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Category: microbes

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Finally, a discussion of the eye microbiome or microbiota (microbial community). Originally eyes were thought not to have much microbial life. But now with modern technology (such as genetic sequencing) it is known that many microbial species live on the eye. And yes, the eye or ocular microbiome can become imbalanced.

From The Scientist: Visualizing the Ocular Microbiome

Ophthalmologists have treated pathogenic eye infections for many decades, and the advent of contact lenses has made such infections more common. But little is known about the bacteria that live on the surface of a healthy human eye, and how this microbial make-up differs when a pathogenic strain takes over. Many bacteria known to live on the eye are difficult to culture, making them virtually invisible to researchers. Adapting sequencing technologies to study the ocular microbiome has opened up new avenues for understanding what’s really happening under the eyelids.

About five years ago, Valery Shestopalov of the Bascom Palmer Eye Institute at the University of Miami was speaking with his microbiology colleagues about what bacteria are found on normal, healthy eyes. Conventional wisdom at that time held that healthy eyes don’t harbor much microbial life, tears and blinking tend to clear away foreign objects, including bacteria. But Shestopalov’s early tests revealed something different. “The tests ran positive. All exposed mucosal epithelium are populated densely,” he said. 

The team found that about a dozen bacteria genera dominated the eye’s conjunctiva, a third of which could not be classified. On the corneal surface, they found a slightly different community. Again, about a dozen genera dominated. And everywhere they’ve looked, the researchers have found more than just bacteria. “We haven't published on this yet, but I have been surprised by how often we find phage or viruses on the normal ocular surface,” Van Gelder told The Scientist in an e-mail.

“People can have a huge variation in microflora and still have healthy eyes, making our job difficult, but really amazing,” Shestopalov said.

The researchers also found that during keratitis infections—infections of the cornea—only about half as many bacterial varieties were present, most prominently Pseudomonas strains. The changes typically occurred well before a diagnosis of an eye infection, suggesting the ocular microbiome could inform future diagnostics, Shestopalov noted. 

One factor that may be expected to impact the composition of the ocular flora is the use of contact lenses. Contact lens wear is one of the biggest factors leading to corneal infection... Researchers believe contact lenses make it easier for pathogens to colonize the surface of the eye by giving the bacteria something to adhere to. Sequencing biofilms from used contact lenses, Shestopalov’s team found evidence of microbial communities that were different from the ocular microbiomes of people who don’t use contacts. On the lenses themselves, the researchers have found much less diversity—many of the bacterial genera that dominate the conjunctiva and cornea were depleted. In their place, Staphylococcus dominated.

Whether the bacteria identified living on the surface of the eye are permanent residents or transient colonizers remains to be seen. The work of deconstructing the ocular microbiome is just getting started, but preliminary results have suggested it is distinct from the rest of the bacterial community that inhabits our bodies. “It stands apart,” Shestopalov said. “There’s statistical evidence of its difference from any other human microbiome.”

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More long-standing medical advice goes out the window. New advice: avoid diet soda and artificial sweeteners. The amazing part is that our gut bacteria are involved.

From Science Daily: Certain gut bacteria may induce metabolic changes following exposure to artificial sweeteners

Artificial sweeteners -- promoted as aids to weight loss and diabetes prevention -- could actually hasten the development of glucose intolerance and metabolic disease, and they do so in a surprising way: by changing the composition and function of the gut microbiota -- the substantial population of bacteria residing in our intestines. These findings, the results of experiments in mice and humans, ...says that the widespread use of artificial sweeteners in drinks and food, among other things, may be contributing to the obesity and diabetes epidemic that is sweeping much of the world.

For years, researchers have been puzzling over the fact that non-caloric artificial sweeteners do not seem to assist in weight loss, with some studies suggesting that they may even have an opposite effect.

Next, the researchers investigated a hypothesis that the gut microbiota are involved in this phenomenon. They thought the bacteria might do this by reacting to new substances like artificial sweeteners, which the body itself may not recognize as "food." Indeed, artificial sweeteners are not absorbed in the gastrointestinal tract, but in passing through they encounter trillions of the bacteria in the gut microbiota.

The researchers treated mice with antibiotics to eradicate many of their gut bacteria; this resulted in a full reversal of the artificial sweeteners' effects on glucose metabolism. Next, they transferred the microbiota from mice that consumed artificial sweeteners to "germ-free," or sterile, mice -- resulting in a complete transmission of the glucose intolerance into the recipient mice. This, in itself, was conclusive proof that changes to the gut bacteria are directly responsible for the harmful effects to their host's metabolism.... A detailed characterization of the microbiota in these mice revealed profound changes to their bacterial populations, including new microbial functions that are known to infer a propensity to obesity, diabetes, and complications of these problems in both mice and humans.

Does the human microbiome function in the same way? Dr. Elinav and Prof. Segal had a means to test this as well. As a first step, they looked at data collected from their Personalized Nutrition Project (www.personalnutrition.org), the largest human trial to date to look at the connection between nutrition and microbiota. Here, they uncovered a significant association between self-reported consumption of artificial sweeteners, personal configurations of gut bacteria, and the propensity for glucose intolerance. They next conducted a controlled experiment, asking a group of volunteers who did not generally eat or drink artificially sweetened foods to consume them for a week, and then undergo tests of their glucose levels and gut microbiota compositions.

The findings showed that many -- but not all -- of the volunteers had begun to develop glucose intolerance after just one week of artificial sweetener consumption. The composition of their gut microbiota explained the difference: the researchers discovered two different populations of human gut bacteria -- one that induced glucose intolerance when exposed to the sweeteners, and one that had no effect either way. Dr. Elinav believes that certain bacteria in the guts of those who developed glucose intolerance reacted to the chemical sweeteners by secreting substances that then provoked an inflammatory response similar to sugar overdose, promoting changes in the body's ability to utilize sugar.

This image depicts gut microbiota. Credit: Weizmann Institute of Science

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This exciting new research is just the beginning knowledge about our virome (the virus community within us). Note that they only looked at viruses in a few areas of our bodies - the rest is still a mystery. But note that it is normal for healthy individuals to carry viruses, and that we have "distinct viral fingerprints". We don't know if the viruses are beneficial or not to us at this time. From Science Daily:

Healthy humans make nice homes for viruses

The same viruses that make us sick can take up residence in and on the human body without provoking a sneeze, cough or other troublesome symptom, according to new research. On average, healthy individuals carry about five types of viruses on their bodies, the researchers report. The study is the first comprehensive analysis to describe the diversity of viruses in healthy people.

The research was conducted as part of the Human Microbiome Project, a major initiative funded by the National Institutes of Health (NIH) that largely has focused on cataloging the body's bacterial ecosystems. ..."Lots of people have asked whether there is a viral counterpart, and we haven't had a clear answer. But now we know there is a normal viral flora, and it's rich and complex."

In 102 healthy young adults ages 18 to 40, the researchers sampled up to five body habitats: nose, skin, mouth, stool and vagina. The study's subjects were nearly evenly split by gender.

At least one virus was detected in 92 percent of the people sampled, and some individuals harbored 10 to 15 viruses...."We only sampled up to five body sites in each person and would expect to see many more viruses if we had sampled the entire body."

Scientists led by George Weinstock, PhD, at Washington University's Genome Institute, sequenced the DNA of the viruses recovered from the body, finding that each individual had a distinct viral fingerprint. (Weinstock is now at The Jackson Laboratory in Connecticut.) About half of people were sampled at two or three points in time, and the researchers noted that some of the viruses established stable, low-level infections.

The researchers don't know yet whether the viruses have a positive or negative effect on overall health but speculate that in some cases, they may keep the immune system primed to respond to dangerous pathogens while in others, lingering viruses increase the risk of disease.

Study volunteers were screened carefully to confirm they were healthy and did not have symptoms of acute infection. They also could not have been diagnosed in the past two years with human papillomavirus infection (HPV), which can cause cervical and throat cancer, or have an active genital herpes infection.

Analyzing the samples, the scientists found seven families of viruses, including strains of herpes viruses that are not sexually transmitted. For example, herpesvirus 6 or herpesvirus 7 was found in 98 percent of individuals sampled from the mouth. Certain strains of papillomaviruses were found in about 75 percent of skin samples and 50 percent of samples from the nose. Novel strains of the virus were found in both sites.

Not surprisingly, the vagina was dominated by papillomaviruses, with 38 percent of female subjects carrying such strains. Some of the women harbored certain high-risk strains that increase the risk of cervical cancer. These strains were more common in women with communities of vaginal bacteria that had lower levels of Lactobacillus and an increase in bacteria such as Gardnerella, which is associated with bacterial vaginosis.

Adenoviruses, the viruses that cause the common cold and pneumonia, also were common at many sites in the body.

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Amazing possibilities, but more studies needed. The key finding: A diversity of the bacterial community in the gut is good, and perhaps can be altered through diet, and so perhaps alter the future risk of developing breast cancer.From Science Daily:

Diverse gut bacteria associated with favorable ratio of estrogen metabolites

Postmenopausal women with diverse gut bacteria exhibit a more favorable ratio of estrogen metabolites, which is associated with reduced risk for breast cancer, compared to women with less microbial variation, according to a new study.

Since the 1970s, it has been known that in addition to supporting digestion, the intestinal bacteria that make up the gut microbiome influence how women's bodies process estrogen, the primary female sex hormone. The colonies of bacteria determine whether estrogen and the fragments left behind after the hormone is processed continue circulating through the body or are expelled through urine and feces. Previous studies have shown that levels of estrogen and estrogen metabolites circulating in the body are associated with risk of developing postmenopausal breast cancer.

"In women who had more diverse communities of gut bacteria, higher levels of estrogen fragments were left after the body metabolized the hormone, compared to women with less diverse intestinal bacteria," said one of the study's authors, James Goedert, MD, of the National Institutes of Health's National Cancer Institute (NCI) in Bethesda, MD. "This pattern suggests that these women may have a lower risk of developing breast cancer."

As part of the cross-sectional study, researchers analyzed fecal and urine samples from 60 postmenopausal women enrolled in Kaiser Permanente Colorado. .

"Our findings suggest a relationship between the diversity of the bacterial community in the gut, which theoretically can be altered with changes in diet or some medications, and future risk of developing breast cancer," Goedert said. 

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An opinion piece from Dr. David Johnson, Prof. of Medicine and Chief of Gastroenterology at Eastern Medical School in Norfolk, Virginia but an interesting one that points out the limitations of current probiotic knowledge and that we shouldn't blindly take probiotics (with only a few bacteria strains) after antibiotic use thinking that they're all good, all the time. I'm including this article to show what many medical professionals think about probiotic use and why.

He discusses 2 large studies, but unfortunately both studies only looked at hospitalized patients - and the large PLACIDE study looked at over-65 year old patients. And in the second large study he discusses the benefits of the antibiotic metronidazole.

I agree with his need for caution and the need for more large studies, but I wish he had discussed children, people NOT hospitalized, people who just had a round of antibiotics without life threatening complications, and not dismissed small studies. Hospitalized vs non-hospitalized people are very, very different groups. Small studies are finding benefits of various bacteria, but yes, the research is in its infancy, especially what are "normal microbial communities" in the gut and in other parts of the body. He does not discuss fecal transplants of entire microbial communities for C. difficile and their over 90% success rate. Dr. S. Lynch has theorized that some bacteria act as "keystone species" that could help repopulate a biome after an insult (such as antibiotics). From Medscape:

Probiotics: Help or Harm in Antibiotic-Associated Diarrhea?

Today I want to discuss the issue of probiotics, and whether probiotics are doing an element of benefit or an element of harm. With access to over-the-counter products, use of probiotics has dramatically increased. Physicians recommend probiotics routinely to patients when they are taking antibiotics to prevent antibiotic-associated diarrhea. I would like to take a time-out and reevaluate what we are doing for these patients.

Not infrequently, antibiotics are associated with Clostridium difficile infections, which occur in up to one third of patients with antibiotic-associated diarrhea.

In 2012, highly publicized meta-analyses were published in JAMA [1] and Annals of Internal Medicine. [2]These studies, and a Cochrane review,[3] suggest that not only can probiotics prevent or diminish antibiotic-associated diarrhea, but probiotics may also be helpful in avoiding C difficile infection.

Enter the most recent study, which is called the PLACIDE study, from the United Kingdom[4] It involved 5 hospitals, 68 different medical and surgical units, and more than 17,000 patients aged 65 years or older. All patients were hospitalized and taking an antibiotic.

These patients were randomly assigned, if they met eligibility criteria, to receive either a microbial preparation (which is the term they used for "probiotic") or an identical placebo. The microbial preparation had 2 strains of Lactobacillus and 2 strains of bifidobacteria, which patients received for 21 days.... Even with evaluation for intention to treat, there was no difference in the outcomes for C difficile infection or antibiotic-associated diarrhea between the microbial preparation (probiotic) and placebo group. Of interest, there was an increase in flatus in the microbial preparation group, and patients with C difficile diarrhea who received the microbial preparation reported a 3-fold increase in bloating. 

Although intended to restore good health, we are seeing a dysbiosis. We have disrupted the microflora in the gut, and are trying to jam it back with strains of bacteria that we think are good bacteria, and it may not be the correct answer. We don't know the right answer. When you alter the microflora, you change some of the metabolism of carbohydrates, bile salts, and complex sugars. We are not clear whether jamming the gut with another strain of bacteria is going to be of benefit.

I want to posit an element of potential harm, and not rush in to recommend probiotics routinely in patients to whom you prescribe antibiotics. I would also caution you not to use probiotics in patients in the intensive care unit, or in any patient with an indwelling prosthesis, particularly an intravascular prosthesis. 

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Reading this is almost guaranteed to make you want to wash your hands. From Science Daily:

How quickly viruses can contaminate buildings -- from just a single doorknob

Using tracer viruses, researchers found that contamination of just a single doorknob or table top results in the spread of viruses throughout office buildings, hotels, and health care facilities. Within 2 to 4 hours, the virus could be detected on 40 to 60 percent of workers and visitors in the facilities and commonly touched objects.

There is a simple solution, though, says Charles Gerba of the University of Arizona, Tucson, who presented the study. "Using disinfecting wipes containing quaternary ammonium compounds (QUATS) registered by EPA as effective against viruses like norovirus and flu, along with hand hygiene, reduced virus spread by 80 to 99 percent," he says.

Norovirus is the most common cause of acute gastroenteritis in the United States, according to the Centers for Disease Control and Prevention (CDC). Each year, it causes an estimated 19-21 million illnesses and contributes to 56,000-71,000 hospitalizations and 570-800 deaths. Touching surfaces or objects contaminated with norovirus then putting your fingers in your mouth is a common source of infection.

In the study, Gerba and his colleagues used bacteriophage MS-2 as a surrogate for the human norovirus, as it is similar in shape, size and resistance to disinfectants. The phage was placed on 1 to 2 commonly touched surfaces (door knob or table top) at the beginning of the day in office buildings, conference room and a health care facility. After various periods of time (2 to 8 hours) they sampled 60 to 100 fomites, surfaces capable of carrying infectious organisms (light switches, bed rails, table tops, countertops, push buttons, coffee pots handles, sink tap handles, door knobs, phones and computer equipment), for the phages.

"Within 2 to 4 hours between 40 to 60% of the fomites sampled were contaminated with virus," says Gerba.

In the intervention phase cleaning personal and employees were provided with QUATS disinfectant containing wipes and instructed on proper use (use of at least once daily). The number of fomites on which virus was detected was reduced by 80% or greater and the concentration of virus reduced by 99% or more.

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Another interesting study that makes you think about our microbiome. From NPR:

Stinky T-Shirt? Bacteria Love Polyester In A Special Way

Anyone with a drawerful of T-shirts knows that the synthetic ones can get sour after just a brief jog, while old-school cotton T-shirts remain relatively stink-free all day. And now science explains why. The bacteria that flourish on a sweaty polyester T-shirt are different from those that grow on cotton, researchers at the University of Ghent in Belgium found. Polyester makes a happy home for Micrococcus bacteria, while Staphylococcus, a common armpit denizen, was found on both poly and cotton.

Microbes love the cozy warmth of the human armpit; it's like a trip to the tropics without ever having to leave home. And it's crowded in there. Those microbes eat compounds in sweat and generate odors, which support a flourishing deodorant industry. 

The scientists asked 26 volunteers to take a spinning class while wearing shirts made of cotton, poly or blends. The shirts were then incubated for a day, and the microbes extracted and DNA fingerprinted. Volunteers also had their armpits swabbed. 

It turns out the bugs on the shirts are different from the bugs in the pits. While Corynebacterium is thought to be the main cause of armpit body odor, there was no Corynebacterium on the clothes. Instead, Staphylococcus flourished on cotton and poly, and Micrococcus, bacteria also known for making malodor, loved polyester.

He's also trying to help people with excessive body odor by giving them armpit bacteria transplants. "We have done transplants with about 15 people, and most of them have been successful," Callewaert, a Ph.D. student in applied biological sciences at the University of Ghent, tells Shots. "All have had an effect short term, but the bad odor comes back after a few months for some people."

Manufacturers have tried to make polyester fabric less hospitable to bacteria by impregnating it with antimicrobials like silver nanoparticles or triclosan. Both products have been criticized as having potentially negative impacts on the environment, and there are few data on how they might affect the wearer. Callewaert thinks the ultimate solution will be something more organic — supplant bad bugs with good ones. 

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Interesting, but does it really mean anything? Just change to a new toothbrush monthly.From Science Daily:

Up to 3,000 times the bacterial growth on hollow-head toothbrushes

Solid-head power toothbrushes retain less bacteria compared to hollow-head toothbrushes, according to new research.

Lead author and professor at the UTHealth School of Dentistry, Donna Warren Morris, R.D.H., M.Ed., notes that microbial counts were lower in the solid-head toothbrush group than in the two hollow-head toothbrush groups in 9 out of 10 comparisons. "Toothbrushes can transmit microorganisms that cause disease and infections. A solid-head design allows for less growth of bacteria and bristles should be soft and made of nylon," Morris said. 

The study was conducted over a three-week period where participants brushed twice daily with one out of three randomly assigned power toothbrushes. Participants used non-antimicrobial toothpaste and continued their flossing routine throughout the study, but refrained from using other dental products like mouthwash.

During the study the brush heads were exposed to five categories of oral microorganisms: anaerobes and facultative microorganisms, yeast and mold, oral streptococci and oral enterococci anaerobes, Porphyromonas gingivalis andFusobacterium species.

The article also states that there is no present or published study that has demonstrated that bacterial growth on toothbrushes can lead to systematic health effects, but as Morris stated, several microorganisms have been associated with systemic diseases.

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Same research study is discussed as in the last post (Your Bacteria All Over Your Home), but different write-up with more and different details. From Washington Post:

Hotel rooms aren’t yucky – you colonize them with your own personal bacteria within hours

When you move from one house to another, you take all your bacteria with you. In fact, your family's microbiome (or your eco-system of inner and outer bacteria) lays claim to hotel rooms with hours. Our bacterial signatures are so persistent and so unique, a new study published Thursday in Science reports, that they could even be used in forensic investigations — and eventually become more useful to police than an old-fashioned fingerprint. And the same research that could track down a serial killer could also help you raise healthier kids.

In studying seven families as they moved from one house to another, the microbiologists had one major takeaway: Bacteria move from your body to your living space at incredible speed.

"Everyone thinks hotels are icky," said Jack Gilbert,, corresponding author of the study and environmental microbiologist at Argonne National Laboratory, "but when one young couple we studied moved into a hotel, it was microbiologically identical to their home within 24 hours." And unpublished further research reveals that the time frame is even swifter than that. "No matter what you do to clean a hotel room," Gilbert said, "your microbial signal has wiped out basically every trace of the previous resident within hours."

What's more, the researchers were able to determine how much individuals in a family interacted, what rooms they used, and even when they'd last been to one part of the house or another. This has obvious applications in forensic science. "We could go all J. Edgar Hoover on this and make a database of microbial fingerprints of people all over the world," Gilbert said, "and it's far more sophisticated than a standard fingerprint, which is just a presence or absence indication. We can see who they are, where they're from, the diet they're eating, when they left, who they may have been interacting with. It gets pretty crazy."

Gilbert and his colleagues are already working with police in Hawaii, hoping to look at the microbiome left on dead bodies. "If someone is, shall we say, recently and inappropriately deceased," Gilbert said, "we can look at their bacterial colonies and try to identify who the last person to come into contact with them was, and when." Based on some promising animal studies, he said, it could be possible. "An actual fingerprint is rarely left on a body," Gilbert said, "but a microbial fingerprint certainly is."

The Home Microbiome Study has more immediate applications, too. Gilbert, a father of two, hopes that fellow parents will use these and future findings to raise their offspring in healthier microbiomes. Before the age of two, the human microbiome remains in flux. Different species of bacteria compete to gain permanent spots — and once the race is run, you're basically stuck with the winners. Research in animals has shown that bacterial exposure in youth can impact physical and mental development and health for the rest of an organism's life.

"Let's say a kid grows up in an apartment block, without going outside much," Gilbert said. "They're just getting this same human bacteria fed back to them, day after day." More exposure is most certainly the better route.

For starters, get a dog. Partway through the study, Gilbert did just that. "We saw dogs acting as a super-charged conduit," he said, "transferring bacteria between one human and another, and bringing in outdoor bacteria. They just run around distributing microbes all willy-nilly." Sure enough, his family saw their home's microbiome benefit from the new addition.

We now know that most bacteria are beneficial to us — and that some can even prevent allergies."Imagine if we could engineer our home environments, optimize our carpeting and air conditioning systems, to bring in the really good bacteria," he said. 

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Exciting research! From Science Daily:

Home is where the microbes are

A person's home is their castle, and they populate it with their own subjects: millions and millions of bacteria. Scientists have detailed the microbes that live in houses and apartments. The study was conducted by researchers from the U.S. Department of Energy's Argonne National Laboratory and the University of Chicago. 

The results shed light on the complicated interaction between humans and the microbes that live on and around us. Mounting evidence suggests that these microscopic, teeming communities play a role in human health and disease treatment and transmission.

"We know that certain bacteria can make it easier for mice to put on weight, for example, and that others influence brain development in young mice," said Argonne microbiologist Jack Gilbert, who led the study. "We want to know where these bacteria come from, and as people spend more and more time indoors, we wanted to map out the microbes that live in our homes and the likelihood that they will settle on us.

The Home Microbiome Project followed seven families, which included eighteen people, three dogs and one cat, over the course of six weeks. The participants in the study swabbed their hands, feet and noses daily to collect a sample of the microbial populations living in and on them. They also sampled surfaces in the house, including doorknobs, light switches, floors and countertops. Then the samples came to Argonne, where researchers performed DNA analysis to characterize the different species of microbes in each sample.

They found that people substantially affected the microbial communities in a house -- when three of the families moved, it took less than a day for the new house to look just like the old one, microbially speaking.

Regular physical contact between individuals also mattered -- in one home where two of the three occupants were in a relationship with one another, the couple shared many more microbes. Married couples and their young children also shared most of their microbial community.

Within a household, hands were the most likely to have similar microbes, while noses showed more individual variation. Adding pets changed the makeup as well, Gilbert said -- they found more plant and soil bacteria in houses with indoor-outdoor dogs or cats.

In at least one case, the researchers tracked a potentially pathogenic strain of bacteria called Enterobacter, which first appeared on one person's hands, then the kitchen counter, and then another person's hands. "It's also quite possible that we are routinely exposed to harmful bacteria -- living on us and in our environment -- but it only causes disease when our immune systems are otherwise disrupted."

Home microbiome studies also could potentially serve as a forensic tool, Gilbert said. Given an unidentified sample from a floor in this study, he said, "we could easily predict which family it came from."

The research also suggests that when a person (and their microbes) leaves a house, the microbial community shifts noticeably in a matter of days."You could theoretically predict whether a person has lived in this location, and how recently, with very good accuracy," he said.