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Category: human microbiome

Published on Leave a comment on Viruses Live in The Guts of Healthy Babies

Yes, even healthy newborns have a diversity of viruses in the gut - this is their virome (community of viruses), and it undergoes changes over time. In fact, the entire infant microbiome (community of microbes) is highly dynamic and the composition of bacteria, viruses and bacteriophages changes with age. One interesting finding is that initially newborn babies have a lot of bacteriophages (viruses that infect bacteria), but that these decline over the first two years of age. From Medical Xpress:

Viruses flourish in guts of healthy babies

Bacteria aren't the only nonhuman invaders to colonize the gut shortly after a baby's birth. Viruses also set up house there, according to new research at Washington University School of Medicine in St. Louis. All together, these invisible residents are thought to play important roles in human health.The study, published online Sept. 14 in Nature Medicine, reports data from eight healthy infants and is one of the first surveys of viruses that reside in the intestine. The investigators analyzed stool samples to track how the babies' bacterial gut microbiomes and viromes changed over the first two years of life.

"We are just beginning to understand the interplay between all the different types of life within our gut," said senior author Lori R. Holtz, MD, assistant professor of pediatrics. "They are not stand-alone communities. We also are seeing that the environment of the infant gut is extremely dynamic, which differs from the relative stability that has been shown in adults."The earliest stool samples were taken at 1-4 days of life, and even at this early time point, Holtz noted, viruses were present.  ...continue reading "Viruses Live in The Guts of Healthy Babies"

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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.”

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 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)

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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"

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The following article excerpts are from the talk "Food and Brain" about the best foods for the brain, at the annual 2015 meeting of the American Psychiatric Association (APA). This is in the new emerging field of food psychiatry, or how certain foods and diet influence the brain. The data is emerging that we can positively influence mental health through dietary interventions. For ex.: recent work reported that adults who followed the Mediterranean dietary pattern the closest over 4.4 years had a significantly reduced risk of developing depression (by 40% to 60%).

One key comment was: "Perhaps diet is the closest we've come to prevention in psychiatry." Some foods that are especially beneficial for the brain: seafood, greens, nuts, legumes (beans) and occasional dark chocolate. Use smaller amounts of meat (more as flavorings rather than just eating huge chunks of it) on top of a plant based diet. Also mentioned were the benefits of turmeric (because of the curcumin in it) and rosemary. And focus on improving the whole dietary pattern rather than just eating or not eating certain foods.

Note that BDNF is Brain-derived neurotrophic factor. This is a protein that acts on the brain, the nervous system, and it is very important for learning, memory, and higher thinking. So increasing BDNF levels is good. And remember, what's good for the brain is also good for the body and microbes - it's all intertwined. From Medscape:

Beans, Greens, and the Best Foods For the Brain

Dr Ramsey, in collaboration with the new International Society for Nutritional Psychiatry, is in the process of developing a standardized "brain food diet." "Food is a very effective and underutilized intervention in mental health," he started off. "We want to help our patients have more resilient brains by using whole foods...by helping get patients off of processed foods, off of white carbohydrates, and off of certain vegetable oils."

Though the field is in its infancy, food psychiatry is increasingly being embraced by clinicians and researchers, as a paper published earlier this year in the Lancet Psychiatry attests. "Although the determinants of mental health are complex," the authors wrote, "the emerging and compelling evidence for nutrition as a crucial factor in the high prevalence and incidence of mental disorders suggests that diet is as important to psychiatry as it is to cardiology, endocrinology, and gastroenterology." ..."The data are very promising that we can positively influence mental health through dietary interventions," commented Dr Ramsey.

"Hominid diets have changed drastically through millions of years of evolution.,,,But only in the past 100 years has our diet drastically switched from a whole foods diet to one that is more processed and high in refined carbohydrates; that includes more vegetable fats rather than meat fats; and preservatives, emulsifiers, and other additives, which appear to have contributed to a decline in our collective health.

Early humans evolved in the African Rift Valley, which is near a seacoast. It's possible that whatever evolutionary spark occurred that made us human occurred here, in part due to reliable access to seafood—oysters in particular—which glutted our brains with omega-3 fatty acids and cholesterol (our brains are composed of 60% fat). Oysters and other mollusks are also very high in nutrients, including B12, which is commonly deficient in people consuming vegan or vegetarian diets and is necessary for myelin and neurotransmitter function. 

A number of studies have linked the Mediterranean diet (high in fish oils, nuts, and grains and including maybe a little red wine) with advantageous effects on neurologic and mental health. Dr Deans cited recent work reporting that adults who followed the Mediterranean dietary pattern the closest over 4.4 years had a significantly reduced risk of developing depression (40%-60%)....When taken together, most of these dietary pattern studies, which have been conducted all over the world, consistently show that traditional, pre-processed diets are the healthiest, including for the brain. ..."Eat the rainbow," he says, given that bold, bright colors in nature tend to signify valuable vitamins and phytonutrients (the reds, purples, and greens in particular).

Seafood: Seafood is packed with brain-healthy omega-3 fatty acids. These healthy fats are also abundant in plants like chia and flax, but plant-based sources aren't as efficiently converted to docosahexaenoic acid (DHA), an important structural component of neuronal membranes. DHA also influences the expression of brain-derived neurotrophic factor (BDNF), which can benefit people who have mood and anxiety disorders. Bivalves like mussels, oysters, and clams are the top source of vitamin B12 as well as zinc: Six oysters (only about 10 calories each) provide 240% of our recommended daily B12 intake and 500% of our recommended zinc intake! Seafood is also a leading dietary source of vitamin D (we don't get it all from the sun) as well as iodine and chromium. Although many people worry about mercury in fish, Dr Ramsey provided an easy way around the concern: Eat small fish like sardines, anchovies, and herring, which typically don't accumulate toxic levels.

Leafy greens: A great base for a brain-food diet, leafy greens are a good source of fiber, folate (derived from the wordfoliage), magnesium, and vitamin K. Perhaps surprising, kale, mustard greens, and bok choy provide the most absorbable form of calcium on the planet, more so than milk. Greens also provide flavanols and carotenoids that have beneficial epigenetic influences (eg, including upping hepatic toxin processing). 

Nuts:... Nuts are packed with healthy monounsaturated fats. They help keep us full and also aid in absorbing fat-soluble nutrients. Nuts also provide fiber as well as minerals like manganese and selenium. A serving of 22 almonds (just 162 calories) contains 33% of our recommended vitamin E, plenty of protein, and minerals, including iron. One study from 2013 found that the Mediterranean diet augmented with nuts is associated with significantly higher BDNF levels in patients with depression.

Legumes: Dr Ramsey is pro-meat, but he acknowledges that many people are eating far too much and the wrong types of meat, and that nuts and legumes are a great alternative source of protein and nutrients...Some data suggest that vegan and vegetarian diets are associated with improved mood. But as previously mentioned, these dietary patterns can result in B12 deficiency, which has been associated with brain atrophy and developmental delay. Hence, supplementation is important in this population. Vegetarianism has also been linked with depression, anxiety, and eating disorders, as well as increased healthcare utilization and worse quality of life. These negative associations also could be due to the fact that it's harder to absorb nutrients like zinc, iron, and certain omega-3s from plants.

"The notion that the vegan diet is the healthiest diet on the planet is probably incorrect," said Dr Ramsey, before explaining that he just feels that we should approach meat in our diets differently....We want to help patients use beef and seafood more as flavorings on top of a plant-based diet." A modest amount of meat in the diet has its benefits, including nutrient availability: Hemoglobin-derived iron is up to 40% more absorbable than plant-based iron. Unlike most plants, meat provides all of the amino acids necessary for protein synthesis. Dr Ramsey emphasized the importance of seeking out leaner, grass-fed meats if one has the means.

The understanding of how microbiota contribute to our mental and medical well-being is rapidly advancing....One of the most powerful interventions to alter our microbiome is diet. Research shows that stressed mice experienced changes in the gastrointestinal microbiota, reflecting the gut-brain relationship. There are 260 million neurons connecting the gut and the brain; furthermore, many commensal gut bacteria make neurotransmitters and communicate with the brain via the vagus nerve....Although the science of probiotic therapies is relatively young, it's clear that these commensal organisms co-evolved with us and are adapted to our diet.

Finally, to close out the session, Dr Ramsey returned to the stage and asked, "So, can you eat to build a better brain? We think that you can if you focus on dietary patterns and not a single food here or there." He also reminded the audience to help their patients identify and increase their consumption of nutrient-dense foods and to "eat the rainbow,"..."I don't know of anything else that can potentially decrease the risk of depression in a population by 40%," he concluded. "Perhaps diet is the closest we've come to prevention in psychiatry."

...Evidence suggests that curcumin, an ingredient in turmeric, increases BDNF. Other research has found that populations that eat more curry have a decreased risk for dementia, while rosemary extract may help prevent cognitive impairment. "Many spices seem to have healing properties," Dr Ramsey commented.

Although the "Food and the Brain" session at the American Psychiatric Association annual meeting focused on what to eat in the interest of brain health, intermittent fasting might also be beneficial for the brain. In addition to helping maintain a healthy weight, fasting induces ketosis. Ketone metabolism has been shown to be beneficial for the brain and improve cognition in patients with mild cognitive impairment or Alzheimer disease. Keep in mind that fasting can come with risks for some people, particularly diabetics, and should be discussed with a healthcare provider.