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Category: microbes

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Published on 6 Comments on Update on Sinusitis Treatment

[UPDATE:  I added an Oct. 2018 update to the post The One Probiotic That Treats Sinusitis, which was originally posted in January 2015.]  Updates incorporate the latest information about treatments and products with Lactobacillus sakei  (kimchi brands, the probiotic Lacto Sinus , the sausage starter culture Bactoferm F-RM-52, etc.). According to research by Abreu et al (2012), Lactobacillus sakei is a bacteria or probiotic (beneficial bacteria) that chronic sinusitis sufferers lack and which treats chronic sinusitis. Chronic sinusitis sufferers also don't have the bacteria diversity in the sinuses that healthy people have.

Many thanks to those who have written to me about their experiences with L. sakei products and sinusitis treatment.  Please keep the updates, results, and progress reports coming. If you have had success with other kimchi brands, please let me know so that I can add it to the list. And I also want to hear if other probiotics work or don't work, or if you have found other sources of Lactobacillus sakei or new ways to use L. sakei. It all adds to the knowledge base which I will continue to update.  You can Comment after posts, the Sinus Treatment Summary page, on the CONTACT page, or write me privately (see CONTACT page).

It is now over 2 1/2 years since my family (4 people) successfully treated ourselves with Lactobacillu sakei for chronic sinusitis and acute sinusitis. We feel great! With each passing year we can tell that our sinus microbial community is bettter, and levels of inflammation are down. As a consequence, we are getting fewer colds or viruses than ever. And best of all - no antibiotics taken in over 2 1/2 years! Yes, Lactobacillus sakei absolutely works as a treatment for sinusitis.

[Read the updated post: The One Probiotic That Treats Sinusitis - with Oct. 2018 update]

Published on Leave a comment on Fungi and Bacteria in Household Dust

Another article from results of the crowdsourced study in which household dust samples were sent to researchers at the University of Colorado from approximately 1200 homes across the United States. Some findings after the dust was analyzed: differences were found in the dust of households that were occupied by more males than females and vice versa, indoor fungi mainly comes from the outside and varies with the geographical location of the house, bacteria is determined by the house's inhabitants (people, pets, and insects), clothes do not prevent the spread of bacteria from our bodies, and dogs and cats had a dramatic influence on bacteria in the home. In other words: where you live determines the fungi in the house and who you live with determines the bacteria in the house. From Discovery News:

Household Dust Packed With Thousands of Microbes

Household dust is full of living organisms that are determined, in large part, by where the home is located and who is living in it, finds a new study that includes some surprising revelations. Homes with a greater ratio of male occupants, for example, were found to contain large amounts of skin and fecal-associated bacteria, while women-dominated households contained an abundance of vaginally shed bacteria that somehow wound up in dust.

He and his colleagues used DNA sequencing and high tech imaging to analyze dust samples from approximately 1,200 homes across the United States. They used volunteers to help collect the material. They discovered that indoor fungi mostly originates outside of the home, such that the geographical location of any home strongly predicts the types of fungi existing within dust.“If you want to change the types of fungi you are exposed to in your home, then it is best to move to a different home, preferably one far away,” Fierer and his team said.

Bacteria, on the other hand, were largely predicted by the home’s possible inhabitants, including humans, pets and even insects. Fierer said, “Our bodies are clearly the source for many bacteria that end up in our homes.” The researchers suspect that body size, relative abundance, and hygiene practices are why men tend to shed more Corynebacterium and Dermabacter (the skin-associated species), as well as the poop-associated Roseburia.

The vaginal-linked bacteria Lactobacillus, discovered in homes with a larger ratio of women, provides evidence that clothes do not fully contain the spread of microorganisms produced by our bodies. Members of this genus are actually thought to protect against allergies and asthma, based on earlier research, but further studies are needed to confirm how this, and other bacteria found in dust, impact human health.

Dogs and cats had such a dramatic effect on dust bacterial communities that the researchers could predict, with around 92 percent accuracy, whether or not such animals were in the home, just based on bacteria alone....So far, the news is good for dog lovers, as he pointed out that “previous work conducted by other groups has shown that living with a dog at a young age can actually reduce allergies.”

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This is a nice study showing cause and effect:  6 hours of sleep or less at night lowers the body's resistance so that the person is more likely to catch a cold virus. From Science Daily:

Short sleepers are four times more likely to catch a cold

A new study led by a UC San Francisco sleep researcher supports what parents have been saying for centuries: to avoid getting sick, be sure to get enough sleep. The team, which included researchers at Carnegie Mellon University and University of Pittsburgh Medical Center, found that people who sleep six hours a night or less are four times more likely to catch a cold when exposed to the virus, compared to those who spend more than seven hours a night in slumber land.

Scientists have long known that sleep is important for our health, with poor sleep linked to chronic illnesses, disease susceptibility and even premature death. Prather's previous studies have shown that people who sleep fewer hours are less protected against illness after receiving a vaccine. Other studies have confirmed that sleep is among the factors that regulate T-cell levels.

Researchers recruited 164 volunteers from the Pittsburgh, PA, area between 2007 and 2011. The recruits underwent two months of health screenings, interviews and questionnaires to establish baselines for factors such as stress, temperament, and alcohol and cigarette use. The researchers also measured participants' normal sleep habits a week prior to administering the cold virus, using a watch-like sensor that measured the quality of sleep throughout the night.

The researchers then sequestered volunteers in a hotel, administered the cold virus via nasal drops and monitored them for a week, collecting daily mucus samples to see if the virus had taken hold. They found that subjects who had slept less than six hours a night the week before were 4.2 times more likely to catch the cold compared to those who got more than seven hours of sleep, and those who slept less than five hours were 4.5 times more likely.

Published on Leave a comment on Vaccines to Battle Tick Diseases?

I recently posted on ways the number of  ticks can be reduced in a backyard. Now an article on vaccines being developed to battle tick borne diseases, especially Lyme disease. However, the bad news is that ticks now transmit 16 diseases in the US (including anaplasmosis, babesiosis, ehrlichiosis), while vaccines typically only focus on one disease at a time. Tick borne diseases are on the rise throughout the world.

We all know about Lyme disease (which is also a problem in Europe, China, and Mongolia), but in parts of Africa, the Middle East, Asia and southern Europe, ticks can spread Crimean–Congo haemorrhagic fever, which is fatal 40% of the time! And while some researchers are focusing on human vaccines, some are focusing on vaccines for mice. Big problem: would we really be able to give the vaccine to enough mice to make a difference? I really like the idea of a vaccine that hampers the ability of ticks to feed on humans. From Nature:

The new war on Lyme and other tick-borne diseases

Williams is testing whether vaccinating mice against Borrelia burgdorferi, the bacterium that causes Lyme disease in the United States, can reduce the proportion of ticks that are infected. ....Borrelia burgdorferi infects an estimated 329,000 people in the United States each year, according to the US Centers for Disease Control and Prevention (CDC) in Atlanta, Georgia. And although most people who get prompt treatment recover quickly — Williams has had Lyme three times — up to one in five develops long-term and potentially life-threatening symptoms, including heart, vision or memory problems, or debilitating joint pain. ...continue reading "Vaccines to Battle Tick Diseases?"

Published on Leave a comment on The Fungi That Live On Our Skin

This article discusses the fungi living on our skin. Recent research (using state of the art genetic analysis) has found that healthy people have lots of diversity in fungi living on their skin. Certain areas seem to have the greatest populations of fungi: in between toes (average of 40 species), the heel (average of 80 species), toenails (average of 80 species), and the genitals. Currently it is thought that there are "intricate interactions between fungi and immune cells on the skin surface", and that often this mutualistic relationship is beneficial, but at other times dysbiosis (when the microbial community is unbalanced or out of whack) can lead to diseases. If the populations get too unbalanced (e.g., antibiotics can kill off bacteria, and then an increase in fungi populations take their place) then ordinarily non-harmful fungi can become pathogenic. Note that: Mutualistic relationship is a relationship between two different species of organisms in which both benefit from the association. From E-Cronicon:

From Head to Toe: Mapping Fungi across Human Skin

The human microbiota refers to the complex aggregate of fungi, bacteria and archaea, found on the surface of the skin, within saliva and oral mucosa, the conjunctiva, the gastrointestinal. When microbial genomes are accounted for, the term microbiome is deployed. In recent years the first in-depth analysis, using sophisticated DNA sequencing, of the human microbiome has taken place through the U.S. National Institutes of Health led Human Microbiome Project. 

Many of the findings have extended, or even turned upside down, what was previously known about the relationship between humans and microorganisms. One of the most interesting areas related to fungi, especially in advancing our understanding about fungal types, locations and numbers and how this affects health and disease....some parts of the body have a greater prevalence of bacteria (such as the arms) whereas fungi are found in closer association with feet.  

A variety of bacteria and fungi are found on the typical 2 square meters that represent the surface of the skin, and within the deeper layers, of a typical adult. These can be considered as ‘residential’ (that is ordinarily found) or ‘transient’ (carried for a period of time by the host.) The resident microorganism types vary in relation to skin type on the human body; between men and women; and to the geographical region in which people live.

The first observation is that many locations across the skin contain considerable populations of fungi. Prime locations, as reported by Findley and colleagues, were inside the ear canal and behind the ear, within the eyebrows, at the back of the head; with feet: on the heel, toenails, between the toes; and with the rest of the body notable locations were the forearm, back, groin, nostrils, chest, palm, and the elbow.

The second observation is that several different species are found, and these vary according to different niches. Focusing on one ecological niche, a study by Oyeka found that the region between toes, taken from a sample of 100 people, discovered 14 genera of fungi. In terms of the individual species recovered, a relatively high number were observed (an average of 40 species.)....the greatest varieties of fungi are to be found on the heel (approximately 80 different species.) The second most populous area is with the toes, where toe nails recover around 80 different species.....With the genitals, where early investigations had suggested that Candida albicans was the most commonly isolated yeasts. However, an investigation of 83 patients by Bentubo., et al.  showed more variety, with high recoveries of Candida parapsilosis, Rhodotorulamucilaginos, Rhodotorulaglutinis, Candida tropicalis and Trichosporoninkin.

The importance of the investigative work into the human skin fungi helps medical researchers understand more fully the connections between the composition of skin-fungi and certain pathologies. Here the intricate interactions between fungi and immune cells on the skin surface is of importance; often this mutualistic relationship is beneficial, at other times dysbiosis can lead to the manifestation of diseases especially when there is a breakdown of the mutualistic relationship.

Changes to fungal diversity can be associated with several health conditions, including atopic dermatitis, psoriasis, acne vulgaris and chronic wounds. Diversity can alter through the over-use of antibiotics, where a decline in bacterial numbers can lead to a rise in fungal populations occupying the same space.

Moreover, research has indicted that patients who have a primary immunodeficiency are host to more populous fungal communities than healthy people. Here it is suggested that the weaknesses in the immune system allow higher numbers of fungi to survive, and, in turn these weaknesses can lead some ordinarily non-harmful species to become pathogenic. Such opportunistic fungi include species of Aspergillus and Candida.

Published on Leave a comment on Some Ways to Get Rid of Ticks

Nice article about ticks, tickborne diseases (of which Lyme disease is one), and possible strategies for coping - whether getting rid of ticks in your yard, or minimizing risk. The only thing I disagreed with is that the author gives the time for transmission of a tick borne disease as needing over 24 hours of the tick being attached (this number is frequently given by authorities). Others disagree (as do I based on experience), and a recent article on transmission time after attachment stated that in animal research, transmission can occur in <16 hours. Some human studies also found transmission times of less than 24 hours (and as little as 6 hours of tick attachment), but so far the minimum attachment time for transmission of infection has never been established. Read the complete article for more pet and tick advice. From Mother Earth News:

How to Get Rid of Ticks and Prevent Lyme Disease 

About 300,000 people are diagnosed with Lyme disease every year, according to new estimates from the Centers for Disease Control and Prevention (CDC). Lyme disease is caused by bacteria that multiply in the bodies of ticks, people and animals, including mice, deer and dogs....  the tiny blacklegged deer tick, which is the most common transmitter of Lyme disease.

These deer ticks pick up Lyme bacteria (Borrelia burgdorferi) when they feed on the blood of infected mice, chipmunks and other hosts. Infected ticks in both the nymphal and adult life stages can then transfer the Lyme bacteria to humans if they latch on for a meal and feed for approximately 36 hours or more. Lyme disease is highly treatable when it’s detected early, but devastating when the infection goes unnoticed for more than a few months.

Let Poultry Help with Tick Prevention  Leafy wooded areas and grassy meadows are the preferred habitats for blacklegged deer ticks and American dog ticks, which both spend their larval stage in leaf litter, their nymphal stage on small animals, and their adult stage in tall grass or other shrubby vegetation. People have learned how to get rid of ticks by keeping foraging chickens and guinea fowl on their property. In April 2015, we launched the MOTHER EARTH NEWS Chickens and Ticks Survey, and responses revealed that: 71 percent had an existing tick problem before they got poultry, 78 percent kept poultry that helped control or eliminate ticks within the birds’ feeding range, 46 percent experienced a drop in tick populations within a month after getting poultry; 45 percent saw good control after several months to a year.Many respondents noted that small bantam chickens and game hens can get into tight spots where larger birds can’t fit, resulting in better tick control....

Permethrin-Treated Clothes and ‘Tick Tubes’  If you live in one of the 13 states where Lyme disease risk is highest, learning how to get rid of ticks should be a top priority. You might want to consider using permethrin, a non-organic pesticide that repels and kills ticks. Permethrin is more potent and persistent than the organic materials we usually recommend. We suggest using a formula designed to be applied to clothing rather than misters, sprayers, foggers or other permethrin products. Clothing products that are pre-treated with permethrin are available, or you can buy permethrin with instructions for how to use it to treat your clothes. Take care to not expose kids to this pesticide...The EPA also classified permethrin as “likely to be carcinogenic to humans,” so weigh the risk of infrequent exposure to the risk of Lyme disease in your area.

You might also consider permethrin-infused “tick tubes,” which are designed to kill ticks on white-footed mice as well as chipmunks and rats, the main animals from which ticks become infected with Lyme. The tick tubes offer nesting materials impregnated with the pesticide to such critters. The animals then take the material back to their nests, where it kills any ticks that may have latched on to the adults and their young. The small amount of permethrin used in tick tubes is not water-soluble, so it’s not likely to end up anywhere but in a nest. Sold commercially as Damminix Tick Tubes, these devices are easy to make yourself....

Herbal Tick Repellents   Many of our survey respondents reported that they apply veterinary-prescribed tick preventatives on their dogs and cats, but would prefer more organic repellents. Two plant-based aromatics — sweet-scented “rose” geranium (Pelargonium graveolens) essential oil and eastern red cedar (Juniperus virginiana; also known as “red cedarwood”) essential oil — were repeatedly recommended by readers who use them as spray-on repellents for pets and family members alike....Both geranium essential oil and eastern red cedar essential oil have proven to be successful repellents against ticks in various life stages, according to the Journal of Agricultural and Food Chemistry and the Journal of Medical Entomology, respectively.

Using full-strength essential oil can injure human skin and overwhelm pets’ sensitive noses, so follow this simple recipe when making a liquid anti-tick spray: In an 8-ounce spray bottle, combine 10 to 20 drops of rose geranium or eastern red cedar essential oil with 1 teaspoon of vodka or rubbing alcohol. Fill the rest of the bottle with water and shake to combine. The spray can be applied to your skin or clothing....

More Tick Prevention Tricks Fencing out deer, the primary host of adult Lyme-infected ticks, can help prevent ticks from reaching your land. Low-cost, plastic-mesh deer fencing is available online and at farm stores. Ticks rarely inhabit lawns that are mowed regularly. Raking up leaves and composting them deprives overwintering ticks of shelter.

When hiking where tick populations are high, stay on the trails and dress defensively — pull your socks up over your pants. When only shorts will do, some people cut off the ankle sections of old socks, spray them with a repellent, and wear the tubes around their calves like tick-deterring leg warmers.

A study published in Experimental and Applied Acarology found that spraying outdoor areas with Safer-brand organic insecticidal soap in spring, when blacklegged deer tick nymphs are active, can provide treatment that is equally as effective as spraying with the insecticide chlorpyrifos.

After you’ve been outdoors, check your dogs for any ticks that may have latched on, and then make your way to a hot, soapy shower followed by a careful body check. You can kill any ticks that have attached to your clothing by immediately putting your clothes into the dryer for 15 minutes on the hottest setting, and then washing them. Most ticks are sensitive to dry heat, but may survive even the hottest wash. 

Published on Leave a comment on A Mix of Bacteria Protect Against Infections?

More research that supports that both more variety (diversity) of microbes and the actual mix of types of microbes are involved in a healthy gut microbiome. Healthy communities don't have just one important species of bacteria, but a mix of bacteria, and some mixes of bacteria work better than others in preventing infections. One can say that some mixes of bacteria are "protective" against infections. And once again, antibiotics screw up the microbial communities and cause imbalances. This study was done in mice looking at gut bacteria and Clostridium difficile (which kills about 14,000 Americans annually), but they are now continuing this research in humans. From Medical Xpress:

It takes a village... to ward off dangerous infections? New microbiome research suggests so

Like a collection of ragtag villagers fighting off an invading army, the mix of bacteria that live in our guts may band together to keep dangerous infections from taking hold, new research suggests. But some "villages" may succeed better than others at holding off the invasion, because of key differences in the kinds of bacteria that make up their feisty population, the team from the University of Michigan Medical School reports. The researchers even show it may be possible to predict which collections of gut bacteria will resist invasion the best—opening the door to new ways of aiding them in their fight.

Working in mice, the team studied one of the most dangerous gut infections around: Clostridium difficile, which kills more than 14,000 Americans a year. C-diff also sickens hundreds of thousands more, mostly hospital patients whose natural collection of gut bacteria—their gut microbiome—has been disturbed by antibiotics prescribed to protect them from other infections.

In a new paper published in the journal mBIO, the team reports the results from tests of seven groups of mice that were given different antibiotics, then were exposed to C-diff spores. The scientists used advanced genetic analysis to determine which bacteria survived the antibiotic challenge, and looked at what factors made it most likely that C-diff would succeed in its invasion.The team also developed a computer model that accurately predicted C-diff's success rate for other mice in the study, based solely on knowing what bacteria the mice had in their natural gut 'village'. The model succeeded 90 percent of the time.

"We know that individual humans all have different collections of gut bacteria, that your internal 'village' is different from mine. But research has mostly focused on studying one collection at a time," says Patrick D. Schloss, Ph.D., the U-M associate professor of microbiology and immunology who led the team. "By looking at many types of microbiomes at once, we were able to tease out a subset of bacterial communities that appear to resist C-diff colonization, and predict to what extent they could prevent an infection."

Schloss, who is a key member of the Medical School's Host Microbiome Initiative, notes that no one species of bacteria by itself protected against colonization. It was the mix that did it. And no one particular mix of specific bacteria was spectacularly better than others - several of the diverse "villages" resisted invasion.

Resistance was associated with members of the Porphyromonadaceae, Lachnospiraceae, Lactobacillus, Alistipes, and Turicibacter families of bacteria. Susceptibility to C. difficile, on the other hand, was associated with loss of these protective species and a rise in Escherichia or Streptococcus bacteria. "It's the community that matters, and antibiotics screw it up," Schloss explains. Being able to use advance genetic tools to detect the DNA of dozens of different bacteria species, and tell how common or rare each one is in a particular gut, made this research possible.

A Clostridium difficile cell.                                                     Credit: Centers for Disease Control and Prevention

Published on Leave a comment on Why Breastfeeding Is So Important

There has been much discussion recently about breastfeeding - why is it so important? Is it really better than formula? The answer is: YES, breastfeeding is the BEST food for the baby, and for a number of reasons. Not only is it nature's perfect food for the baby, but it also helps the development of the baby's microbiome or microbiota (the community of microbes that live within and on humans).

Specifically, breast milk transmits about 700 species of bacteria to the baby - bacteria that are important in developing the baby's microbiota, bacteria that are important for the baby's development and health in many ways (including the immune system). No formula does that. Not even close.

There is obviously much we don't know or understand yet, but finding 700 species in breast milk is a big deal. The most variety was in colostrum (the first milk), but even after 6 months (mature milk) they found hundreds of species of bacteria. What was also interesting was that the bacteria species in the breast milk varied whether the baby was born by vaginal birth, unplanned cesarean, or planned cesarean (this last had a somewhat different bacterial community which persisted through the 6 months of the study).

By the way, in the original study, the authors made a point of saying that the 700 bacteria species are NOT bacterial contaminants, but meant to be there! (for those who want to sterilize and pasteurize everything because they think that all bacteria are bad).

This study is from 2013, but well worth reading. From Science Daily: Breast milk contains more than 700 species of bacteria, Spanish researchers find

Researchers have traced the bacterial microbiota map in breast milk and identified the species of microbes taken from breast milk by infants. The study has revealed a larger microbial diversity than originally thought: more than 700 species. The breast milk received from the mother is one of the factors determining how the bacterial flora will develop in the newborn baby.

A group of Spanish scientists have now used a technique based on massive DNA sequencing to identify the set of bacteria contained within breast milk called microbiome.  Colostrum is the first secretion of the mammary glands after giving birth. In some of the samples taken of this liquid, more than 700 species of these microorganisms were found, which is more than originally expected by experts.

"This is one of the first studies to document such diversity using the pyrosequencing technique (a large scale DNA sequencing determination technique) on colostrum samples on the one hand, and breast milk on the other, the latter being collected after one and six months of breastfeeding," explain the coauthors, María Carmen Collado, researcher at the Institute of Agrochemistry and Food Technology (IATA-CSIC) and Alex Mira, researcher at the Higher Public Health Research Centre (CSISP-GVA).

The most common bacterial genera in the colostrum samples were Weissella, Leuconostoc, Staphylococcus, Streptococcus and Lactococcus. In the fluid developed between the first and sixth month of breastfeeding, bacteria typical of the oral cavity were observed, such as Veillonella, Leptotrichia and Prevotella....The study also reveals that the milk of overweight mothers or those who put on more weight than recommended during pregnancy contains a lesser diversity of species.

The type of labour also affects the microbiome within the breast milk: that of mothers who underwent a planned caesarean is different and not as rich in microorganisms as that of mothers who had a vaginal birth. However, when the caesarean is unplanned (intrapartum), milk composition is very similar to that of mothers who have a vaginal birth.

These results suggest that the hormonal state of the mother at the time of labour also plays a role: "The lack of signals of physiological stress, as well as hormonal signals specific to labour, could influence the microbial composition and diversity of breast milk," state the authors.

And yes, what you eat while breastfeeding has an effect on the breast milk. From Science Daily:  Carotenoid levels in breast milk vary by country, diet

A Purdue University-led analysis of breast milk concludes that levels of health-promoting compounds known as carotenoids differ by country, with the U.S. lagging behind China and Mexico, a reflection of regional dietary habits. Carotenoids are plant pigments that potentially play functional roles in human development and are key sources of vitamin A, an essential component of eye health and the immune system.

The carotenoid content of a woman's breast milk is determined by her consumption of fruits and vegetables such as squash, citrus, sweet potatoes and dark, leafy greens.

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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)

Published on

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.