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

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

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

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

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

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

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

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

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

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

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

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

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Lactobacilli

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

From The Scientist: Characterizing the “Healthy” Vagina

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

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

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

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

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

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

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

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

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

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

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

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

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

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Informing pregnant women about environmental health hazards is absolutely necessary, especially because steps can be taken to avoid them (such as pesticides, mercury in fish, lead and BPA). Why isn't it happening routinely? Hey obstetricians - are you listening? From Huffington Post:

Doctors Fail To Counsel Pregnant Women On Toxic Chemical Risks

...dozens of environmental chemicals can course through a pregnant woman's body, cross the umbilical cord and wreck havoc on a developing fetus. Birth defects, IQ losses and childhood cancers are just some of the potential risks scientists have now tied to even low levels of exposure.

Among more than 2,500 doctors consulted for the survey, nearly all of them reported counseling patients on factors such as diet, exercise and cigarette smoking. However, only about 20 percent said they addressed environmental exposures. They pegged their hesitation to a number of factors, from the fear of overwhelming patients with anxiety-inducing worries to limited appointment time to a lack of environmental health education.

Just one in 15 doctors said they had received training on the harmful reproductive effects of toxic chemicals. "Medical school and residencies tend to frame their curriculum around the boards and required licensing exams," said Stotland. "This material is not yet on those tests." ... The American College of Obstetrics and Gynecologists (ACOG) and the American Society for Reproductive Medicine (ASRM) issued a statement in October that underscored mounting evidence of "significant and long-lasting effects" caused by industrial chemicals, and emphasized doctors' role in protecting pregnant women.

The actual study from Plos One summed up the importance of knowing about exposures to environmental hazards during pregnancy very nicely in the introduction:

Counseling Patients on Preventing Prenatal Environmental Exposures - A Mixed-Methods Study of Obstetricians

Exposure to hazardous environmental chemicals, i.e., manufactured chemicals and metals, is linked to adverse health outcomes across all stages of the human life cycle including fertility, conception, pregnancy, child and adolescent development, and adult health [1]–[5]. Human exposure to environmental chemicals is ubiquitous. A population-based study found that virtually all pregnant women in the U.S. had measureable levels of at least 43 different environmental chemicals in their bodies, including chemicals that were measured at levels similar to those associated with adverse developmental and reproductive health outcomes in epidemiologic studies [6]. There are currently over 80,000 chemicals in commerce [7], [8], and exposure occurs through air, water, food and consumer products in the home and workplace. The majority of industrial chemicals have not been tested for potential reproductive/developmental harm [9].

Obstetricians are uniquely positioned to help prevent exposures to environmental chemicals with adverse developmental and reproductive health effects [2]. Pregnancy is a time when exposure to environmental contaminants can disrupt or interfere with the physiology of a cell, tissue, or organ [4], leading to permanent and lifelong adverse health outcomes that may be passed down to future generations [10]. Pregnancy is also an opportune time to prevent harmful exposures as it is a period when patient interest about health can be extremely high.

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The worrisome results are adding up for BPA and BPS. From Environmental Health News:

Miscarriage risk rises with BPA exposure, study finds

Women exposed to high levels of bisphenol A early in their pregnancy had an 83 percent greater risk of miscarriage than women with the lowest levels, according to new research. The scientists said their new study adds to evidence that low levels of the ubiquitous chemical, used to make polycarbonate plastic and found in some food cans and paper receipts, may affect human reproduction. The study involved 115 pregnant women who had visited a Stanford University fertility clinic within about four weeks of fertilization. The more BPA detected in the women’s blood, the higher their risk of miscarriage, according to the researchers.

“Couples suffering from infertility or recurrent miscarriages would be best advised to reduce BPA exposure because it has the potential to adversely affect fetal development,” wrote the scientists, led by Dr. Ruth Lathi, a Stanford University associate professor of obstetrics and gynecology. 

In 2005, a smaller study in Japan found that 45 women who had three or more first-trimester miscarriages had three times more BPA in their blood than 32 women with no history of pregnancy problems. 

From Science Daily:

BPA increases risk of cancer in human prostate tissue, study shows

Fetal exposure to a commonly used plasticizer found in products such as water bottles, soup can liners and paper receipts, can increase the risk for prostate cancer later in life, according to a study. Exposure of the fetus to BPA in utero is of particular concern, because the chemical, which mimics the hormone estrogen, has been linked to several kinds of cancer, including prostate cancer, in rodent models. The new findings show that human prostate tissue is also susceptible.

"Our research provides the first direct evidence that exposure to BPA during development, at the levels we see in our day-to-day lives, increases the risk for prostate cancer in human prostate tissue," Prins said

This study was done in rats, but thought to also apply to humans. From Science Daily:

Common BPA substitute, BPS, disrupts heart rhythms in females

Bisphenol S (BPS), a common substitute for bisphenol A (BPA) in consumer products, may have similar toxic effects on the heart as previously reported for BPA, a new study finds.

There is implied safety in BPA-free products. The thing is, the BPA analogs -- and BPS is one of them -- have not been tested for safety in humans." "Our findings call into question the safety of BPA-free products containing BPS," he said. "BPS and other BPA analogs need to be evaluated before further use by humans."

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Another reason to try to avoid BPA. From Medical Xpress:

BPA stimulates growth of breast cancer cells, diminishes effect of treatment

Bisphenol A (BPA), a chemical commonly used in plastics, appears to increase the proliferation of breast cancer cells, according to Duke Medicine researchers presenting at an annual meeting of endocrine scientists.

The researchers found that the chemical, at levels typically found in human blood, could also affect growth of an aggressive hormone-independent subtype of  cells called inflammatory breast cancer and diminish the effectiveness of treatments for the disease.

"We set out to determine whether routine exposures to common chemicals such as those in plastics, pesticides and insecticides could influence the effectiveness of breast cancer treatments," said corresponding author Gayathri Devi, Ph.D., associate professor of surgery at Duke. "BPA was one of the top chemicals to show growth stimulatory effects in breast cancer cells."

Screenings identified several agents that appeared to increase the proliferation of inflammatory breast cancer cells. Among the most active was BPA, a chemical known to disrupt hormones. The researchers found that it caused breast cancer cells to grow at a faster rate in both estrogen-receptor positive and estrogen-receptor negative breast cancer cells.

The researchers also found that BPA doses in the range observed in human blood lowered the efficacy of FDA-approved anti-cancer drugs used in breast cancer therapy, notably lapatinib.

"These studies provide the foundation for additional research to develop tools that can be used to identify patients who may be at greater risk of developing treatment resistance," Devi said. "The findings could also lead to biomarkers that identify patients who have heavy exposure to compounds that could diminish the effectiveness of their cancer therapy."

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The researchers of this study looked at proximity to farm fields (how close a pregnant woman lives to a farm) and certain farm pesticides and found a link between exposure to farm pesticides during pregnancy and having a child with autism. But too bad they didn't also include pesticide exposures from homes (for pest control), gardens, and yards which would have given a more accurate measure of total exposure. However, it's a start. From Science Daily:

Association found between maternal exposure to agricultural pesticides and autism

Pregnant women who lived in close proximity to fields and farms where chemical pesticides were applied experienced a two-thirds increased risk of having a child with autism spectrum disorder or other developmental delay, a study by researchers with the UC Davis MIND Institute has found. The associations were stronger when the exposures occurred during the second and third trimesters of the women's pregnancies.

The large, multisite California-based study examined associations between specific classes of pesticides, including organophosphates, pyrethroids and carbamates, applied during the study participants' pregnancies and later diagnoses of autism and developmental delay in their offspring. It is published online in Environmental Health Perspectives. "... the message is very clear: Women who are pregnant should take special care to avoid contact with agricultural chemicals whenever possible."

California is the top agricultural producing state in the nation, grossing $38 billion in revenue from farm crops in 2010. Statewide, approximately 200 million pounds of active pesticides are applied each year, most of it in the Central Valley, north to the Sacramento Valley and south to the Imperial Valley on the California-Mexico border. While pesticides are critical for the modern agriculture industry, certain commonly used pesticides are neurotoxic and may pose threats to brain development during gestation, potentially resulting in developmental delay or autism.

The study was conducted by examining commercial pesticide application using the California Pesticide Use Report and linking the data to the residential addresses of approximately 1,000 participants in the Northern California-based Childhood Risk of Autism from Genetics and the Environment (CHARGE) Study. The study includes families with children between 2 and 5 diagnosed with autism or developmental delay or with typical development. "We mapped where our study participants' lived during pregnancy and around the time of birth. In California, pesticide applicators must report what they're applying, where they're applying it, dates when the applications were made and how much was applied," Hertz-Picciotto said. "What we saw were several classes of pesticides more commonly applied near residences of mothers whose children developed autism or had delayed cognitive or other skills."

Organophosphates applied over the course of pregnancy were associated with an elevated risk of autism spectrum disorder, particularly for chlorpyrifos applications in the second trimester. Pyrethroids were moderately associated with autism spectrum disorder immediately prior to conception and in the third trimester. Carbamates applied during pregnancy were associated with developmental delay.

Exposures to insecticides for those living near agricultural areas may be problematic, especially during gestation, because the developing fetal brain may be more vulnerable than it is in adults. Because these pesticides are neurotoxic, in utero exposures during early development may distort the complex processes of structural development and neuronal signaling, producing alterations to the excitation and inhibition mechanisms that govern mood, learning, social interactions and behavior.

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

Gut microbe levels are linked to type 2 diabetes and obesity

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

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

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

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

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

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

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But I wonder if the results would be different if the only processed meat (cold cuts, salami, prosciutto) you ate came from antibiotic, hormone, additive, and nitrate-free meat. From Science Daily:

Processed red meat linked to higher risk of heart failure, death in men

Men who regularly eat moderate amounts of processed red meat such as cold cuts (ham/salami) and sausage may have an increased risk of heart failure incidence and a greater risk of death from heart failure. 

Processed meats are preserved by smoking, curing, salting or adding preservatives. Examples include cold cuts (ham, salami), sausage, bacon and hot dogs."Processed red meat commonly contains sodium, nitrates, phosphates and other food additives, and smoked and grilled meats also contain polycyclic aromatic hydrocarbons, all of which may contribute to the increased heart failure risk," said Alicja Wolk, D.M.Sc., senior author of the study and professor in the Division of Nutritional Epidemiology at the Institute of Environmental Medicine, Karolinska Institutet in Stockholm, Sweden. "Unprocessed meat is free from food additives and usually has a lower amount of sodium."

The Cohort of Swedish Men study -- the first to examine the effects of processed red meat separately from unprocessed red meat -- included 37,035 men 45-79 years old with no history of heart failure, ischemic heart disease or cancer. 

After almost 12 years of follow-up, researchers found:  - Men who ate the most processed red meat had more than a 2-fold increased risk of death from heart failure compared to men in the lowest category. - For each 50 gram (e.g. 1-2 slices of ham) increase in daily consumption of processed meat, the risk of heart failure incidence increased by 8 percent and the risk of death from heart failure by 38 percent. - The risk of heart failure or death among those who ate unprocessed red meat didn't increase.

"To reduce your risk of heart failure and other cardiovascular diseases, we suggest avoiding processed red meat in your diet, and limiting the amount of unprocessed red meat to one to two servings per week or less," said Joanna Kaluza, Ph.D., study lead author and assistant professor in the Department of Human Nutrition at Warsaw University of Life Sciences in Poland. "Instead, eat a diet rich in fruit, vegetables, whole grain products, nuts and increase your servings of fish."

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Everyone worries and talks about Lyme disease on the east coast of the U.S., but it appears that they should be worrying about multiple infections (including Lyme disease) when bitten by a tick. From Science Daily:

Single tick bite can pack double pathogen punch

People who get bitten by a blacklegged tick have a higher-than-expected chance of being exposed to more than one pathogen at the same time.

"We found that ticks are almost twice as likely to be infected with two pathogens -- the bacterium that causes Lyme disease and the protozoan that causes babesiosis -- than we would have expected," said Felicia Keesing, a professor of biology at Bard College, Adjunct Scientist at the Cary Institute, and co-author of the paper. "That means health care providers and the public need to be particularly alert to the possibility of multiple infections coming from the same tick bite."

Almost 30 percent of the ticks were infected with the agent of Lyme disease. One-third of these were also infected with at least one other pathogen. The agents of Lyme disease and babesiosis were found together in 7 percent of ticks.

"Mice and chipmunks are critical reservoirs for these two pathogens, so ticks that have fed on these animals are much more likely to be co-infected," ...

Not only was co-infection with the agents of Lyme disease and babesiosis greater than expected, but rates of triple infection with the agents of Lyme, babesiosis, and anaplasmosis were about twice as likely as expected. "People in tick-infested parts of the United States such as the Northeast, Mid-Atlantic, and Upper Midwest, are vulnerable to being exposed to two or three diseases from a single tick bite," said Keesing. "And, of course, that risk increases when they're bitten by more than one tick."

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

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

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

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

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

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

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

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

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

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

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