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Category: human microbiome

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.

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This new research suggests possible future treatments in treating urinary tract infections (UTIs) by manipulating the person's diet and so influencing gut microbes and urinary pH (how acidic is the urine). These possible future treatments are different than what others are looking for, which are bacteria (probiotics) that one can take to prevent or treat UTIs. (Earlier posts on treating UTIs are here and here,)

The researchers found that during UTIs, humans secrete siderocalin which helps the body fight infection by depriving bacteria of iron (a mineral necessary for bacterial growth), and that samples that were less acidic, and closer to the neutral pH of pure water, showed higher activity of the protein siderocalin and were better at restricting bacterial growth than the more acidic samples.

The researchers found that the presence of small metabolites called aromatics, which vary depending on a person's diet, also contributed to variations in bacterial growth. Samples that restricted bacterial growth had more aromatic compounds, and urine that permitted bacterial growth had fewer. Stay tuned for follow-up research. 

One of the researchers, Dr. Jeffrey P. Henderson, pointed out that physicians already know how to raise urinary pH with things like calcium supplements, and alkalizing agents are already used in the U.K. as over-the-counter UTI treatments. But knowing how to encourage the metabolites is trickier, but will involve dietary changes. Some good food sources include those rich in antioxidants: coffee, tea, colorful berries, cranberries, and red wine.

From Science Daily: A person's diet, acidity of urine may affect susceptibility to UTIs

The acidity of urine -- as well as the presence of small molecules related to diet -- may influence how well bacteria can grow in the urinary tract, a new study shows. The research may have implications for treating urinary tract infections, which are among the most common bacterial infections worldwide. Urinary tract infections (UTIs) often are caused by a strain of bacteria called Escherichia coli (E. coli), and doctors long have relied on antibiotics to kill the microbes. But increasing bacterial resistance to these drugs is leading researchers to look for alternative treatment strategies.

"Many physicians can tell you that they see patients who are particularly susceptible to urinary tract infections," said senior author Jeffrey P. Henderson​, MD, PhD,...With this in mind, Henderson and his team, including first author Robin R. Shields-Cutler, a graduate student in Henderson's lab, were interested in studying how the body naturally fights bacterial infections. They cultured E. coli in urine samples from healthy volunteers and noted major differences in how well individual urine samples could harness a key immune protein to limit bacterial growth. "We could divide these urine samples into two groups based on whether they permitted or restricted bacterial growth," Henderson said. "Then we asked, what is special about the urine samples that restricted growth?"

The urine samples that prevented bacterial growth supported more activity of this key protein, which the body makes naturally in response to infection, than the samples that permitted bacteria to grow easily. The protein is called siderocalin, and past research has suggested that it helps the body fight infection by depriving bacteria of iron, a mineral necessary for bacterial growth. Their data led the researchers to ask if any characteristics of their healthy volunteers were associated with the effectiveness of siderocalin.

"Age and sex did not turn out to be major players," Shields-Cutler said. "Of all the factors we measured, the only one that was really different between the two groups was pH -- how acidic or basic the urine was."Henderson said that conventional wisdom in medicine favors the idea that acidic urine is better for restricting bacterial growth. But their results were surprising because samples that were less acidic, closer to the neutral pH of pure water, showed higher activity of the protein siderocalin and were better at restricting bacterial growth than the more acidic samples.

Importantly, the researchers also showed that they could encourage or discourage bacterial growth in urine simply by adjusting the pH, a finding that could have implications for how patients with UTIs are treated.

"Physicians are very good at manipulating urinary pH," said Henderson, who treats patients with UTIs. "If you take Tums, for example, it makes the urine less acidic. But pH is not the whole story here. Urine is a destination for much of the body's waste in the form of small molecules. It's an incredibly complex medium that is changed by diet, individual genetics and many other factors."

After analyzing thousands of compounds in the samples, the researchers determined that the presence of small metabolites called aromatics, which vary depending on a person's diet, also contributed to variations in bacterial growth. Samples that restricted bacterial growth had more aromatic compounds, and urine that permitted bacterial growth had fewer.

Henderson and his colleagues suspect that at least some of these aromatics are good iron binders, helping deprive the bacteria of iron. And perhaps surprisingly, these molecules are not produced by human cells, but by a person's gut microbes as they process food in the diet."Our study suggests that the body's immune system harnesses dietary plant compounds to prevent bacterial growth," Henderson said. "We identified a list of compounds of interest, and many of these are associated with specific dietary components and with gut microbes."

Indeed, their results implicate cranberries among other possible dietary interventions. Shield-Cutler noted that many studies already have investigated extracts or juices from cranberries as UTI treatments but the results of such investigations have not been consistent.

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Drawing of colon seen from front (the appendix is colored red). Credit: Wikipedia.

For more than 100 years, the standard treatment for appendicitis has been surgery. Now a large Finnish study provides the best evidence to date that most patients can be treated with antibiotics alone.

How did the usual treatment of doing an appendectomy (appendix removal) arise? In 1886 Dr. Reginald Fitz, while investigating pelvic infections (which resulted in many deaths in those days), decided that an inflamed appendix progresses from a mild inflammation, to gangrene, then perforation, which would result in pelvic abscess.

This reason for an appendectomy (that it would prevent serious infection) became established in medical thought and still guides appendicitis management today. But nowadays we have antibiotics! And the researchers noted that some cases resolved on their own without any treatment.

And instead of the prevailing view for many years that the appendix is a "vestigial organ with no purpose",  it turns out that the appendix has a great reason for existence. It seems to provide a safe haven for good bacteria when gastrointestinal illness flushes those bacteria from the rest of the intestines. This reservoir of gut microbes then repopulates the digestive system following the illness.

It makes me wonder why some people get appendicitis and others don't - do they have inflammation for some reason so that their bacterial communities are out of whack (dysbiosis)? Would dietary changes help prevent recurrences?

From the NY Times: Antibiotics Are Effective in Appendicitis, Study Says

For more than 100 years, the standard treatment for appendicitis has been surgery. Now a large Finnish study provides the best evidence to date that most patients can be treated with antibiotics alone. The study, published Tuesday in JAMA, involved 530 patients aged 18 to 60 who agreed to have their treatment — antibiotics or surgery — decided at random. Three out of four who took antibiotics recovered easily, the researchers found. And none who had surgery after taking antibiotics were worse off for having waited.

The new study comes amid growing questions about the routine use of surgery to treat appendicitis, which strikes about 300,000 Americans a year, afflicting one out of 10 adults at some point in their lives.

The results only apply to uncomplicated appendicitis, stressed Dr. Paulina Salminen, a surgeon at Turku University Hospital in Finland and lead author of the new study. She and her colleagues excluded from their trial the 20 percent of patients with complicated cases — people with perforated appendices or abdominal abscesses, and those with a little, rock like blockage of the appendix called an appendicolith.

In the 1950s, soon after antibiotics were discovered, some doctors reported success using them to treat patients with appendicitis. But, Dr. Livingston wrote in his editorial, “So powerful is the perceived benefit of appendectomy for appendicitis that surgical treatment for appendicitis remains unquestioned, with seemingly little interest in studying the problem.”

Dr. Livingston also found that most appendices that perforate have already done so by the time the patient shows up at an emergency room. Those that have not perforated when the patient seeks medical help almost never do so. People with so-called uncomplicated appendicitis, he concluded, seem to have a different disease — one that can be treated with antibiotics.

“The reason we take the appendix out and do it as an emergency is the belief, dating back to 1886, that the appendix will eventually become gangrenous and cause a pelvic abscess,” Dr. Livingston said.

Even with the results of the Finnish study, many questions remain. A person who has had one episode of appendicitis is at higher than usual risk for another....Accumulating data has led other experts to raise an even more controversial idea: Perhaps antibiotics aren’t always necessary, either. It is possible, some researchers say, that most people with appendicitis would get better on their own if doctors did nothing. The Finnish team is now planning a clinical trial to test that theory.

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Could this be true? Eating fermented foods linked to fewer social anxiety symptoms? Fifteen years ago before the world of bacteria could be explored with state of the art genetic tests, this would have sounded too woo-woo. And now we say - could be. Next the researchers will test an experimental version of this study to see if they find causation. Right now all we can say they are linked or that we see an association.

But note that exercise also reduced social anxiety (this was also a finding in other studies). From Science Daily:

Decreased social anxiety among young adults who eat fermented foods

A possible connection between fermented foods, which contain probiotics, and social anxiety symptoms, is the focus of recent study...The researchers found that young adults who eat more fermented foods have fewer social anxiety symptoms, with the effect being greatest among those at genetic risk for social anxiety disorder as measured by neuroticism. "It is likely that the probiotics in the fermented foods are favorably changing the environment in the gut, and changes in the gut in turn influence social anxiety," said Hilimire. "I think that it is absolutely fascinating that the microorganisms in your gut can influence your mind."

The researchers designed a questionnaire that was included in a mass testing tool administered in the university's Introduction to Psychology courses during the fall 2014 semester; about 700 students participated. The questionnaire asked students about the fermented foods over the previous 30 days; it also asked about exercise frequency and the average consumption of fruits and vegetables so that the researchers could control for healthy habits outside of fermented food intake, said Hilimire.

"The main finding was that individuals who had consumed more fermented foods had reduced social anxiety but that was qualified by an interaction by neuroticism. What that means is that that relationship was strongest amongst people that were high in neuroticism," Hilimire said.The secondary finding was that more exercise was related to reduced social anxiety. 

"However, if we rely on the animal models that have come before us and the human experimental work that has come before us in other anxiety and depression studies, it does seem that there is a causative mechanism," said Hilimire. "Assuming similar findings in the experimental follow-up, what it would suggest is that you could augment more traditional therapies (like medications, psychotherapy or a combination of the two) with fermented foods -- dietary changes -- and exercise, as well."

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This month more research from researcher JJ Goedert about gut microbes in postmenopausal women and breast cancer. Very suggestive research was published September 2014 about the possibility of increasing a person's gut bacteria diversity to lower breast cancer risk. And even earlier research found that the human breast has a microbiome (community of microbes) that is different in healthy breasts as compared to cancerous breasts.

Now JJGoedert and others investigated whether the gut microbiota differed in 48 postmenopausal breast cancer case patients (before treatment) as compared to 48 control patients (women without breast cancer). The average age of both groups was 62 years.The researchers analyzed the estrogens in the women's urine and the bacterial diversity in fecal samples using modern genetic analysis (such as 16S rRNA sequencing). They found in this study that postmenopausal women with breast cancer had lower gut bacteria diversity and somewhat different composition of gut bacteria as compared to women without breast cancer. They also said that what this means is unknown, that is,"whether these affect breast cancer risk and prognosis is unknown." Some differences in gut bacteria composition: women with breast cancer had lower levels of Clostridiaceae, Faecalibacterium, and Ruminococcaceae; and they had higher levels of Dorea and Lachnospiraceae.

Excerpt is from the Journal of the National Cancer Institute:

Investigation of the association between the fecal microbiota and breast cancer in postmenopausal women: a population-based case-control pilot study.

We investigated whether the gut microbiota differed in 48 postmenopausal breast cancer case patients, pretreatment, vs 48 control patients. Microbiota profiles in fecal DNA were determined by Illumina sequencing and taxonomy of 16S rRNA genes. Estrogens were quantified in urine....  Compared with control patients, case patients had statistically significantly altered microbiota composition  and lower α-diversity. Adjusted for estrogens and other covariates, odds ratio of cancer was 0.50 per α-diversity tertile. Differences in specific taxa were not statistically significant when adjusted for multiple comparisons. This pilot study shows that postmenopausal women with breast cancer have altered composition and estrogen-independent low diversity of their gut microbiota. Whether these affect breast cancer risk and prognosis is unknown.

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New research shows that wearing contact lenses could significantly change the bacteria of the eye’s surface, making it more susceptible to infection. NYU Langone Medical Center researchers analyzed swabs from both contact-wearers and non-wearers to determine the number and type of bacterial species that lived on the surface of their eyes—the eye’s microbiome as well as the skin below the eye.

They found that the eye microbiome of contact lens wearers is more similar in composition to the microbiome of their skin than the eye microbiome of non-lens wearers.

Note that infections often come when people don’t take proper care of their lenses—sleeping in them overnight, or not cleaning them well or often enough so most eye doctors have shifted to recommending daily lenses. 

From Medical News Today: Alterations to the eye microbiome of contact lens wearers may increase infections

Contact lens wearers - ever wondered why you are more likely to experience eye infections than your contacts-less friends? Researchers from NYU Langone Medical Center in New York City think they may have found the answer, in a study that used high-precision genetic tests to map the human microbiome....the NYU Langone researchers report that micro-organisms residing in the eyes of people who wear contact lenses daily more closely resemble micro-organisms residing in eyelid skin than the bacteria usually found in the eyes of people who do not wear contacts.

The researchers took hundreds of swabs of different parts of the eye, including the skin directly beneath the eye. Genetic analysis of swabs and used contact lenses allowed the team to identify which bacteria were present. Comparing nine contact lens wearers with 11 non-contacts users, the team found three times the usual proportion of the bacteria Methylobacterium, Lactobacillus, Acinetobacter and Pseudomonas on the eye surfaces (conjunctiva) of contact lens wearers than on the eye surfaces of the control group.

Examining the bacterial diversity using a plotted graph, the team observed that the eye microbiome of contact lens wearers is more similar in composition to the microbiome of their skin than the eye microbiome of non-lens wearers. 

Interestingly, the researchers say, Staphylococcus bacteria was found in greater amounts in the eyes of non-lens wearers. Staphylococcus is linked with eye infections, but is usually more prominent on the skin. However, the researchers are unable to explain why non-lens wearers have greater amounts of this bacteria, despite this group traditionally having fewer eye infections than people who wear contacts.

Study author Dr. Jack Dodick, professor and chair of ophthalmology at NYU Langone, says:"There has been an increase in the prevalence of corneal ulcers following the introduction of soft contact lenses in the 1970s. A common pathogen implicated has been Pseudomonas. This study suggests that because the offending organisms seem to emanate from the skin, greater attention should be directed to eyelid and hand hygiene to decrease the incidence of this serious occurrence."