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The results of a recent study makes sense - that different microbes are found in city and town apartments and homes versus rural homes and jungle huts. And of course one would expect these different exposures to have an effect on our health. Guess where one gets more fresh air and sunlight, and where one has more chemical exposures?

Inside modern city and town buildings is lots of exposure to all sorts of plastics, human made chemicals, cleaners (and disinfectants), pesticides, medications, lack of fresh air, and along with lack of sunlight - all sorts of fungi. On the other hand, in rural areas there is fresher air, more sunlight, and more natural materials. [Remember: it's plastics and modern chemical compounds that outgas into the air and are a cause of air pollution. And yes, get into our bodies and affect our health negatively.]

The study was conducted in Peru and Brazil by several big names in the microbiome field, including Martin Blaser, Rob Knight, and Maria Dominguez-Bello. As the researchers point out, we have replaced a natural environment with a synthetic environment. Bottom line: get out into nature as much as possible, even if it's just walks. Try to use natural materials in your home (e.g., wood and not just plastic furniture), try to use "natural" products, and fewer chemicals routinely (pesticides, disinfectants, etc)

From Futurity: More Fungi Live In Urban Homes Than In Jungle Huts  ...continue reading "Different Microbes Live In Urban Homes Versus Really Rural Homes"

Researchers in Canada found that sunlight (or UVB light) on the skin changes the gut microbes (gut microbiome), especially in people with lower levels of vitamin D, that is, who are vitamin D deficient. UVB (Ultraviolet B light) exposure increased beneficial gut microbe diversity and richness in these people, as well as increasing their vitamin D levels. However, people who had been taking vitamin D supplements prior to the study, and who had sufficient vitamin D levels, did not have significant gut microbiome changes.

The researchers viewed the study results as evidence that there may be a skin-gut axis. As the researcher Vallance said: “It is likely that exposure to UVB light somehow alters the immune system in the skin initially, then more systemically, which in turn affects how favorable the intestinal environment is for the different bacteria,” suggested Vallance.

The researchers also thought that these study results (which was conducted in Vancouver, Canada, in healthy human volunteers) could help explain the protective effect of UVB light against inflammatory diseases such as multiple sclerosis (MS) or inflammatory bowel disease (IBD). And how did the researchers know what bacteria were in the gut in the study participants? They analyzed the feces with modern genetic sequencing methods. By the way, these results match what has been found in earlier studies in humans and mice.

Bottom line: Sunlight on the skin is beneficial to the gut microbiome, by increasing gut bacteria linked to health. In the study the increases in bacteria (after UVB light exposures) were in the Lachnospiraceae, Ruminococcus, and Clostridiaeae families. And nope, none of those are found in currently available probiotics. By the way, this study was conducted in winter in Canada, so the effects of UVB light were clearly seen in the healthy volunteers. This study supports getting some sunlight exposure (on the skin), and perhaps supplementing with vitamin D in the winter.

From Medical Xpress: Where the sun doesn't shine? Skin UV exposure reflected in poop  ...continue reading "Exposure To Sunlight Improves Gut Microbes and Vitamin D Levels"

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Researchers are starting to raise concerns about routine daily intake of probiotics for "gut health". Much is still unknown, but problems are starting to appear. A healthy gut contains hundreds of species (bacteria, fungi, viruses), and taking megadoses of a few species (a probiotic supplement) can overwhelm the normal gut microbial community. A healthy gut is one with a greater diversity of species, not just some species.

For example, one study found that daily probiotic ingestion can result in overgrowth of some bacterial species in the intestines, resulting in such symptoms as brain fogginess, bloating, and gas. Successful treatment was antibiotics and stopping the use of probiotics.   Another recent study found that after using antibiotics, those who took probiotics (thinking it would help microbial recolonization of the gut microbes) actually had slower recovery of the gut microbiome (microbial community).  The best recovery was in those who took nothing, no supplements at all, or those who received a fecal microbial transplant (where an entire microbial community is transplanted).

The evidence is showing that for gut microbial health, the best thing to do is eat a variety of real whole foods (and not highly processed foods) that have lots of fiber, such as whole grains, fruits, vegetables, seeds, nuts, and legumes (beans). In other words, feed the beneficial bacteria. A Mediterranean style diet is good.

A recent article in Medscape (the medical site) highlights these same concerns. [See below.] A study that looked at the gut microbiome of people who were about to undergo treatment for melanoma found that those who were taking probiotics actually had worse gut microbial diversity. [Remember, gut microbial diversity is considered an indicator of gut health.] And the cancer treatment (immunotherapy) did not work as well on them.

Bottom line: The evidence is showing that for gut microbial health, the best thing to do is eat a variety of real whole foods (and not highly processed foods) that have lots of fiber, such as whole grains, fruits, vegetables, seeds, nuts, and legumes (beans). In other words, feed the beneficial bacteria. A Mediterranean style diet is good. Don't take routine daily supplements or probiotics for  "gut health" - they won't help. Instead, if you want - only take probiotics for a short while for a specific symptom or problem.

Dr. Lorenzo Cohen wrote a piece for the Wall Street Journal laying out those same points. Some excerpts from: Those Probiotics May Actually Be Hurting Your ‘Gut Health’  ...continue reading "Daily Use of Probiotics Can Hurt Gut Health"

Bacterial vaginosis is a problem for many women, with estimates that up to a third of women of reproductive age get it at some point in life. Bacterial vaginosis is a condition where the microbes in the vagina are imbalanced or out-of-whack, especially with diminishing numbers and types of Lactobacillus species. Lactobacillus species are typically the dominant bacteria in healthy vaginal microbiomes.

Unfortunately, some women have recurring bacterial vaginosis (BV), many who wind up taking course after course of antibiotics to try to deal with it. Symptoms can include thin gray, white, or green vaginal discharge, vaginal itching, burning during urinbation, and a smelly fishy vaginal odor. Which is why a small study done in Israel finding success with vaginal microbial transplantation (VMT) from healthy donors to women with BV is very exciting.

Researchers transplanted vaginal fluid (with all its microbes) from 3 healthy women (and thus a healthy vaginal microbial community) into 5 women with severe BV that did not respond well to antibiotics. Afterwards four of the  recipients had long-lasting (up to 21 months) vaginal microbial changes and complete remission of BV (2 after the first transplant, 2 after 3 transplants) - becoming more like the donors' vaginal microbiome, and also rich in Lactobacillus. The 5th person had partial improvement of BV, but there were complications - she took a course of antibiotics for a throat infection, her BV symptoms returned, and then she received another vaginal microbiome transplant, after which her vaginal microbes were a mix of her original and the donors.

Of course larger studies are now needed, especially because there can be risks when receiving another person's microbes (e.g. accidental transfer of viruses). But I also want to point out that some of these Lactobacillus species (especially Lactobacillus crispatus) are easily available without a prescription, and women have been self-experimenting with them, many with good success.

Excerpts from Ars Technica - Vaginal-fluid transplants treat incurable condition in pilot study   ...continue reading "Vaginal Fluid Transplants Successfully Treat Bacterial Vaginosis"

We have trillions of bacterial cells from thousands of different strains of bacteria living in our gut! Researchers at MIT (Massachusetts Institute of Technology) collected stool samples from 90 people living in the Boston area (some for as long as 2 years), did modern genetic sequencing, and in this way isolated nearly 8000 strains of bacteria.  These bacterial strains were from the six major phyla of bacteria (e.g. Bacteroidetes and Firmicutes) that dominate the human gastrointestinal tract. Just remember that the human gut also has fungi, archaea, and viruses living there. Yes, it is crowded in the gut!

The researchers took repeated stool samples from about a dozen of the volunteers and so were able to study bacterial changes within individuals over time. They are making all the data about the gut bacterial strains available to other researchers, with the hope that this will help scientists develop new treatments for a variety of diseases. This data set is called the Broad Institute-OpenBiome Microbiome Library (BIO-ML). This is important information to have because study after study is finding that there are gut microbial differences in people with a number of diseases as compared to healthy individuals.

BOTTOM LINE: The goal should be to feed and nurture beneficial gut microbes, ones that are associated with health. The best way to feed your beneficial gut microbes is to have a diet with lots of whole, real foods and fiber - which means a diet rich in fruits, vegetables, whole grains, nuts, legumes (beans), and seeds. (Think Mediterranean style dietary pattern.) And to eat less (a lot less) highly processed, low fiber, refined grains, and sugary foods. In other words, you don't want to feed microbes linked to chronic inflammation and diseases, but instead want to feed beneficial microbes linked to health (and not chronic inflammation). For example, choose the apple and not the candy bar. Your gut microbes will thank you.

From MIT News Office: A comprehensive catalogue of human digestive tract bacteria   ...continue reading "There Are Thousands of Human Gut Bacteria Strains"

A really interesting study found that in humans, taking antibiotics (which reduces the gut bacteria) may result in the flu vaccine not being as effective as in people who did not take antibiotics. An earlier similar study had found that this was true for mice, which is why the researchers did the study on humans.

The Stanford University and Emory University researchers studied healthy people who had recent (in last few years) flu vaccinations and those who hadn't had a flu vaccine for several years prior to the study. Some individuals took 5 days of broad spectrum antibiotics, and on day 4 received a flu vaccine, while others did not take antibiotics, but did receive the flu vaccine on day 4.

Not surprisingly: The antibiotics lowered the gut-bacterial population by 10,000-fold. While month by month there was increasing recovery, the resulting loss of overall diversity was detectable for up to one year after the antibiotics were taken. Keep in mind that they found that: "Notably, species richness and biodiversity were not fully recovered at 6 months, indicating long-lasting loss of unique bacterial species, consistent with previous studies." [BOTTOM LINE: Only take antibiotics when necessary.]

Interestingly, after antibiotic use, the researchers found other changes besides an alteration in gut bacteria populations. They also found changes within the immune system which resulted in an inflammatory state, which was due to "impairments in bile acid metabolism by the gut flora". In other words, taking antibiotics has a number of effects beyond treating an infection (the reason they were taken).

By the way, those who had taken flu vaccines in prior years had much better responses to the vaccines - they only had a minimal impact on vaccine response, even though they took antibiotics, than those who had not. Those who had not received flu vaccines or the flu in recent years had "low preexisting immunity", and taking the antibiotics (which resulted in loss of gut bacterial species) impaired their antibody response to the flu  vaccine. The researchers said: "The results of this study are consistent with the concept of immune responses in adults being largely determined by immune history and resilient to transient changes in the microbiome."

From Medical Xpress: Individual response to flu vaccine influenced by gut microbes   ...continue reading "Antibiotics, Flu Vaccines, and Gut Bacteria"

The evidence is growing. Another recent study found that exposure to dirt and animals in the first year of life is beneficial for development of a a rich and diverse gut microbiome - that is, for greater species "richness" as well as more beneficial microbes. This is linked to lower levels of allergies and asthma in children.

So don't worry about children being exposed to animal "germs" and getting dirty! Instead, consider the microbes as having health benefits, such as developing a "robust immune system". In summary, it now appears that in the first year of life the immune system needs lots of exposure to all sorts of microbes (e.g. from pets, animals, dirt)  to "train it" to develop normally.

The Ohio State University researchers compared 5 healthy rural Amish infants to 5 healthy non-Amish urban infants in Ohio, also found that all of the rural (Amish) children were breastfed, while 2 of the urban (non-Amish) children were only formula fed (some microbial differences there). The Amish households had farm animals (cattle, sheep, and/or horses) and pets (dogs and/or cats), while the non-Amish households had no contact with livestock, but did have a pet dog or cat. Just like in other studies, one pet doesn't seem to be enough - even more animal exposure in early childhood is best for the gut microbiome. [One study found a dose-dependent effect with exposure to 5 furry pets in early childhood was needed to prevent all allergies.]

Studies find that rural (Amish) children have a low incidence of allergies and asthma, while urban children have a high incidence of allergies and asthma. In this study, an example of microbial differences in the 2 groups of children was that Bifidobacterium bacteria were "enriched" in non-Amish (urban) infants, while Roseburia species were "enriched" in Amish (rural, farm-raised) infants. Similar gut microbe differences have been observed in other studies comparing rural and urban children, and both dietary differences (e.g. farm raised children eat lots of homegrown produce) and environmental differences (animal exposure) are thought to be responsible for the differences.

From Science Daily: Keeping livestock in the yard just might help your baby's immune system  ...continue reading "Children, Animals, and Gut Microbes"

The Paleo diet has been around for years and yet it continues to be controversial. The debate is whether following the Paleo diet long-term has health benefits or not? Supporters of the Paleo (Paleolothic) diet say it promotes gut health and is good for gut microbes, but recent research findings are a strike against this claim. The Paleo diet is based on the hypothesis that humans have not adapted to eating products of agricultural farming such as grains, dairy products, or legumes (beans), as well as all processed foods, so they should be avoided. Instead it stresses eating meat, fish, eggs, nuts, (some) fruits, and vegetables.

So what were the new research findings?  Australian researchers found that people who had been on a Paleo diet for more than a year ate lower amounts of resistant starch, and so had a different bacteria profile in the gut - with lower levels of some beneficial species. They also had high levels of a biomarker in the blood (trimethylamine-n-oxide or TMAO) that is linked to heart disease.

The problem seems to be the lower intake of resistant starch - which is a carbohydrate that resists digestion in the small intestine and ferments in the large intestine. As the fibers ferment they act as a prebiotic and feed the beneficial bacteria in the gut. More than one type of resistant starch can be present in a single food. And what foods contain resistant starches? Precisely some foods avoided in the Paleo diet: grains, rice, beans, peas, lentils, plantains, and green bananas. A number of studies find health benefits (e.g. gut health) from eating foods with resistant starches.

From Medical Xpress: Heart disease biomarker linked to paleo diet

People who follow the paleo diet have twice the amount of a key blood biomarker linked closely to heart disease, the world's first major study examining the impact of the diet on gut bacteria has found.  ...continue reading "Problems With Paleo Diet?"

New research once again confirms that raw fruits and vegetables result in a person ingesting lots of microbes. Millions of bacteria. Which is considered beneficial for our gut microbiome! What's interesting in the latest study looking at bacteria in both conventionally and organically grown apples is that organic apples are a better source of bacteria - that their bacteria are more diverse, distinct, and balanced (when compared to conventionally grown apples).

The Austrian researchers (Wassermann et al) wrote in the Frontiers In Microbiology: "Our results suggest that we consume about 100 million bacterial cells with one apple. Although this amount was the same, the bacterial composition was significantly different in conventionally and organically produced apples."

Interestingly, there were a lot of beneficial Lactobacillus species in the organic apples, but not conventionally grown ones. The researchers thought that the diverse microbiome of organic apples probably limits or hampers harmful microbes (human pathogens). The researchers also wrote: "The described microbial patterns in organic apples resemble the impact of apple polyphenols on human health, which have not only been shown to alleviate allergic symptoms (Zuercher et al., 2010), but also to promote growth of Lactobacillus and Bifidobacterium in the human gut and to reduce abundance of food-borne pathogens."

Another bonus of eating organic apples is that it means avoiding pesticides that are routinely sprayed on conventional fruit. So eat away! Microbes, fiber, and nutrients all in one small fruit!

Fun fact: The researchers write that apples are the most consumed fruit world-wide. Excerpts from Science Daily: An apple carries about 100 million bacteria -- good luck washing them off  ...continue reading "Excellent Reason To Eat Apples: The Bacteria"

New research is raising questions about the role of gut bacteria in how people react to medications and whether the medicines are effective, at least some medications such as L-dopa treatment for Parkinson's disease. Why do medicines work for some people and not others? Perhaps the gut microbes are playing a part by interacting with the medicines! The gut microbes may actually be breaking down medicines and preventing them from reaching their target.

Researchers from Harvard University and University of California found that the composition of the gut microbes has an effect on whether the medicine L-dopa is effective or becomes ineffective as a Parkinson's disease treatment. They found that some bacteria can inactivate the medicine. Definitely research that needs following up on. Also, which medications is this true for?

Excerpts from Science Daily: Gut microbes eat our medication    ...continue reading "Gut Bacteria Has An Effect On Some Medicines?"