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Published on 2 Comments on Good Books About the Human Microbiome

Recently several good books have been published about the community of microbes within us - our microbiota or microbiome. Originally I mainly saw the term human microbiome used everywhere. It referred to all the organisms living within and on us that are identified by their genomes (genetic material within the organism such as DNA and RNA). However, recently I'm seeing the term microbiota being used more. The microbiota refers to the community of microbes within and on us. Think of it this way: the human microbiota is the collection of all the microbes within and on us, and their genes are called the human microbiome. So there's a difference, but both refer to all the microbes within and on us.

The human body contains over 10 times more microbial cells than human cells - thus 90% microbes (about 100 trillion microbial cells), and 10% human cells (about ten trillion human cells). It is estimated that the weight of all these microbes in an adult is about 3 pounds, which is about the weight of the adult human brain. Different communities of microbes live in different parts of the body - and each little part of the body has its own ecosystem or community. And there is variation from person to person in the types of microbes in each niche in the body. So knowing all this, it is time that to stop thinking about yourself as ME or I, but more of a collective WE.

It is great to see some recently published books that explore this new and emerging field, discuss the importance of feeding and nurturing the microbes (and how), look at current and future medical uses of microbes. Because that's the exciting stuff. As I've been posting all along, our microbes seem to be intimately linked with our health - whether cancer or sinusitis (think how Lactobacillus sakei successfully treats chronic sinusitis) or many other ailments. I enjoyed all the books, I liked that the material was presented a little differently (as well as some different material) by each author, and that each book had reference lists.

Martin Blaser, MD - Missing Microbes: How the Overuse of Antibiotics is Fueling Our Modern Plagues   This is the most scholarly of the books (published 2014, and with lots of references), because he is writing not just from his own extensive personal and professional experiences, but also as director of the New York University Human Microbiome Program. He discusses the dangers of some modern medical advances (such as frequent use of antibiotics and Cesarean sections)  to the human microbiome and how this may ultimately result in various diseases (modern plagues). I have posted about him various times, including an NPR interview about his book. The CDC (Centers for Disease Control) book review page also said: "Despite his emphasis on missing microbes, however, Blaser is wary of using probiotics, prebiotics, and synbiotics to restore microbial balance. He reasonably cites the challenges arising from the unsubstantiated claims of manufacturers and the paucity of well-designed trials to evaluate probiotics."

Justin Sonnenburg and Erica Sonnenburg, PhDs - The Good Gut: Taking Control of Your Weight, Your Mood, and Your Long-term Health This interesting book written is  meant for the general reader, and they incorporate their personal stories (they are both PhDs working at Stanford University while raising 2 children) as well as what the latest microbiota research is regarding our health and bodies. They make the case that "caring for our gut microbes may be the most important health choice we make". They, like Dr. Blaser, argue that our microbiota are in peril from changes to the diet, overuse of antibiotics, and oversterilization, and is facing a "mass extinction event" which is leading to a number of modern ailments (allergies, asthma, etc). They even provide some menus and recipes to feed our microbes, recipes that stress dietary fiber. Some posts in the past year mentioned his research (especially the importance of dietary fiber in health).

Alanna Collen -  10% Human: How Our Body's Microbes Hold the Key to Health and Happiness  (Published 2015) This book is written in a chatty style by Alanna Collen, a British science writer with a PhD in evolutionary biology. She incorporates both her personal story and experiences with the scientific literature. There was much to like about the book and that it was "easy to read", but there were a few moments that I thought that the research in a discussion was incomplete (urinary tract infections come to mind).

This last one I haven't yet read, but Dr. Rob Knight is such a BIG name in this emerging field  (and I heard his wonderful lectures in the Coursera course on the human microbiome) that I'm including this TED talk book. He is also a co-founder of the American Gut Project. I've mentioned his work in a number of posts this past year. Rob Knight with Brendan Buhler - Follow Your Gut: The Enormous Impact of Tiny Microbes (TED BOOKS) (Published 2015)

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 The following article supported what I have been reading over the past few years: that medical tests and treatments also have downsides, that it is possible to "know too much", that more harm than benefits can occur from certain tests, procedures, and medicines, and lifestyle changes (eat a less processed more plant-based diet, move more, and don't smoke) can be better than some medicines or certain procedures. The doctor mentioned in this article (Dr. H. Gilbert Welch) recently published a book aimed at the general public which I just read and highly recommend: Less Medicine, More Health. Dr. Welch is an academic physician, a professor at Dartmouth Medical School, and a nationally recognized expert on the effects of medical testing. In 2012 he published the well regarded and more technical and in-depth book on this issue: Overdiagnosed: Making People Sick in the Pursuit of Health. From The Atlantic:

The Downside of Medical Screening

If you had a disease, and you could find out sooner rather than later, why wouldn’t you?Medicine has long focused on early detection of diseases as part of a move toward preventive care. But imperfect tests, false positives, and overdiagnosis mean that sometimes the tests do more harm than good, and in recent years, there have been more recommendations to reduce some kinds of screening, including pap smears, colonoscopies, mammograms, and even annual pelvic exams.

“This is something we all need to understand, the two sides of early detection. It does help people, but it’s almost guaranteed to harm others,” said H. Gilbert Welch, a professor of medicine, public policy, and business administration at Dartmouth College, and author of the book Should I Be Tested for Cancer? (He reveals his answer in the book’s subtitle: “Maybe not.”)

The more you look for disease, the more you find it. And in the case of cancer, it’s hard for doctors to know if what they find is dangerous and needs to be addressed, or if it’s just a small tumor that won’t grow and poses no threat. “We can’t be sure which is which, so we treat everybody,” Welch explained at the Aspen Ideas Festival’s Spotlight Health session. “That means we’re treating people who will never experience problems from their disease.”

But they may experience problems from the treatment.The panel gave the example of prostate cancer, which is very common in men—one in seven American men will be diagnosed with it in their lifetimes. “But it turns out a lot of these cancers are very indolent,” said Jessica Herzstein, a preventive-medicine consultant and member of the U.S. Preventive Services Task Force. Around 30 to 40 percent of men who’ve been treated for prostate cancer likely had “slow-growing tumors that would never have become a threat to the man’s lifespan or health,” according to the Prostate Cancer Foundation.

In other words, “you’re going to die with them, not of them,” Herzstein said, “and the treatments are very very harmful.” Radiation therapy, for example, can cause incontinence and erectile dysfunction, and hormone therapy can cause osteoporosis and depression.

The possibility of a false positive is another downside. Not only could it lead to more invasive follow-up tests or treatments that aren’t needed, but it can also give patients unnecessary anxiety.“If we resolve the test by saying ‘The test was wrong, you’re fine!’, that’s one thing,” Welch said. “But most false alarms aren’t resolved that way. [It’s more like] ‘You don’t have cancer, but you have some abnormality that possibly puts you at a higher risk for cancer, but we’re not going to do anything about it. I think that’s where there can be [mental] harm.”

Ultimately, it comes down to a weighing of the benefits and the harms, and, in the absence of clear evidence, the preferences of the patient. The U.S. Preventive Services Task Force helps identify which tests are beneficial by evaluating and grading them. It gives tests an A if there’s a high certainty of substantial benefit, a B if there’s moderate certainty of substantial benefit, a C if there’s moderate certainty of a small benefit, a D if there’s moderate or high certainty of no benefit, and an I if the evidence is just too insufficient to say.

The task force gave prostate cancer screening a D. HIV screening got an A. For breast cancer screening, an always-controversial topic, the results vary. Breast self-exams got a D. Mammograms got a B, but only for women between 50 and 74 years old. For women in their 40s, the grade is a C, meaning the task force recommends patients and physicians discuss and decide together.

Before getting a screening test, patients should think about what would happen if they get a positive result, and if they’d be ready for it, Welch advised. “If I were to go through this, and have this diagnosis, would I want to have this surgery?” Herzstein asked, posing a hypothetical. Would you want to undergo the biopsy, the chemo, whatever treatments come next? “Maybe you don’t even want to go there if there is no treatment for the disease,” she added. Welch gives an example. “With Alzheimer’s disease that’s a fundamental question: What are you going to do with a positive result?” he asked. 

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Recently I've seen a number of published studies that found benefits to someone being bilingual or benefits in learning a new language. Some benefits recently found in bilinguals (or the "billngual advantage"): more gray matter in the executive control area of the brain, 4 to 5 year delay in onset of Alzheimer's symptoms, processing of information more efficiently and more easily, and young bilingual children are more likely to think that everything is learned (while monolinguals more likely to think things are innate). From Science Daily:

Bilinguals of two spoken languages have more gray matter than monolinguals

A new study published in the journal Cerebral Cortex suggests people who speak two languages have more gray matter in the executive control region of the brain...Early on, bilingualism was thought to be a disadvantage because the presence of two vocabularies would lead to delayed language development in children. However, it has since been demonstrated that bilingual individuals perform better, compared with monolinguals, on tasks that require attention, inhibition and short-term memory, collectively termed "executive control."

This "bilingual advantage" is believed to come about because of bilinguals' long-term use and management of two spoken languages. But skepticism still remains about whether these advantages are present, as they are not observed in all studies...."Given this concern, we took a different approach and instead compared gray matter volume between adult bilinguals and monolinguals. We reasoned that the experience with two languages and the increased need for cognitive control to use them appropriately would result in brain changes in Spanish-English bilinguals when compared with English-speaking monolinguals. And in fact greater gray matter for bilinguals was observed in frontal and parietal brain regions that are involved in executive control."

Gray matter of the brain has been shown to differ in volume as a function of people's experiences. A prominent finding of this type was a report that London taxi drivers have more gray matter in brain areas involved in spatial navigation.

What about being bilingual leads to these advantages?....The researchers compared gray matter in bilinguals of American Sign Language (ASL) and spoken English with monolingual users of English...."Unlike the findings for the Spanish-English bilinguals, we found no evidence for greater gray matter in the ASL-English bilinguals," Olulade says. "Thus we conclude that the management of two spoken languages in the same modality, rather than simply a larger vocabulary, leads to the differences we observed in the Spanish-English bilinguals."

Science Daily: Bilingualism delays Alzheimer's manifestation by more than four years

The symptoms of Alzheimer disease (AD) manifest themselves about four to five years later in bilinguals as opposed to monolinguals. In bilinguals, the disease onset was estimated at the age of 77, while in monolinguals, this was at the age of 73.

From Science Daily:  Bilingual brains better equipped to process information

Speaking more than one language is good for the brain, according to new research that indicates bilingual speakers process information more efficiently and more easily than those who know a single language. The benefits occur because the bilingual brain is constantly activating both languages and choosing which language to use and which to ignore, said a researcher.

From Science daily:  Bilingualism changes children's beliefs

Most young children are essentialists: They believe that human and animal characteristics are innate. That kind of reasoning can lead them to think that traits like native language and clothing preference are intrinsic rather than acquired. But a new study suggests that certain bilingual kids are more likely to understand that it's what one learns, rather than what one is born with, that makes up a person's psychological attributes.

White and gray matter of the human brain. Credit: Medline Plus, US National Library of Medicine

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Huh - all that talk and research for years about the first born being the smartest and most responsible. Yes...but according to this large study comparing 377,00 high school students from different families, the differences are so small as to be meaningless (1 IQ point!). Researchers looking within-families (studying siblings within families) say that the effects are larger. Depends on who you want to believe. And this study did not look at the siblings later in life - at achievements, etc. From Medical Xpress:

Birth order has no meaningful effect on personality or IQ, massive study reports

For those who believe that birth order influences traits like personality and intelligence, a study of 377,000 high school students offers some good news: Yes, the study found, first-borns do have higher IQs and consistently different personality traits than those born later in the family chronology. However, researchers say, the differences between first-borns and "later-borns" are so small that they have no practical relevance to people's lives. The analysis found - as a previous large-scale study did - that first-borns enjoy a one-IQ-point advantage over later-borns, Damian said. The difference is statistically significant but meaningless, she said.

The analysis also revealed consistent differences in personality traits between first-borns and later-borns - first-borns tended to be more extroverted, agreeable and conscientious, and had less anxiety than later-borns, for example - but those differences were "infinitesimally small," amounting to a correlation of 0.02, Roberts said. "But in terms of personality traits and how you rate them, a 0.02 correlation doesn't get you anything of note. You are not going to be able to see it with the naked eye. You're not going to be able to sit two people down next to each other and see the differences between them.."

The study controlled for potentially confounding factors - such as a family's economic status, the number of children and the relative age of the siblings at the time of the analysis - that might skew the results, Damian said. For example, wealthier families tend to have fewer children than other families, and so have a higher proportion of first-borns who also have access to more resources that may influence their IQ or personality, she said.

Many previous studies of birth order suffered from small sample sizes, Damian said. Many compared children with their siblings - a "within-family" design that some assert is better than comparing children from different families, as the new analysis did.

The team also evaluated a subset of the children in the study - those with exactly two siblings and living with two parents. This allowed the researchers to look for specific differences between first- and second-borns, or second- and third-borns. The findings confirmed those seen in the larger study, with specific differences between the oldest and a second child, and between second and third children. But the magnitude of the differences was, again, "minuscule," Roberts said.

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A recent report found that when a person is exposed to a little bit (or low doses) of a lot of different commonly encountered chemicals, than the combinations over time may cause changes that increase the risk of cancer (they may initiate cancer). Think about it - we are not exposed to just one chemical at a time (which is how chemicals are tested), but to mixtures or a "chemical soup". It is almost impossible to avoid them. As one of the researchers said: "We urgently need to focus more resources to research the effect of low dose exposure to mixtures of chemicals in the food we eat, air we breathe and water we drink." Testing mixtures of chemicals is currently not required by law.

The effects may be synergistic  - an enhanced effect that is more than the sum of the individual chemicals. And some chemicals may have bigger effects at smaller doses (typical of endocrine or hormone disruptors), than at larger doses - which is not how chemicals are typically viewed (typical view: the more you are exposed to a chemical, the greater the effect). A global task force of 174 scientists looked at 85 common everyday chemicals (at everyday low doses), and 50 were found to support cancer-related mechanisms (processes essential to cancer development). Examples of problematic chemicals that are common in everyday life: triclosan (in many soaps and personal care products), bisphenol A (in many plastics, including can linings), and atrazine (common herbicide or weedkiller). From the LA Times:

Combinations of 'safe' chemicals may increase cancer risk, study suggests

Lots of chemicals are considered safe in low doses. But what happens when you ingest a little bit of a lot of different chemicals over time? In some cases, these combinations may conspire to increase your risk of cancer, according to a new report. “Many [chemicals] have the possibility, when they are combined, to cause the initiation of cancer,” said Hemad Yasaei, a cancer biologist at Brunel University in England, one of the authors of the report. “They could have a synergistic or enhanced effect.”

This is not the way regulators typically think about cancer risk when they evaluate a compound’s safety.Normally, they test an individual chemical on laboratory animals, exposing them to progressively smaller amounts until it no longer causes malignant tumors to grow. Then they take that dose, determine the equivalent for humans, and apply what is called a “margin of safety” by declaring that some small fraction of that low dose is safe for people.

The big assumption driving the margin of safety is that a smaller amount of a chemical is less dangerous than a larger amount. (Think of the familiar axiom, “The dose makes the poison.”) But that’s not true for all chemicals, experts say. Some chemicals, such as those that mimic hormones, may actually be more dangerous at lower doses because the human body is exquisitely attuned to respond to minute amounts of natural hormones such as estrogen and testosterone.

And regulators haven’t required testing of mixtures of chemicals at all...Leroy Lowe, president of Canadian nonprofit Getting to Know Cancer and leader of the report published this week by the journal Carcinogenesis. The new report raises questions about whether this approach is adequate...Humans are exposed to about 80,000 man-made chemicals over their lifetimes, experts say. These chemicals are in the foods we eat, the water we drink and the air we breathe. "We live in a chemical soup,” said toxicologist Linda Birnbaum, director of the National Institute of Environmental Health Sciences, who was not involved in the new study.

The research team — a coalition of 174 researchers from 28 countries — set out to determine whether mixtures of these chemicals, at the very tiny concentrations found in the environment, could plausibly trigger the formation of cancerous tumors. They focused on 85 particular chemicals that were impossible to avoid in modern life, that were likely to disturb biological function and were not thought to pose cancer risks at the very low doses that people tend to ingest them.

The researchers scoured the scientific literature to understand how each of these chemicals could affect 10 important processes that are essential to cancer development. Among them: tumor-promoting inflammation, resistance to cell death and the formation of new blood vessels to feed malignant cells. In addition, they categorized whether each of the chemicals exerted biological effects at very low doses to which humans are ubiquitously exposed. (These doses are so small that they tend to be measured in parts per million or parts per billion.)
Of the 85 chemicals researchers examined, 50 were found to affect cancer-causing processes in the body, even at very low doses.

These 50 everyday chemicals included bisphenol A (used in manufacturing plastics), triclosan (often found in hand sanitizer and anti-bacterial soap) and atrazine (a commonly used herbicide). Since each of these chemicals affects different processes that could lead to cancer — bisphenol A makes cells less sensitive to signals to stop reproducing, for example, while atrazine encourages inflammation — it’s plausible that consuming mixtures of these chemicals is riskier than consuming any one individually.

More details about this report. From Science Daily: Cocktail of common chemicals may trigger cancer

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Again, more research finding that being overweight or obese is associated with an increased risk of breast cancer - specifically higher risk of invasive breast cancer in postmenopausal women. They found that the heavier the woman, the higher the risk, but the risk did not vary with hormone therapy use or race and ethnicity. From Medical Xpress:

Obesity associated with increased breast cancer risk in postmenopausal women

An analysis of extended follow-up data from the Women's Health Initiative clinical trials suggests that postmenopausal women who were overweight and obese had an increased risk of invasive breast cancer compared to women of normal weight, according to an article published online by JAMA Oncology. Obesity is a major public health problem in the United States and obesity has been associated with breast cancer risk in observational studies, systematic reviews and meta-analyses.

The Women's Health Initiative (WHI) protocol measured height and weight, baseline and annual or biennial mammograms, and breast cancer in 67,142 postmenopausal women enrolled from 1993 to 1998 with a median of 13 years of follow-up. There were 3,388 invasive breast cancers. Analysis by the authors found:

  • Women who were overweight (body mass index [BMI] 25 to < 30); obese, grade 1 (BMI 30 to < 35); and obese, grade 2 plus 3 (BMI > 35) had an increased risk of invasive breast cancer compared to women of normal weight (BMI < 25)
  • The risk was greatest for women with a BMI greater than 35; those women had a 58 percent increased risk of invasive breast cancer compared with women of normal weight (BMI < 25)....
  • Obesity was associated with markers of poor prognosis; women with a BMI greater than 35 were more likely to have large tumors, evidence of lymph node involvement and poorly differentiated tumors
  • Women with a baseline BMI of less than 25 who gained more than 5 percent of body weight during the follow-up period had an increased risk of breast cancer....

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Eating green leafy vegetables and other brightly colored fruits and vegetables containing vitamin K, lutein, folate and beta-carotene were linked to keeping the brain healthy in older adults and slowing cognitive decline. Researchers found that older people who ate one to two servings per day had the cognitive ability of a person 11 years younger than those who consumed none. From Science Daily:

Eating green leafy vegetables keeps mental abilities sharp

Something as easy as adding more spinach, kale, collards and mustard greens to your diet could help slow cognitive decline, according to new research. The study also examined the nutrients responsible for the effect, linking vitamin K consumption to slower cognitive decline for the first time...."Since declining cognitive ability is central to Alzheimer's disease and dementias, increasing consumption of green leafy vegetables could offer a very simple, affordable and non-invasive way of potentially protecting your brain from Alzheimer's disease and dementia."

The researchers tracked the diets and cognitive abilities of more than 950 older adults for an average of five years and saw a significant decrease in the rate of cognitive decline for study participants who consumed greater amounts of green leafy vegetables. People who ate one to two servings per day had the cognitive ability of a person 11 years younger than those who consumed none. When the researchers examined individual nutrients linked with slowing cognitive decline, they found that vitamin K, lutein, folate and beta-carotene were most likely helping to keep the brain healthy.

To conduct the study, Morris' research team gathered data from 954 participants from the Memory and Aging Project, which aims to identify factors associated with the maintenance of cognitive health. The participants, whose age averaged 81, reported their daily food and beverage intake by answering a detailed 144-item questionnaire at the beginning of the study.... They followed participants for 2 to 10 years, assessing cognition annually with a comprehensive battery of 19 tests and adjusted for age, sex, education, smoking, genetic risk for Alzheimer's disease and participation in physical activities when estimating the effects of diet on cognitive decline.

"With baby boomers approaching old age, there is huge public demand for lifestyle behaviors that can ward off loss of memory and other cognitive abilities with age," said Morris. "Our study provides evidence that eating green leafy vegetables and other foods rich in vitamin K, lutein and beta-carotene can help to keep the brain healthy to preserve functioning." In addition to green leafy vegetables, other good sources of vitamin K, lutein, folate and beta-carotene include brightly colored fruits and vegetables.

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Women: if you sit at work all day, and then you sit 6 or more hours during your leisure time, then you are at significantly greater risk of developing any cancer (compared to women who sit for fewer than 3 hours a day during leisure time). And the odds for certain cancers (multiple myeloma, ovarian cancer, and invasive breast cancer) are greatly increased. That 30 minutes at the gym doesn't cancel out the negative effects of sitting all day. But interestingly, this pattern didn't apply to men. From Medscape:

Leisure Time Sitting Increases Cancer Risk in Women

Women who sit 6 or more hours a day during their leisure time have a 10% greater risk of developing any cancer compared with women who sit for fewer than 3 hours a day. In addition, they are more likely to develop certain site-specific cancers, such as invasive breast cancer, ovarian cancer, and multiple myeloma. However, no similar pattern emerged for men.

"So when we think about independent risk factors for many types of cancer, and definitely for invasive breast cancer, you want to tell women to maintain a physically active lifestyle, to maintain a healthy weight, to limit their alcohol consumption, and now you also want to tell them to reduce their time spent sitting," she said.

The findings come from an analysis of data on some 69,260 men and 77,462 women enrolled in the American Cancer Society Cancer Prevention Study II Nutrition. All participants were cancer-free on enrolment. Between 1992 and 2009, 18,555 men and 12,236 women were diagnosed with cancer. On average, men were followed for 13.2 years, and women were followed for an average of 15.8 years.

"In women, leisure-time spent sitting was associated with a statistically significant higher risk of total cancer incidence...after adjustment for physical activity, [body mass index (BMI)], and other potential confounders," the authors report. Sitting 6 or more hours a day during leisure time was also associated with a 65% greater risk for multiple myeloma, a 43% greater risk for ovarian cancer, and a 10% greater risk for invasive breast cancer compared with women who sat less than 3 hours a day during leisure time. The association between longer sitting times and endometrial cancer was statistically significant before adjusting for BMI, but was attenuated when adjusted for BMI.

The same pattern was not seen in men in this study. Leisure time spent sitting was not associated with cancer risk in men, with the exception of an 11% higher risk associated with sitting time among obese men.

"There are a lot of individuals whom I would describe as 'an active couch potato.' " Dr Patel said. "People are going to the gym and maintaining a healthy weight, but they spend the majority of the rest of their time in sedentary activities — sitting at work, sitting in the car, sitting at home — so you really have to think not just of that 30 minutes a day where you are intentionally engaging in physical activity, but what does the rest of your day look like?"

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The key finding in this research (they studied mice, but this process would also happen in humans) is that: the presence of microbes specifically blocks the immune cells responsible for triggering allergies. Once again we see the importance of a healthy and diverse microbiota (the community of microbes within us), and the need to nurture it from birth. Studies have shown the importance of the first year of life in establishing a healthy microbiome and the development of the immune system. A number of studies have shown that the presence of pets or animals (e.g., living on a farm) reduces the incidence of allergies in children.From Science Daily:

Role of microbiota in preventing allergies

The human body is inhabited by billions of symbiotic bacteria, carrying a diversity that is unique to each individual. The microbiota is involved in many mechanisms, including digestion, vitamin synthesis and host defense. It is well established that a loss of bacterial symbionts promotes the development of allergies. Scientists at the Institut Pasteur have succeeded in explaining this phenomenon, and demonstrate how the microbiota acts on the balance of the immune system: the presence of microbes specifically blocks the immune cells responsible for triggering allergies. 

The hygiene hypothesis suggests a link between the decline in infectious diseases and the increase in allergic diseases in industrialized countries. Improvements in hygiene levels necessarily lead to reduced contact with microbes that is paralleled by an increased incidence in allergic and autoimmune diseases, such as type 1 diabetes.

Epidemiological studies have substantiated this hypothesis, by showing that children living in contact with farm animals -- and therefore with more microbial agents -- develop fewer allergies during their lifetime. Conversely, experimental studies have shown that administering antibiotics to mice within the first days of life results in a loss of microbiota, and subsequently, in an increased incidence in allergy.

However, until now, the biological mechanisms underlying this phenomenon remained unclear. In this study published in Science, the team led by Gérard Eberl (head of the Microenvironment and Immunity Unit at the Institut Pasteur) shows that, in mice, symbiotic intestinal microbes act on the immune system by blocking allergic reactions.

Several types of immune response can be generated in order to defend the organism. The presence of bacterial or fungal microbes provokes a response from immune cells known as type 3 cells. These immune cells coordinate the phagocytosis and killing of the microbes. However, in the case of infection by pathogenic agents that are too large to be handled by type 3 cells (such as parasitic worms and certain allergens), the cells that organize the elimination of the pathogen, but also allergic reactions, are known as type 2 cells.

In this study, scientists at the Institut Pasteur have shown that type 3 cells activated during a microbial aggression act directly on type 2 cells and block their activity. Type 2 cells are consequently unable to generate allergic immune responses. This work demonstrates that the microbiota indirectly regulates type 2 immune responses by inducing type 3 cells.

These results explain how an imbalance in microbiota triggers an exaggerated type 2 immune response normally used to fight large parasites, but that also leads to allergic responses....In terms of allergy treatment, a hitherto unexplored therapeutic approach consists therefore in stimulating type 3 cells by mimicking a microbial antigen in order to block allergy-causing type 2 cells.

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It turns out that we also have microbes called archaea living in and on our bodies. They are part of our microbiome (community of microbes living in and on us, which also includes bacteria, viruses, and fungi). Archaea constitute a domain or kingdom of single-celled microorganisms. These microbes are prokaryotes, meaning that they have no cell nucleus or any other membrane-bound organelles in their cells. Archaeal cells have unique properties that separate them from bacteria and eukaryotes. Archaea were initially classified as bacteria and thought to only exist in extreme environments (such as hot springs and salt lakes), and given the name archaebacteria, but this classification is now outdated. We now know that archaea live in less extreme places, including oceans, marshlands, animals, and humans.

So little is known about archaea that not even medical schools discuss this topic. This may be due to the fact that we currently don't know of any archaea that are human pathogens (that is, that cause illness) or parasitic. They are generally viewed as mutuals (the relationship is beneficial to both organisms) or commensals (they benefit, but don't help or harm the other organism). Humans appear to have low levels of archaea, and so far they have  been found in the human gut (part of digestion and metabolism), on the skin, and in subgingival dental plaque (and perhaps involved with periodontal disease). But studies rarely look for them. We don't know the importance or roles that they play in our bodies (but there are suspicions), but it turns out that drugs such as statins and the antibiotic metronidazole  are eliminating them.

Note that methanogens are archaea that excrete or produce methane as a metabolic byproduct in anoxic (no oxygen) conditions such as the gut. They help digest our food. The species Methanobrevibacter smithii  has been shown to be present in up to 95.7% of humans studied, and found to be the most abundant methanogen in the human gut, comprising up to as much as 10% of all anaerobes found in a healthy individual's colon. Anaerobes are organisms that require oxygen-free conditions to live. Some of the June 2015 article (by M. N. Lurie-Weinberger and U. Goph) excerpts from PLOS:

Archaea in and on the Human Body: Health Implications and Future Directions

Although they are abundant and even dominant members of animal microbiomes (microbiotas), from sponges and termites to mice and cattle, archaea in our own microbiomes have received much less attention than their bacterial counterparts. The fact that human-associated archaea have been relatively little-studied may be at least partially attributed to the lack of any established archaeal human pathogens. Clinically oriented microbiology courses often do not mention archaea at all, and most medical school and biology students are only aware of archaea as exotic extremophiles that have strange and eukaryotic-like molecular machinery. Since archaea have been known to be associated with the human gut for several decades, one would think that human microbiome studies may unravel new facets of archaea–human interactions...  ...continue reading "We Have Archaea In and On Our Bodies"