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Category: microbes

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Another article stating that the future is feces in treating a number of diseases. From Pacific Standard:

Medicine’s Dirty Secret: Fecal Transplants Are the Next Big Thing in Health Care

POO IS A DECIDEDLY IMPERFECT delivery vehicle for a medical therapy. It’s messy. It stinks. It’s inconsistent, not to mention a regulatory nightmare. But it can be incredibly potent. A classic study of nine healthy British volunteers found that bacteria accounted for more than half of the mass of their fecal solids. That astonishing concentration of microorganisms, both living and dead, makes sense when you consider that the microbial colonists inhabiting our gastrointestinal tract outnumber our own cells roughly three to one, on recent estimates.

In the ideal conditions of the human gut, a thriving ecosystem of 1,000 or more bacterial species that rivals the complexity of a rainforest has co-evolved with us. This microscopic jungle is constantly adapting in response to our diet, antibiotic use and other environmental influences. As the science has progressed, researchers are now comparing the entire collection of microbial inhabitants of the human gut, our microbiome, to a “hidden metabolic organ.” Scientists have linked disruptions to this organ, a condition known as dysbiosis, to everything from inflammatory bowel disease and high blood pressure to diabetes and obesity.

Viewed in this light, a fecal microbiota transplant is nothing more than an attempt to reseed an intestinal tract, often after antibiotics have killed off the native flora that might have kept invasive species at bay. No other medical therapy can claim such a high cure rate for the infection widely known as C. diff.

Some doctors have likened the recoveries of desperately ill patients to those seen with anti-HIV protease inhibitors in the mid-1990s. After the Mayo Clinic in Scottsdale, Arizona, performed its first fecal microbiota transplant in 2011, a patient who had been bed-ridden for weeks left the hospital 24 hours later. And in 2013, researchers in the Netherlands halted a landmark C. diff. clinical trial early for ethical reasons when they saw that the overall cure rate of 94 percent with donor feces had far outpaced the 31 percent cured with the antibiotic vancomycin.

Yet few other interventions elicit such disgust, revulsion, and ridicule. Chronicling a potential advance by a team of Canadian scientists, one newspaper account warned readers: “Hold your nose and don’t spit out your coffee.” In 2013, the founder of a patient advocacy blog called The Power of Poop wrote an open letter to 13 gastroenterology associations detailing the story of a Kentucky man who contracted an acute case of C. diff. Despite his family’s pleas, his doctor dismissed the idea of a fecal transplant as “quackery.” The man died the next day.

Although most providers haven’t published their overall success rates, their self-reported results are surprisingly similar, and consistent with what published reports there are. Khoruts says he has achieved a success rate of about 90 percent after one infusion, 99 percent after two. “In medicine, it’s pretty startling to have therapy that’s that effective for the most refractory patients with that condition,” he says. Colleen Kelly, a gastroenterologist with the Women’s Medicine Collaborative in Providence, Rhode Island, has performed the procedure on 130 patients with recurrent C. diff., with a success rate of about 95 percent. Most of the transplants have taken after just one attempt.

For a relatively simple bacterial infection, Petrof says, the potential remedy may be fairly straightforward. “With recurrent C. diff. what you’ve done is you’ve basically torched the forest,” she says. Nearly everything has been killed off by the antibiotics, leaving very low bacterial diversity. “So the C. diff. can just take root and grow.” Adding back almost any other flora—the equivalent of planting seedlings in the dirt—could help the ecosystem keep interloping pathogens at bay.

For more complicated conditions, though, a simple fecal transplant may not be enough, at least with donors from the Western world. One hypothesis suggests that people in lower-income countries might harbor more diverse bacterial populations in their guts than those who have grown up in a more sterile, antibiotic-rich environment. And in fact, a 2012 study found that residents of Venezuela’s Amazonas state and rural Malawi had markedly more diverse gut microbiomes than people living in three U.S. metropolitan areas. Scientists have already raised the idea that a rise in allergies and autoimmunity in industrialized nations may derive from a kind of collective defect of reduced microbial diversity.

“We cannot find people who’ve never been on antibiotics,” Khoruts says of his donors. For complex autoimmune diseases such as ulcerative colitis, fecal transplants may offer only a partial solution. And with some data suggesting that susceptibility may be linked in part to past antibiotic exposure, perhaps no Western donor can provide the microbes needed to fully reseed the gut.

What then? Khoruts says it may be necessary to seek out ancestral microbial communities—the ones all humans hosted before the advent of the antibiotic era—within people in Africa or the Amazon. “It’s just a disappearing resource,” he says.

By the beginning of April 2014, nearly 30 fecal transplant clinical trials were underway around the world. Roughly half were aimed at C. diff., including two testing the therapy in combination with vancomycin, and another multi-center trial evaluating the effectiveness of fresh versus frozen donor poo.

As the therapy becomes more widely established, via something akin to a “poop pill” or “crapsule,” perhaps the infectious pool of C. diff. patients may start to dwindle. More clinicians, then, might feel emboldened to explore how our bowel flora may affect not only the gastrointestinal system but also the immune and neurological systems. At least a dozen trials are now investigating whether fecal transplants can help treat some form of inflammatory bowel disease, be it Crohn’s disease or ulcerative colitis. Another is looking into Type 2 diabetes, and one is even using lean donors to test fecal transplants on patients with metabolic syndrome. Researchers say it won’t be along before they’re joined by studies investigating whether the therapy might aid diseases like multiple sclerosis and autism.

For those who want to know more, another article form The Pacific Standard:

6 Ways to Transplant Fecal Matter, at Home or at the Hospital

And the following two groups:  The Fecal Transplant Foundation

The Power of Poop

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Of course we should expect to find bacteria in a healthy placenta. It only makes sense. But this is interesting stuff - the possibility that the placental biome being out of whack playing a role in preterm birth. From Medical Xpress:

Bacteria live even in healthy placentas, study finds

Surprising new research shows a small but diverse community of bacteria lives in the placentas of healthy pregnant women, overturning the belief that fetuses grow in a pretty sterile environment. These are mostly varieties of "good germs" that live in everybody. But the study also hints that the make-up of this microbial colony plays a role in premature birth.

We share our bodies with trillions of microbes—on the skin, in the gut, in the mouth. These communities are called our microbiome, and many bacteria play critical roles in keeping us healthy, especially those in the intestinal tract. Healthy newborns pick up some from their mother during birth, different bugs depending on whether they were delivered vaginally or by C-section. What about before birth?

Aagard's team earlier had studied the microbiome of the vagina, and learned that its composition changes when a woman becomes pregnant. The puzzle: The most common vaginal microbes weren't the same as the earliest gut bacteria that scientists were finding in newborns. What else, Aagaard wondered, could be "seeding" the infants' intestinal tract?

With colleagues from Baylor and Texas Children's Hospital, Aagaard analyzed 320 donated placentas, using technology that teases out bacterial DNA to evaluate the type and abundance of different microbes. The placenta isn't teeming with microbes—it harbors a low level, Aagaard stressed. Among them are kinds of E. coli that live in the intestines of most healthy people. But to Aagaard's surprise, the placental microbiome most resembled bacteria frequently found in the mouth, she reported in the journal Science Translational Medicine. The theory: Oral microbes slip into the mother's bloodstream and make their way to the placenta.

Why does the body allow them to stay? Aagaard said there appears to be a role for different microbes. Some metabolize nutrients. Some are toxic to yeast and parasites. Some act a bit like natural versions of medications used to stop preterm contractions, she said. In fact, among the 89 placentas that were collected after preterm births, levels of some of the apparently helpful bacteria were markedly lower, she said.

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Most of us are infected with human papilloma viruses. But the really interesting part is that the researchers found that the various HPV strains tend to interact, coexist, and offset symptoms in a balancing act - a HPV viral biome. From Medical Xpress:

More than two-thirds of healthy Americans are infected with human papilloma viruses

In what is believed to be the largest and most detailed genetic analysis of its kind, researchers at NYU Langone Medical Center and elsewhere have concluded that 69 percent of healthy American adults are infected with one or more of 109 strains of human papillomavirus (HPV). Only four of the 103 men and women whose tissue DNA was publicly available through a government database had either of the two HPV types known to cause most cases of cervical cancer, some throat cancers, and genital warts.

Researchers say that while most of the viral strains so far appear to be harmless and can remain dormant for years, their overwhelming presence suggests a delicate balancing act for HPV infection in the body, in which many viral strains keep each other in check, preventing other strains from spreading out of control. Although infection is increasingly known to happen through skin-to-skin contact, HPV remains the most common sexually transmitted infection in the United States. 

"Our study offers initial and broad evidence of a seemingly 'normal' HPV viral biome in people that does not necessarily cause disease and that could very well mimic the highly varied bacterial environment in the body, or microbiome, which is key to maintaining good health," says senior study investigator and NYU Langone pathologist Zhiheng Pei, MD, PhD. 

Lead study investigator and NYU Langone research scientist Yingfei Ma, PhD, says "the HPV 'community' in healthy people is surprisingly more vast and complex than previously thought, and much further monitoring and research is needed to determine how the various non-cancer-causing HPV genotypes interact with the cancer-causing strains, such as genotypes 16 and 18, and what causes these strains to trigger cancer."

Among the study's other key findings: - Some 109 of 148 known HPV types were detected in study participants. - Most study participants had HPV infections in the skin (61 percent); then vagina (41 percent), mouth (30 percent), and gut (17 percent). - Skin samples contained the most varied HPV strains (80 types of HPV, including 40 that were found only in the skin). Vaginal tissue had the second most numerous strains (43 types of HPV, with 20  exclusive to the organ), followed by mouth tissue (33 types, of which five were exclusively oral in origin), and gut tissue (six types, all of which were found in other organs).

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Several interesting bacteria studies. Who knew that dental caries (tooth decay that causes cavities) is contagious? From Science Daily:

Bacteria can linger on airplane surfaces for days

Disease-causing bacteria can linger on surfaces commonly found in airplane cabins for days, even up to a week, according to research. In order for disease-causing bacteria to be transmitted from a cabin surface to a person, it must survive the environmental conditions in the airplane. In this study, MRSA lasted longest (168 hours) on material from the seat-back pocket while E. coli O157:H7 survived longest (96 hours) on the material from the armrest.

From Science Daily: Cavities are contagious, research shows

Dental caries, commonly known as tooth decay, is the single most common chronic childhood disease. In fact, it is an infectious disease, new research demonstrates. Mothers with cavities can transmit caries-producing oral bacteria to their babies when they clean pacifiers by sticking them in their own mouths or by sharing spoons. Parents should make their own oral health care a priority in order to help their children stay healthy.

From Science Daily: Physicians' stethoscopes more contaminated than palms of their hands

Although healthcare workers' hands are the main source of bacterial transmission in hospitals, physicians' stethoscopes appear to play a role. To explore this question, investigators assessed the level of bacterial contamination on physicians' hands and stethoscopes following a single physical examination. Two parts of the stethoscope (the tube and diaphragm) and four regions of the physician's hands (back, fingertips, and thenar and hypothenar eminences) were measured for the total number of bacteria present in a new study. The stethoscope's diaphragm was more contaminated than all regions of the physician's hand except the fingertips. Further, the tube of the stethoscope was more heavily contaminated than the back of the physician's hand.

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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.