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Published on Leave a comment on Should We Be Worried That Humans Are Losing Many Species of Gut Microbes?

An article was just published in a research journal to discuss the fact that humans - in part due to lifestyles which include less dietary fiber (due to eating fewer varieties and amounts of plants) and due to medical practices (such as frequent use of antibiotics) has resulted in gut "bacterial extinctions". In other words, humans (especially those living an urban industrialized Western lifestyle) have fewer gut bacterial species than those living a more traditional lifestyle, and this loss of bacterial species is linked to various diseases. Humans can increase the number of certain bacterial species, but the loss of some bacterial species is forever. 

The researchers discuss that humans have the "lowest level of gut bacterial diversity"  of any hominid and primate. They stated that the shrinking of the variety of microbial species in the human gut (the gut microbiome) began early in human evolution (as humans started eating more meat), but that it has accelerated dramatically within industrialized societies. And that evidence is accumulating that this gut bacterial "depauperation" - the loss of a variety of bacterial species - may predispose humans to a range of diseases.  Some of it is due to evolution (as humans ate more meat), and some to lifestyle changes. A term is used throughout this paper: depauperate - which means lacking in numbers or variety of species in the gut microbiome (the microbial community or ecosystem).

Other research has also shown that eating a highly processed Western diet results in gut microbial changes that are linked to various diseases (here, here, here) - that is, the microbes being fed are those associated with diseases. Also, certain diets encourage certain microbial species to flourish (here, here).  Bottom line: studies find health benefits from higher levels of dietary fiber - from fruits, vegetables, seeds, nuts, whole grains, and legumes (beans). From Current Opinion In Microbiology:

The shrinking human gut microbiome

Highlights: Humans harbor the lowest levels of gut bacterial diversity of any hominid. Humans in industrialized nations harbor fewer gut bacterial taxa than any primate. Medical practices and lack of dietary fiber may drive gut bacterial extinctions. Depauperate microbiotas may predispose entire human populations to certain diseases.

Mammals harbor complex assemblages of gut bacteria that are deeply integrated with their hosts’ digestive, immune, and neuroendocrine systems. Recent work has revealed that there has been a substantial loss of gut bacterial diversity from humans since the divergence of humans and chimpanzees. This bacterial depauperation began in humanity’s ancient evolutionary past and has accelerated in recent years with the advent of modern lifestyles. Today, humans living in industrialized societies harbor the lowest levels of gut bacterial diversity of any primate for which metagenomic data are available, a condition that may increase risk of infections, autoimmune disorders, and metabolic syndrome. Some missing gut bacteria may remain within under-sampled human populations, whereas others may be globally extinct and unrecoverable.

A typical human harbors on the order of 1013 bacterial cells in the large intestine. This gut microbiota, which can contain over a thousand species, is deeply integrated with virtually every tissue and organ system in the body. Gut bacteria process difficult to digest components of the diet, promote angiogenesis in the intestine, train the immune system, regulate metabolism, and even influence moods and behaviors.

In contrast to hunter–gatherer to agricultural transitions, adoptions of industrial and post-industrial lifestyles have led to massive reductions in bacterial richness within human gut microbiotas. Individuals living in urban centers in the United States harbor fewer gut bacterial species on average than do individuals living more traditional lifestyles in Malawi , Venezuela, Peru, and Papua New Guinea.....Industrialized and traditional lifestyles differ in many respects, confounding the identification of the specific practices that have led to decreases in gut bacterial diversity within industrialized societies. One potential cause is the rise of food processing and the corresponding reductions in the intake of dietary fiber in favor of simple sugars. Recently, studies in model systems have indicated that long-term reductions in dietary fiber can lead to the extirpation of gut bacterial taxa from host lineages. 

Other potential causes of reduced gut bacterial diversity within industrialized human populations include certain modern medical practices. For example, longitudinal studies in humans have shown that levels of gut bacterial diversity decrease drastically after antibiotic use. Although bacterial richness may recover after treatment is completed, the timeline and extent of the restoration is highly subject-dependent. The consequences of antibiotic use on gut bacterial diversity may be most severe when treatment is administered during the early years of life, before the adult microbiota has fully formed .

Published on Leave a comment on Why Are Inflammatory Bowel Diseases In Very Young Canadian Children Increasing?

Sooo.....what is going on here? Why are very early onset (5 years and younger) pediatric inflammatory bowel diseases (IBD) in children increasing so rapidly in Canada? Inflammatory bowel diseases include Crohn's disease and ulcerative colitis. In the last two decades there has been an increase of 7.2% per year- to the point that it is among the highest in the world (9.68 per 100,000 children). Only Norway has a similar incidence (10.6 per 100,000 children under the age of 16 years), with Sweden having an incidence  of 12.8 per 100,000. Research studies find that the microbial communities are out of whack (dysbiosis) in IBD.

But why is the rate of IBD increasing in these northern countries? The researchers mention that rates are also increasing in the northern states in the US. Currently the reasons for the higher rates in Canadian and northern European children are not known. Some environmental factors such as lack of sunlight exposure and high rates of vitamin D deficiency, antibiotic use, and diet have been hypothesized as contributing to the pediatric IBD increase. Stay tuned... From Science Daily:

Inflammatory bowel diseases on the rise in very young Canadian children

Canada has amongst the highest rates of pediatric inflammatory bowel disease (IBD) in the world, and the number of children under five years old being diagnosed increased by 7.2 per cent every year between 1999 to 2010, according to a new study by researchers at the Institute for Clinical Evaluative Sciences (ICES), Children's Hospital of Eastern Ontario (CHEO) Research Institute and the Canadian Gastro-Intestinal Epidemiology Consortium.

"The number of children under five being diagnosed with IBD is alarming because it was almost unheard of 20 years ago, and it is now much more common," says Dr. Eric Benchimol, lead author of the study, scientist at ICES and a pediatric gastroenterologist at the Children's Hospital of Eastern Ontario Inflammatory Bowel Disease Centre, in Ottawa. IBD primarily includes Crohn's disease and ulcerative colitis, which are lifelong conditions that cause inflammation in the digestive tract, leading to chronic diarrhea, blood in the stool, abdominal pains and weight loss.

Researchers say a change in the bacterial composition of the gut may be to blame for the increase in IBD cases but they don't know what is causing the change. They suspect a combination of environmental risk factors could be to blame, such as early life exposure to antibiotics, diet, or lower levels of Vitamin D in Canadians.

The researchers found that the incidence of IBD has stabilized in children over the age of five, but in children under five it continues to rise rapidly. The researchers estimate that approximately 600 to 650 children are diagnosed with IBD every year in Canada. [Original study.]

Published on Leave a comment on Gut Microbes of Babies Exposed to Pets

More research supports that being exposed to pets during pregnancy or in the first months of life changes the gut bacteria, and in a way that is thought to be beneficial. The researchers found that infants exposed to pets prenatally or after birth (or both) had higher levels of two microbes that are associated with a lower risk of allergies and obesity. The two microbes are Ruminococcus and Oscillospira, but in case you're wondering - they are not (yet) available in probiotics.

And these differences in gut bacteria occurred no matter how the infants were born or fed (C-section, vaginal, breastfed, formula fed), or whether they received antibiotics at birth or not  - it was the pet exposure that was most important. The evidence is building that if one wants to avoid allergies in children - to have them exposed to furry pets in the first  year of life, and according to this study - perhaps before birth also. From Science Daily:

Pet exposure may reduce allergy and obesity

A new University of Alberta study showed that babies from families with pets -- 70 per cent of which were dogs -- showed higher levels of two types of microbes associated with lower risks of allergic disease and obesity.

"There's definitely a critical window of time when gut immunity and microbes co-develop, and when disruptions to the process result in changes to gut immunity," said Anita Kozyrskyj, a U of A pediatric epidemiologist....The latest findings from Kozyrskyj and her team's work on fecal samples collected from infants registered in the Canadian Healthy Infant Longitudinal Development study build on two decades of research that show children who grow up with dogs have lower rates of asthma. 

Her team of 12, including study co-author and U of A post-doctoral fellow Hein Min Tun, take the science one step closer to understanding the connection by identifying that exposure to pets in the womb or up to three months after birth increases the abundance of two bacteria, Ruminococcus and Oscillospira, which have been linked with reduced childhood allergies and obesity, respectively.

"The abundance of these two bacteria were increased twofold when there was a pet in the house," said Kozyrskyj, adding that the pet exposure was shown to affect the gut microbiome indirectly -- from dog to mother to unborn baby -- during pregnancy as well as during the first three months of the baby's life. In other words, even if the dog had been given away for adoption just before the woman gave birth, the healthy microbiome exchange could still take place.

The study also showed that the immunity-boosting exchange occurred even in three birth scenarios known for reducing immunity, as shown in Kozyrskyj's previous work: C-section versus vaginal delivery, antibiotics during birth and lack of breastfeeding. What's more, Kozyrskyj's study suggested that the presence of pets in the house reduced the likelihood of the transmission of vaginal GBS (group B Strep) during birth, which causes pneumonia in newborns and is prevented by giving mothers antibiotics during delivery. [Original study.]

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Published on 12 Comments on Kimchi Is Also Antifungal?

Last week a person told an amazing story in the comments section after a post on this site. After suffering from a "constant runny nose and a bad smell" in the nose for 2 years - which was diagnosed as "fungi and staph" in the sinuses - the person started doing "kimchi treatments" (as discussed in the Sinusitis Treatment Summary page). After 2 weeks a fungal ball was loosened, which came out of the sinuses and into the mouth, and was then spit out. About an inch in size - a smelly, grey/green, round fungal ball. Wow. Which leads to the question: Are any of the microbes in live kimchi anti-fungal?

Kimchi is an amazing live fermented food, typically made with cabbage and other vegetables and a variety of seasonings. Kimchi is the national dish of Korea and so there is tremendous interest in Korea in studying kimchi to learn about the many different microbial species in kimchi, including how they change over the course of fermentation.

It turns out that kimchi contains many species of bacteria, including various species of Lactobacillus - which are considered beneficial. Of course one of the species found in kimchi over the course of fermentation is Lactobacillus sakei - the bacteria that successfully treats sinusitis, and which I have written about extensively. L. sakei predominates over pathogenic bacteria (antibacterial) - which is why it is also used as a sausage starter culture (to kill off bacteria such as Listeria). One study found that the garlic, ginger, and leek used in making kimchi were the sources of L. sakei bacteria found in fermented kimchi.

Studies show that a number of the Lactobacillus species found in kimchi are antifungal against a number of different kinds of fungi.  Some of these antifungal bacteria are: Lactobacillus plantarum, L. cruvatus, L. lactis, L. casei, L. pentosus, L. acidophilus, and L. sakei (here, here).

A study from 2005 found that some Lactobacillus species found in kimchi are predominant over a fungi known to cause health problems in humans - Aspergillus fumigatus, a mold (fungi) which is the most common cause of Aspergillus infections. Aspergillus (of which there are many species) is very common both indoors and outdoors (on plants, soil, rotting plants, household dust, etc.), so people typically breathe in these fungal spores daily and without any negative effects. However, sometimes Aspergillus can cause allergic reactions, infections in the lungs and sinuses (including fungal balls), and other infections. (more information at CDC site).

The study found that 5 bacterial species in kimchi were also antifungal against other species of fungi (Aspergillus flavus, Fusarium moniliforme, Penicillium commune, and Rhizopus oryzae). The 5 bacterial species in kimchi that they found to be antifungal were: Lactobacillus cruvatus, L. lactis subsp. lactis, L. casei, L. pentosus, and L. sakei.

Just keep in mind that fungi are everywhere around us, and even part of the microbes that live in and on us - this is our mycobiome. We also breathe in a variety of fungi (mold spores) every day. In healthy individuals (even babies) 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.

If the populations get too unbalanced (e.g., antibiotics can kill off bacteria, and then an increase in fungi populations take their place) then ordinarily non-harmful fungi can become pathogenic. Or other pathogenic microbes can enter the community (e.g., through infection), and the person becomes ill.

IN SUMMARY: Kimchi has beneficial bacteria in it that are effective not just against bacteria (antibacterial), but also against some kinds of fungi (antifungal). One 2016 review study went so far as to say: "Kimchi possesses anti-inflammatory, antibacterial, antioxidant, anticancer, antiobesity, probiotic properties, cholesterol reduction, and antiaging properties."

Experiences of my family and people writing suggest that the L. sakei in kimchi (and other products) is also antibiofilm. Hopefully, there will be some research on this in the future. But in the meantime, please keep writing to me about fungal complications of sinusitis, and especially if kimchi, L. sakei products, or other probiotics helped.

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)

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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 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"