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Author: Sima

Published on Leave a comment on Are Antibiotics Used In Agriculture Causing Harm?

Image result for apple tree wikipedia This post continues the discussion of antibiotics and their overuse. Antibiotic resistance is increasing due to misuse of antibiotics (or antimicrobials), and this is occurring throughout the world (post with video of how superbugs evolve). This is because bacteria are constantly evolving against the antibiotics they're exposed to. We may reach a point where simple cuts or infections could lead to death because no antibiotics will work. The World Health Organization (WHO) in 2016 said that bacterial resistance to antibiotics is “one of the biggest threats to global health." Especially scary are the bacteria resistant to numerous antibiotics - the superbugs. 

According to the CDC: "Each year in the United States, at least 2 million people become infected with bacteria that are resistant to antibiotics and at least 23,000 people die each year as a direct result of these infections."

Part of the problem is that farmers are still giving antibiotics (antimicrobials) to farm animals unnecessarily, typically as "growth promoters" or to try to prevent disease. Currently about 80% of all antibiotics used in the US are given to livestock animals (of which nearly 70 percent of those used are considered “medically important” for humans). But what is typically ignored is that farmers also use antibiotics, or antimicrobials, on crops (plant agriculture). In both instances - conventional farming uses antibiotics, but NOT organic farming. Another reason to support organic farming and to eat organic foods.

The nonprofit organization Beyond Pesticides has just released a report discussing antibiotic use in conventional farming (both crops and animals), and how this is contributing to "bacterial resistance to critical life-saving human medicines", and also how organic farming does not use antibiotics. The report discusses that while antibiotic use in animal agriculture is widely acknowledged as harmful, the use of antibiotics in conventional crop production is also harmful. Antibiotics are used because plants can get bacterial diseases (e.g.,bacterial canker, soft rot, and bacterial wilt) The report even discusses fish farming, how antibiotics are used routinely in seafood imported from other countries, and also how some fungicides are used as antibiotics (to "manage" or kill bacteria).

What antibiotics are used in agriculture? For starters - glyphosate (in the pesticide Roundup), which is the most widely used pesticide in the world. Glyphosate is patented by its manufacturer (Monsanto) for its antibacterial properties - thus an antibiotic. As a result, glyphosate is the most widely used antibiotic in agriculture and around homes, gardens, schools, and communities in the U.S. Other antibiotics used widely in farming (especially for fruit trees) are oxytetracycline and streptomycin - which are used in the production of apples, pears, peaches, beans, celery, peppers, tomatoes, and potatoes. The government allows antibiotic residues to remain on the foods ("tolerances for residues on foods") when we buy them in grocery stores.

The report also points out that: The main health impacts of antibiotic residues in food are the promotion of antibiotic resistance and disruption of the microbiota in the human gut. Which means that the microbial communities in our gut can be affected in a negative way. It's well worth reading the 7 page easy to read report - with lots of photos, graphs, and good explanations. Beyond Pesticides: Agricultural Uses of Antibiotics Escalate Bacterial Resistance

Published on Leave a comment on Probiotics For Allergies?

Could this be true? Probiotics for seasonal allergies? A study by Univ. of Florida researchers reported that taking a combination probiotic of Lactobacillus gasseri, Bifidobacterium bifidum, and Bifidobacterium longum (sold as Kyo-Dophilus) for 8 weeks during spring allergy season resulted in an improvement in seasonal allergy symptoms. It must be noted that the people participating had mild seasonal allergies, not severe allergies. While they reported overall allergy symptom improvement, there was no significant improvement with eye symptoms. Too bad, because for those suffering from itchy eyes, it is a symptom that causes anguish during allergy season.

All participants had their stool (fecal) samples tested (with modern genetic sequencing) and it was found that the group taking the probiotic supplements had a beneficial shift in their overall microorganisms in the gut - with some bacteria such as Escherichia coli decreasing and the very beneficial and anti-inflammatory bacteria Faecalibacterium prausnitzii increasing. (See posts here and here on F. prausnitzii.) What was really good about the study was that it was a "double-blind, randomized clinical trial", meaning that people were randomly  assigned to the probiotic treatment or placebo group, and no one knew who was getting a placebo or the probiotic until the end of the study. The researchers say that why the probiotics improved allergy symptoms is s till not clear, but they have some theories. From Science Daily:

Allergies? Probiotic combination may curb your symptoms, new study finds

As we head into allergy season, you may feel less likely to grab a hanky and sneeze. That's because new University of Florida research shows a probiotic combination might help reduce hay fever symptoms, if it's taken during allergy season. Many published studies have shown a probiotic's ability to regulate the body's immune response to allergies, but not all of the probiotics show a benefit, UF researchers say. Scientists already know that the probiotic combination of lactobacilli and bifidobacteria, sold as Kyo-Dophilus in stores, helps maintain digestive health and parts of the immune system. They suspect that probiotics might work by increasing the human body's percentage of regulatory T-cells, which in turn might increase tolerance to hay fever symptoms.

UF researchers wanted to know if the components in this combination probiotic would help alleviate allergy symptoms. To do that, they enrolled 173 healthy adults who said they suffered seasonal allergies and randomly split them into two groups: Some took the combination probiotic; others took a placebo. Each week during the eight-week experiment, participants responded to an online survey to convey their discomfort level. Scientists also analyzed DNA from participants' stool samples to determine how their bacteria changed, because probiotics aim to deliver good bacteria to the human's intestinal system.

Participants who took the probiotic reported improvements in quality of life, compared to those taking the placebo, the study showed. For example, participants suffered fewer allergy-related nose symptoms, which meant that they were less troubled during daily activities. Researchers note that this study did not include severe allergy sufferers. But the combination of probiotics showed clinical benefit for those with more mild seasonal allergies, Langkamp-Henken said. [Original study.]

Published on Leave a comment on Four Years of Sinusitis Treatment Success

It's now 4 years being free of chronic sinusitis and off all antibiotics! Four amazing years since I (and then the rest of my family) started using easy do-it-yourself sinusitis treatments containing the probiotic (beneficial bacteria) Lactobacillus sakei. My sinuses feel great! And yes, it still feels miraculous.

After reading the original ground-breaking research on sinusitis done by Abreu et al (2012), it led to finding and 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.

I just updated the post The One Probiotic That Treats Sinusitis (originally posted January 2015) using my family's experiences (lots of self-experimentation!) and all the information that people have sent me. 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 so much!

Thank you all who have written to 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, there is also an updated  Sinusitis Treatment Summary page with the various treatment methods quickly discussed, and latest information on everything: The Best Probiotic For Sinus Infections. One can also click on SINUSITIS under CATEGORIES to see more posts about what is going on in the world of sinusitis research.)

Published on Leave a comment on New Antibiotics Are Needed For Twelve Scary Superbugs

Image result for Acinetobacter baumannii Many posts on this blog are about beneficial microbes, and the many species of microbes (bacteria, fungi, viruses) living within and on us. But there are also bacteria in the world that pose a serious threat to human health, and the list of these are growing due to antibiotic resistance. This week the World Health Organization (WHO) officials came out with a list of a dozen antibiotic-resistant "priority pathogens" that pose the greatest threats to human health. These are bacteria resistant to multiple antibiotics - thus superbugs.

Antibiotic resistance is increasing due to misuse of antibiotics (or antimicrobials), and this is occurring throughout the world (post with video of how superbugs evolve). This is because bacteria are constantly evolving against the antibiotics they're exposed to. We may reach a point where simple cuts or infections could lead to death because no antibiotics will work. The World Health Organization said in a 2014 report that: "The problem is so serious that it threatens the achievements of modern medicine. A post-antibiotic era—in which common infections and minor injuries can kill—far from being an apocalyptic fantasy, is instead a very real possibility for the twenty-first century."

Part of the problem is that farmers are still giving antibiotics (antimicrobials) to farm animals unnecessarily, typically as "growth promoters" or to try to prevent disease. Currently about 80% of all antibiotics used in the US are given to livestock animals (of which nearly 70 percent of those used are considered “medically important” for humans).

New antibiotic development is not keeping pace with the emergence of new antibiotic resistant bacteria. According to the CDC: "Each year in the United States, at least 2 million people become infected with bacteria that are resistant to antibiotics and at least 23,000 people die each year as a direct result of these infections."

According to WHO officials "The bacteria on the list are responsible for severe infections and high mortality rates mostly in hospitalized patients, transplant recipients, those receiving chemotherapy or patients in intensive care units." They have also been seen in our hospitalized and returning military service people. The WHO list is meant to steer public and private research dollars toward developing new antibiotics for these particular families of bacteria. Pharmaceutical companies currently lack financial incentives to develop new drugs aimed at these superbugs. Currently too few new antibiotics are under development. From World Health Organization:

WHO publishes list of bacteria for which new antibiotics are urgently needed

WHO today published its first ever list of antibiotic-resistant "priority pathogens" – a catalogue of 12 families of bacteria that pose the greatest threat to human health. The list was drawn up in a bid to guide and promote research and development (R&D) of new antibiotics, as part of WHO’s efforts to address growing global resistance to antimicrobial medicines. The list highlights in particular the threat of gram-negative bacteria that are resistant to multiple antibiotics. These bacteria have built-in abilities to find new ways to resist treatment and can pass along genetic material that allows other bacteria to become drug-resistant as well.....The WHO list is divided into three categories according to the urgency of need for new antibiotics: critical, high and medium priority.

The most critical group of all includes multidrug resistant bacteria that pose a particular threat in hospitals, nursing homes, and among patients whose care requires devices such as ventilators and blood catheters. They include Acinetobacter, Pseudomonas and various Enterobacteriaceae (including Klebsiella, E. coli, Serratia, and Proteus). They can cause severe and often deadly infections such as bloodstream infections and pneumonia. These bacteria have become resistant to a large number of antibiotics, including carbapenems and third generation cephalosporins – the best available antibiotics for treating multi-drug resistant bacteria. The second and third tiers in the list – the high and medium priority categories – contain other increasingly drug-resistant bacteria that cause more common diseases such as gonorrhoea and food poisoning caused by salmonella.

WHO priority pathogens list for R&D of new antibiotics: Priority 1: CRITICAL - Acinetobacter baumannii, carbapenem-resistant, Pseudomonas aeruginosa, carbapenem resistant, Enterobacteriaceae, carbapenem-resistant, ESBL-producing. Priority 2: HIGH - Enterococcus faecium, vancomycin-resistant, Staphylococcus aureus, methicillin-resistant, vancomycin-intermediate and resistant, Helicobacter pylori, clarithromycin-resistant, Campylobacter spp., fluoroquinolone-resistant, Salmonellae, fluoroquinolone-resistant, Neisseria gonorrhoeae, cephalosporin-resistant, fluoroquinolone-resistant. Priority 3: MEDIUM - Streptococcus pneumoniae, penicillin-non-susceptible, Haemophilus influenzae, ampicillin-resistant, Shigella spp., fluoroquinolone-resistant.

Image result for Acinetobacter baumannii Acinetobacter baumannii  Credit: Centers for Disease Control and Prevention (CDC)

Published on Leave a comment on Ten Portions of Fruits and Vegetables Daily?

 This past week a study was published linking 8 to 10 portions of fruits and vegetables per day with a lower risk of early death, cancer, heart disease, and stroke. This confirms other research linking many daily servings of fruits and vegetables with various health benefits. For example, the study findings discussed in the Nov. 2, 2016 post: "Eating lots of fruits and vegetables (more than 10 servings a day!)  is linked to better cognitive functioning in both normal weight and overweight adults (both young and older adults), and may delay the onset of cognitive decline that occurs with aging and also dementia."

This new study led by researchers from the Imperial College London reviewed 95 previous studies of the relationship between diet and health. They found that people who ate 10 portions of fruits and vegetables a day had nearly a third lower risk of premature death and stroke than those who ate very little or no fruits and vegetables. The researchers pointed out that as the amount of fruits and vegetables eaten daily went up, the health benefits also increased (lower risk of heart disease, stroke, cardiovascular disease, cancer), and the risk of premature death decreased - thus a dose related relationship. So better to eat some fruits and vegetables than none! A portion is about 80 grams, equivalent to a medium apple, 1 banana, or generally about 1/2 cup of vegetables or fruits.

From Science Daily: Eating up to ten portions of fruit and vegetables a day may prevent 7.8 million premature deaths worldwide

A fruit and vegetable intake above five-a-day shows major benefit in reducing the chance of heart attack, stroke, cancer and early death. This is the finding of new research, led by scientists from Imperial College London, which analysed 95 studies on fruit and vegetable intake....the greatest benefit came from eating 800 g a day (roughly equivalent to ten portions -- one portion of fruit or vegetables if defined as 80 g).

The results revealed that even a daily intake of 200 g was associated with a 16 per cent reduced risk of heart disease, an 18 per cent reduced risk of stroke, and a 13 per cent reduced risk of cardiovascular disease. This amount, which is equivalent to two and a half portions, was also associated with 4 per cent reduced risk in cancer risk, and 15 per cent reduction in the risk of premature death. Further benefits were observed with higher intakes. Eating up to 800 g fruit and vegetables a day -- or 10 portions -- was associated with a 24 per cent reduced risk of heart disease, a 33 per cent reduced risk of stroke, a 28 per cent reduced risk of cardiovascular disease, a 13 per cent reduced risk of total cancer, and a 31 per cent reduction in dying prematurely. This risk was calculated in comparison to not eating any fruit and vegetables. [Original study.]

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Published on 14 Comments on Do Probiotic Supplements Stick Around In the Gut?

People assume that taking probiotics results in the beneficial probiotic bacteria colonizing and living in the gut (or sinuses when using L. sakei). It is common to hear the phrase "take probiotics to repopulate the gut" or "improve the gut microbes". The human gut microbiota (human gut microbiome) refers to all the microbes that reside inside the gut (hundreds of species). Probiotics are live bacteria, that when taken or administered, result in a health benefit. But what does the evidence say?

First, it is important to realize that currently supplements and foods contain only a small variety of probiotic species, with some Lactobacillus and Bifidobacterium species among the most common. But they are not the most common bacteria found in the gut. And very important bacteria such as Faecalibacterium prausnitzii (a reduction of which is associated with a number of diseases) are not available at all in supplements. One problem is the F. prausnitzii are "oxygen sensitive" and they die within minutes upon exposure to air, a big problem when trying to produce supplements.

The evidence from the last 4 years  of L. sakei use for sinusitis treatment is that for some reason, the L. sakei is not sticking around long-term and permanently colonizing in the sinuses. My family's experiences and the experience of other people contacting me is that every time a person becomes sick with a cold or sore throat, it once again results in sinusitis, and then another treatment with a L. sakei product is needed to treat the sinusitis, even though less is needed over time. And of course this has been a surprise and a big disappointment. [See Dec. 2020 update below.]

The same appears to be true for probiotics (whether added to a food or in a supplement) that are taken for other reasons, including intestinal health. Study after study, and a review article, finds that the beneficial bacteria do not colonize in the gut even if there are health benefits from the probiotics. That is, there may be definite health benefits from the bacteria, but within days of stopping the probiotic (whether in a food or a supplement) it is no longer found in the gut. Researchers know this because they can see what bacteria are in the gut by analyzing (using modern genetic sequencing tests) what is in the fecal matter (the stool).

However, the one exception to all of the above is a fecal microbiota transplant (FMT) - which is transfer of fecal matter from one person to another. There the transplanted microbes of the donor do colonize the recipient's gut, referred to as "engraftment of microbes". Some researchers found that viruses in the fecal matter helped with the engraftment. So it looks like more than just some bacterial strains are involved. Another thing to remember is that study after study finds that dietary changes result in microbial changes in the gut, and these changes can occur very quickly.

[Dec. 2020 update: A few recent studies are now suggesting that if a person takes or uses a bacterial species that naturally occurs in the body and is depleted, than it may stick around for a while - this is colonization, even if only short-term. We also find this occurring with L. sakei - while we may need to use it now and then, this is occurring less frequently over time, and we need to use a much smaller amount when needed. Colonization! Overall, there has been major improvement of our sinuses over time - and yes, they feel great.]

From Gut Microbiota News Watch: Learning what happens between a probiotic input and a health output

What scientists know is that probiotics in healthy individuals are associated with a number of benefits. Meta-analyses of randomized, controlled trials show that probiotics help prevent upper respiratory tract infections, urinary tract infections, allergy, and cardiovascular disease risk in adults. But between the input and the output, what happens? A common assumption is that probiotics work by influencing the gut microbe community, leading to an increase in the diversity of bacterial species in the gut ecosystem and measurable excretion in the stool.

But this theory doesn’t seem to be true, according to a recently published systematic review by Kristensen and colleagues in Genome Medicine. Authors of the review analyzed seven studies and found no evidence that probiotics have the ability to change fecal microbiota composition. So even though individuals in the different studies were ingesting live bacterial species, the bacteria didn’t stick around to increase the diversity of the gut fecal microbiota.

“Do probiotics alter the fecal composition of healthy adults? The answer seems to be no,” says Dr. Mary Ellen Sanders, Executive Science Officer for the International Scientific Association for Probiotics and Prebiotics (ISAPP)....Dr. Dan Merenstein, Research Division Director and Associate Professor of Family Medicine at Georgetown University Medical Center in Washington, DC (USA), agrees. “Initially when probiotics were studied, some people expected to see permanent colonization. We now realize that is unlikely to occur,” he says. “This study shows that the probiotics tested to date do not result in overarching bacterial community structure changes in healthy subjects. But clinical effects are clearly demonstrated for probiotics, and likely some are mediated by microbiome changes.”

At issue, then, is not what probiotics do for healthy individuals, but exactly how they work: the so-called ‘mechanism’. Sanders, who described some alternative mechanisms in her BMC Medicine commentary about the Kristensen review, points out a logical error in news stories worldwide that covered the article: the assumption that if probiotics fail to change the microbiota composition, they fail to have any health effects. Sanders emphasizes that probiotics might work in many possible ways. “Probiotics may act through changing the function of the resident microbes, not their composition. They may interact with host immune cells,” she says. “They may inhibit opportunistic pathogens that are not dominant members of the microbiota. They may promote microbiota stability… .” 

Published on Leave a comment on Health Benefits of 5 Days of Calorie Restriction

Do you want to live longer and be healthy at the same time? Some possible ways may be to restrict the calories in the diet (every day) or to practice intermittent calorie restriction (a fasting mimicking diet a few days a month or even each week, such as the 5:2 diet). Previous studies in animals and humans have suggested that periodic fasting can reduce body fat, cut insulin levels, and provide other benefits. Studies in animals found that sharply restricting calories (calorie restriction or CR) daily resulted in longer, healthier lives, but it is unknown if the benefits of chronic calorie restriction also holds true for humans, and even if it might be dangerous. And really - how many people would actually want to reduce their calorie intake by 25% or more day in and day out for years? Intermittent calorie restriction seems much, much easier.

Two recently published studies suggest health benefits of calorie restriction diets - chronic calorie restriction in adult rhesus monkeys, and intermittent calorie restriction (a fasting mimicking diet a few days a month) in humans.

Researchers at the Univ. of Wisconsin–Madison and National Institute of Aging reanalyzed two studies they had originally done with conflicting results, and now they reported in Nature Communications that chronic calorie restriction produced health benefits (such as lower incidence of cancer, cardiovascular problems) and longer life in rhesus monkeys. Since these primates have human-like aging patterns, they thought that CR would also have similar benefits in humans - a longer, healthier life.  The researchers describe one monkey they started on a 30 percent calorie restriction diet when he was 16 years old (late middle age for rhesus monkeys), and that he is now 43 (a longevity record for the species). They found that in nonhuman primates calorie restriction is beneficial when started in adulthood (especially late middle age in males), but does not improve survival when started in juveniles (young animals) - and in fact they tended to die at an earlier age than the normal diet group of primates.

In the other study (in Science Translational Medicine), research suggests it is possible to gain anti-aging benefits with a “fasting-mimicking diet,” practiced just five days a month. 100 healthy adults (aged 20 to 70) were randomly assigned to either a group following a low-calorie "fasting-mimicking" diet (FMD) five days a month, for 3 months, or a normal diet control group. After 3 months, the control group also went on the fasting mimicking diet. Test subjects followed a 50 percent calorie restricted diet (totaling about 1,100 calories on the first day) and 70 percent diet (about 700 calories) on the next four days, then ate whatever they wanted for the rest of the month. The calorie-restricted diet was low in calories, sugars, and protein, was 100 percent plant-based, and featured vegetable soups, energy bars, energy drinks, and a chip snack, as well as mineral and vitamin supplements. (Note that Longo and Univ. of Southern California are both owners of L-Nutra, the company that manufactures the diet. But Longo says he takes no salary or consulting fees from the company.)

But it still wasn't easy for the test subjects to follow the 5 days of restricted calories per month because there was a 25% drop out rate. Health benefits (about a 6 pound weight loss, smaller waistlines, lower blood pressure, lower levels of inflammation, and better levels of glucose, triglycerides and cholesterol, etc.), showed up after the third month and persisted for at least three months—even after subjects had returned full-time to a normal diet. They lost body fat, but lean muscle mass remained unchanged. They found that the benefits were greater for people who were obese or otherwise unhealthy. In summary, the researchers said that 3 cycles of the 5 days per month of fasting-mimicking diet improved the levels of a variety of "markers/risk factors associated with poor health and aging and with multiple age-related diseases" (such as cancer, diabetes, heart disease, etc).

Other researchers say there is no need to suffer through such extreme diets, but to instead follow a healthy lifestyle, which includes a healthy diet (with lots of vegetables, fruits, legumes, seeds, whole grains, and nuts), and to exercise. And remember - nowhere does following restricted calorie diets mean you'll live longer - just that you should be healthier as you age (hopefully). There are no guarantees in life...

From Science Translational Medicine: Fasting-mimicking diet and markers/risk factors for aging, diabetes, cancer, and cardiovascular disease

Mice that fast periodically are healthier, metabolically speaking. To explore whether fasting can help people as well, Wei et al. studied 71 people who either consumed a fasting-mimicking diet for 5 days each month for 3 months or maintained their normal diet for 3 months and then switched to the fasting schedule. The fasting-like diet reduced body weight and body fat, lowered blood pressure, and decreased the hormone IGF-1, which has been implicated in aging and disease. A post hoc analysis replicated these results and also showed that fasting decreased BMI, glucose, triglycerides, cholesterol, and C-reactive protein (a marker for inflammation). These effects were generally larger in the subjects who were at greater risk of disease at the start of the study. A larger study is needed to replicate these results, but they raise the possibility that fasting may be a practical road to a healthy metabolic system.

From Nature Communications:  Caloric restriction improves health and survival of rhesus monkeys

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Published on 5 Comments on Vitamin B3 and Glaucoma

Image result for eyes A recent study had great results in preventing glaucoma or stopping the progress of glaucoma by supplementing the diet of mice with vitamin B3 (nicotinamide). But now the research needs to see if this also holds true for humans.

Glaucoma is a common neurodegenerative disease that results in vision loss. Two main risk factors are increasing age and high intraocular pressure (pressure in the eye). The researchers said that their next step is testing B3 in human glaucoma patients. So stay tuned...

Vitamin B3, also known as niacin, is an essential vitamin for health, but both deficiencies and too high doses have negative health effects. It is recommended that adults get between 14 mg to 18 mg of niacin per day. Since it is not stored in the body (the excess will be excreted in urine), then you need to get a continuous supply from your diet.

As seen in so many other studies of vitamins and minerals, there is no evidence of adverse effects from the consumption of naturally occurring niacin in foods, but one can get too much from supplements (along with negative health effects).

What foods are good sources of B3 (niacin)? Foods highest in B3 (niacin) are tuna, chicken, turkey, but other good sources are anchovies, salmon, sardines, red meat, peanuts, nuts, seeds, eggs, mushrooms, dairy foods. lentils, beans, potatoes, and grain products.

From Medical Xpress: Vitamin B3 prevents glaucoma in laboratory mice

In mice genetically predisposed to glaucoma, vitamin B3 added to drinking water is effective at preventing the disease, a research team led by Jackson Laboratory Professor and Howard Hughes Medical Investigator Simon W.M. John reports in the journal Science. ...continue reading "Vitamin B3 and Glaucoma"

Published on Leave a comment on All Babies Have Fungi Living In Them

A new study has summarized what we know about fungi that live in and on babies - and yes, we all have fungi both on and within us. It's called the mycobiome. In healthy individuals all the microbes (bacteria, viruses, fungi, etc) live in balanced microbial communities, but the communities can become "out of whack" (dysbiosis) for various reasons, and microbes that formerly co-existed peacefully can multiply and become problematic. Or other pathogenic microbes can enter the community, and the person becomes ill.

In healthy adults, approximately 0.1% of the microbes in the adult intestine are fungi, from approximately 60 unique species. Most species live peacefully in the body, and some fungi even have health benefits (e.g., Saccharomyces boulardii prevents gastrointestinal disease). Some fungi that many view as no good and involved with diseases (e.g., Candida and Aspergillus) are also found normally in healthy people. Studies show that normally infants also have fungi. Some fungi that live in the baby's gut (thus detected in fecal samples) are Candida (including C. albicans), Saccharomyces, and Cladosporium. The researchers (from the Univ. of Minnesota) point out that the study of fungi in babies has been neglected and much more research needs to be done.

Whether an infant is born vaginally or through cesarean delivery (C-section) affects the composition of the baby's bacterial communities over the first 6 months of life. And similarly, it looks like when the baby passes through the birth canal, the baby is exposed to the mother's mycobiota (fungi), and then these colonize in the infant's gut. Babies born by C-section have some differences in their fungi, such as being colonized by the mother's skin fungi (such as Malassezia fungi). After birth, a parent kissing and touching the baby (skin to skin contact) also transmits microbes, including fungi, to the baby.

Whether a baby drinks breast milk or formula strongly affects the infant's bacteria within the GI tract. For example, breast-fed infants have more Bifidobacteria and Labctobacilli in their gut compared to formula-fed infants. One study found about 700 species of bacteria in breast milk. Thus, scientists think that human breast milk also influences the infant gut mycobiota (fungi), although this research still needs to be done.

Whether a baby is born prematurely or at term (gestational age) is important. For infants born prematurely, intestinal fungi can cause big problems, such as an overgrowth in the gut. For example, 10% of premature babies get invasive, systemic Candidiasis, and about 20% die. Some factors leading to this are: a naïve immune system, bacterial communities out of whack (dysbiosis) due to antibiotic exposure, and use of parenteral nutrition (because this doesn't contain all the microbes from the mother that are in breast milk). In premature infants, beneficial fungi such as S. boulardii, may help to regulate the growth of opportunistic fungal colonizers such as Candida.

it is clear that whether the baby received antibiotics is important. The bacterial community of infants is altered by exposure to antibiotics in both term and preterm infants. For example, in a lengthy study over the first 3 years of life, infants receiving multiple courses of antibiotics had bacterial community changes following antibiotics and their gut bacterial microbiome became less diverse (fewer species). Although most commonly used antibiotics do not directly act on fungi, anti-bacterial antibiotic exposure is associated with alterations to the mycobiota (fungi) -  such as increased rates of fungal colonization, fungal overgrowth, and changes in the fungal community. For ex., premature infants exposed to cephalosporin antibiotics have an increased risk for invasive Candidiasis (a fungal overgrowth).

Out of whack (dysbiotic) microbial communities, incuding fungi, are found in IBD (intestinal bowel diseases) in children. They have more of some fungi (e.g. Pichia jadinii and Candida parapsilosis) and less of Cladosporium cladosporiodes, and an overall decrease in fungal diversity in the gut, as compared to healthy children.

From BMC Medicine: Infant fungal communities: current knowledge and research opportunities

The microbes colonizing the infant gastrointestinal tract have been implicated in later-life disease states such as allergies and obesity. Recently, the medical research community has begun to realize that very early colonization events may be most impactful on future health, with the presence of key taxa required for proper immune and metabolic development. However, most studies to date have focused on bacterial colonization events and have left out fungi, a clinically important sub-population of the microbiota. A number of recent findings indicate the importance of host-associated fungi (the mycobiota) in adult and infant disease states, including acute infections, allergies, and metabolism, making characterization of early human mycobiota an important frontier of medical research. This review summarizes the current state of knowledge with a focus on factors influencing infant mycobiota development and associations between early fungal exposures and health outcomes. We also propose next steps for infant fungal mycobiome research....

Published on Leave a comment on Gut Microbe Differences Between Active and Sedentary Women

A new study found differences in gut microbes between active women (they exercised at least the recommended amount) and those that are sedentary. When the gut bacteria were analyzed with modern tests (genetic sequencing) the active women had more of the health promoting beneficial bacteria such as Faecalibacterium prausnitzii, Roseburia hominis, and Akkermansia muciniphila than the sedentary women. The sedentary women also had some bacterial species not seen in the active women. The researchers said that exercise "modifies the composition of gut microbiota" (the gut microbes) in a way beneficial for health.

And what is the recommended minimal amount of exercise? The World Health Organization recommends at least 3 days of exercise per week for 30 minutes at a moderate intensity. Note that exercise can mean doing exercises, but it can also include walking briskly, intense housework (scrubbing, vacuuming with lots of bending, etc.), gardening (digging, raking, etc), or shoveling snow, etc. In this study the group of active women had at least 3 hours of physical exercise per week. Note that a sedentary lifestyle is associated with a high incidence of chronic diseases such as cardiovascular disease, cancer and diabetes, while physical exercise or activity has metabolic and immune health benefits (prevents disease).

But...reading the full study, the research also showed that the active group ate more fruits and vegetables - which we know has an effect on the gut microbiome and feeds beneficial bacteria. Although the diets of the 2 groups of women were similar in total carbohydrates, protein and fat content eaten, the active women ate more fruits, vegetables, and fiber, and the sedentary group ate more processed meat. So it looks like both exercise and a good amount of fruits and vegetables may be important for nurturing beneficial bacteria. By the way, the 3 species of beneficial bacteria mentioned currently are not found in any probiotic supplements on the market. (Earlier posts on the beneficial F. prausnitzii and Akkermansia muciniphila). From C. Bressa et al research article in PLoS ONE:

Differences in gut microbiota profile between women with active lifestyle and sedentary women

Physical exercise is a tool to prevent and treat some of the chronic diseases affecting the world’s population. A mechanism through which exercise could exert beneficial effects in the body is by provoking alterations to the gut microbiota, an environmental factor that in recent years has been associated with numerous chronic diseases. Here we show that physical exercise performed by women to at least the degree recommended by the World Health Organization can modify the composition of gut microbiota. Using high-throughput sequencing of the 16s rRNA gene, eleven genera were found to be significantly different between active and sedentary women. Quantitative PCR analysis revealed higher abundance of health-promoting bacterial species in active women, including Faecalibacterium prausnitzii, Roseburia hominis and Akkermansia muciniphila. Moreover, body fat percentage, muscular mass and physical activity significantly correlated with several bacterial populations. In summary, we provide the first demonstration of interdependence between some bacterial genera and sedentary behavior parameters, and show that not only does the dose and type of exercise influence the composition of gut microbiota, but also the breaking of sedentary behavior. ...continue reading "Gut Microbe Differences Between Active and Sedentary Women"