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Category: microbes

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It is estimated that between 14,000 to 30,000 Americans die each year from Clostridium difficile infections. So finding a bacteria that could protect people from C. difficile is a big deal. However, it is only one bacteria, and sick people typically are depleted of a microbial community, not just one bacteria. From Science News:

Harmless bacterium edges out intestinal germ

Gut infections from the bacterium Clostridium difficile can be fought with a closely related but harmless microbe known as C. scindens. The friendly bacterium combats infection in mice by converting molecules produced in the liver into forms that inhibit C. difficile growth,researchers report October 22 in Nature.

C. scindens also appears to protect people from infection, the researchers found in a preliminary study in humans. The new findings could begin a path to the next generation of therapies using gut bacteria, says Alexander Khoruts, a gastroenterologist at the University of Minnesota in Minneapolis.

People who become infected with C. difficile typically have taken antibiotics, which wipe out the beneficial microbes in the gut, giving C. difficile a chance to take root. The infection can lead to cramps, diarrhea and even death. An estimated 500,000 to 1 million people get C. difficile infections each year in the United States. People with C. difficile receive more antibiotics to treat the infection or a fecal transplant to restore healthy microbes to the gut.

Several research groups have been trying to identify gut bacteria that are resilient in the face of C. difficile so that physicians can give patients those bacteria as a treatment, says Eric Pamer, an immunologist at Memorial Sloan Kettering Cancer Center. Single strains of bacteria such as C. scindens would offer significant advantages over fecal transplants: With a transplant, doctors screen the donated feces for pathogens that might sicken the recipient. But, Pamer says, “there are many things, viruses that have yet to be identified, that could be in a crude fecal product that might cause trouble.”  

Pamer and his team gave mice antibiotics to deplete beneficial microbes but not wipe them out completely. The researchers then fed the mice C. difficile spores and identified microbes that appeared in mice with lower amounts of C. difficile in their guts. C. scindens was the clear victor. It is harmless and present in most people, but in very low numbers.

The researchers also examined the microbial populations of 24 patients undergoing stem cell transplants. Those patients had lowered microbial diversity after receiving combinations of antibiotics, radiation and chemotherapy. The patients who didn’t develop C. difficile after the transplant were more likely to have C. scindens in their guts.

The researchers also investigated how C. scindens combats C. difficile. C. difficile begins growing after it is exposed to certain molecules secreted in bile after a meal. However, another form of the molecule inhibits C. difficile growth. C. scindens transforms the molecule from one form to the other, boosting resistance to C. difficile.  

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This research supports the growing evidence for the importance of microbes in the health of young children. Even the type of milk a child drinks is important. From Science Daily:

Pediatric allergology: Fresh milk keeps infections at bay

A study by researchers of Ludwig-Maximilians-Universitaet (LMU) in Munich shows that infants fed on fresh rather than UHT (ultra-pasteurized) cow's milk are less prone to infection. 

A pan-European study, led by Professor Erika von Mutius, Professor of Pediatric Allergology at LMU and Head of the Asthma and Allergy Department at Dr. von Hauner's Children's Hospital, reports that fresh cow's milk protects young children from respiratory infections, febrile illness and inflammation of the middle ear. As untreated cow's milk may itself contain pathogenic microorganisms and could pose a health risk, the researchers argue for the use of processing methods that preserve the protective agents present in raw milk.

The findings are the latest to emerge from the long-term PASTURE study, which is exploring the role of dietary and environmental factors in the development of allergic illness. The study initially recruited 1000 pregnant women who were asked to document their children's diet and state of health at weekly intervals during the first year of life.

"Among children who were fed on fresh, unprocessed cow's milk the incidence of head colds and other respiratory infections, febrile and middle-ear inflammation was found to be significantly lower than in the group whose milk ration consisted of the commercially processed ultra-pasteurized product," says Dr. Georg Loss. Ingestion of farm milk reduced the risk of developing these conditions by up to 30%, and the effect was diminished if the milk was heated at home before consumption. Conventionally pasteurized milk retained the ability to reduce the risk of febrile illness, while exposure to the higher temperatures used in UHT processing eliminated the effect altogether. 

"The effects of diverse milk treatments are presumably attributable to differentially heat-resistant components present in fresh milk. Compounds that are sensitive to heating seem to play a particularly important role in protection against respiratory-tract and ear infections," says Loss.

At the end of the first year of life, blood samples were obtained from the children enrolled in the study, and tested for biochemical indicators of immunological function. Infants fed on unprocessed milk were found to have lower levels of the C-reactive protein, which is a measure of inflammation status. "Other studies have shown that higher levels of inflammation are related to the subsequent emergence of chronic conditions such as asthma and obesity. Consumption of unprocessed milk may therefore reduce the risk of developing asthma," Loss explains.

Industrial processing of milk involves short-term heating of the raw product. Conventionally pasteurized milk has been exposed to temperatures of 72-75°C for 15 seconds, while ultra-pasteurized milk undergoes heating at around 135°C for a few seconds. The latter is also homogenized to disperse the milk fats, which prevents the formation of cream. 

In addition to fats and carbohydrates, cow's milk contains proteins that can modulate the function of the immune system. "In many respects, the composition of cow's milk is similar to that of human milk," says Loss. It has long been known that breast-feeding protects infants from infection, although how milk actually affects the early immune function remains unclear. It is possible that some of the factors involved interact directly with viruses or that they promote the development of a healthy immune system by altering the composition of the gut microflora.

That living in the country has positive effects on the immune system has been demonstrated in several previous studies. Together these investigations show, as Erika von Mutius notes, that "children who grow up on traditional dairy farms are least likely to develop allergies.

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The possibilities are exciting. See my earlier posts on psychobiotics for more information. From Medical Xpress:

How gut bacteria ensures a healthy brain – and could play a role in treating depression

But medicine in the 21st century is rethinking its relationship with bacteria and concluding that, far from being uniformly bad for us, many of these organisms are actually essential for our health. Nowhere is this more apparent than in the human gut, where the microbiome  – the collection of bacteria living in the gastrointestinal tract - plays a complex and critical role in the health of its host.

The microbiome interacts with and influences organ systems throughout the body, including, as research is revealing, the brain. This discovery has led to a surge of interest in potential gut-based treatments for neuropsychiatric disorders and a new class of studies investigating how the gut and its microbiome affect both healthy and diseased brains.

The lives of the bacteria in our gut are intimately entwined with our immune, endocrine and nervous systems. The relationship goes both ways: the microbiome influences the function of these systems, which in turn alter the activity and composition of the bacterial community. We are starting to unravel this complexity and gain insight into how gut bacteria interface with the rest of the body and, in particular, how they affect the brain.

The microbiome-immune system link is established early on. Over the first year of life, bacteria populate the gut, which is largely sterile at birth, and the developing immune system learns which bacteria to consider normal residents of the body and which to attack as invaders. This early learning sets the stage for later immune responses to fluctuations in the microbiome's composition.

When a normally scarce strain becomes too abundant or a pathogenic species joins the community of gut bacteria, the resulting response by the immune system can have wide-reaching effects. Depression has been linked with elevated levels of such molecules in some individuals, suggesting that treatments that alter the composition of the microbiome could alleviate symptoms of this disorder.

Such an intervention could potentially be achieved using either prebiotics – substances that promote the growth of beneficial bacteria – or probiotics – live cultures of these bacteria. It is even possible that the microbiome could be manipulated by dietary changes.

In one experiment, researchers transplanted the human microbiome into germ-free mice (animals that have no gut bacteria) in order to study it in a controlled setting. They found that, simply by changing the carbohydrate and fat content of the mice's food, they could alter basic cellular functions and gene expression in the microbiome.

Depression is not the only psychiatric disorder in which the microbiome may play a role.Research in rodents, as well as a few preliminary studies in humans, indicate that the state of our resident microbes is tied to our anxiety levels.

This research also reveals the complexity of the relationship between the microbiome and psychological state. ...Researchers have shown that the presence or absence of microbes in young mice affects the sensitivity of the hypothalamic-pituitary-adrenal (HPA) axis – a key pathway in the body's stress response system. The activity of the microbiome during development thus sways how we respond to future stressors and how much anxiety they cause us.

How do the bacteria in our gut wield such influence over our brains and bodies? The mechanisms of microbiome-host interactions appear to be as numerous and varied as the interactions themselves.

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Another interesting factoid about the human gut microbiome - it has circadian rhythms. This also has implications for timing of medical treatments and medicines. From Science Daily:

Jet lag can cause obesity by disrupting the daily rhythms of gut microbes

Organisms ranging from bacteria to humans have circadian clocks to help them synchronize their biological activities to the time of day. A study now reveals that gut microbes in mice and humans have circadian rhythms that are controlled by the biological clock of the host in which they reside. Disruption of the circadian clock in the host alters the rhythms and composition of the microbial community, leading to obesity and metabolic problems.

Disruption of the circadian clock in humans is a hallmark of relatively recent lifestyle changes involving chronic shift work or frequent flights across time zones. These widespread behavioral patterns have been linked to a wide range of diseases, including obesity, diabetes, cancer, and cardiovascular disease. But, until now, it has not been clear how changes in circadian rhythms increase the risk for these diseases.

In the new study, Elinav and his team set out to determine whether gut microbes could be the missing link. When they analyzed microbes found in fecal samples collected from mice and humans at different times of day, they discovered rhythmic fluctuations in the abundance of microbes and their biological activities. The host's circadian clock and normal feeding habits were required for the generation of these rhythmic fluctuations in the gut microbes.

When mice were exposed to changing light-dark schedules and abnormal 24 hr feeding habits, the microbial community lost its rhythmic fluctuations and changed in composition. Moreover, a high-fat diet caused these jet-lagged mice to gain weight and develop metabolic problems associated with diabetes. Similarly, jet lag in two humans who had traveled from the United States to Israel changed the composition of gut microbes, favoring the growth of bacteria that have been linked to obesity and metabolic disease.

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Maybe bacteria are involved in Multiple sclerosis (MS). From Scientific American:

Could Multiple Sclerosis Begin in the Gut?

MS researchers are focusing on the content of the gut’s microbiome as a possible contributor to the body’s autoimmune attack on its nervous system.

Multiple sclerosis (MS) is an electrical disorder, or rather one of impaired myelin, a fatty, insulating substance that better allows electric current to bolt down our neurons and release the neurotransmitters that help run our bodies and brains. Researchers have speculated for some time that the myelin degradation seen in MS is due, at least in part, to autoimmune activity against the nervous system. Recent work presented at the MS Boston 2014 Meeting suggests that this aberrant immune response begins in the gut.

Eighty percent of the human immune system resides in the gastrointestinal tract. Alongside it are the trillions of symbiotic bacteria, fungi and other single-celled organisms that make up our guts’ microbiomes. Normally everyone wins: The microorganisms benefit from a home and a steady food supply; we enjoy the essential assistance they provide in various metabolic and digestive functions. Our microbiomes also help calibrate our immune systems, so our bodies recognize which co-inhabitants should be there and which should not. Yet mounting evidence suggests that when our resident biota are out of balance, they contribute to numerous diseases, including diabetes, rheumatoid arthritis, autism and, it appears, MS by inciting rogue immune activity that can spread throughout the body and brain.

One study presented at the conference, out of Brigham and Women’s Hospital (BWH), reported a single-celled organism called methanobrevibacteriaceae that activates the immune system is enriched in the gastrointestinal tracts of MS patients whereas bacteria that suppress immune activity are depleted. Other work, which resulted from a collaboration among 10 academic researcher centers across the U.S. and Canada, reported significantly altered gut flora in pediatric MS patients while a group of Japanese researchers found that yeast consumption reduced the chances of mice developing an MS-like disease by altering gut flora.

Sushrut Jangi, a staff physician at Beth Israel Deaconess Medical Center in Boston who co-authored the BWH study, thinks that regional dietary influences might even be at play. “The biomes of people living in different areas and who consume Western versus non-Western diets are demonstratively different,” he says. “People who emigrate from non-Western countries, including India, where MS rates are low, consequently develop a high risk of disease in the U.S. One idea to explain this is that the biome may shift from an Indian biome to an American biome,” although there is not yet data to support this theory.

The microbiome theory is gaining so much steam in academia that a coalition of four U.S. research centers called the MS Microbiome Consortium recently formed to investigate the role of gut microorganisms in the disease. The group presented data in Boston showing significantly different gastrointestinal bacterial populations in patients treated with the MS drug glatiramer acetate compared with untreated subjects. How exactly the drug suppresses MS activity is unknown but the findings suggest that perhaps it works in part by altering gut flora and, as a result, suppressing abnormal immune activity. “But important questions remain, such as how MS medications affect the microbiome, how an individual’s microbiome may affect treatment responses, whether particular bacterial species are associated with more severe disease and ultimately whether we can manipulate the microbiome to benefit our patients.”

Katz Sand says that dietary and probiotic approaches to treating MS are worth pursuing, as is a less palatable approach: fecal transplantation.Yet answers in science and medicine are rarely simple, she added, pointing out that in all likelihood MS arises from a complicated confluence of genetic and environmental influences that might ultimately trigger autoimmune activity. Beyond just our gut flora well over 100 genetic variants —many related to immune function—are now known to contribute to the disease as are external factors including vitamin D deficiency  (MS is more common at higher latitudes), smoking and increased salt intake. 

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Very exciting new way to use probiotics! Huge potential. From Science Daily:

Probiotics protect children, pregnant women against heavy metal poisoning

Yogurt containing probiotic bacteria successfully protected children and pregnant women against heavy metal exposure in a recent study. Canadian and Tanzanian researchers created and distributed a special yogurt containing Lactobacillus rhamnosus bacteria and observed  the outcomes against a control group.

A research team from the Canadian Centre for Human Microbiome and Probiotics, led by Dr. Gregor Reid, studied how microbes could protect against environmental health damage in poor parts of the world. Their lab research indicated that L. rhamnosus had a great affinity for binding toxic heavy metals. Working with this knowledge, the team hypothesized that regularly consuming this probiotic strain could prevent metals from being absorbed from the diet.

Working with the Western Heads East organization, Dr. Reid had already established a network of community kitchens in Mwanza, Tanzania to produce a probiotic yogurt for the local population. Mwanza is located on the shores of Lake Victoria, which is known to be polluted with pesticides and toxic metals including mercury. The team utilized this network to produce and distribute a new type of yogurt containing L. rhamnosus. The special yogurt was distributed to a group of pregnant women and a group of children. The researchers measured the baseline and post-yogurt levels of toxic metals.

The team found a significant protective effect of the probiotic against mercury and arsenic in the pregnant women. This is important as "reduction in these compounds in the mothers could presumably decrease negative developmental effects in their fetus and newborns," according to Dr. Reid. While the results obtained in the children studied showed benefits and lower toxin levels, the sample size and duration of treatment did not allow statistical significance.

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Of course there is a lung microbiome. From The Scientist:

Breathing Life into Lung Microbiome Research

Although it’s far less populated than the mouth community that helps feed it, researchers increasingly appreciate the role of the lung microbiome in respiratory health.

“There’s a constant flow into [the] lungs of aspirated bacteria from the mouth,” he said. But through the action of cilia and the cough reflex, among other things, there’s also an outward flow of microbes, making the lung microbiome a dynamic community.

Like the placenta, urethra, and other sites of the body now known to harbor commensal bacteria, researchers and clinicians once considered the lung to be sterile in the absence of infection. Over the last 10 years, however, evidence has been building that, although it is far less-populated than the mouth or gut, the disease-free lung, too, is populated by a persistent community of bacteria. Shifts in the lung microbiome have been correlated with the development of chronic lung conditions like cystic fibrosis (CF) or chronic obstructive pulmonary disease (COPD), although the relationship between the lung microbiome and disease is complicated.

The surface area of the healthy lung is a dynamic environment. The respiratory organ is constantly bombarded by debris and microbes that make their way from the mouth and nose through the trachea. Ciliated cells on branching bronchioles within the lungs beat rhythmically to move debris and invading microbes, while alveolar macrophages constantly patrol for and destroy unwelcome bugs.

The lung microbiome is about 1,000 times less dense than the oral microbiome and about 1 million to 1 billion times sparser than the microbial community of the gut, said Huffnagle. That is in part because the lung lacks the microbe-friendly mucosal lining found in the mouth and gastrointestinal tract, instead harboring a thin layer of much-less-inviting surfactant to keep the respiratory organs from drying out. ... It appears that the lung microbiome is populated from the oral microbiome, and among this population exists a small subset of bacteria that can survive the unique environment of the lung. The most common bacteria found in healthy lungs are Streptococcus, Prevotella, and Veillonella species.

Segal, who studies small airway disorders with an eye toward early detection of COPD, has found in a series of studies that inflammation of the lungs is often accompanied by a shift in their bacterial makeup. The mechanism behind these changes and consequences of them are still not well understood, however. Other studies have uncovered associations between changes in the lung microbiome and HIV or asthma, but again, causality has been difficult to elucidate.

According to Yvonne Huang  from the University of California San Francisco Medical Center, who is working to characterize lung microbiomes in relation to health and disease progression, “this field is where studies of gut microbiome were 10 to 15 years ago. 

  Human lungs. Credit: Wikipedia

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Sad, but not surprising results. It highlights the damage repeated courses of antibiotics, and even illness, do to gut microbial communities. The researchers write that during a prolonged stay in ICU they found the emergence of "ultra-low-density communities" (only 1 to 4 bacteria species) in patients. From Science Daily:

Critically ill ICU patients lose almost all of their gut microbes and the ones left aren't good

Researchers at the University of Chicago have shown that after a long stay in the Intensive Care Unit (ICU) only a handful of pathogenic microbe species remain behind in patients' intestines. The team tested these remaining pathogens and discovered that some can become deadly when provoked by conditions that mimic the body's stress response to illness.

"Our hypothesis has always been that the gut microflora in these patients are very abnormal, and these could be the culprits that lead to sepsis," he says. The current study supports this idea. Alverdy and Olga Zaborina, a microbiologist, wanted to know what happens to the gut microbes of ICU patients, who receive repeated courses of multiple antibiotics to ward off infections.

They found that patients with stays longer than a month had only one to four types of microbes in their gut, as measured from fecal samples -- compared to about 40 different types found in healthy volunteers.

Four of these patients had gut microbe communities with just two members-- an infectious Candida yeast strain and a pathogenic bacterial strain, such as Enterococcus faecium or Staphylococcus aureus and other bugs associated with hospital-associated infections. Not surprisingly, almost all of the pathogenic bacteria in these patients were antibiotic resistant.

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Published on 4 Comments on Which Probiotic Treatment is Best For Sinusitis?

[PLEASE NOTE THAT AN UPDATED VERSION OF THIS POST WITH NEW INFORMATION, INCLUDING NEW PRODUCTS, WAS PUBLISHED IN MAY 2018: The One Probiotic That Treats Sinusitis. Comments can be posted there.]

We now know that antibiotics, especially repeated courses of antibiotics, kills off bacteria and alters the microbial community in the sinuses (sinus biome). Research by Abreu et al (in 2012) showed that it is Lactobacillus sakei that is missing in chronic sinusitis sufferers, and that Lactobacillus sakei successfully treats sinusitis. From this research it is clear that Lactobacillus sakei is a  beneficial bacteria that can be used as a probiotic to cure sinustis.

It turns out that many brands of live fermented kimchi contain Lactobacillus sakei, and this is what my family used to treat and cure ourselves of chronic sinusitis (and acute sinusitis). So yes, kimchi can be probiotics for sinusitis. It is now over 85 weeks since I've been off all antibiotics and feeling great!

Until now I avoided naming the kimchi brand we used on this site because I believe that many brands of fermented kimchi (with cabbage) contain Lactobacillus sakei, and should be effective in curing sinusitis (this is by dabbing or smearing it in the nostrils - see Sinusitis Treatment Summary link for the METHOD and details).

WHAT BRANDS OR PRODUCTS WITH Lactobacillus sakei WORK?

The brand I use is Sunja's Kimchi (from Vermont). We originally were successful with the Medium Spicy Cabbage Kimchi and when that stopped being fully effective last winter (from overuse? recipe change?), we switched to Sunja's Medium Spicy Cucumber Kimchi (fermented at least 14 days and the jar opened less than 1 week).

Recently I heard from a woman in Nevada who wrote me stating that smearing/dabbing Sinto Gourmet Mild White Napa Cabbage Kimchi into her nostrils was successfully treating her chronic sinusitis (using the method described in the Sinusitis Treatment page)

One person wrote that he successfully cured chronic and acute sinusitis with a fermented sausage starter from Chr. Hansen containing L. sakei and another bacteria. He used it after mixing very small amounts in his  Neti pot - initially used it 1 x per day until cured, and then sparingly only as needed (after a cold) or as a maintenance booster once every 3 or 4 months (see his comment in the Contact page for more details). (UPDATE: one name for this product is Bactoferm F-RM-52, which contains Lactobacillus sakei and Staphylococcus carnosus  . See 1/12/15 post for more, including my experience with it.)

Eating kimchi does not seem to treat sinusitis, even though it may be good for the gut. Only smearing or dabbing it in the nostrils works.

Several people have reported that using sauerkraut has not helped their sinusitis, and scientific studies report that sauerkraut contains minimal L.sakei, if at all.

Others have also mentioned thinking about using lactic acid starter cultures containing L. sakei , whether using it alone or making kimchi with it, but I don't know how it went.

Finally, I would like feedback from you: 1) What brands of kimchi have worked for you in treating or curing sinusitis?     2) What other products containing Lactobacillus sakei have worked successfully for you? And how did you use it?   3) What other bacteria have worked for you in curing sinusitis?

Please let me know by commenting in the comments section or writing me an email. This way I can update this list.  The goal is to find ways to improve the beneficial bacteria in the sinuses and so treat, cure, and eventually prevent sinusitis.   Thanks!

[PLEASE NOTE THAT AN UPDATED VERSION OF THIS POST WITH NEW INFORMATION WAS PUBLISHED IN MAY 2018: The One Probiotic That Treats Sinusitis. Comments can be posted there.]

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I mentioned these studies earlier in July, but this write-up (from Sept. 17, 2014) gives the reader some new information. From Gut Microbiota Watch:

Studies uncover 500 “hidden” microbes in the gut

Over the last few years, scientists have found that the microbes hosted in the digestive tract (the gut microbiota or gut flora) perform key functions for health. Digestion, immunity and even mental health are extremely dependent on tasks carried out by the gut bacteria.

Now, two studies have found that the human gut hosts five hundred species of microbes – and seven million microbial genes – that were unknown until now. The proportion of the gut flora that had been hidden until now may hold essential information on the origin of a range of diseases (IBD and metabolic syndrome, among others), as well as the clues on how to cure them.

The two studies were published in Nature Biotechnology in July, and come from the efforts of the MetaHIT(METAgenomics of the Human Intestinal Tract) project, a European consortium working to explore the composition of human gut microbiota.

The first of the two studies focuses on expanding the catalogue of genes that belong to microbes of the gut flora....As a result, the catalogue has increased to 10 million genes. The next step for the scientists is to find what these genes do, in order to have a better understanding of the functions performed by the microbiota.

The second of the two studies pursues an even more ambitious goal: identifying new organisms in the microbiota, rather than identifying new genes....By applying this method, the authors have found 500 species whose existence in the microbiota was previously unknown.

Interestingly, some of the subjects analysed in the study had very few of these new species. By checking who these individuals were, the authors found that they all had Crohn’s disease, ulcerative colitis, or metabolic syndrome with an inflammatory component. These findings suggest that there is a correlation between suffering from these diseases and having less diversity in these unknown species. “These species, unknown until now, will possibly make the difference between healthy and unhealthy people”, said Guarner.

This information may open the door to new strategies aimed at recovering the presence of these species through nutritional intervention. In particular, providing patients with probiotics or prebiotics,  that may help to balance their microbiota.