The New York Times, July 19, 2010, by Carl Zimmer  —  Dr. Alexander Khoruts had run out of options.

In 2008, Dr. Khoruts, a gastroenterologist at the University of Minnesota, took on a patient suffering from a vicious gut infection of Clostridium difficile,  and used bacteriotherapy to help cure a patient suffering from a gut infection.

She was crippled by constant diarrhea, which had left her in a wheelchair wearing diapers. Dr. Khoruts treated her with an assortment of antibiotics, but nothing could stop the bacteria. His patient was wasting away, losing 60 pounds over the course of eight months. “She was just dwindling down the drain, and she probably would have died,” Dr. Khoruts said.

Dr. Khoruts decided his patient needed a transplant. But he didn’t give her a piece of someone else’s intestines, or a stomach, or any other organ. Instead, he gave her some of her husband’s bacteria.

Dr. Khoruts mixed a small sample of her husband’s stool with saline solution and delivered it into her colon. Writing in the Journal of Clinical Gastroenterology last month, Dr. Khoruts and his colleagues reported that her diarrhea vanished in a day. Her Clostridium difficile infection disappeared as well and has not returned since.

The procedure — known as bacteriotherapy or fecal transplantation — had been carried out a few times over the past few decades. But Dr. Khoruts and his colleagues were able to do something previous doctors could not: they took a genetic survey of the bacteria in her intestines before and after the transplant.

Before the transplant, they found, her gut flora was in a desperate state. “The normal bacteria just didn’t exist in her,” said Dr. Khoruts. “She was colonized by all sorts of misfits.”

Two weeks after the transplant, the scientists analyzed the microbes again. Her husband’s microbes had taken over. “That community was able to function and cure her disease in a matter of days,” said Janet Jansson, a microbial ecologist at Lawrence Berkeley National Laboratory and a co-author of the paper. “I didn’t expect it to work. The project blew me away.”

Scientists are regularly blown away by the complexity, power, and sheer number of microbes that live in our bodies. “We have over 10 times more microbes than human cells in our bodies,” said George Weinstock of Washington University in St. Louis. But the microbiome, as it’s known, remains mostly a mystery. “It’s as if we have these other organs, and yet these are parts of our bodies we know nothing about.”

Dr. Weinstock is part of an international effort to shed light on those puzzling organs. He and his colleagues are cataloging thousands of new microbe species by gathering their DNA sequences. Meanwhile, other scientists are running experiments to figure out what those microbes are actually doing. They’re finding that the microbiome does a lot to keep us in good health. Ultimately, researchers hope, they will learn enough about the microbiome to enlist it in the fight against diseases.

“In just the last year, it really went from a small cottage industry to the big time,” said David Relman of Stanford University.

The microbiome first came to light in the mid-1600s, when the Dutch lens-grinder Antonie van Leeuwenhoek scraped the scum off his teeth, placed it under a microscope and discovered that it contained swimming creatures. Later generations of microbiologists continued to study microbes from our bodies, but they could only study the ones that could survive in a laboratory. For many species, this exile meant death.

In recent years, scientists have started to survey the microbiome in a new way: by gathering DNA. They scrape the skin or take a cheek swab and pull out the genetic material. Getting the DNA is fairly easy. Sequencing and making sense of it is hard, however, because a single sample may yield millions of fragments of DNA from hundreds of different species.

A number of teams are working together to tackle this problem in a systematic way. Dr. Weinstock is part of the biggest of these initiatives, known as the Human Microbiome Project. The $150 million initiative was started in 2007 by the National Institutes of Health. The project team is gathering samples from 18 different sites on the bodies of 300 volunteers.

To make sense of the genes that they’re gathering, they are sequencing the entire genomes of some 900 species that have been cultivated in the lab. Before the project, scientists had only sequenced about 20 species in the microbiome. In May, the scientists published details on the first 178 genomes. They discovered 29,693 genes that are unlike any known genes. (The entire human genome contains only around 20,000 protein-coding genes.)

“This was quite surprising to us, because these are organisms that have been studied for a long time,” said Karen E. Nelson of the J. Craig Venter Institute in Rockville, Md.

The new surveys are helping scientists understand the many ecosystems our bodies offer microbes. In the mouth alone, Dr. Relman estimates, there are between 500 and 1,000 species. “It hasn’t reached a plateau yet: the more people you look at, the more species you get,” he said. The mouth in turn is divided up into smaller ecosystems, like the tongue, the gums, the teeth. Each tooth—and even each side of each tooth—has a different combination of species.

Scientists are even discovering ecosystems in our bodies where they weren’t supposed to exist. Lungs have traditionally been considered to be sterile because microbiologists have never been able to rear microbes from them. A team of scientists at Imperial College London recently went hunting for DNA instead. Analyzing lung samples from healthy volunteers, they discovered 128 species of bacteria. Every square centimeter of our lungs is home to 2,000 microbes.

Some microbes can only survive in one part of the body, while others are more cosmopolitan. And the species found in one person’s body may be missing from another’s. Out of the 500 to 1,000 species of microbes identified in people’s mouths, for example, only about 100 to 200 live in any one person’s mouth at any given moment. Only 13 percent of the species on two people’s hands are the same. Only 17 percent of the species living on one person’s left hand also live on the right one.

This variation means that the total number of genes in the human microbiome must be colossal. European and Chinese researchers recently catalogued all the microbial genes in stool samples they collected from 124 individuals. In March, they published a list of 3.3 million genes.

The variation in our microbiomes emerges the moment we are born.

“You have a sterile baby coming from a germ-free environment into the world,” said Maria Dominguez-Bello, a microbiologist at the University of Puerto Rico. Recently, she and her colleagues studied how sterile babies get colonized in a hospital in the Venezuelan city of Puerto Ayacucho. They took samples from the bodies of newborns within minutes of birth. They found that babies born vaginally were coated with microbes from their mothers’ birth canals. But babies born by Caesarean section were covered in microbes typically found on the skin of adults.

“Our bet was that the Caesarean section babies were sterile, but it’s like they’re magnets,” said Dr. Dominguez-Bello.

We continue to be colonized every day of our lives. “Surrounding us and infusing us is this cloud of microbes,” said Jeffrey Gordon of Washington University. We end up with different species, but those species generally carry out the same essential chemistry that we need to survive. One of those tasks is breaking down complex plant molecules. “We have a pathetic number of enzymes encoded in the human genome, whereas microbes have a large arsenal,” said Dr. Gordon.

In addition to helping us digest, the microbiome helps us in many other ways. The microbes in our nose, for example, make antibiotics that can kill the dangerous pathogens we sniff. Our bodies wait for signals from microbes in order to fully develop. When scientists rear mice without any germ in their bodies, the mice end up with stunted intestines.

In order to co-exist with our microbiome, our immune system has to be able to tolerate thousands of harmless species, while attacking pathogens. Scientists are finding that the microbiome itself guides the immune system to the proper balance.

One way the immune system fights pathogens is with inflammation. Too much inflammation can be harmful, so we have immune cells that produce inflammation-reducing signals. Last month, Sarkis Mazmanian and June L. Round at Caltech reported that mice reared without a microbiome can’t produce an inflammation-reducing molecule called IL-10.

The scientists then inoculated the mice with a single species of gut bacteria, known as Bacteroides fragilis. Once the bacteria began to breed in the guts of the mice, they produced a signal that was taken up by certain immune cells. In response to the signal, the cells developed the ability to produce IL-10.

Scientists are not just finding new links between the microbiome and our health. They’re also finding that many diseases are accompanied by dramatic changes in the makeup of our inner ecosystems. The Imperial College team that discovered microbes in the lungs, for example, also discovered that people with asthma have a different collection of microbes than healthy people. Obese people also have a different set of species in their guts than people of normal weight.

In some cases, new microbes may simply move into our bodies when disease alters the landscape. In other cases, however, the microbes may help give rise to the disease. Some surveys suggest that babies delivered by Caesarian section are more likely to get skin infections from multiply-resistant Staphylococcus aureus. It’s possible that they lack the defensive shield of microbes from their mother’s birth canal.

Caesarean sections have also been linked to an increase in asthma and allergies in children. So have the increased use of antibiotics in the United States and other developed countries. Children who live on farms — where they can get a healthy dose of microbes from the soil — are less prone to getting autoimmune disorders than children who grow up in cities.

Some scientists argue that these studies all point to the same conclusion: when children are deprived of their normal supply of microbes, their immune systems get a poor education. In some people, untutored immune cells become too eager to unleash a storm of inflammation. Instead of killing off invaders, they only damage the host’s own body.

A better understanding of the microbiome might give doctors a new way to fight some of these diseases. For more than a century, scientists have been investigating how to treat patients with beneficial bacteria. But probiotics, as they’re sometimes called, have only had limited success. The problem may lie in our ignorance of precisely how most microbes in our bodies affect our health.

Dr. Khoruts and his colleagues have carried out 15 more fecal transplants, 13 of which cured their patients. They’re now analyzing the microbiome of their patients to figure out precisely which species are wiping out the Clostridium difficile infections. Instead of a crude transplant, Dr. Khoruts hopes that eventually he can give his patients what he jokingly calls “God’s probiotic” — a pill containing microbes whose ability to fight infections has been scientifically validated.

Dr. Weinstock, however, warns that a deep understanding of the microbiome is a long way off.

“In terms of hard-boiled science, we’re falling short of the mark,” he said. A better picture of the microbiome will only emerge once scientists can use the genetic information Dr. Weinstock and his colleagues are gathering to run many more experiments.

“It’s just old-time science. There are no short-cuts around that,” he said.

15 Tips to Freshen Your Breath

  

Reviewed by Brunilda Nazario, MD

WebMD.com, July 19, 2010, by Debra Fulghum Bruce, PhD  —  The kiss. The smile. The breath. What’s most important to you (and to your significant other)? Chances are it’s good breath.

Let’s get personal. Bad breath (halitosis) may be common in dogs — but for people, bad breath affects how you feel about yourself, not to mention how others perceive you. In fact, you may not know you have halitosis until a brave friend tells you.

How can you tell if you have bad breath? A simple way is to stick a clean finger in your mouth and scrape saliva from the back of your tongue. Put it on the back of your hand, wait a minute, then smell your hand. Is it something you’d want to kiss?

 If not, check out these 15 tips about causes and cures for bad breath. Start freshening your breath today!

5 Common Causes of Bad Breath

1. Blame bacteria for bad breath. Bacteria breed inside your mouth. These micro organisms lurk between your teeth and cover your tongue. When bacteria stagnate, they multiply and give off toxins and stinky odors.

 2. Say “Ahhh.” The deep holes in your tonsils, called crypts, are a common cause of halitosis. If your tonsils are too wide and pitted, a cheese-like smelly substance collects in these holes. These nuggets sometimes smell, and may cause bad breath.

 3. Pungent foods and bad breath. Foods such as onion, garlic, and fish can cause bad breath — even hours after you brush your teeth.

4. Bad habits = bad breath. Any type of smoking (cigarettes, cigars, pipe) or chewing tobacco can leave you with a really nasty taste — and smell — in your mouth. 

5. Tummy troubles. Sometimes GI problems such as GERD or an ulcer can cause bad breath when you burp and gas is released. Also blame low-carb diets, which cause ketosis, a fat-burning state in the body that produces dragon breath.

 

10 Tips to Banish Bad Breath

Now for the fix, here are some simple tips from oral health experts on how to have breath that’s “kissing fresh”:

1. Brush your teeth — and tongue — twice a day to banish bad breath. While you’re brushing your teeth with a fluoride toothpaste, brush your tongue – especially the back of the tongue. Brushing your tongue will remove smelly bacteria that cause bad breath. One study found that by brushing the tongue, volunteers reduced their perception of bad breath by 70%. You can also buy inexpensive tongue scrapers at most pharmacies. 

2. Floss once a day for fresh breath. Flossing is must-do. Flossing gets out hidden food particles and removes plaque, a coating of bacteria that forms around the tooth. Flossing also helps prevent periodontal disease — another common cause of bad breath.

 3. Gargle with peroxide to fight halitosis. An antimicrobial mouthwash is important if you have a problem with excess plaque. “You can also gargle with peroxide for fresher breath,” says Mike McIlwain, DMD, a dentist at McIlwain Dentistry and an assistant clinical professor in Pediatric Dentistry at the University of Florida. McIlwain recommends gargling with peroxide to his patients. “Treat it like your favorite mouthwash. Just swig, swish, and spit. The oxygen in the hydrogen peroxide kills mouth bacteria that cause bad breath,” McIlwain says. 

 

4. Use a fluoride mouth rinse for sweeter breath. Not only do decayed teeth hurt, they have an awful odor. Tooth decay can be prevented with fluoride toothpaste and proper dental care. 

5. Drink lots of water to avert bad breath. “Lack of fluids can lead to dry mouth (xerostomia) and cause bad breath,” says Murray Grossan, MD, a board certified otolaryngologist at Cedars Sinai Medical Center in Los Angeles and coauthor of The Sinus Cure. Dry mouth or reduced saliva can be the result of not drinking enough liquids, mouth breathing, or medications like antihistamines.

6. Reduce upset stomachs to ease bad breath. Over-the-counter antacids may ease a sour or acidic stomach, which can cause halitosis when you burp. If you are milk intolerant and have GI problems, try lactase tablets.

7. Check your sinuses; infections cause bad breath. Bad breath is often a clue to an underlying sinus infection. “The purulent post-nasal drip is the culprit,” says William Sears, MD, also known as “America’s Pediatrician,” an associate clinical professor of Pediatrics at the University of California, Irvine, School of Medicine. Post-nasal drip is most noticeable after sleeping at night, which is why many people rush to brush their teeth first thing in the morning.

8. Eat yogurt for sweeter breath. Yogurt replenishes the good bacteria in the gut and “promotes a healthier mouth,” McIlwain says. Sears recommends celery “to remove stinky bacteria.” You may also try eating parsley between meals to fresh breath. Parsley reportedly has antibacterial and antifungal properties.

9. Chew gum with xylitol to banish bad breath. Chewing gum makes you salivate if your mouth is dry and causing bad breath. Saliva is what washes away the bacteria in your mouth. 

10. See your dentist. At least every six months, see your dentist for teeth cleaning and an oral exam. Your dentist can check your mouth and teeth for open cavities and gum disease that cause bad breath.

If self-care tips don’t work to stop your bad breath, see your doctor. Occasionally bad breath is a sign of a more serious problem, such as an infection, chronic bronchitis, diabetes, or kidney or liver disease.

GoogleNews.com, FORBES.COM, PITTSBURGH — Generic drugmaker Mylan Inc. said Monday that regulators approved its generic version of Catapres-TTS high blood pressure patches.

Mylan said its patches are available for immediate shipment.

The patch delivers a drug called clonidine through the skin. The brand name version of the drug is made by German drugmaker Boehringer Ingelheim. Mylan said U.S. sales of clonidine patches totaled $313 million in the 12 months ended March 31. Par Pharmaceutical Cos. began selling a generic version last year.

FOUR OAKS, N.C. —

GoggleNews.com, FORBES.COM, July 19, 2010  —  A global medical device maker plans to expand in North Carolina, building a new East Coast distribution center in return for a promised state gift of $600,000.

Gov. Beverly Perdue’s office said Monday that Becton, Dickinson and Co. will add nearly 190 jobs by 2015.

The Franklin Lakes, N.J., company would pay an average salary of nearly $29,000 a year plus benefits, below Johnston County’s average annual wage of $31,000.

The site in Four Oaks about 30 miles south of Raleigh is expected to open in 2012.

The News & Observer of Raleigh reports that Becton Dickinson began operations in Research Triangle Park almost four decades ago and employs more than 700 people in RTP, Durham, Burlington and Mebane.

Summer Sunset Through a Dandelion

By Vicki France