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Category: human microbiome

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An exciting research study which finds that it is normal for bacteria to live in the bladders of healthy women, and that urine is not sterile. After further studies on the microbial communities in the bladder, perhaps bacterial treatments for various urinary problems? From Science Daily:

Study debunks common myth that urine is sterile: Bacterial differences found in urine of healthy women and women with overactive bladder

Bacteria live in the bladders of healthy women, discrediting the common belief that normal urine is sterile. This study also revealed that bladder bacteria in healthy women differ from the bladder bacteria in women affected by overactive bladder (OAB), which causes a sudden need to urinate.

Approximately 15 percent of women suffer from OAB and yet an estimated 40 -- 50 percent do not respond to conventional treatments. One possible explanation for the lack of response to medication may be the bacteria present in these women.

"If we can determine that certain bacteria cause OAB symptoms, we may be able to better identify those at risk for this condition and more effectively treat them," said Alan Wolfe, PhD, co-investigator and professor of Microbiology and Immunology, SSOM.

This study evaluated urine specimens of 90 women with and without OAB symptoms. Urine samples were collected through a catheter and analyzed using an expanded quantitative urine culture (EQUC) technique. This EQUC technique was able to find bacteria that are not identified by the standard urine culture techniques typically used to diagnose urinary tract syndromes.

Loyola researchers now plan to determine which bacteria in the bladder are helpful and which are harmful. They also will look at how these bacteria interact with each other and with their host, and how we can use this information to help patients. 

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Now we need ways to nurture our skin bacteria. From Science Daily:

Bacteria on the skin: Our invisible companions influence how quickly wounds heal

A new study suggests microbes living on our skin influence how quickly wounds heal. The findings could lead to new treatments for chronic wounds, which affect 1 in 20 elderly people.

We spend our lives covered head-to-toe in a thin veneer of bacteria. But despite a growing appreciation for the valuable roles our resident microbes play in the digestive tract, little is known about the bacteria that reside in and on our skin. A new study suggests the interplay between our cells and these skin-dwelling microbes could influence how wounds heal.

Chronic wounds -- cuts or lesions that just never seem to heal -- are a significant health problem, particularly among elderly people. An estimated 1 in 20 elderly people live with a chronic wound, which often results from diabetes, poor blood circulation or being confined to bed or a wheelchair."These wounds can literally persist for years, and we simply have no good treatments to help a chronic wound heal," said Hardman, who added that doctors currently have no reliable way to tell whether a wound will heal or persist. 

In their recent study, Hardman and his colleagues compared the skin bacteria from people with chronic wounds that did or did not heal. The results showed markedly different bacterial communities, suggesting there may be a bacterial "signature" of a wound that refuses to heal. "Our data clearly support the idea that one could swab a wound, profile the bacteria that are there and then be able to tell whether the wound is likely to heal quickly or persist, which could impact treatment decisions," said Hardman.

The team also conducted a series of studies in mice to shed light on the reasons why some wounds heal while others do not. They found that mice lacking a single gene had a different array of skin microbiota -- including more harmful bacteria -- and healed much more slowly than mice with a normal copy of the gene. The gene, which has been linked to Crohn's disease, is known to help cells recognize and respond to bacteria. Hardman said the findings suggest that genetic factors influence the makeup of bacteria on a person's skin, which in turn influences how they heal.

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Another reason to breastfeed infants. From Medical Xpress:

Breastfeeding promotes the growth of beneficial bacteria in the gut

A number of studies have shown that breastfed babies grow slightly slower and are slightly slimmer than children who are fed with infant formula. Children who are breastfed also have a slightly lower incidence of obesity, allergies, diabetes and inflammatory bowel disease later in life. According to a new study by the National Food Institute and the University of Copenhagen this may be due to the fact that breastfeeding promotes the development of beneficial bacteria in the baby's gut.

"We have become increasingly aware of how crucially important a healthy gut microbial population is for a well-functioning immune system. Babies are born without bacteria in the gut, and so it is interesting to identify the influence dietary factors have on gut microbiota development in children's first three years of life," research manager at the National Food Institute Tine Rask Licht says.

The study shows that there are significant changes in the intestinal bacterial composition from nine to 18 months following cessation of breastfeeding and other types of food being introduced. However, a child's gut microbiota continues to evolve right up to the age of three, as it becomes increasingly complex and also more stable.

"The results help to support the assumption that the gut microbiota is not - as previously thought - stable from the moment a child is a year old. According to our study important changes continue to occur right up to the age of three.

More information: The study has been described in a scientific article in Applied and Environmental Microbiology: Establishment of intestinal microbiota during early life: A longitudinal, explorative study of a large cohort of Danish infants:www.ncbi.nlm.nih.gov/pubmed/24584251

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Some information about toothbrushes and bacteria. From Science Daily:

Clean before you clean: What's on your toothbrush just might surprise you

Do you know Staphylococci, coliforms, pseudomonads, yeasts, intestinal bacteria and -- yes -- even fecal germs may be on your toothbrush?

Appropriate toothbrush storage and care are important to achieving personal oral hygiene and optimally effective plaque removal, says Maria L. Geisinger, DDS, assistant professor of periodontology in the School of Dentistry at the University of Alabama at Birmingham.

"The oral cavity is home to hundreds of different types of microorganisms, which can be transferred to a toothbrush during use," Geisinger said. "Furthermore, most toothbrushes are stored in bathrooms, which exposes them to gastrointestinal microorganisms that may be transferred via a fecal-oral route. The number of microorganisms can vary wildly from undetectable to 1 million colony-forming units (CFUs). Proper handling and care of your toothbrush is important to your overall health."

What constitutes proper care and handling? Geisinger answers several questions that may help better protect families from toothbrush germs.

Q. Can bacteria from your toilet really reach your toothbrush?

A. "The short answer is 'yes.' Enteric bacteria, which mostly occur in the intestines, can transfer to toothbrushes and thus into your mouth. This may occur through inadequate hand-washing or due to microscopic droplets released from the toilet during flushing. The topic of dirty toothbrushes was a recent subject of the popular Discovery Channel show "Mythbusters," when 24 toothbrushes were tested, and all of them demonstrated enteric microorganisms -- even those that had not been inside of a bathroom. In fact, toothbrushes may be contaminated with bacteria right out of the box, as they are not required to be packaged in a sterile manner."

Q. What is the proper way to clean your toothbrush to help remove germs?

A. "You should thoroughly rinse toothbrushes with potable tap water after brushing to remove any remaining toothpaste and debris. Additionally, soaking toothbrushes in an antibacterial mouth rinse has been shown to decrease the level of bacteria that grow on toothbrushes."

Q. How should you to store your toothbrush to avoid germ and bacteria buildup?

A. "The American Dental Association recommends that you not store your toothbrush in a closed container or routinely cover your toothbrush, as a damp environment is more conducive to the growth of microorganisms. Also, storing toothbrushes in an upright position and allowing them to air dry until the next use is recommended, if possible. If more than one brush is stored in an area, keeping the toothbrushes separate can aid in preventing cross-contamination."

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Another reason to wash your hands before handling food. From The Scientist:

Money Microbiome

Analyzing the genetic material on 80 $1 bills sampled from a Manhattan bank, researchers from New York University (NYU) have discovered a diverse array of microbes, most of which are relatively harmless to humans, but a few that may leave you washing your hands after every cash transaction. It total, they found more than 3,000 bacterial types, including some drug-resistant species, and known microbes accounted for just 20 percent of the non-human DNA the researchers isolated; the rest belongs to as-yet unidentified species.

The most abundant species the researchers identified were those that cause acne, followed by benign skin flora. More alarming discoveries included pathogenic Staphylococcus species as well as bacteria associated with gastric ulcers, pneumonia, and food poisoning. The researchers also found DNA from antibiotic-resistance genes, such as those carried by the deadly methicillin-resistantStaphylococcus aureus (MRSA).

The researchers even found evidence of anthrax, although Carlton notes this shouldn’t necessarily be cause for concern. “Anthrax is a very common bacteria in soil."

Nevertheless, the microbial diversity identified highlights the likelihood that cash—one of the most common items to be distributed internationally—could spread disease around the world. A 2010 study that investigated currencies from 10 different countries, including Australia, China, the U.K., Ireland, Mexico, and the U.S., found similarly dirty money, and the authors recommended “that current guidelines as they apply in most countries with regard to the concurrent hygienic handling of foods and money should be universally adopted.”

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Flatulence is good, and up to 18 a day is totally normal! From NPR:

Got Gas? It Could Mean You've Got Healthy Gut Microbes

We know that air often comes after eating nutrient-packed vegetables, such as cabbage, kale and broccoli. And researchers have found that fiber-rich foods, like beans and lentils, boost the levels of beneficial gut bacteria after only a few days, as we reported in December.

So all this got us wondering: Could passing gas, in some instances, be a sign that our gut microbes are busy keeping us healthy? Absolutely, says Purna Kashyap, a gastroenterologist at the Mayo Clinic in Rochester, Minn. "Eating foods that cause gas is the only way for the microbes in the gut to get nutrients," he says. "If we didn't feed them carbohydrates, it would be harder for them to live in our gut."

And we need to keep these colon-dwelling critters content, Kashyap says. When they gobble up food — and create gas — they also make molecules that boost the immune system, protect the lining of the intestine and prevent infections.

"A healthy individual can have up to 18 flatulences per day and be perfectly normal," he adds.

Gas gets into the digestive tract primarily through  two routes: Swallowing air (which we all do when we eat and chew gum) and your microbiome. That's the collection of organisms in the GI tract that scientists and doctors are currently all fired up about. (Check our colleague Rob Stein's recent series on it.) That microbiome includes hundreds of different bacteria. But there are also organisms from another kingdom shacking up with them: the archaea.

All these microbes are gas-making fools. They eat up unused food in your large intestine, like fiber and other carbohydrates we don't digest, and churn out a bunch of gases as waste. But that's not all they make. They also produce a slew of molecules (called short chain fatty acids) that may promote the growth of other beneficial bacteria and archaea.

And the more fiber you feed these friendly inhabitants, the more types of species appear, studies have found. "Undigested carbohydrates allow the whole ecosystem to thrive and flourish," Kashyap says. Most gas made by the microbiome is odorless. It's simply carbon dioxide, hydrogen or methane. But sometimes a little sulfur slips in there."That's when it gets smelly," Kashyap says.

But here's the hitch: Many of the smelly sulfur compounds in vegetables have healthful properties. Take for instance, the broccoli, mustard and cabbage family. These Brassica vegetables are packed with a sulfur compound, called sulforaphane, that is strongly associated with a reduced risk of cancer. Another possible benefit of a little smelly gas? It may reduce the total volume of air in the gut, Kashyap says. 

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Excerpts from a very interesting NPR interview with Dr. Martin Blaser and his views on the human microbiome. The big take-away: our modern life-style is not good for the gut microbiome. His recently published book is Missing Microbes: How the Overuse of Antibiotics is Fueling Our Modern Plagues.

From NPR News: Modern Medicine May Not Be Doing Your Microbiome Any Favors

There are lots of theories about why food allergies, asthma, celiac disease and intestinal disorders like Crohn's disease have been on the rise. Dr. Martin Blaser speculates that it may be connected to the overuse of antibiotics, which has resulted in killing off strains of bacteria that typically live in the gut.

Blaser is an expert on the human microbiome, which is the collection of bacteria, viruses, fungi and other microbes that live in and on the body. In fact, up to 90 percent of all the cells in the human body aren't human at all — they're micro-organisms. Blaser is the director of NYU's Human Microbiome Program and a former chairman of medicine there. His new book is called Missing Microbes: How the Overuse of Antibiotics Is Fueling Our Modern Plagues.

"Since World War II, we've seen big rises in a number of diseases: asthma, allergies, food allergies, wheat allergy, juvenile diabetes, obesity. ... These are all diseases that have gone up dramatically in the last 50 or 70 years. One of the questions is: Why are they going up? Are they going up for 10 different reasons, or perhaps there is one reason that is fueling all of them."

"My theory is that the one reason is the changing microbiome; that we evolved a certain stable situation with our microbiome and with the modern advances of modern life, including modern medical practices, we have been disrupting the microbiome. And there's evidence for that, especially early in life, and it's changing how our children develop."

"There's a choreography; there's a normal developmental cycle of the microbiome from birth over the first few years of life, especially the first three years, [that] appear[s] to be the most important. And that's how nature has, how we have, evolved together so that we can maximize health and create a new generation, which is nature's great purpose. And because of modern practices, we have disrupted that. And then the question is: Does that have consequence[s]?"

"As far as we know, when the baby is inside the womb it is apparently sterile. ... The big moment of truth is when the membranes rupture, the water breaks, and the baby starts coming out. And that's where they first get exposed to the bacteria of the world, and the first bacteria they're exposed to is their mother's bacteria in the birth canal. So as labor proceeds, the babies are in contact with the microbes lining their mother's vagina and, as they're going out, they're covered by these bacteria. They swallow the bacteria; it's on their skin. ..."

"That's their initial exposure to the world of bacteria. That's how mammals have been doing it for the last 150 million years, whether they're dolphins or elephants or humans. ... And we know a little about what those bacteria are. The most common bacteria are lactobacillus and there's evidence that over the course of pregnancy the microbiome in the vagina changes, just as many other parts of the body are changing. The microbiome is changing in its composition in terms of maximizing lactobacilli, and these are bacteria that eat lactose, which is the main component of milk. So the baby's mouth is filled with lactobacilli. The first thing that happens is they go up against their mom's breast and they inoculate the nipple with lactobacilli and now milk and lactobacilli go into the new baby and that's the foundation for their microbiome and that's how they start their life. ..."

"You could project that if they didn't acquire these organisms or they didn't acquire them normally or at the normal time, then the foundations might be a little shaky."

"Shortly after birth, they compared the microbiomes in the babies that came out. The babies that were born vaginally, their microbiome, not surprisingly, looked like the mom's vagina everywhere in the body — in their GI tract, on their skin, in their mouth. But the babies born by C-section, their microbiome looked like skin and it didn't even necessarily look like the mom's skin, maybe it was somebody else in the operating room. So it's clear that the microbiome is different immediately depending on the kind of birth."

"What I can tell you is that our immune system is quite complex. There are many kinds of immune cells. There are cells that strongly recognize foreign substances, there are ones that try to damp [the immune system] and down-regulate it. There's what we call innate immunity, which is the immunity we're all born with, and then there's adaptive immunity — the immunity that develops when we experience different kinds of exposures. So it's very complex."

"There are many different probiotics.  I think I can say three things: The first is that they're almost completely unregulated; second is that they seem to be generally safe; and third is that they're mostly untested. ... I'm actually a big believer in probiotics; I think that's going to be part of the future of medicine, that we're going to understand the science of the microbiome well enough so that we can look at a sample from a child and say this child is lacking such-and-such an organism and now we're going to take it off the shelf and we're going to give it back to that child. ... "

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An argument for the need for human exposure to the microbes in rural environments. However, the role of diesel exhaust and other urban air pollutants is not discussed here (for example, diesel exhaust is linked to asthma). From Science Daily:

Rural microbes could boost city dwellers' health, study finds

The greater prevalence of asthma, allergies and other chronic inflammatory disorders among people of lower socioeconomic status might be due in part to their reduced exposure to the microbes that thrive in rural environments, according to a new scientific paper co-authored by a University of Colorado Boulder researcher.

The article, published in the journal Clinical & Experimental Immunology, argues that people living in urban centers who have less access to green spaces may be more apt to have chronic inflammation, a condition caused by immune system dysfunction.

When our immune systems are working properly, they trigger inflammation to fight off dangerous infections, but the inflammation disappears when the infection is gone. However, a breakdown in immune system function can cause a low level of inflammation to persist indefinitely. Such chronic inflammation can cause a host of health disorders.

Some scientists have hypothesized that the increase of chronic inflammation in wealthier Western countries is connected to lifestyles that have essentially become too clean. The so-called "hygiene hypothesis" is based on the notion that some microbes and infections interact with the immune system to suppress inflammation and that eliminating exposure to those things could compromise your health.

The authors agree that microbes and some types of infections are important because they can keep the immune system from triggering inflammation when it's not necessary, as happens with asthma attacks and allergic reactions.

But they say the infections that were historically important to immune system development have largely been eliminated in developed countries. The modern diseases we pick up from school, work and other crowded areas today do not actually lead to lower instances of inflammatory disorders.

During our evolutionary history, the human immune system was exposed to microbes and infections in three important ways: commensal microbes were passed to infants from their mothers and other family members; people came into contact with nonpathogenic microbes in the environment; and people lived with chronic infections, such as helminths, which are parasitic worms found in the gut and blood.

In order for those "old infections" to be tolerated in the body for long periods of time, they evolved a mechanism to keep the human immune system from triggering inflammation. Similarly, environmental bacteria, which were abundant and harmless, were tolerated by the immune system. According to Rook, a professor at UCL, "Helminthic parasites need to be tolerated by the immune system because, although not always harmless, once they are established in the host efforts by the immune system to eliminate them are futile, and merely cause tissue damage."

In contrast, relatively modern "crowd infections," such as measles or chicken pox, cause an inflammatory response. The result is that either the sick person dies or the infection is wiped out by the inflammation and the person becomes immune from having the same infection again in the future.

Collectively, the authors refer to the microbes and old infections that had a beneficial impact on the function of our immune systems as "old friends." Exposure to old friends plays an important role in guarding against inflammatory disorders, the authors said. Because the "old infections" are largely absent from the developed world, exposure to environmental microbes -- such as those found in rural environments, like farms and green spaces -- has likely become even more important.

The authors say this would explain why low-income urban residents -- who cannot easily afford to leave the city for rural vacations -- are more likely to suffer from inflammatory disorders. The problem is made worse because people who live in densely populated areas also are more likely to contract crowd infections, which cause more inflammation.

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Important to know about this nasty bacterial strain for those who use contact lenses. From Science Daily:

Bacteria survive longer in contact lens cleaning solution than previously thought, study shows

Each year in the UK, bacterial infections cause around 6,000 cases of a severe eye condition known as microbial keratitis -- an inflammation and ulceration of the cornea that can lead to loss of vision. The use of contact lenses has been identified as a particular risk factor for microbial keratitis. New research, presented today at the Society for General Microbiology Annual Conference in Liverpool, shows that a bacterial strain associated with more severe infections shows enhanced resistance to a common contact lens disinfectant solution.

Researchers from The University of Liverpool and The Royal Liverpool University NHS Trust tested different strains of the keratitis-causing bacterium Pseudomonas aeruginosa for their ability to survive in a commonly used contact lens cleaning solution. The team compared nine clinical strains of P. aeruginosa, taken from hospital patients in the UK, with P. aeruginosa strain 9027, the standard strain used by lens solution manufacturers.

The results showed that the majority of clinical strains tested were killed within 10 minutes of being immersed in the contact lens solution, comparable with the standard reference strain. However, one clinical isolate, P. aeruginosa strain 39016 -- associated with a more severe case of keratitis with a prolonged healing time -- was able to survive for over four hours, much longer than the reference strain.

Professor Craig Winstanley, who led the research, says: "Microbial keratitis can be devastating for a patient -- it is important that the risk of developing this condition is reduced in contact lens wearers by improving contact lens disinfectant solutions."

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Another reason to avoid products with Triclosan. From Science Daily:

Antimicrobial from soaps promotes bacteria buildup in human noses

An antimicrobial agent found in common household soaps, shampoos and toothpastes may be finding its way inside human noses where it promotes the colonization of Staphylococcus aureus bacteria and could predispose some people to infection. 

Triclosan, a human-made compound used in a range of antibacterial personal care products such as soaps, toothpastes, kitchen surfaces, clothes and medical equipment, was found in nasal passages of 41% of adults sampled. A higher proportion of subjects with triclosan also had S. aureus colonization. S. aureus could promote infection in some populations such as people undergoing surgery.

Triclosan has been around for the past 40 years, says senior study author Blaise Boles, PhD, an assistant professor of molecular, cellular and developmental biology at the university, and has been incorporated into many antibacterial household products within the past decade. Other studies have found traces of triclosan in human fluids including serum, urine and milk, and studies in mammals have found that high concentrations of triclosan can disrupt the endocrine system and decrease heart and skeletal muscle function.

"It's really common in hand soaps, toothpastes and mouthwashes but there's no evidence it does a better job than regular soap," Boles says. "This agent may have unintended consequences in our bodies. It could promote S. aureus nasal colonization, putting some people at increased risk for infection."

Additional experiments found that S. aureus grown in the presence of triclosan was better able to attach to human proteins, and that rats exposed to triclosan were more susceptible to S. aureus nasal colonization.