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Category: microbes

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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.

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Finally, a discussion of the eye microbiome or microbiota (microbial community). Originally eyes were thought not to have much microbial life. But now with modern technology (such as genetic sequencing) it is known that many microbial species live on the eye. And yes, the eye or ocular microbiome can become imbalanced.

From The Scientist: Visualizing the Ocular Microbiome

Ophthalmologists have treated pathogenic eye infections for many decades, and the advent of contact lenses has made such infections more common. But little is known about the bacteria that live on the surface of a healthy human eye, and how this microbial make-up differs when a pathogenic strain takes over. Many bacteria known to live on the eye are difficult to culture, making them virtually invisible to researchers. Adapting sequencing technologies to study the ocular microbiome has opened up new avenues for understanding what’s really happening under the eyelids.

About five years ago, Valery Shestopalov of the Bascom Palmer Eye Institute at the University of Miami was speaking with his microbiology colleagues about what bacteria are found on normal, healthy eyes. Conventional wisdom at that time held that healthy eyes don’t harbor much microbial life, tears and blinking tend to clear away foreign objects, including bacteria. But Shestopalov’s early tests revealed something different. “The tests ran positive. All exposed mucosal epithelium are populated densely,” he said. 

The team found that about a dozen bacteria genera dominated the eye’s conjunctiva, a third of which could not be classified. On the corneal surface, they found a slightly different community. Again, about a dozen genera dominated. And everywhere they’ve looked, the researchers have found more than just bacteria. “We haven't published on this yet, but I have been surprised by how often we find phage or viruses on the normal ocular surface,” Van Gelder told The Scientist in an e-mail.

“People can have a huge variation in microflora and still have healthy eyes, making our job difficult, but really amazing,” Shestopalov said.

The researchers also found that during keratitis infections—infections of the cornea—only about half as many bacterial varieties were present, most prominently Pseudomonas strains. The changes typically occurred well before a diagnosis of an eye infection, suggesting the ocular microbiome could inform future diagnostics, Shestopalov noted. 

One factor that may be expected to impact the composition of the ocular flora is the use of contact lenses. Contact lens wear is one of the biggest factors leading to corneal infection... Researchers believe contact lenses make it easier for pathogens to colonize the surface of the eye by giving the bacteria something to adhere to. Sequencing biofilms from used contact lenses, Shestopalov’s team found evidence of microbial communities that were different from the ocular microbiomes of people who don’t use contacts. On the lenses themselves, the researchers have found much less diversity—many of the bacterial genera that dominate the conjunctiva and cornea were depleted. In their place, Staphylococcus dominated.

Whether the bacteria identified living on the surface of the eye are permanent residents or transient colonizers remains to be seen. The work of deconstructing the ocular microbiome is just getting started, but preliminary results have suggested it is distinct from the rest of the bacterial community that inhabits our bodies. “It stands apart,” Shestopalov said. “There’s statistical evidence of its difference from any other human microbiome.”

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More long-standing medical advice goes out the window. New advice: avoid diet soda and artificial sweeteners. The amazing part is that our gut bacteria are involved.

From Science Daily: Certain gut bacteria may induce metabolic changes following exposure to artificial sweeteners

Artificial sweeteners -- promoted as aids to weight loss and diabetes prevention -- could actually hasten the development of glucose intolerance and metabolic disease, and they do so in a surprising way: by changing the composition and function of the gut microbiota -- the substantial population of bacteria residing in our intestines. These findings, the results of experiments in mice and humans, ...says that the widespread use of artificial sweeteners in drinks and food, among other things, may be contributing to the obesity and diabetes epidemic that is sweeping much of the world.

For years, researchers have been puzzling over the fact that non-caloric artificial sweeteners do not seem to assist in weight loss, with some studies suggesting that they may even have an opposite effect.

Next, the researchers investigated a hypothesis that the gut microbiota are involved in this phenomenon. They thought the bacteria might do this by reacting to new substances like artificial sweeteners, which the body itself may not recognize as "food." Indeed, artificial sweeteners are not absorbed in the gastrointestinal tract, but in passing through they encounter trillions of the bacteria in the gut microbiota.

The researchers treated mice with antibiotics to eradicate many of their gut bacteria; this resulted in a full reversal of the artificial sweeteners' effects on glucose metabolism. Next, they transferred the microbiota from mice that consumed artificial sweeteners to "germ-free," or sterile, mice -- resulting in a complete transmission of the glucose intolerance into the recipient mice. This, in itself, was conclusive proof that changes to the gut bacteria are directly responsible for the harmful effects to their host's metabolism.... A detailed characterization of the microbiota in these mice revealed profound changes to their bacterial populations, including new microbial functions that are known to infer a propensity to obesity, diabetes, and complications of these problems in both mice and humans.

Does the human microbiome function in the same way? Dr. Elinav and Prof. Segal had a means to test this as well. As a first step, they looked at data collected from their Personalized Nutrition Project (www.personalnutrition.org), the largest human trial to date to look at the connection between nutrition and microbiota. Here, they uncovered a significant association between self-reported consumption of artificial sweeteners, personal configurations of gut bacteria, and the propensity for glucose intolerance. They next conducted a controlled experiment, asking a group of volunteers who did not generally eat or drink artificially sweetened foods to consume them for a week, and then undergo tests of their glucose levels and gut microbiota compositions.

The findings showed that many -- but not all -- of the volunteers had begun to develop glucose intolerance after just one week of artificial sweetener consumption. The composition of their gut microbiota explained the difference: the researchers discovered two different populations of human gut bacteria -- one that induced glucose intolerance when exposed to the sweeteners, and one that had no effect either way. Dr. Elinav believes that certain bacteria in the guts of those who developed glucose intolerance reacted to the chemical sweeteners by secreting substances that then provoked an inflammatory response similar to sugar overdose, promoting changes in the body's ability to utilize sugar.

This image depicts gut microbiota. Credit: Weizmann Institute of Science

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This exciting new research is just the beginning knowledge about our virome (the virus community within us). Note that they only looked at viruses in a few areas of our bodies - the rest is still a mystery. But note that it is normal for healthy individuals to carry viruses, and that we have "distinct viral fingerprints". We don't know if the viruses are beneficial or not to us at this time. From Science Daily:

Healthy humans make nice homes for viruses

The same viruses that make us sick can take up residence in and on the human body without provoking a sneeze, cough or other troublesome symptom, according to new research. On average, healthy individuals carry about five types of viruses on their bodies, the researchers report. The study is the first comprehensive analysis to describe the diversity of viruses in healthy people.

The research was conducted as part of the Human Microbiome Project, a major initiative funded by the National Institutes of Health (NIH) that largely has focused on cataloging the body's bacterial ecosystems. ..."Lots of people have asked whether there is a viral counterpart, and we haven't had a clear answer. But now we know there is a normal viral flora, and it's rich and complex."

In 102 healthy young adults ages 18 to 40, the researchers sampled up to five body habitats: nose, skin, mouth, stool and vagina. The study's subjects were nearly evenly split by gender.

At least one virus was detected in 92 percent of the people sampled, and some individuals harbored 10 to 15 viruses...."We only sampled up to five body sites in each person and would expect to see many more viruses if we had sampled the entire body."

Scientists led by George Weinstock, PhD, at Washington University's Genome Institute, sequenced the DNA of the viruses recovered from the body, finding that each individual had a distinct viral fingerprint. (Weinstock is now at The Jackson Laboratory in Connecticut.) About half of people were sampled at two or three points in time, and the researchers noted that some of the viruses established stable, low-level infections.

The researchers don't know yet whether the viruses have a positive or negative effect on overall health but speculate that in some cases, they may keep the immune system primed to respond to dangerous pathogens while in others, lingering viruses increase the risk of disease.

Study volunteers were screened carefully to confirm they were healthy and did not have symptoms of acute infection. They also could not have been diagnosed in the past two years with human papillomavirus infection (HPV), which can cause cervical and throat cancer, or have an active genital herpes infection.

Analyzing the samples, the scientists found seven families of viruses, including strains of herpes viruses that are not sexually transmitted. For example, herpesvirus 6 or herpesvirus 7 was found in 98 percent of individuals sampled from the mouth. Certain strains of papillomaviruses were found in about 75 percent of skin samples and 50 percent of samples from the nose. Novel strains of the virus were found in both sites.

Not surprisingly, the vagina was dominated by papillomaviruses, with 38 percent of female subjects carrying such strains. Some of the women harbored certain high-risk strains that increase the risk of cervical cancer. These strains were more common in women with communities of vaginal bacteria that had lower levels of Lactobacillus and an increase in bacteria such as Gardnerella, which is associated with bacterial vaginosis.

Adenoviruses, the viruses that cause the common cold and pneumonia, also were common at many sites in the body.

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Amazing possibilities, but more studies needed. The key finding: A diversity of the bacterial community in the gut is good, and perhaps can be altered through diet, and so perhaps alter the future risk of developing breast cancer.From Science Daily:

Diverse gut bacteria associated with favorable ratio of estrogen metabolites

Postmenopausal women with diverse gut bacteria exhibit a more favorable ratio of estrogen metabolites, which is associated with reduced risk for breast cancer, compared to women with less microbial variation, according to a new study.

Since the 1970s, it has been known that in addition to supporting digestion, the intestinal bacteria that make up the gut microbiome influence how women's bodies process estrogen, the primary female sex hormone. The colonies of bacteria determine whether estrogen and the fragments left behind after the hormone is processed continue circulating through the body or are expelled through urine and feces. Previous studies have shown that levels of estrogen and estrogen metabolites circulating in the body are associated with risk of developing postmenopausal breast cancer.

"In women who had more diverse communities of gut bacteria, higher levels of estrogen fragments were left after the body metabolized the hormone, compared to women with less diverse intestinal bacteria," said one of the study's authors, James Goedert, MD, of the National Institutes of Health's National Cancer Institute (NCI) in Bethesda, MD. "This pattern suggests that these women may have a lower risk of developing breast cancer."

As part of the cross-sectional study, researchers analyzed fecal and urine samples from 60 postmenopausal women enrolled in Kaiser Permanente Colorado. .

"Our findings suggest a relationship between the diversity of the bacterial community in the gut, which theoretically can be altered with changes in diet or some medications, and future risk of developing breast cancer," Goedert said. 

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An opinion piece from Dr. David Johnson, Prof. of Medicine and Chief of Gastroenterology at Eastern Medical School in Norfolk, Virginia but an interesting one that points out the limitations of current probiotic knowledge and that we shouldn't blindly take probiotics (with only a few bacteria strains) after antibiotic use thinking that they're all good, all the time. I'm including this article to show what many medical professionals think about probiotic use and why.

He discusses 2 large studies, but unfortunately both studies only looked at hospitalized patients - and the large PLACIDE study looked at over-65 year old patients. And in the second large study he discusses the benefits of the antibiotic metronidazole.

I agree with his need for caution and the need for more large studies, but I wish he had discussed children, people NOT hospitalized, people who just had a round of antibiotics without life threatening complications, and not dismissed small studies. Hospitalized vs non-hospitalized people are very, very different groups. Small studies are finding benefits of various bacteria, but yes, the research is in its infancy, especially what are "normal microbial communities" in the gut and in other parts of the body. He does not discuss fecal transplants of entire microbial communities for C. difficile and their over 90% success rate. Dr. S. Lynch has theorized that some bacteria act as "keystone species" that could help repopulate a biome after an insult (such as antibiotics). From Medscape:

Probiotics: Help or Harm in Antibiotic-Associated Diarrhea?

Today I want to discuss the issue of probiotics, and whether probiotics are doing an element of benefit or an element of harm. With access to over-the-counter products, use of probiotics has dramatically increased. Physicians recommend probiotics routinely to patients when they are taking antibiotics to prevent antibiotic-associated diarrhea. I would like to take a time-out and reevaluate what we are doing for these patients.

Not infrequently, antibiotics are associated with Clostridium difficile infections, which occur in up to one third of patients with antibiotic-associated diarrhea.

In 2012, highly publicized meta-analyses were published in JAMA [1] and Annals of Internal Medicine. [2]These studies, and a Cochrane review,[3] suggest that not only can probiotics prevent or diminish antibiotic-associated diarrhea, but probiotics may also be helpful in avoiding C difficile infection.

Enter the most recent study, which is called the PLACIDE study, from the United Kingdom[4] It involved 5 hospitals, 68 different medical and surgical units, and more than 17,000 patients aged 65 years or older. All patients were hospitalized and taking an antibiotic.

These patients were randomly assigned, if they met eligibility criteria, to receive either a microbial preparation (which is the term they used for "probiotic") or an identical placebo. The microbial preparation had 2 strains of Lactobacillus and 2 strains of bifidobacteria, which patients received for 21 days.... Even with evaluation for intention to treat, there was no difference in the outcomes for C difficile infection or antibiotic-associated diarrhea between the microbial preparation (probiotic) and placebo group. Of interest, there was an increase in flatus in the microbial preparation group, and patients with C difficile diarrhea who received the microbial preparation reported a 3-fold increase in bloating. 

Although intended to restore good health, we are seeing a dysbiosis. We have disrupted the microflora in the gut, and are trying to jam it back with strains of bacteria that we think are good bacteria, and it may not be the correct answer. We don't know the right answer. When you alter the microflora, you change some of the metabolism of carbohydrates, bile salts, and complex sugars. We are not clear whether jamming the gut with another strain of bacteria is going to be of benefit.

I want to posit an element of potential harm, and not rush in to recommend probiotics routinely in patients to whom you prescribe antibiotics. I would also caution you not to use probiotics in patients in the intensive care unit, or in any patient with an indwelling prosthesis, particularly an intravascular prosthesis.