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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"


It's official. This month is 5 whole years being free of chronic sinusitis and off all antibiotics! Yes, that's correct - 5 whole years for all 4 family members, and our sinuses feel great!

Back in February 2013 - first I, and then the rest of my family, started using easy do-it-yourself sinusitis treatments containing the probiotic (beneficial bacteria) Lactobacillus sakei. Now we only treat with a L. sakei  product when occasionally needed - and it still works great. And it still feels miraculous.

After reading the original ground-breaking research on sinusitis done by Abreu et al (2012), it led to me trying L. sakei as a sinusitis treatment. Of course, there is an entire community of microbes (bacteria, fungi, viruses) that live in healthy sinuses - the sinus microbiome - but L. sakei seems to be a key one for sinus health. Since that original 2012 study, other studies have also found that in people with chronic sinusitis, the sinus microbial community is out of whack (dysbiosis). 

The one thing different this past year is that our sinus microbial community (sinus microbiome) seems better. If we need to treat (for example, after a virus that goes into sinusitis), then all four of us noticed that we need to use much less of a product than in the past. Incredibly little. So it seems that our sinus microbial community has definitely improved over time.

The post The One Probiotic That Treats Sinusitis (originally posted January 2015 and with many updates since then) contains information using my family's experiences (lots of self-experimentation!) and all the information that people have given me over the years. Thanks everyone! The post has a list of brands and products with L. sakei, treatment results, as well as information about some other promising probiotics (beneficial bacteria).

Thank you all who have contacted me  - whether publicly or privately. Please keep writing and tell me what has worked or hasn't worked for you as a sinusitis treatment. If you find another bacteria or microbe or product that works for you - please let me know. It all adds to the sinusitis treatment knowledge base. I will keep posting updates. 

(NOTE: I wrote our background story - Sinusitis Treatment Story back in December 2013, and there is also a  Sinusitis Treatment Summary page with the various treatment methods quickly discussed. One can also click on SINUSITIS under CATEGORIES to see more posts about what is going on in the world of sinusitis research.)

There have been many posts on this blog about diet, fiber, microbes, and the association of diet with various diseases, such as cancer. A recent journal article by M. Song and A. Chan reviewed studies that looked at the link between diet, gut microbes (the gut microbiota or gut microbiome), and colorectal cancer (what we typically call colon cancer).

In summary, research from the last 20 years has found that diet and colorectal cancer (CRC) go hand in hand, and that diet determines the microbes (microbiota) living in the gut - that is, what you feed the microbes determines what microbes will live and thrive in the gut. Also, certain microbes in the gut are linked to inflammation and cancer formation, and others to its prevention. In other words, there is potential to prevent colorectal cancer with certain diets, and to increase the odds of colorectal cancer with other diets.

What are main dietary factors linked to colorectal cancer? Western diet (lots of processed foods, red and processed meat, low in fiber, refined grains), low levels of dietary fiber, low intake of omega-3 fatty acids from seafood (or fish oil), and obesity. The researchers point out that a Western diet is associated with gut dysbiosis (microbial imbalance), loss of gut barrier integrity, and increased levels of inflammation. What should one do? Basically think to yourself: "I need to feed the beneficial microbes in my gut, so I need to eat lots of fruits, vegetables, whole grains, and seafood (omega-3 fatty acids)" - this is what the researchers call a "prudent pattern diet". And try to maintain a normal weight. Some excerpts from Current Colorectal Cancer Reports:

Diet, Gut Microbiota, and Colorectal Cancer Prevention: a Review of Potential Mechanisms and Promising Targets for Future Research

AbstractDiet plays an important role in the development of colorectal cancer. Emerging data have implicated the gut microbiota in colorectal cancer. Diet is a major determinant for the gut microbial structure and function. Therefore, it has been hypothesized that alterations in gut microbes and their metabolites may contribute to the influence of diet on the development of colorectal cancer.We review several major dietary factors that have been linked to gut microbiota and colorectal cancer, including major dietary patterns, fiber, red meat and sulfur, and obesity

Colorectal cancer (CRC) is the third most commonly diagnosed cancer and the fourth leading cause of cancer death in the world. Over the past few decades, numerous epidemiologic studies have identified a range of dietary factors that may potentially promote or prevent CRC. Likewise, increasing evidence has implicated the gut microbiota in CRC development. Biological plausibility is supported by habitation of numerous gut microbes in the large intestine and the functional importance of the gut microbiota in maintenance of the gut barrier integrity and immune homeostasis, the disruptions of which are among the most important mechanisms in colorectal carcinogenesis. Given the critical role of diet in the configurations of gut microbial communities and production of bacterial metabolites, it has been proposed that diet may influence CRC risk through modulation of the gut microbial composition and metabolism that in turn shape the immune response during tumor development.

Although gut bacterial abundance may respond rapidly to extreme changes in diet, predominant microbial community membership is primarily determined by long-term diet, and substantial inter-individual variation persists despite short-term dietary change. .... Thus, this review focuses on the dietary factors that have strong mechanistic support, including dietary pattern, fiber, red meat and sulfur, and omega-3 fatty acid. Given the close link between diet and obesity and the predominant role of obesity in CRC as well as the substantial data linking the gut microbiome to obesity, we also include obesity at the end of the review.

DIETARY PATTERNS: Convincing data indicate that a “Western dietary pattern,” characterized by high intake of red or processed meat, sweets, and refined grains, is associated with higher risk of colorectal neoplasia; in contrast, diets that are rich in fruits, vegetables, and whole grains (“prudent pattern diet”) are associated with lower risk of CRC. Western diets are associated with gut dysbiosis (microbial imbalance), loss of gut barrier integrity, increased levels of inflammatory proteins, and dysregulated immune signatures.

A potential role of the gut microbiota in mediating the dietary associations with CRC risk is suggested by the dramatic difference of the gut microbial structures between populations consuming different diets. Rural Africans, whose diet is high in fiber and low in fat, have a strikingly different gut microbial composition than urban Europeans or African Americans consuming a Western diet, which parallels the lower CRC rates in Africa than Western countries. For example, the African gut microbiota is characterized by a predominance of Prevotella genus that are involved in starch, hemicellulose, and xylan degradation, whereas the American microbiota is predominated by Bacteroides genus with a higher abundance of potentially pathogenic proteobacteria, such as Escherichia and Acinetobacter. .... Moreover, a crossover study indicates that switching African Americans to a high-fiber, low-fat diet for 2 weeks increases production of SCFAs, suppresses secondary bile acid synthesis, and reduces colonic mucosal inflammation and proliferation biomarkers of cancer risk.

Fiber: Numerous prospective studies have linked higher fiber intake to lower risk of CRC. The most recent expert report from the World Cancer Research Fund and the American Institute for Cancer Research in 2011 concludes that evidence that consumption of foods containing dietary fiber protects against CRC is convincing. Besides systemic benefits for insulin sensitivity and metabolic regulation, which have been implicated in colorectal carcinogenesis, fiber possesses gut-specific activities, such as diluting fecal content, decreasing transit time, and increasing stool weight, thereby minimizing exposure to intestinal carcinogens.

Moreover, soluble fiber can be fermented by bacteria in the lumen of the colon into SCFAs [short-chain fatty acids], including butyrate, acetate,and propionate. Higher fiber intake has been shown to enrich butyrate-producing bacteria in the gut, such as Clostridium, Anaerostipes, Eubacterium, and Roseburia species, and increase production of SCFAs. SCFAs have been suggested as the key metabolites linking the gut microbes to various health conditions, especially CRC

Red Meat and Sulfur: There is convincing evidence that red and processed meats are associated with increased risk of CRC. Recently, the Int. Agency for Research on Cancer has classified processed meat as a carcinogen to humans. Mechanisms underlying the pro-cancer effects of red or processed meats include heme iron, N-nitroso compounds, or heterocyclic amines, and hydrogen sulfide production. Hydrogen sulfide has been implicated in inflammatory disorders associated with risk of CRC, such as ulcerative colitis, and directly with CRC.

Omega-3 Fatty Acid: Marine omega-3 polyunsaturated fatty acid, including eicosapentaenoic acid, docosahexaenoic acid, and docosapentaenoic acid, possesses potent anti-inflammatory activity and may protect against CRC. Fish oil, a rich source of omega-3 fatty acid, is the most popular natural product used by US adults. Substantial data support the beneficial effect of omega-3 fatty acid on CRC prevention and treatment.

Dietary fat composition is a major driver of the gut microbial community structure. Compared to other types of fat, omega-3 fatty acid have been associated with higher intestinal microbiota diversity and omega-3 fatty acid-rich diet ameliorates the gut dysbiosis induced by omega-6 polyunsaturated fatty acid or antibiotics.

Obesity: Since the 1970–1980s, the prevalence of obesity has markedly increased worldwide. The obesity epidemic is believed to be largely driven by global westernization characterized by overconsumption of easily accessible and energy-dense food and a sedentary lifestyle. Obesity is an established risk factor for CRC and several other cancers. Possible mechanisms include increased insulin levels and bioavailability of insulin-like growth factor 1, altered secretion of adipokines and inflammatory cytokines, and changes in sex hormone levels.

A recent study tested a variety of probiotic (beneficial) Lactobacillus and Bifidobacteria species of bacteria as a treatment for chronic sinusitis. Unfortunately, it found that the microbes tested had NO effect on chronic sinusitis symptoms. It was a nice study conducted in Sweden, with 21 people with chronic sinusitis (but without nasal polyps) randomly assigned to receive a nasal spray (that they used 2 x daily for 14 days) containing either a mixture of 13 bacteria or a "sham" nasal spray. No one knew who received what, and then after a few weeks they did a crossover - meaning who got what was switched for another 2 weeks.

But...the main finding is that after 14 days of using the nasal sprays, there was no improvement in either group, no improvement in symptoms, no effect on the sinus "microbial flora", and no effect on inflammation. In fact, 2 individuals wound up taking antibiotics while testing the bacteria nasal spray. In other words, a big fat zero.

The bacteria tested were what the researchers called a honeybee lactic acid (LAB) microbiome, with both Lactobacillus and Bifidobacteria species: Lactobacillus apinorumL. melliferL. mellis, L. kimbladiiL. melliventrisL. helsingborgensisL. kullabergensisL. kunkeei, L. apisBifidobacterium asteroidesB. coryneforme, Bifidobacterium Bin7N, and Bifidobacterium Hma3N. These species are not typically found in probiotic supplements.

Why did they choose those strains of bacteria? Because "in vitro" testing (meaning in a test tube or culture dish) suggested that they would be effective against the pathogenic bacteria frequently found in chronic sinusitis (that they were antimicrobial). But real world testing in actual humans in this study showed that those specific Lactobacillus and Bifidobacteria microbes had no effect on sinusitis symptoms. Their premise was good - that the sinus microbiome was "disturbed" or out of whack (dysbiosis) in chronic sinusitis, but unfortunately they chose the wrong bacteria to test as a treatment.

The SNOT-22 questionnaire that asked questions of sinusitis sufferers at several points in the study to see if there was improvement in sinusitis symptoms, is one typically given to those with chronic sinusitis. [By the way, when reviewing the questionnaire, I realized it left out some major sinusitis symptoms such as "gagging on phlegm", "waking up with sore throat", "teeth hurt", "headache" - all of which are frequently mentioned by many contacting me, and which I remember well from pre-L. sakei days. In other words - it is incomplete, yet it is the questionnaire typically used to assess quality of life and symptoms for those with chronic sinusitis.]

The researchers end the journal article by stating "Further studies are warranted to explore whether other tentative probiotic assemblages [other bacterial species] can confer positive health effects to patients suffering from inflammatory conditions of the upper airways." Huh... If only they had asked...  I've been writing about Lactobacillus sakei as an excellent treatment for chronic sinusitis since 2013 (based on results of Abreu et al study), and I've been getting positive feedback from others about L. sakei since early 2014. For those who find that L. sakei works as a sinusitis treatment, the results seem miraculous - typically with major improvement within a few days. (Please note: Perhaps other microbes may also work as a sinusitis treatment.) Excerpts from Laryngoscope Investigative Otolaryngology:

Clinical efficacy of a topical lactic acid bacterial microbiome in chronic rhinosinusitis: A randomized controlled trial

A locally disturbed commensal microbiome might be an etiological factor in chronic rhinosinusitis (CRS) in general and in CRS without nasal polyps (CRSsNP) in particular. Lactic acid bacteria (LAB) have been suggested to restore commensal microbiomes. A honeybee LAB microbiome consisting of various lactobacilli and bifidobacteria have been found potent against CRS pathogens in vitro. Recently, we examined effects of single nasal administrations of this microbiome in healthy subjects and found it inert. In this study, we examined effects of repeated such administrations in patients with CRSsNP.

The study was of a randomized, double‐blinded, crossover, and sham‐controlled design. Twenty patients received 2 weeks' treatment administered using a nasal spray‐device. The subjects were monitored with regard to symptoms (SNOT‐22 questionnaire, i.e., the primary efficacy variable), changes to their microbiome, and inflammatory products (IL‐6, IL‐8, TNF‐, IL‐8,a, and MPO) in nasal lavage fluids.

ResultsNeither symptom scores, microbiological explorations, nor levels of inflammatory products in nasal lavage fluids were affected by LAB (c.f. sham). Conclusion: Two weeks' nasal administration of a honeybee LAB microbiome to patients with CRSsNP is well tolerated but affects neither symptom severity nor the microbiological flora/local inflammatory activity.

 In this study, involving patients with well‐defined CRSsNP, we demonstrate that repeated nasal administration of a LAB microbiota composed of several species of lactobacilli and bifidobacteria over 2 weeks neither affects symptoms as assessed by SNOT‐22 questionnaire nor the bacterial composition or the inflammatory activity in the nasal cavity. The observations are of relevance to the evaluation of topical LAB treatment in the management of upper respiratory tract conditions such as CRS.

Just read a small study that compared the microbes in the sinus microbiome between 12 healthy people with no sinusitis (controls) and 14 with chronic sinusitis, their neurotransmitter levels (serotonin, dopamine, and GABA), and also looked at depression scores in the 2 groups. Well, of course they found some microbial differences between healthy people and those with chronic rhinosinusitis (CRS), but they also found that those with the most severe chronic sinusitis tended to have the most depressive symptoms, and lower amounts of the neurotransmitters studied, but they did not find significant differences overall.

I found their summary and conclusions problematic, since they discussed that "possibly" the sinus microbes influence brain neurotransmitters. And they pointed out that as certain disease associated microbes increased (especially Moraxella), the neurotransmitter concentrations tended to decrease in those with sinusitis. But since there were no significant group differences, they did not prove their hypotheses, and conclusions can not be made. So saying there is "the potential for downstream effects of the sinonasal microbiota on neural signaling and, subsequently, brain function and behavior" is misleading and overreaching. The researchers also said it was "difficult to discern disease associations from natural variation." Hah!

It should be obvious that the worse the chronic sinusitis, the more depressive symptoms, because having chronic sinusitis is DEPRESSING. One suffers with it. Some people have told me how chronic sinusitis has destroyed their life - whether their health, financially, with relationships, etc. Of course they will have higher depressive scores! And when a Lactobacillus sakei product or other probiotic successfully treats sinusitis (usually very quickly), then the mood is one of elation as symptoms go away (finally health!).

All one can say (based on studies) is: the sinus microbiomes in healthy people (normal sinus microbial community) are somewhat different from those with chronic sinusitis (out-of-whack microbial community or dysbiosis). And one would expect that those with less severe/milder sinusitis have a "better" community of sinus microbes - that is, more microbes that are associated with health, and fewer of those associated with sickness, than sicker people. Which is what this study suggested. Excerpts from the International Forum of Allergy & Rhinology:

The sinonasal microbiota, neural signaling, and depression in chronic rhinosinusitis

The complex relationships between the human microbiota, the immune system, and the brain play important roles in both health and disease, and have been of increasing interest in the study of chronic inflammatory mucosal conditions. We hypothesized that the sinonasal microbiota may act as a modifier of interkingdom neural signaling and, subsequently, mental health, in the upper respiratory inflammatory condition chronic rhinosinusitis (CRS). In this study we investigated associations between the sinonasal microbiota; local concentrations of the neurotransmitters serotonin, dopamine, and γ-aminobutyric acid (GABA); and depression severity in a cohort of 14 CRS patients and 12 healthy controls.

Several commonly “health-associated” sinonasal bacterial taxa were positively associated with higher neurotransmitter concentrations and negatively associated with depression severity. In contrast, several taxa commonly associated with an imbalanced sinonasal microbiota negatively associated with neurotransmitters and positively with depression severity. Few significant differences were identified when comparing between control and CRS subject groups, including neurotransmitter concentrations, depression scores, or sinonasal microbiota composition or abundance. Conclusion: The findings obtained lend support to the potential for downstream effects of the sinonasal microbiota on neural signaling and, subsequently, brain function and behavior.

SOME OTHER EXCERPTS: Depression scores were also not significantly different between controls and CRS patients. .... The serotonin levels in CRS patients compared with control subjects tended to be lower, but not significantly so. Although median values for dopamine, GABA, and serotonin were generally lower in CRS patients than controls, all 3 neurotransmitters had a greater range among those with CRS, and no differences were significant. ... For both CRS and control individuals, bacterial communities were generally dominated by OTUs of the genera Corynebacterium and Staphylococcus.

Correlation analyses identified associations between members of the genera Staphylococcus, Finegoldia, Propionibacterium, Peptoniphilus, and Anaerococcus, as well as bacterial community diversity overall. Members of these genera have been previously identified as representative of more “health-associated” sinonasal bacterial community types, whereas their depletion has been associated with lower bacterial community diversity, increased bacterial load, increased rates of asthma, and elevated markers of inflammation. Similarly, members of the genera Burkholderia and Propionibacterium have been identified as 2 potential “gatekeepers” that help maintain bacterial community stability in the sinonasal tract. In the present study, several of these same bacterial taxa were significantly positively correlated with neurotransmitter levels and negatively with depression severity, whereas several other OTUs (including members of Streptococcus, Rothia, Enterobacteriaceae, Corynebacterium, and Moraxella) showed the opposite pattern (negatively associated with neurotransmitter levels and positively with depression severity). 

Two studies (one in mice and one in humans) from researchers at the University of Illinois found that no matter what your diet - exercise changes the gut bacteria in a beneficial way. And when you go back to a sedentary lifestyle, your gut microbes change again and beneficial microbes such as short chain fatty acids (SCFAs), especially butyrates, decline. The effect was more pronounced in lean sedentary adults (as compared to obese sedentary adults).

Beneficial microbes that increased with exercise in humans were species of Faecalibacterium, Roseburia, Lachnospira, Lachnospiraceae, and Clostridiales. Faecalibacterium prausnitzii has been discussed in earlier posts as a beneficial keystone species in the gut (here, here, and here). What kind of exercises did they do? They did three supervised 30 to 60 minute moderate to vigorous intensity aerobic/endurance exercise sessions per week for 6 weeks, and they could use a cycle ergometer (stationary bicycle) or treadmill each session.

Besides beneficial microbial changes, 6 weeks of exercising resulted in improved body composition (total lean body mass, decreased body fat, increased bone mineral density), and an improvement in cardiorespiratory fitness. These changes reversed in everyone when they went back to 6 weeks of a sedentary lifestyle. Bottom line: get out and move, move, move. Your gut microbes and your body will thank you. From Science Daily:

Exercise changes gut microbial composition independent of diet, team reports

Two studies -- one in mice and the other in human subjects -- offer the first definitive evidence that exercise alone can change the composition of microbes in the gut. The studies were designed to isolate exercise-induced changes from other factors -- such as diet or antibiotic use -- that might alter the intestinal microbiota.

In the first study, scientists transplanted fecal material from exercised and sedentary mice into the colons of sedentary germ-free mice, which had been raised in a sterile facility and had no microbiota of their own. In the second study, the team tracked changes in the composition of gut microbiota in human participants as they transitioned from a sedentary lifestyle to a more active one -- and back again.

Recipients of the exercised mouse microbiota also had a higher proportion of microbes that produce butyrate, a short-chain fatty acid that promotes healthy intestinal cells, reduces inflammation and generates energy for the host. They also appeared to be more resistant to experimental ulcerative colitis, an inflammatory bowel disease.

In the human study, the team recruited 18 lean and 14 obese sedentary adults, sampled their gut microbiomes, and started them on an exercise program during which they performed supervised cardiovascular exercise for 30-60 minutes three times a week for six weeks. The researchers sampled participants' gut microbiomes again at the end of the exercise program and after another six weeks of sedentary behavior. Participants maintained their usual diets throughout the course of the study. Fecal concentrations of SCFAs, in particular butyrate, went up in the human gut as a result of exercise. These levels declined again after the participants reverted to a sedentary lifestyle.

The most dramatic increases were seen in lean participants, who had significantly lower levels of SCFA-producing microbes in their guts to begin with. Obese participants saw only modest increases in the proportion of SCFA-producing microbes. The ratios of different microbes in the gut also differed between lean and obese participants at every stage of the study, the researchers said. "The bottom line is that there are clear differences in how the microbiome of somebody who is obese versus somebody who is lean responds to exercise," Woods said. " [Original study in humans.]

Another study has shown health benefits from eating a diet rich in whole grains, as compared to one with lots of refined grains (think bagels, muffins, white bread). Fifty overweight Danish adults were randomly assigned to either a group where all grains eaten were whole grains or a group where all grain products were of refined grains. They did this for 8 weeks, then ate their usual diet for a few weeks (the "washout period"), and then were assigned to the other dietary group for 8 weeks.

They found that eating the diet rich in whole grains resulted in: consuming fewer calories (the whole grains made them feel fuller), losing weight, and a decrease in chronic low-grade inflammation (by measuring blood inflammation markers). The whole grain rye seemed to be especially beneficial. But interestingly, the researchers found that the whole grain diet did not significantly change the gut microbe composition. But they did find that 4 strains of Faecalibacterium prausntzii and one of Prevotella copri increased in abundance after whole grain and decreased after refined grain consumption. F.prausnitzii is a desirable and beneficial keystone species in the gut (here and here).

Other studies show that eating a diet rich in whole grains (rather than refined grains) is associated with a decreased risk of several diseases, including type 2 diabetes and cardiovascular diseases. Bottom line: choose whole grains whenever possible. From Science Daily:

Several reasons why whole grains are healthy

When overweight adults exchange refined grain products -- such as white bread and pasta -- with whole grain varieties, they eat less, they lose weight and the amount of inflammation in their bodies decreases. These are some of the findings of a large Danish study headed by the National Food Institute, Technical University of Denmark. 

The study included 50 adults at risk of developing cardiovascular disease or type 2 diabetes. Blood tests showed that the participants had less inflammation in their bodies when eating whole grains. In particular, it appeared that rye had a beneficial effect on the blood's content of inflammatory markers. Inflammation is the natural response of the body to an infection, but some people have slightly elevated levels of inflammation (so-called low-grade inflammation) even though there is no infection. This is particularly the case in overweight people. In overweight people, an increased level of 'unnecessary' (subclinical) inflammation may lead to increased risk of developing type 2 diabetes.

The study also shows that participants eat less when whole grain products are on the menu -- presumably because whole grain consumption causes satiety. While eating the whole grain diet, participants have generally lost weight. The researchers used DNA sequencing to analyze stool samples from the participants in order to examine whether the different diet types affected the participants' gut bacteria composition. Overall, the analysis did not shown major effects of the dietary grain products on the composition of the gut bacteria. [Original study.]