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An interesting study about exposure to household cleaning products (regular cleaning products compared to eco-friendly products) and the gut microbiomes of young children was recently published. Canadian researchers found that the use of household cleaning disinfectants in the home was associated with changes in gut microbial communities in infants (more of some bacteria and less of others) - when compared to infants living in homes where eco-friendly cleaners were used. These changes occurred in a dose dependent manner (the more they were used, the bigger the changes).

Also interesting was that the more disinfectants (which are antibacterial) were used in a home, the more Lachnospiraceae was found in the infant's gut microbiota in infancy (age 3 to 4 months), and this was associated with a higher body mass of the child at 1 and 3 years, and increased odds of being overweight or obese at age 3. Use of eco-friendly products was associated with decreased odds of the child being overweight or obese at age 3. What was heavy use of household disinfectants? Daily or weekly. Just keep in mind that these are associations - not a definite cause and effect. But animal studies find similar results. And I wonder - what is frequent use of disinfectants doing to adult gut microbiomes? From Medical Xpress:

Household cleaning products may contribute to kids' overweight by altering their gut microbiota

Commonly used household cleaners could be making children overweight by altering their gut microbiota, suggests a Canadian study published in CMAJ (Canadian Medical Association Journal). The study analyzed the gut flora of 757 infants from the general population at age 3-4 months and weight at ages 1 and 3 years, looking at exposure to disinfectants, detergents and eco-friendly products used in the home. 

...continue reading "What Are Household Disinfectants Doing To Our Gut Microbes?"

Two recent studies caught my eye – both reviews of scientific research that looked at the issue of diet and whether it contributes to the development of Intestinal Bowel Disease (IBD), specifically Crohn’s disease and ulcerative colitis. These are chronic inflammatory disorders of the gastrointestinal tract, and which are rapidly increasing in developed countries (over 1 million individuals in the US). The main question is: Does a person’s diet contribute to the development of IBD?

Both articles (one in the journal Nature Reviews and one in Immunology) said: YES, there is growing evidence that a person’s diet has a role in the development of IBD. Both articles stated that the current view is that some individuals may be genetically susceptible, and their diet (which feeds the microbes in the gut) then makes them more prone to the disease due to the mucosal lining becoming permeable and inflamed. Studies have shown that people with IBD have gut microbial communities that are imbalanced or out of whack (dysbiosis).

What does this mean? A person’s diet has a key role in what microbes live in the gut (human gut microbiome) – what one eats feeds the microbes in the gut, and a person’s general dietary pattern feeds some types of microbes and not others. So what one eats determines what lives in the gut microbial community. Unfortunately a fiber-deficient diet (typical Western diet) is both linked to increased mucosal inflammation (the mucus layer of the intestines) and it makes it leaky. In other words, a fiber deficient diet impairs the mucus layer of the intestines. Animal studies also support this (that the diet regulates mucosal barrier function).

People in developed countries such as the US typically eat a Western style diet. A Western diet is characterized by high amounts of red meat, processed food, high-fat foods, refined grains, sugary desserts, and low intakes of dietary fiber. However, the Western style diet has been linked to increased mucosal inflammation of the intestines, and to a higher incidence of a number of diseases, including ulcerative colitis and Crohn’s disease.

What diet is best? A diet rich in fruits and vegetables, whole grains, nuts, seeds, legumes (beans), and fish. Low in red meat, but moderate amounts of poultry. High in vitamin D, and high in omega-3 fatty acids. High in dietary potassium and zinc. Eat the foods, not supplements. One good example to follow is the Mediterranean diet. Think of it this way: high fiber diets lower inflammation in the gut, low fiber diets increase inflammation.

Both articles had similar diagrams showing that diet has an effect on the microbes in the gut (the microbiome), which results in either 1) a healthy mucosal lining of the intestines, or 2) a disturbed mucosal lining, disturbed permeability, and inflammation. The one article calls it the “mucinous layer” and the other calls it the gut “barrier” in the diagrams, but both are talking about the mucosal lining of the intestines.

The following image contrasts the effects on the intestines of the two types of diet - the intestines on the left have "homeostasis" (balance) from a healthy dietary pattern (lots of fiber, fruits& vegetables, etc) , and the one on the right has inflammation from a Western dietary pattern.  To see it more clearly, go to the original Figure 1. in the article by L. Celiberto et al: Inflammatory bowel disease and immunonutrition: novel therapeutic approaches through modulation of diet and the gut microbiome

The other review:  The role of diet in the aetiopathogenesis of inflammatory bowel disease

The last few days a number of articles appeared in the news about the official US government's opposition to a WHO (World Health Organization)  resolution supporting breastfeeding. Huh? Apparently this was because the US government decided that supporting formula companies was more important than the health of mothers and babies. The US government went so far as to threaten other countries if they supported the resolution.

Medical and scientific studies have clearly established that breast milk is best for a baby for numerous short and long-term health benefits. There are also health benefits to the mother from breastfeeding (e.g. lower incidence of breast and ovarian cancer, and type 2 diabetes). Of course there are many women who can't or won't breastfeed for various reasons (including they can't because of lack of maternity leave or support at their workplace) and their babies will drink infant formula and do well. But .... in general women should be encouraged to breastfeed because of the numerous health benefits, and they shouldn't just hear nonsense (e.g.lies)  from infant formula companies. Below are links to articles explaining what happened in the US vs the WHO and other countries in the breastfeeding controversy, and some reasons why breast milk  is better than formula.

But what these news articles didn't mention is another really important health benefit: mothers transmit hundreds of species of microbes to their babies in breast milk. Yes, hundreds of microbial species which help "seed" the infant's microbiome (microbial communities). [Some research posts: more than 700 species of bacteria in breast milk, and gut microbiota development,]

From Quartz:  All the scientific support for breastfeeding that the US apparently didn’t read  ...continue reading "Why Are Formula Company Profits More Important Than the Health of Babies?"

A recent large study (using health data from the United Kingdom) found that children and adults who took five commonly prescribed types of antibiotics had an increased risk of developing kidney stones, compared to people who didn't take these antibiotics. The five types of antibiotics were sulfas, cephalosporins, fluoroquinolones, nitrofurantoin, and broad-spectrum penicillins. The antibiotics were taken orally (by mouth).

However, not all antibiotics were associated with an increased risk of kidney stones. The study examined 12 types of antibiotics, and found seven types that didn’t appear to influence the risk of kidney stones.The strongest risks for kidney stones were in children and adolescents, and with more recent exposure. The risk of kidney stones decreased over time, but remained elevated several years after antibiotic use.

The researchers pointed out that recent studies have found differences in the gut microbiome (community of microbes) between patients with kidney stones and those without kidney stones. And that studies find that the use of antibiotics disrupts the microbiome. (here and here) Another reason to only take antibiotics when absolutely necessary. From Science Daily:

Oral antibiotics may raise risk of kidney stones

Pediatric researchers have found that children and adults treated with some oral antibiotics have a significantly higher risk of developing kidney stones. This is the first time that these medicines have been linked to this condition. The strongest risks appeared at younger ages and among patients most recently exposed to antibiotics ...continue reading "Antibiotics and Kidney Stones"

Once again, a study finds that consumption of nuts is beneficial to health - this time by impacting the gut microbiome (community of microbes) in a beneficial way. This was a nicely done study -18 healthy adults randomly assigned first to either eating about a handful of walnuts daily (42 g) or zero nuts daily for 3 weeks, and then assigned to the other group for 3 weeks, with a "washout period" of 1 week in-between. Walnut consumption resulted in higher amounts of beneficial gut bacteria (Faecalibacterium, Clostridium, Dialister, and Roseburia) which are butyrate producing (beneficial!), and lowering of proinflammatory secondary bile acids and LDL cholesterol (both beneficial).

As seen in this walnut study from the University of Illinois, adding walnuts to the diet has quick effects on the gut microbiome. Other studies find that diets rich in nuts (which are a source of dietary fiber and unsaturated fatty acids) are associated with a reduced risk of death from cancer and heart disease. Bottom line: eating some nuts daily feeds beneficial bacteria in the gut, and so has beneficial health effects. This walnut study had everyone eating about a handful of walnut halves a day (42 g, which is a little less than 1/2 cup walnut halves).

From Science Daily: Walnuts impact gut microbiome and improve health

Diets rich in nuts, such as walnuts, have been shown to play a role in heart health and in reducing colorectal cancer. According to a new study from the University of Illinois, the way walnuts impact the gut microbiome -- the collection of trillions of microbes or bacteria in the gastrointestinal tract -- may be behind some of those health benefits.  ...continue reading "Walnuts Feed Beneficial Gut Bacteria and Other Health Benefits"

People ask me: what's going on with research in the treatment of sinusitis with probiotics? Well, the answer is that things are moving along slowly - very slowly, but there are good signs. Earlier this year an interesting article by researcher Anders U. Cervin at the University of Queensland (Australia) was published that specifically talked about "topical probiotics" as a potential treatment for chronic sinusitis. By this he means that probiotics (beneficial bacteria) could be directly applied to the nasal passages in the nose, such as a nasal spray. And he discussed how the prevailing view nowadays, based on scientific evidence, is that in sinusitis there is an "imbalance of the sinus microbiome" - the community of microbes living in the sinuses. Yes!!!

Cervin mentioned all sorts of research showing beneficial effects of using different strains of probiotics for various illnesses, mentioned the Abreu et al study (which is the reason I focused on Lactobacillus sakei as a sinusitis treatment, and which works successfully for many people), but.... nowhere did he mention Lactobacillus sakei by name. What???

Cervin discusses how studies are needed to test nasal sprays for the treatment of sinusitis, and made a lot of good points. He looked at studies already done, wondered what bacterial strains might be beneficial, but obviously didn't read the Abreu et al study carefully to see that L. sakei might be a good candidate to test. And he didn't do an internet search to see what probiotics people are using already as a successful treatment for sinusitis (see post). He did mention that the only good trial using nasal spray probiotics in humans with sinusitis found no effect - because they tested the wrong Lactobacillus strains - they were honeybee strains [see post], and not ones found in humans.

Eh... So once again I'm heartened by the focus on the microbial community in sinusitis, and heartened that he said there it was time to get out of the laboratory and start testing probiotics as treatments on people. But I'm dismayed that the focus is so narrow that he's missing what is in front of him - what is already out there. He also missed that a "snot transplant" study is now going on in Europe, which is sure to have interesting results.

By the way, some of the questions the article raises are ones which, based on the experiences of myself and others over the past 5 years, we can already answer: living bacteria as a treatment are better than dead bacteria (using dead bacteria doesn't work), nasal treatments work but just swallowing a probiotic pill doesn't, Lactobacillus sakei works as a treatment for many, the L. sakei bacteria reduces inflammation in the nasal passages, the probiotic can be used in place of an antibiotic, and only treat when needed and not continuously (continuously treating can also result in an imbalance in the sinus microbiome). [See post The One Probiotic That Treats Sinusitis where these issues are discussed.] ...continue reading "Researcher Sees Potential for Sinusitis Nasal Probiotics"


Study after study, and such influential researchers as Dr. Martin Blaser (at New York University) have warned about antibiotics having a negative effect on the human microbiome - that they kill off gut microbes. And all conclude that therefore antibiotics should be used carefully - only when needed. But there are other reasons to be cautious about antibiotics as a recent article warned. Some people who take the class of antibiotics called fluoroquinolones develop a syndrome called fluoroquinolone-associated disability (FQAD) which causes crippling side-effects, including irreversible nerve damage. People who have fallen ill after taking fluoroquinolones call it being "floxed".

The FDA currently has "black box" warnings about fluoroquinolones - that they can cause tendon rupture or a risk of irreversible nerve damage in those taking the antibiotics. Black box warnings are placed inside a black box on drug labels and call attention to serious or life-threatening risks. Millions have taken these drugs, but some (the FDA considers it a rare event) develop the serious side-effects.

Many people (myself included) have taken fluoroquinolones, such as Levaquin, over the years for sinusitis treatment. Some have taken them multiple times. Most have not reported side-effects (including myself), but those who developed serious side-effects (floxed) are desperate for sinusitis treatments that don't involve taking antibiotics. Which is where alternative treatments using probiotics such as Lactobacillus sakei come in (yes, it works for sinusitis!). Excerpts from Nature (the international journal of science):

When Antibiotics Turn Toxic

In 2014, Miriam van Staveren went on holiday to the Canary Islands and caught an infection. Her ear and sinuses throbbed, so she went to see the resort doctor, who prescribed a six-day course of the popular antibiotic levofloxacin. Three weeks later, after she had returned home to Amsterdam, her Achilles tendons started to hurt, then her knees and shoulders. She developed shooting pains in her legs and feet, as well as fatigue and depression. “I got sicker and sicker,” she says. “I was in pain all day.” Previously an active tennis player and hiker, the 61-year-old physician could barely walk, and had to climb the stairs on all fours. Since then, she has seen a variety of medical specialists. Some dismissed her symptoms as psychosomatic. Others suggested diagnoses of fibromyalgia or chronic fatigue syndrome. Van Staveren is in no doubt, however. She’s convinced that the antibiotic poisoned her.

She’s not alone. Levofloxacin is one of a class of drugs called fluoroquinolones, some of the world’s most commonly prescribed antibiotics. In the United States in 2015, doctors doled out 32 million prescriptions for the drugs, making them the country’s fourth-most popular class of antibiotic. But for a small percentage of people, fluoroquinolones have developed a bad reputation. On websites and Facebook groups with names such as Floxie Hope and My Quin Story,thousands of people who have fallen ill after fluoroquinolone treatment gather to share experiences. Many of them describe a devastating and progressive condition, encompassing symptoms ranging from psychiatric and sensory disturbances to problems with muscles, tendons and nerves that continue after people have stopped taking the drugs. They call it being ‘floxed’.  ...continue reading "Some Antibiotics Can Have Crippling Side Effects"

Once again a study found that a high fiber diet feeds beneficial gut microbes and causes changes in the gut microbe community (the microbiome). What's new in this study is that eating the high fiber diet had health benefits for people with type 2 diabetes - that it lowered their blood sugar levels (better blood glucose control), resulted in  greater weight loss, and better lipid levels. And that when these gut microbes were transplanted into mice - they had similar health effects (better regulation of blood sugar). Which showed it was the microbes that caused the beneficial effects.

What foods are high-fiber foods? Fruits, vegetables, whole grains, nuts, seeds, and legumes (beans). [See Feeding Your Gut Microbes] From The Scientist:

High-Fiber Diet Shifts Gut Microbes, Lowering Blood Sugar in Diabetics

A diet high in fiber can reshape the gut microbiome, helping people with type 2 diabetes stay healthy. A study published yesterday (March 8) in Science found that when patients with the condition ate a high-fiber diet, they had an abundance of microbial species that helped to reduce blood sugar and regulate weight compared with cohorts who ate a less fiber-rich diet ...continue reading "High Fiber Diet Is Beneficial For Those With Type 2 Diabetes"


Recently I was asked about the human skin microbiome (skin microbial communities) and whether the things we do frequently (e.g. use soap and shampoo, go swimming in a pool) has an effect on our skin microbiome. As I've posted earlier, human skin microbes include bacteria, fungi, viruses, and  archaea. Most of these microbes are harmless or beneficial, but when the microbial communities are out of whack (dysbiosis), then there are diseases or skin disorders (such as acne, psoriasis, and eczema). The human skin acts as a physical barrier, a first line of defense, to pathogens (microbes that can cause disease). Studies have found that using soaps, lotions, make-up, our diet and lifestyle all have some effect on skin microbial communities. Even living with someone results in some microbial exchange. Spending more time outdoors, owning pets, and drinking less alcohol (or none) are all associated with higher levels of microbial skin diversity.

But then I came across a small study from 2016 (National Human Genome Research Institute, NIH, Bethesda, MD) in Cell - Temporal Stability of the Human Skin Microbiome. The researchers found that skin microbial communities are "surprisingly stable over time" (the study lasted 2 years), even though the humans were typically exposed to things daily that could disrupt their skin microbial communities (other people, clothing, the environments). But some individuals had more stable communities than others, and stability varied from site to site (the feet had the least stable microbial communities). Also, they found that bacterial, fungal, and viral communities not only show a strong preference for inhabiting specific skin sites, but also serve as "microbial fingerprints" that are highly unique to individuals. They did point out that "immunosuppression, illness, or the occurrence of disease have been shown to cause major shifts in skin communities".

Then there is a recent 2018 review article - but behind a paywall even though the researchers worked for NIH, thus paid for with our tax dollars (!!).They also discussed all the microbes living on the skin, and how when the microbial communities are out of whack (dysbiosis), then there is disease (whether acne, or eczema, etc.). Microbes that are beneficial in healthy people can become pathogenic, e.g. when the person has a disease. It also pointed out that only with modern genetic sequencing methods (rather than old style "cultures") can one really see what makes up the skin microbial communities. And that using these methods we can compare the skin microbes of healthy persons with those with a disease. And yes, there then is also the possibility of finding protective, beneficial microorganisms which are in healthy persons, but absent or under-represented in those with a disease. Sounds  like probiotics for the skin! ...continue reading "Microbes of the Skin"


Research has found that antibiotics disrupt a person's normal gut microbiome (microbial community), especially because the antibiotics kill both bad (pathogenic) and beneficial bacteria. But what about other medicines? Do they also have an effect?

A recently published study that reviewed the research looked precisely at that topic and found that YES - other medicines (besides antibiotics) also have an effect on (disrupt) the gut microbiome. The different categories of drugs - proton pump inhibitors (PPIs), metformin, nonsteroidal anti-inflammatory drugs (NSAIDs), opioids, statins and antipsychotics - all had different kinds of impacts on the gut microbiome.

The researchers also suggest that other types of commonly prescribed medicines now need to be examined for their impact on the intestinal (gut) microbiome, such as thyroid hormones, contraceptive drugs, and antihypertensive (high blood pressure) drugs. Excerpts from Dr. Paul Enck's article about the study at Gut Microbiota Research and Practice:

A systematic review explores the role of non-antibiotic prescription drugs in gut microbiota dysbiosis

Both diet and medications are among the strongest variables affecting the gut microbiome. When it comes to medications, although antibiotics have been repeatedly shown to affect the human gut microbiome, little is known regarding the impact of non-antibiotic prescription drugs on the gut microbiome.

review, led by Dr. Emmanuel Montassier from the MiHAR Lab at Institut de Recherche en Santé 2, Université de Nantes (Nantes, France), has concluded that some non-antibiotic prescription drugs have a notable impact on the gut microbiome to the same extent as antibiotics ...continue reading "Common Medicines That Disrupt the Normal Gut Microbiome"