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Category: microbes

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Published on 4 Comments on Which Product Will Better Treat UTIs?

Image result for pills wikipedia Hah!  A study that builds on what is already known by many women - that the non-prescription product D-mannose works for urinary tract infections (UTIs). D-mannose is amazingly effective for urinary tract infections caused by E. coli bacteria (up to 90% of UTIs), even infections that  keep recurring (30 to 50% of infections), and which don't respond to numerous antibiotics.

D-mannose is effective because it attaches to E. coli bacteria, and prevents them from attaching to the walls of the urinary tract. But as women know, there are many (all effective) D-mannose products on the market - so the big pharmaceutical companies can't claim it as their own (with patents) for the big bucks $$$.

So... this study is basically chemically reformulating the mannose sugar (which is in D-mannose) for a new product (mannosides) - one that they can claim as their own. Maybe it'll be a little better than ordinary D-mannose, and maybe not. Human studies are needed.

By the way, this study may be big news to physicians because most don't seem to know about D-mannose as a treatment for UTIs - they all seem to focus just on antibiotics and perhaps cranberry juice in treating UTIs. This may be because D-mannose is considered as an "alternative treatment". And I could find only one study that compares antibiotics and D-mannose for recurrent UTIs - and guess which one did a little better?  Yup...D-mannose (see post). From Medical Xpress:

New treatment reduces E. coli, may offer alternative to antibiotics

Urinary tract infections (UTIs) are among the most common infections, and they tend to come back again and again, even when treated. Most UTIs are caused by E. coli that live in the gut and spread to the urinary tract. A new study from Washington University School of Medicine in St. Louis has found that a molecular decoy can target and reduce these UTI-causing bacteria in the gut. With a smaller pool of disease-causing bacteria in the gut, according to the researchers, the risk of having a UTI goes down...."This compound may provide a way to treat UTIs without the use of antibiotics."

Close to 100 million people worldwide acquire UTIs each year, and despite antibiotic treatment, about a quarter develop another such infection within six months. UTIs cause painful, burning urination and the frequent urge to urinate. In serious cases, the infection can spread to the kidneys and then the bloodstream, where it can become life-threatening. Most UTIs are caused by E. coli that live harmlessly in the gut. However, when shed in the feces, the bacteria can spread to the opening of the urinary tract and up to the bladder, where they can cause problems. Conventional wisdom holds that UTIs recur frequently because bacterial populations from the gut are continually re-seeding the urinary tract with disease-causing bacteria.

Hultgren, graduate student Caitlin Spaulding, and colleagues reasoned that if they could reduce the number of dangerous E. coli in the gut, they could reduce the likelihood of developing a UTI and possibly prevent some recurrent infections. First, the researchers identified genes that E. coli need to survive in the gut. One set of genes coded for a kind of pilus, a hairlike appendage on the surface of E. coli that allows the bacteria to stick to tissues, like molecular velcro. Without this pilus, the bacteria fail to thrive in the gut. Earlier studies found that the identified pilus attaches to a sugar called mannose that is found on the surface of the bladder. Grabbing hold of mannose receptors on the bladder with the pilus allows the bacteria to avoid being swept away when a person urinates. Bacteria that lack this pilus are unable to cause UTIs in mice.

Previously, Hultgren and co-author, James W. Janetka, PhD, an associate professor of biochemistry and molecular biophysics at Washington University, chemically modified mannose to create a group of molecules, called mannosides, that are similar to mannose but changed in a way that the bacteria latch onto them more tightly with their pili. Unlike mannose receptors, though, these mannosides are not attached to the bladder wall, so bacteria that take hold of mannosides instead of mannose receptors are flushed out with urine.

Since the researchers found that this same pilus also allows the bacteria to bind in the gut, they reasoned that mannoside treatment could reduce the number of E. coli in the gut and perhaps prevent the spread of the bacteria to the bladder. To test this idea, they introduced a disease-causing strain of E. coli into the bladders and guts of mice to mirror the pattern seen in people. In women with UTIs, the same bacteria that cause problems in the bladder usually also are found living in the gut.

The researchers gave the mice three oral doses of mannoside, and then measured the numbers of bacteria in the bladders and guts of the mice after the last dose of mannoside. They found that the disease-causing bacteria had been almost entirely eliminated from the bladder and reduced a hundredfold in the gut, from 100 million per sample to 1 million. .... researchers measured the composition of the gut microbiome after mannoside treatment. They found that mannoside treatment had minimal effect on intestinal bacteria other than the ones that cause most UTIs. This is in stark contrast to the massive changes in the abundance of many microbial species seen after treatment with antibiotics. Furthermore, since mannoside is not an antibiotic, it potentially could be used to treat UTIs caused by antibiotic-resistant strains of bacteria, a growing problem. 

Published on Leave a comment on Will We Use Predator Bacteria To Destroy Superbugs In the Future?

Great idea and one that this blog has been pushing for a long time - the use of beneficial bacteria to get rid of other harmful bacteria. Some researchers refer to the bacteria acting as "living antibiotics" when they overpower harmful bacteria.

Researchers such as Daniel Kadouri, a micro-biologist at Rutgers School of Dental Medicine in Newark, are studying bacteria that aggressively attack harmful  bacteria, and calling them "predator bacteria". They are focusing on one specific bacteria - Bdellovibrio bacteriovorus, a gram-negative bacteria that dines on other gram-negative bacteria. They hope to eventually be able to give this bacteria as a medicine to humans , and then this predator bacteria would overpower and destroy "superbugs" (pathogenic bacteria that are resistant to many antibiotics). A great idea, but unfortunately the researchers think that it'll take about 10 more years of testing and development before it's ready for use in humans. From Science News:

Live antibiotics use bacteria to kill bacteria

The woman in her 70s was in trouble. What started as a broken leg led to an infection in her hip that hung on for two years and several hospital stays. At a Nevada hospital, doctors gave the woman seven different antibiotics, one after the other. The drugs did little to help her. Lab results showed that none of the 14 antibiotics available at the hospital could fight the infection, caused by the bacterium Klebsiella pneumoniae.... The CDC’s final report revealed startling news: The bacteria raging in the woman’s body were resistant to all 26 antibiotics available in the United States. She died from septic shock; the infection shut down her organs.  ...continue reading "Will We Use Predator Bacteria To Destroy Superbugs In the Future?"

Published on Leave a comment on Big Pharma’s Pollution Leading To Superbugs

Image result for pills wikipedia Nowadays there is tremendous concern about the spread of antibiotic resistant bacteria  or "superbugs" throughout the world. Articles frequently mention India being at the epicenter of this crisis - that is, the source of many antibiotic resistant strains (both in and out of hospitals), which then travel throughout the world due to global travel. The massive overuse and misuse of antibiotics (whether in humans, animals, and even crops) is usually given as the major reason for the development of antibiotic resistant strains of bacteria (here, here, and here).

Thus the following article about unchecked pollution from pharmaceutical companies in India fueling the creation of deadly superbugs was shocking to read - and it may explain why the problem is so severe there. Note that the Indian companies supply just about all the world's major drug companies with antibiotics and anti-fungals. It appears that the companies are ignoring local laws (which have been called "toothless") which would cut down on the pollution. What is stressed in the article is that one of the world’s biggest drug production hubs (the Indian city of Hyderabad) is producing dangerous levels of pharmaceutical pollution, and the international agencies that ensure drug safety are basically ignoring this problem (and doing little to address it).

Thousands of tons of pharmaceutical waste is produced each day by the many pharmaceutical companies in Hyderabad, India, which is then contaminating the water sources in the area. With the result that water samples (from rivers, lakes, groundwater, drinking water, surface water, treated sewage water) in  that area contain bacteria and fungi resistant to multiple drugs (superbugs), and these superbugs then get spread to humans throughout India and eventually globally.   This article is definitely worth reading in its entirety. Excerpts from The Bureau of Investigative Journalism:

Big Pharma's Pollution Is Creating Deadly Superbugs While The World Looks The Other Way

Industrial pollution from Indian pharmaceutical companies making medicines for nearly all the world’s major drug companies is fueling the creation of deadly superbugs, suggests new research. Global health authorities have no regulations in place to stop this happening. A major study published today in the prestigious scientific journal Infection found “excessively high” levels of antibiotic and antifungal drug residue in water sources in and around a major drug production hub in the Indian city of Hyderabad, as well as high levels of bacteria and fungi resistant to those drugs. Scientists told the Bureau the quantities found meant they believe the drug residues must have originated from pharmaceutical factories.

The presence of drug residues in the natural environment allows the microbes living there to build up resistance to the ingredients in the medicines that are supposed to kill them, turning them into what we call superbugs. The resistant microbes travel easily and have multiplied in huge numbers all over the world, creating a grave public health emergency that is already thought to kill hundreds of thousands of people a year.

When antimicrobial drugs stop working common infections can become fatal, and scientists and public health leaders say the worsening problem of antibiotic resistance (also known as AMR) could reverse half a century of medical progress if the world does not act fast. Yet while policies are being put into place to counter the overuse and misuse of drugs which has propelled the crisis, international regulators are allowing dirty drug production methods to continue unchecked. Global authorities like the Food and Drug Administration and the European Medicines Agency strictly regulate drug supply chains in terms of drug safety - but environmental standards do not feature in their rulebook. Drug producers must adhere to Good Manufacturing Practices (GMP) guidelines - but those guidelines do not cover pollution.

The international bodies say the governments of the countries where the drugs are made are the ones responsible for stopping pollution - but domestic legislation is having little impact on the ground, say the study's authors. The lack of international regulation must be addressed, they argue, highlighting the grave public health threat faced by antibiotic resistance as well as the rampant global spread of superbugs from India, which has become an epicentre of the crisis.

A group of scientists based at the University of Leipzig worked with German journalists to take an in-depth look at pharmaceutical pollution in Hyderabad, where 50% of India’s drug exports are produced. A fifth of the world’s generic drugs are produced in India, with factories based in Hyderabad supplying Big Pharma and public health authorities like World Health Organisation with millions of tons of antibiotics and antifungals each year.

The researchers tested 28 water samples in and around the Patancheru-Bollaram Industrial zone on the outskirts of the city, where more than than 30 drug manufacturing companies supplying nearly all the world’s major drug companies are based. Thousands of tons of pharmaceutical waste are produced by the factories each day, the paper says. Almost all the samples contained bacteria and fungi resistant to multiple drugs (known as MDR pathogens, the technical name for superbugs). Researchers then tested 16 of the samples for drug residues and found 13 of them were contaminated with antibiotics and antifungals. Previous studies have shown how exposure to antibiotics and antifungals in the environment causes bacteria and fungi to develop immunity to those drugs.

Environmental pollution and poor management of wastewater in Hyderabad is causing “unprecedented antimicrobial drug contamination” of surrounding water sources, conclude the researchers - contamination which appears to be driving the creation and spread of dangerous superbugs which have spread across the world. Combined with the mass misuse of antibiotics and poor sanitation, superbugs are already having severe consequences in India - an estimated 56,000 newborn babies die from resistant infections there each year.

The companies in question strongly deny that their factories pollute the environment, and the sheer number of factories operating in Hyderabad means it is impossible to identify exactly which companies are responsible for the contamination found in the samples tested. What is clear is one of the world’s biggest drug production hubs is producing dangerous levels of pharmaceutical pollution, and the international bodies tasked with ensuring drug safety are doing little to address it.

Around 170 companies making bulk drugs like antibiotics operate in and around Hyderabad, the majority clustered in sprawling industrial estates along the banks of the Musi river. Companies in Europe and the US, as well as health authorities like WHO and the UK’s NHS are reliant on drugs being produced in these factories.

The area has long been criticised for its pollution, which has continued unabated despite decades of campaigning by Indian NGOs, say the report authors. In 2009 the Patancheru-Bollaram zone was classified as “critically polluted” in India’s national pollution index and construction in the area was banned. But the government relaxed the rules in 2014 and building was allowed to begin again. Last year India’s Supreme Court ordered the country’s pharmaceutical companies to operate a zero liquid waste policy, but “massive violations” have reportedly occurred, says the Infection report....India has become the epicentre of the global drug resistance crisis, with 56,000 newborn Indian babies estimated to die each year from drug-resistant blood infections, and 70 to 90% of people who travel to India returning home with multi-drug-resistant bacteria in their gut, according to the study.

Researchers took water samples from rivers, lakes, groundwater, drinking water and surface water from rural and urban areas in and around the industrial estate, as well as pools near factories and water sources contaminated by sewage treatment plants. Four were taken from taps, one from a borehole, and the remaining 23 were classed as environmental samples. The samples were tested for bacteria resistant to multiple drugs (known as MDR pathogens, the technical name for superbugs). The researchers then tested 16 of the samples for the antibiotics and antifungals used to treat infections. All samples apart from one taken from tap water at a four star hotel were found to contain drug-resistant bacteria. All 23 environmental samples contained carbapenemase-producing bacteria - a group of bugs dubbed the “nightmare bacteria” because they are virtually untreatable and kill 40-50% of people whose blood gets infected with them.

Of the 16 samples then tested for drug residue, 13 were found to be contaminated with antibiotics and antifungals, some in disturbingly high levels. The researchers compared the levels of residue to limits recommended by leading microbiologists; once levels exceed those limits it is likely that superbugs will develop. The amounts of antimicrobials found in the new tests were “eye-wateringly high”, said Dr Mark Holmes, a microbiologist at the University of Cambridge. “The quantities involved mean the amount in the water is almost the same as a therapeutic dose,” he said, calling on the Indian authorities to investigate immediately by testing each factory’s effluent. 

There are reams of regulations and stipulations that manufacturers have to adhere to in order to export their products to the US and Europe – known as the Good Manufacturing Practices (GMP) framework. These focus on making sure drugs are safe, pure, and effective. Stringent inspections by the FDA, WHO and European authorities check that these rules are being followed. However these regulations do not address environmental concerns. Inspectors have no mandate to sanction a factory for polluting, failing to treat its waste or other environmental problems – this falls within the remit of local governments.

Published on Leave a comment on Stop Using Antimicrobial Containing Products

Stop using the damn antibacterial products! Yes, stop using stuff that says "antibacterial", "antimicrobial", "germ-killing",  or "anti-odor". Whether in personal care items, or bedding, or socks, or hand wipes, or wherever else you see those labels - don't buy them and try to avoid using them. Plain soap works just as well for cleaning hands (see FDA page). The "antibacterial" chemicals in soaps, toothpastes, body washes, etc. are absorbed by the body where they may do harm. Yes - HARM. The harms may not be known initially, but over and over, at some later point, the various chemicals are shown to cause harm - whether in humans or the environment, or both.

A case in point is the antimicrobial triclosan. It has been used for years in soooo many products, and religiously used by those concerned with "killing germs". It is now finally banned by the FDA from soaps and body washes because of the harms it causes. These include various health effects - and also because it's an endocrine disruptor (disrupts hormones).  And yes, it also crosses the placenta and has been associated with effects on the developing baby. For example, a recent study found an "inverse relationship" - that higher levels of triclosan in the mothers' urine during pregnancy (meaning they had used and absorbed more triclosan products) were associated with lower birth weight, length, head circumference, and gestational age (length of pregnancy). Of special concern to us at Lacto Bacto is that it also disrupts our microbes - remember that antimicrobial products (whether Triclosan in soap or antibiotics) kill off both beneficial and harmful bacteria.

As a recent study shows - triclosan is absorbed by pregnant women (and can be measured in their urine) and, it is absorbed and found in the urine of children who washed their hands or brushed their teeth with products containing triclosan.  And the higher the socioeconomic status, the more triclosan in the body - after all, people pay a premium for products that are "antimicrobial". While triclosan is now banned from being used in certain products (soaps and body washes), it is still allowed in many, many other products. And there are all those other antimicrobials that also should NOT be used. So please read the labels, especially the ingredient lists, and try to avoid antimicrobial, antibacterial, germ-killing, and anti-odor products. From Environmental health News:

Hygiene leaves kids with loads of triclosan

Levels of a controversial chemical meant to kill bacteria spike in the bodies of young children after they brush their teeth or wash their hands, according to a new study. U.S. manufacturers are phasing triclosan out of hand soaps after the Food and Drug Administration banned it effective last year amid concerns that the compound disrupted the body's hormone systems. It remains in Colgate Total toothpaste, some cleaning products and cosmetics. Health experts say exposure is best avoided for babies in the womb and developing children.

The latest study, published in the journal Environmental Science & Technology, is one of the first to show that children’s levels rise through their first few years of life. Hand washing and teeth brushing have speedy, significant impact on levels, the researchers found. Braun and colleagues tested the urine of 389 mothers and their children from Cincinnati, collecting samples from the women three times during pregnancy and from the children periodically between 1 and 8 years old.

They found triclosan in more than 70 percent of the samples. Among 8 year olds, levels were 66 percent higher in those that used hand soap. And more washing left the children with higher loads—those who reported washing their hands more than five times per day had more than four times the triclosan concentrations than those washing once or less per day. Children who had brushed their teeth within the last day had levels 2.5 times higher than those who had a toothpaste-free 24-hour span.

Braun said the levels of triclosan rose as the children aged, eventually leveling off. “Their levels were almost to moms’ levels by the time they reached 5 to 8 years of age.” This, he said, is likely due to more frequent use of personal care products as the kids aged. Despite the hand soap ban, triclosan remains on the market because it is effective at fighting plaque and gingivitis. Colgate uses 0.3 percent of the antibacterial to “fight harmful plaque germs.”.

Braun, however, said there is “quite compelling” evidence from animal studies that triclosan decreases thyroid hormone levels. Properly functioning thyroid hormones are critical for brain development. Just last month, using the same mothers and children, Braun and others reported that mothers’ triclosan exposure during pregnancy was linked to lower birth weights, smaller heads and earlier births. In addition, Pessah and colleagues reported triclosan hinders proper muscle development. The researchers used mice and fish, finding that triclosan affects the process responsible for muscle contraction.

Published on Leave a comment on Cold Water Versus Hot Water In Removing Bacteria From Hands

Image result for washing hands OK,  the study results sound promising: that washing with cold water is as good as washing with warm or hot water for removing bacteria from the hands. And that type of soap didn't matter - both the anti-microbial soap and ordinary soap were equally effective. But...the researchers only looked at one strain of bacteria - E. coli (full name Escherichia coli (ATCC 11229)), and there are MANY microbes and viruses out there that cause problems. So I would view it as a nice start ( a preliminary study), but not the final word. From Science Daily:

Handwashing: Cool water as effective as hot for removing germs

We all know that washing our hands can keep us from spreading germs and getting sick. But a new Rutgers-New Brunswick study found that cool water removes the same amount of harmful bacteria as hot. ....In the Rutgers study, published in the June issue of the Journal of Food Protection, high levels of a harmless bacteria were put on the hands of 21 participants multiple times over a six-month period before they were asked to wash their hands in 60-degree, 79-degree or 100-degree water temperatures using 0.5 ml, 1 ml or 2 ml volumes of soap.

 "Also we learned even washing for 10 seconds significantly removed bacteria from the hands." While the study indicates that there is no difference between the amount of soap used, more work needs to be done to understand exactly how much and what type of soap is needed to remove harmful microbes from hands, said co-author Jim Arbogast, vice president of Hygiene Sciences and Public Health Advancements for GOJO. "This is important because the biggest public health need is to increase handwashing or hand sanitizing by food service workers and the public before eating, preparing food and after using the restroom," Arbogast said.

These findings are significant, particularly to the restaurant and food industry, because the U.S. Food and Drug Administration issues guidelines, every four years, to states. Those guidelines currently recommend that plumbing systems at food establishments and restaurants deliver water at 100 degrees Fahrenheit for handwashing.

Schaffner said the issue of water temperature has been debated for a number of years without enough science to back-up any recommendation to change the policy guidelines or provide proof that water temperature makes a difference in hand hygiene. Many states, in fact, interpret the FDA guidelines as a requirement that water temperature for handwashing must be 100 degrees, he said. [Original study.]

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Published on 7 Comments on Will Snot Transplants Work In Treating Chronic Sinusitis?

An amazing new study is about to start in Sweden - this study will see if "snot transplants" work for the treatment for chronic sinusitis! Will this turn out to be a permanent treatment? While studies show that probiotic supplements tend not to stick around in the gut (they're gone after about a week), people receiving a fecal microbiota transplant (FMT) find that these microbial communities do stick around (colonize).  So there is something about getting an entire microbial community (bacteria, fungi, viruses) that is more effective than just a few species that are in typical probiotic supplements.

We have found the same problem in sinusitis treatment - the Lactobacillus sakei treatment works to treat sinusitis, but then doesn't stick around - as evidenced by having to treat again after a cold or sore throat.  And so we treat again - and again it's successful. And this happens again and again. Sooo.... it's important to find out if a transplant of the entire microbial community of snot (the sinonasal microbiome) works. And if works, will the treatment be a permanent one? I also wonder.... Several people have mentioned this idea to me, but has anyone with sinusitis tried a "snot transplant" at home? (And yes, this is self-experimentation.)

The description and purpose of the study refer to what this site has discussed for several years: the sinus microbiome is out of whack (dysbiosis) in chronic rhinosinusitis (CRS), whether due to antibiotics or something else (viruses, etc). The study will enroll 30 people, start May 15, 2017, and end December 31, 2018. The purpose of the study is to have patients with chronic rhinosinusits without nasal polyps (CRSsNP) receive microbiome transplants from healthy donors without any sinus problems. They would receive a snot transplant for 5 days in a row. Unfortunately we'll have to wait at least 1 1/2 years for any results. Excerpts from clinical trails.gov:

Sinonasal Microbiome Transplant as a Therapy for Chronic Rhinosinusitis Without Nasal Polyps (CRSsNP)

Purpose: Chronic rhinosinusitis (CRS) is a disease associated with impaired quality of life and substantial societal costs. Though sometimes co-appearing with other conditions, such as asthma, allergy, and nasal polyps, many cases present without co-morbidities. Micro-biological diagnostic procedures are frequently undertaken, but the results are often inconclusive. Nevertheless, antibiotics are usually prescribed, but invariably with limited and temporary success. Accordingly, there is a need for new treatments for CRS.

Recent studies indicate that the sinuses are colonized by a commensal microbiome of bacteria and that damage to this natural microbiome, by pathogens or antibiotics, may cause an imbalance that may promote CRS. Therefore, treatments that restore the commensal microbiome may offer an alternative to current protocols. Arguably, as suggested by studies on patients with intestinal infections (next paragraph), one such possibility may be to transfer a "normal microbiome" to patients with CRS.

A disrupted microbiome is linked to intestinal clostridium difficile infections. Probiotic restitution therapy may be effective even in cases recalcitrant to antibiotic treatment. However, a key to effective probiotic restitution is selecting the bacteria that facilitate regrowth of normal microbiome. As an answer to this, researchers have chosen to simply transplant the entire microbiome from a healthy donor. In the case of clostridium difficile infection in the form of faecal transplants.

In this study, we will examine the possibility to treat patients with chronic rhinosinusitis without polyps (CRSsNP) with complete sinonasal microbiomes obtained from healthy donors. Our analysis will focus on symptoms and signs of disease as well as on nasal inflammatory and microbiological indices.

Detailed Description: Over the last few years the theory of a damaged microbiome as a cause or promoting factor behind chronic rhinosinusitis has gained increasing interest from the scientific community. A number of studies aimed at investigating the microbiota of the nose and paranasal sinuses in health and disease has been published with very varying outcomes. Furthermore, other studies have been aimed at probiotic treatment of sinonasal disease either locally or through immunologic manipulation via the gastrointestinal microbiota.

A problem common to all these studies is that studies examining the normal nasal microbiota have identified a great amount of different bacterial species. It is as of today not known which individual species or combinations of species that promotes health. 

In this study the investigators aim at recruiting patients suffering from chronic rhinosinusitis without polyps (CRSsNP) and healthy participants without any history sinonasal disease. The patients and the healthy participants will be examined for infectious diseases in a manner similar to other medical transplant procedures to minimize the risk for the recipients. The patients will then be treated with antibiotics to reduce the bacterial load of the nose and the paranasal sinuses. After the patient has finished the antibiotic treatment a microbiome transplant will be harvested from the healthy participant as a nasal lavage. The raw lavage fluid will then be used to transplant the microbiome to the patient. The procedure will be repeated for five consecutive days. The outcome measures analysed will focus on subjective sinonasal health and symptoms of the patients but also include nasal inflammatory and microbiological indices.

Published on Leave a comment on The Importance of Dirt

Great article about the importance of both dirt (it's alive!) and exposure to nature. Main points: It’s estimated that children now spend less time outside than the average prisoner, and that that the average American adult now spends 93 percent of their life indoors (in our homes, workplaces, cars, etc.). It is now thought that human beings need to be exposed to lots of microbes when young for proper immune system development - and this means exposure to the microbes in dirt (for example, young children benefit from playing in the dirt!). There is much harm on many levels from monocultures (whether huge fields of only one crop or "perfect" lawns) sustained by large amounts of chemicals (pesticides and fertilizers). In contrast, a lawn with diversity (clover, flowering "weeds", etc) avoids the use of dangerous chemicals, has benefits to wildlife and humans, and is also a "bee habitat".

Also, what is rarely discussed, but very important to the health of our environment: An estimated quarter of a million acres are paved or repaved in the United States each year - so that “asphalt is the land’s last crop". Paving over the land is "soil sealing", because this cuts off air and water, and kills the microorganisms and insects that live there. This results in dirt being killed off forever. Yikes! Why isn't this discussed more? Excerpts from National Geographic:

WHY YOU NEED MORE DIRT IN YOUR LIFE

It’s estimated that children now spend less time outside than the average prisoner. This could have devastating effects: Kids need to be exposed to the microbes in the soil to build up their defences against diseases that may attack them later. But it’s not just children, Paul Bogard explains in his new book, The Ground Beneath Us. The EPA estimates that the average American adult now spends 93 percent of their life indoors. As we retreat indoors, more and more of the earth is disappearing, with an estimated quarter of a million acres paved or repaved in the United States each year. 

When National Geographic caught up with Bogard by phone at his home in Minnesota, the author explained why Iowa is the most transformed state in the U.S., how soil is alive but we’re killing it, and how places where terrible things happened can become sacred ground.

You write, “We are only just now beginning to understand the vast life in the soil, what it does, and how our activities on the surface may affect it.” Talk us through some highlights of the new science—and how you became so passionate about dirt.

It began with this statistic: that those of us in the Western world now spend about 90-95 percent of our time inside, in our houses, workplaces, in our cars. We’re living our lives separated from the natural world. When we walk outside, many of us walk on pavement. There’s this literal separation from the natural ground, from the soil, the dirt. It made me think, what are the costs of this separation? And it struck me as symbolic of our separation of these many different kinds of grounds that sustain us. Our food, water, energy, even our spirits come from these different grounds.

One of the first scientific discoveries I found was the hypothesis that human beings need to be exposed to the biota in the dirt, on the ground, especially when they’re kids, as a way of inoculating us to diseases that appear later in life. Kids these days are not being exposed to dirt because they’re not allowed to play outside. Their parents think dirt is dirty. But both the newest science and the oldest traditions tell us the same thing, which is that the ground is alive. The ground gives us life. And in the book, I tried to touch on both of those things.

One expert you quote says, “asphalt is the land’s last crop.” Talk about “soil sealing” and how roads and suburbs are literally eating away at the ground beneath our feet.

Soil sealing is one of the most shocking things I learned about. When we pave over the natural ground, we cut it off from the air and water that the life in the ground needs to stay alive. We essentially kill that ground. There is an argument that, if we pulled up the pavement and worked hard to rejuvenate that ground, we could bring it back. But the scientists I talked to said, when you pave it over, it’s the last crop, the last thing that’s going to grow there. We’re not moving in the direction of pulling pavement up. We’re moving in the opposite direction where we’re paving some of our most fertile ground, the ground that we’re going to need to feed a growing population.

You also had childhood affection for Iowa. But when you went back to research your book, you changed your mind. Why?

As a child, I was enamoured with the beauty of the green corn stalks, the black dirt, and what I thought was the natural topography. Coming back older and with a new understanding of the ground, it made me uncomfortable because Iowa is the most transformed state in the union. Some 97 percent of the natural ground has been altered, changed, or transformed. As one biologist said, “it’s an open air monoculture owned by monopolies.” So, instead of my romantic, childhood view of miles of corn stalks, the beauty of life growing, and the colour green, I saw it as this monoculture where another life isn’t allowed to grow.

Americans love their lawns and spend billions of dollars keeping them green and weed free. But we are also paying a high price for this perfect turf, aren’t we?

Oh my! We really are, certainly ecologically, paying a high price. America’s greatest crop, the thing we grow the most of, is our turf grass lawns. And the amounts of pesticides and chemical fertilisers we dump onto these lawns, and the amount of water that we use to grow them, is enormous. As a result, we have problems with runoff draining into our rivers and the lawns themselves tend to become monocultures, where nothing else grows but the turf grass. What a massive opportunity is being lost! We could have lawns that are more biologically diverse and pollinator-friendly. There’s also evidence that a number of illnesses are associated with coming into contact with these chemical fertilisers and pesticides.

Published on Leave a comment on We All Have Biofilms In Our Sinuses

Once again a study looked at biofilms in sinuses - but this time in the sinuses of healthy people and not those with sinusitis. Various different species of bacteria and small size "microcolonies" or biofilms were found in the healthy maxillary sinuses of all 30 people - so yes, it appears that the presence of biofilms in the sinuses is normal in healthy people. And yes, the presence of bacteria (even some low levels of species which are typically associated with sinusitis) are normally found in the sinuses of healthy people.  (Earlier research also found this last finding.)

The researchers state that it is normal for people to have "small size bacterial microcolonies" (of different kinds of bacteria) in the sinuses. The researchers theorized that the biofilms are probably "in equilibrium" under the influence of  "inhibiting defensive factors of the body", but they can become a source of infection if there are favorable conditions (such as illness). In other words, the researchers said that these biofilms are more like "bacteria films" in that they contain bacteria, but they live in small colonies that don't cause an inflammatory response with sinusitis symptoms.

One negative of this study was that advanced genetic sequencing was not done on the samples. Instead all samples taken from the people were cultured, which we now know misses a lot of bacterial and other microbial species (fungi, viruses). They looked at the microcolonies (biofilms) with scanning microscopes. Thus, while they found an assortment of bacteria on the sinuses of each person - they only found a total of 41 bacterial species among 30 persons. This is in contrast to studies using modern genetic sequencing that found hundreds of microbial species in healthy sinus microbiomes (microbial communities).

The other issue is that it is not clear to me if there were biofilms or  microcolonies that contained "beneficial" species in any of the samples. Other research suggests that biofilms of beneficial bacteria are also found in humans, and that this is one way beneficial bacteria that normally can't survive with exposure to oxygen can survive oxygen (the slime coating on the colony protects the bacteria within).

Other studies also stress that in healthy people there is "homeostasis" or "equilibrium" among all the microbes living in the sinuses, - a microbial community (which includes biofilms), and which helps maintain sinus health. See post with discussion of Mackenzie et al 2017 study: "A stable network of microbial interactions, established through processes such as niche competition, nutrient cycling, immune evasion, and biofilm formation help maintain homeostasis during health." But, as has been usual in recent sinus research, the current study also stated that much is unknown, that there are theories which are not yet proven one way or another, and more research needs to be done. Of course.... Excerpts from Morawska-Kochman et al research article in PLoS ONE:

The presence of bacterial microcolonies on the maxillary sinus ciliary epithelium in healthy young individuals

The aim of this cross-sectional in vitro study was to evaluate the mucosal surfaces of healthy maxillary sinuses, explore different forms of bacterial microorganism colonies present on the mucous membrane, and determine a mucosal surface area they occupy. Samples of the maxillary sinus mucosa were collected from 30 healthy patients (M = 11; F = 19). The material was obtained during the Le Fort I osteotomy performed during corrective jaw surgery. The morphological and morphometric analysis of sinus mucosa and bacterial film that was grown on it was performed using scanning electron microscopy (SEM) as well as imaging software.

Scanning electron microscopy analysis showed the presence of different bacterium and bacteria-like structures in all the analyzed samples. In most cases, the bacterial film was mostly composed of diplococci-like and streptococci-like structures on the mucosa of the paranasal sinus. In any case, the mucous layer did not cover the whole lining of the evaluated sample. Each colony consists of more than 20 single bacterial cells, which has grown in aggregates.

Under the conditions of normal homeostasis of the body, the maxillary sinuses present diverse bacterial colonization. The bacteria are dispersed or concentrated in single microcolonies of the biofilm on the border of the mucous covering the ciliary epithelium. There is no uniform layer of the biofilm covering the mucosa of the maxillary sinuses. Because the biofilm is detected on healthy individuals sinus mucosa, the clinical question if it may become pathogenic is unclear and require an explanation.

It should also be noted that pathogenic organisms, such as Pseudomonas aeruginosa, Haemophilus influenzae, Streptococcus pneumoniae, or Staphylococcus aureus can be found in patients without active symptoms of the disease. Usually, colonization is defined as the presence of bacteria on the mucous membrane, and the lack of the inflammatory response distinguishes it from an infection.

However, the bacteria film in contrast to typical biofilm might be defined by the presence of bacteria, that growth in colonies without inducing the inflammatory response. Thus, the aim of the study was to evaluate the mucosal surfaces of the healthy maxillary sinuses (without any history of recent acute sinus inflammations or chronic inflammation in the past), to identify different forms of bacterial microorganisms which could, under certain conditions, become opportunistic or pathogenic and determine a mucosal surface of the area they occupy.

Scanning electron microscope investigations revealed the presence of bacterial film on the surface of maxillary sinus mucosa in 30 patients. Moreover, microbiological examinations of specimens taken from study participants revealed the presence of various types of aerobic and anaerobic bacteria in 28 cases (93.34%) out of 30 studied samples. All samples had mixed flora. In total, 41 different microorganisms were isolated. The most frequently found microorganism was Streptococcus spp. in over 90% of all samples, while Propionibacterium acnes were present in 29,2% of samples, and Staphylococcus spp. was present in 17% of the samples.

Scanning electron microscopy analysis showed that the mucous layer has a thickness of 200 nm (± 40), which is covered up to 5% of the surface of each sample. The analysis showed the presence of bacteria-like microcolony structures in all analyzed samples.....Each colony consisted of more than 20 single bacterial cells, that had grown in aggregates. These clearly indicate the existence of a bacterial-like microcolony on maxillary sinus mucosa.

Bacterial microcolonies on the maxillary sinus ciliary epithelium in healthy young individuals. Credit: Morawska-Kochman et al.

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.]