain all the microbes from the mother that are in breast milk). In premature infants, beneficial fungi such as S. boulardii, may help to regulate the growth of opportunistic fungal colonizers such as Candida.

it is clear that whether the baby received antibiotics is important. The bacterial community of infants is altered by exposure to antibiotics in both term and preterm infants. For example, in a lengthy study over the first 3 years of life, infants receiving multiple courses of antibiotics had bacterial community changes following antibiotics and their gut bacterial microbiome became less diverse (fewer species). Although most commonly used antibiotics do not directly act on fungi, anti-bacterial antibiotic exposure is associated with alterations to the mycobiota (fungi) -  such as increased rates of fungal colonization, fungal overgrowth, and changes in the fungal community. For ex., premature infants exposed to cephalosporin antibiotics have an increased risk for invasive Candidiasis (a fungal overgrowth).

Out of whack (dysbiotic) microbial communities, incuding fungi, are found in IBD (intestinal bowel diseases) in children. They have more of some fungi (e.g. Pichia jadinii and Candida parapsilosis) and less of Cladosporium cladosporiodes, and an overall decrease in fungal diversity in the gut, as compared to healthy children.

From BMC Medicine: Infant fungal communities: current knowledge and research opportunities

The microbes colonizing the infant gastrointestinal tract have been implicated in later-life disease states such as allergies and obesity. Recently, the medical research community has begun to realize that very early colonization events may be most impactful on future health, with the presence of key taxa required for proper immune and metabolic development. However, most studies to date have focused on bacterial colonization events and have left out fungi, a clinically important sub-population of the microbiota. A number of recent findings indicate the importance of host-associated fungi (the mycobiota) in adult and infant disease states, including acute infections, allergies, and metabolism, making characterization of early human mycobiota an important frontier of medical research. This review summarizes the current state of knowledge with a focus on factors influencing infant mycobiota development and associations between early fungal exposures and health outcomes. We also propose next steps for infant fungal mycobiome research....

 A new study found differences in gut microbes between active women (they exercised at least the recommended amount) and those that are sedentary. When the gut bacteria were analyzed with modern tests (genetic sequencing) the active women had more of the health promoting beneficial bacteria such as Faecalibacterium prausnitzii, Roseburia hominis, and Akkermansia muciniphila than the sedentary women. The sedentary women also had some bacterial species not seen in the active women. The researchers said that exercise "modifies the composition of gut microbiota" (the gut microbes) in a way beneficial for health.

And what is the recommended minimal amount of exercise? The World Health Organization recommends at least 3 days of exercise per week for 30 minutes at a moderate intensity. Note that exercise can mean doing exercises, but it can also include walking briskly, intense housework (scrubbing, vacuuming with lots of bending, etc.), gardening (digging, raking, etc), or shoveling snow, etc. In this study the group of active women had at least 3 hours of physical exercise per week. Note that a sedentary lifestyle is associated with a high incidence of chronic diseases such as cardiovascular disease, cancer and diabetes, while physical exercise or activity has metabolic and immune health benefits (prevents disease).

But...reading the full study, the research also showed that the active group ate more fruits and vegetables - which we know has an effect on the gut microbiome and feeds beneficial bacteria. Although the diets of the 2 groups of women were similar in total carbohydrates, protein and fat content eaten, the active women ate more fruits, vegetables, and fiber, and the sedentary group ate more processed meat. So it looks like both exercise and a good amount of fruits and vegetables may be important for nurturing beneficial bacteria. By the way, the 3 species of beneficial bacteria mentioned currently are not found in any probiotic supplements on the market. (Earlier posts on the beneficial F. prausnitzii and Akkermansia muciniphila). From PLoS ONE:

Differences in gut microbiota profile between women with active lifestyle and sedentary women

Physical exercise is a tool to prevent and treat some of the chronic diseases affecting the world’s population. A mechanism through which exercise could exert beneficial effects in the body is by provoking alterations to the gut microbiota, an environmental factor that in recent years has been associated with numerous chronic diseases. Here we show that physical exercise performed by women to at least the degree recommended by the World Health Organization can modify the composition of gut microbiota. Using high-throughput sequencing of the 16s rRNA gene, eleven genera were found to be significantly different between active and sedentary women. Quantitative PCR analysis revealed higher abundance of health-promoting bacterial species in active women, including Faecalibacterium prausnitzii, Roseburia hominis and Akkermansia muciniphila. Moreover, body fat percentage, muscular mass and physical activity significantly correlated with several bacterial populations. In summary, we provide the first demonstration of interdependence between some bacterial genera and sedentary behavior parameters, and show that not only does the dose and type of exercise influence the composition of gut microbiota, but also the breaking of sedentary behavior.

Sedentary lifestyle is associated with a high incidence of chronic diseases such as cardiovascular disease, cancer and diabetes. Physical exercise is a powerful preventative and treatment intervention that is known to be effective in generating metabolic and immune health benefits. The gut microbiota is essential for processing dietary components and has a major role in shaping the immune system.... Dysbiosis or imbalance in gut microbiota has been associated with many diseases, among which are ulcerative colitis, Crohn's disease, colon cancer, metabolic syndrome, type I and type II diabetes, cardiovascular disease, allergy, asthma, eczema and autism.....Several studies in experimental models have addressed the relationship between gut microbiota composition and physical exercise....Collectively, these findings indicate that modulation of the microbiota by exercise depends not only on the physiological state of the individual, but also on the diet.

A total of 15 phyla were detected, in order of presence: Bacteroidetes (54%), Firmicutes (44%), Proteobacteria (0.96%), Tenericutes (0.39%), Verrucomicrobia (0.11%), Euryarchaeota (0.08%), Actinobacteria (0.07%), Lentisphaerae (0.06%), Cyanobacteria (0.050%), Spirochaetes (0.04%), Fusobacteria (0.014%), Elusimicrobia (0.009%), Synergistetes (0.007%), kTM7 (0.003%), and Acidobacteria (0.0001%). Acidobacteria (2 subjects), Elusimicrobia (2 subjects) and Spirochaetes (2 subjects) phyla were detected only in sedentary subjects.... At the genus level, there were significant differences in eleven genera: Bifidobacterium, Barnesiellaceae, Odoribacter, Paraprevotella, Turicibacter, Clostridiales, Coprococcus, Ruminococcus, and two unknown genera of Ruminococcaceae family. Given the importance of some bacterial species in health, the presence of Bifidobacterium longum, Faecalibacterium prausnitzii, Roseburia hominis, Akkermansia muciniphila was measured by qPCR. Analyses revealed a more significant abundance of F. prautznnii, R. hominis and A. muciniphila in active than in sedentary women.

Among all the genera studied, the abundance of eleven of them was significantly different between the active and sedentary group, with Paraprevotella and an unclassified genus of the Desulfovibrionaceae family specifically associated with sedentarism parameters, while the remaining genera where largely associated with diet parameters.....Nonetheless, as exercise and diet often go hand in hand, an active lifestyle is frequently associated with a high consumption of fruits and vegetables, whereas sedentarism is associated with the consumption of high-calorie and fatty foods. Indeed, exercise interventions in human populations have resulted in an improvement in diet habits. Although the diets were similar in our study regarding total carbohydrates, protein and fat content, significant differences were observed for fiber (higher in the active group) and processed meat (higher in the sedentary group).