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A recently released report from the American Academy of Microbiology explains the basics of the human microbiome (the collection of trillions of microbes living in and on the human body) and its role in human health in easy to understand language and illustrations. It's a primer for the general public that addresses questions about this growing area of research. There is also a section on the role of the microbiome in human conditions such as obesity and inflammatory bowel disease, and there are general tips on what can be done to maintain a healthy microbiome. It is well worth reading. Below is part of the answer to the question "How big is the microbiome?" The answer shows that it is amazingly big by all measures.

FAQ: HUMAN MICROBIOME

3) How big is the microbiome?

The microbiome is big by almost any measure — number of organisms, total volume, species diversity, and genetic diversity.

NUMBER OF ORGANISMS:
The microbiome includes approximately 100 trillion bacterial cells.                                                   That’s 100,000,000,000,000! You may have heard that there are 10 times more microbial cells than human cells in the human body, but that commonly cited ratio was based on an estimate of 10 trillion cells in the human body. More recent estimates suggest that the human body actually is made up of about 37 trillion human cells. Thus at any given time, the average human body is carrying around 3 times more bacterial cells than human ones. But the microbiome includes more than just bacteria. Remember that it also includes plenty of viruses, fungi, archaea, and single-celled eukaryotes. There is general agreement that viruses outnumber bacterial cells, maybe by as much as 5 to 1. There are thought to be about 10-fold fewer fungal cells than bacteria. All of these numbers are estimates and because the microbiome is a dynamic community, the numbers may change under different circumstances. 
TOTAL VOLUME:
The microbiome is also pretty big in terms of the space it occupies and its total weight. Even though each individual member is microscopic, those large numbers do add up. Most estimates put the weight of an average human microbiome at about 2.5 pounds. In volume, if consolidated, the microbiome would occupy about 3 pints. Keep in mind though, that the microbiome is not all consolidated in one place, and the density of the various microbial communities varies greatly from body site to body site. Blood and lymphatic fluids are practically sterile, while the intestines and colon contain one of the densest known microbial communities on Earth. What is the secret to that high density in the intestinal tract?
Surface area. The inner surfaces of the human intestine and colon are highly convoluted. If you were to flatten out the entire inner surface of the intestine, it would be the size of a tennis court! Dense microbial communities coat that entire surface and also fill the interior spaces of the intestines, resulting in a very dense community.

SPECIES DIVERSITY:
The microbiome is also diverse — a normal microbiome includes around a thousand different species. Thinking back again to your high school biology class, you might recall learning about three basic kinds of bacteria: rods, spheres, and spirals. Certainly bacteriologists developed and used a much more detailed classification system that took into account bacterial physiology and metabolism, but until quite recently, known bacterial diversity was confined to the approximately 5,000 bacterial species that could be grown in the laboratory. Technological advances, especially the capacity to sequence genetic material from environmental samples, have allowed scientists to explore the bacterial world at much greater depth and resolution. 

Very interesting research that may change how we view Lyme Disease - that the bacterium Borrelia burgdorferi — the cause of Lyme disease — may be a contagious illness, sexually transmitted between partners. From the January 27, 2014 Medical Daily:

Is Lyme Disease Contagious? Clues Hint That It May Be A Sexually Transmitted Disease

 A new study published in the Journal of Investigative Medicine suggests the bacterium Borrelia burgdorferi — the cause of Lyme disease — may be a contagious illness, sexually transmitted between partners.

The transmission from person-to-person has been an idea refuted by the CDC who believes it is solely transmitted to humans through the bite of an infected blacklegged tick. “The CDC position on sexual intra-human Borrelia burgdorferi transmission is that it does not occur,” the agency said in a 2011 statement.

The study — presented at the annual Western Regional Meeting of the American Federation for Medical Research — a collaborative effort by an international team of scientists — tested semen samples and vaginal secretions of three groups of patients to investigate whether passing Lyme disease to a partner through unprotected sex is a possibility. The study observed control subjects without evidence of Lyme disease, random subjects who tested positive for Lyme disease, and married heterosexual couples engaging in unprotected sex who tested positive for the disease. The presence of B. burgdorferi and identical strains of the bacterium were of particular interest to the researchers in unprotected sex in spouses.

The control subjects were found to test negative for the bacterium in semen samples or vaginal secretions, as expected by the researchers. The researchers found traces of B. burgdorferi in the vaginal secretions of all women with Lyme disease. In contrast, approximately half of the men with the disease tested positive for the bacterium in semen samples. In addition, one of the heterosexual couples with Lyme disease were found to have identical strains of the bacterium in their genital secretions.

A surprising finding for the researchers was why women with Lyme disease had consistently positive vaginal secretions, compared with the semen samples that showed greater variability. Although this warrants further research, overall, the results indicate the presence of the bacterium in genital secretions and identical strains in married couples, which means the disease may be contracted through sexual transmission. “Our findings will change the way Lyme disease is viewed by doctors and patients,” said Marianne Middelveen, lead author of the study presented in Carmel, 

The possibility of Lyme disease being a sexually transmitted disease could help explain the increase in reported cases throughout the years, suggesting ticks aren’t the only way of infection. The disease is commonly undiagnosed due to the signature “bull’s eye rash” absence in nearly half of those who are infected. 

Another inadvertent way to kill off good bacteria. From the January 27, 2014 Medical Daily:

Antiseptic Mouthwash Raises Heart Attack Risk, Blood Pressure: Chlorhexidine Kills Off 'Good' Bacteria That Helps Blood Vessels Relax

Antiseptic mouthwash is commonly used to quickly refresh and clean the mouth after brushing your teeth in the morning, after eating, and before going to bed. According to a recent study published in the journal Free Radical Biology and Medicine, using a mouthwash twice daily — such as Corsodyl — may increase blood pressure up to 3.5 millimeters of mercury (mmHg), raising your heart attack risk.

Now a team of researchers at Queen Mary University of London believe using antiseptic mouthwash daily could increase the odds of HBP (high blood pressure) due to a chemical that kills the “good” bacteria responsible for helping the blood vessels relax.

Professor Amrita Ahluwalia, lead author of the study, and her team of researchers, observed the effects of a chlorhexidine-based antiseptic mouthwash — Corsodyl — by measuring the blood pressure of a small cohort of healthy participants during a two-week period. Chlorhexidine is an antiseptic that treats gingivitis and others problems of the mouth and gums. A total of 19 participants were recruited for the study during an initial seven-day control period followed by a seven-day treatment period with the antiseptic mouthwash. 

The findings revealed Cordosyl use retracts the oral bacterial conversion from nitrate to nitrate which reduces the plasma nitrate levels that are associated with increases in blood pressure. The mouthwash led the participants’ blood pressure to rise between 2 to 3.5 mmHg, with a noticeable effect found within one day of using the mouthwash twice.

The study authors believe killing off “good” oral bacteria plays a vital role in determining the plasma nitrate levels, and the bodily control of blood pressure. “Killing off all these bugs each day is a disaster, when small rises in blood pressure have significant impact on morbidity and mortality from heart disease and stroke,” said Ahluwalia, the Daily Mail reported. However, she adds, “We are not telling people to stop using antiseptic mouthwashes if they have a gum or tooth infection — but we would ask why anyone else would want to.”

The findings of the study do not apply to all mouthwashes because not all mouthwashes contain the chemical chlorhexidine, such as the popular Listerine. The study authors caution other mouthwashes could still produce the same effects as Corsodyl by damaging the mouth’s healthy bacteria.

If you missed these recent articles about weight and gut bacteria, please go read them now. Amazing stuff. From the December 9, 2013 Washington Post:

The microbes in your gut may be making you fat or keeping you thin

 ...a growing body of evidence suggesting that naturally occurring bacteria and other microbes in the body, and possibly even viruses, can influence weight in ways that scientists are only just beginning to understand. Numerous studies are underway looking at the role of intestinal organisms in obesity, with a focus on how they extract energy from food and how this affects weight gain or loss.

From September 5, 2013 Science News: Gut infections keep mice lean

Skinniness could be contagious. Gut bacteria from thin people can invade the intestines of mice carrying microbes from obese people. And these invaders can keep mice from getting tubby, researchers report in the Sept. 6 Science.

But the benefits come with a catch. The invading microbes drop in and get to work only when mice eat healthy food. Even fat-blocking bacteria can’t fight a bad diet, suggests study leader Jeffrey Gordon, a microbiologist at Washington University in St. Louis. 

Fat and thin people have different microbes teeming in their intestines, for example. And normal-weight mice given microbes from obese mice pack on extra fat, says coauthor Vanessa Ridaura, also of Washington University.

Breast milk contains hundreds of species of bacteria.From the December 8, 2013 Scientific American:

The bacteria in breast milk

Several recent studies have found that breast milk contains a healthy dose of commensal bacteria; all the staphylococci, streptococci, and lactic acid bacteria that are found in the infant gut. This isn’t just bacteria from the skin which have contaminated the samples, but bacteria that have come from inside the breast as an integral component of the milk.

In a study of 16 women it was found that while each milk sample contained hundreds of different bacterial species, around half of the microbiotic community was made up of nine species present in all samples. The other half varied from person to person. This pattern is also found in human gut microbes; a core set present in all individuals along with a large diversity of separate species to make up a unique individual microbiome.

So how do bacteria get into breast milk? Some of them may come from the mouth of the baby. During feeding the skin of both the mother and baby will be in contact with the baby’s open mouth and a certain amount of flow-back can occur between the mouth and nipple. More excitingly it’s been suggested that immune cells in the mothers gut may be able to pick up bacteria and carry them around the body using the lymphatic system. The lymphatic system is a network of vessels used to transport blood plasma. It’s a main highway for immune cells inside the body and is also involved in the absorption and transports of fats.

Like all humans, infants have a range of bacteria within their gut. It looks like these bacteria are initially supplied from the mother’vaginal and skin bacteria, before being replaced by bacteria from the breast milk. Researchers also found that when babies started eating solid food a whole new range of bacteria was introduced, forming the gut microbiome that persisted into adulthood.

From the December 11, 2013 National Geographic:

You Are What You Eat, All 100 Trillion Of You

By setting ten volunteers on either a vegetarian menu or a carnivorous one,Lawrence David from Duke University and Harvard University’s Peter Turnbaugh have shown that when our diet changes, our gut bacteria react very quickly. Within days, some species step into the limelight, while others fade into the background. They activate different genes, pull off different metabolic tricks, and secrete different substances. Our microbiome, it seems, can rapidly switch between plant-eating and meat-eating modes.

David’s team wanted to see what happens over days. If you flood your gut with different food, how long does it take for your microbiome to react?

They did this by recruiting ten volunteers who were willing to collect daily faecal samples. They each ate two different diets for five straight days —a plant-based one that was rich in grains, legumes, fruit and vegetables, and an animal-based one composed of meat, eggs and cheese.

In general, the animal diet led to more dramatic changes than the plant one. 

David and Turnbaugh’s team also found that the altered gut communities did different things. During the plant diet, they became better at breaking down carbohydrates; during the animal diet, protein digestion was their forte. On the meat-heavy days, they activated more genes for breaking down harmful chemicals found in charred meat, and for making vitamins.

And these changes happened very quickly. Some were obvious by day one. By day four, you could pick up a stool sample, list the active genes within it, and predict with total accuracy which diet the owners had been on.

Just two days after the volunteers stopped their diets, things were back to normal. The gut microbiome, it seems, is a fickle beast—easily changed, but not permanently so. The team also found that our food doesn’t just change the microbes that already exist in the gut—they also add some new ones. 

The point is that our gut microbiomes are more flexible than we previously thought. A recent study showed that most of the strains in our guts stay there for decades or more. But while the roster is clearly stable, their relative numbers fluctuate a lot, and food-borne newcomers can gain a foothold.

Some recent studies have explored the link between bacteria in the gut and colorectal cancer. The beneficial Prevotellaceae bacteria (mentioned in the Nov. 5 study below) have been discussed elsewhere as liking whole grain foods. So go feed your gut with some nice whole grain bread or cereal. And some fruits and veggies while you're at it. As mom used to say: "You are what you eat."

A study published December 6, 2013 found that decreased diversity of the gut microbiome and the presence of certain types of bacteria were associated with colorectal cancer in humans: Decreased Diversity of Bacteria Microbiome in Gut Associated Colorectal Cancer

From the November 5, 2013 Science Daily: Microbes in the Gut Help Determine Risk of Tumors

Transferring the gut microbes from a mouse with colon tumors to germ-free mice makes those mice prone to getting tumors as well, according to the results of a study published in mBio®, the online open-access journal of the American Society for Microbiology. The work has implications for human health because it indicates the risk of colorectal cancer may well have a microbial component.

Scientists have known for years that inflammation plays a role in the development of colorectal cancer, but this new information indicates that interactions between inflammation and subsequent changes in the gut microbiota create the conditions that result in colon tumors.

Known risk factors for developing colorectal cancer include consuming a diet rich in red meat, alcohol consumption, and chronic inflammation in the gastrointestinal tract (patients with inflammatory bowel diseases, such as ulcerative colitis, are at a greater risk of developing colorectal cancer, for instance).

The results were stark: mice given the microbiota of the tumor-bearing mice had more than two times as many colon tumors as the mice given a healthy microbiota. What's more, normal mice that were given antibiotics before and after inoculation had significantly fewer tumors than the mice that got no antibiotics, and tumors that were present in these antibiotic-treated mice were significantly smaller than tumors in untreated mice. This suggests that specific populations of microorganisms were essential for the formation of tumors...

Looking at the microorganisms, they found that tumor-bearing mice harbored greater numbers of bacteria within the Bacteroides, Odoribacter, and Akkermansia genera, and decreased numbers of bacteria affiliated with members of the Prevotellaceae and Porphyromonadaceae families. Three weeks after they were inoculated with the communities from the tumor-bearing mice, the germ-free mice had a gut microbiome that was very similar to the tumor-bearing mice, and they had a greater abundance of the same bacterial groups associated with tumor-formation. 

This is the story of my family's successful Sinusitis Treatment using an all natural, easy home remedy. (UPDATE: The treatment worked so well that we all have been cured of chronic sinusitis, and we have been off all antibiotics for over 3 years.)

Ten months ago my family was struggling with chronic sinusitis that no longer responded well to antibiotics. My oldest son had just been told to get another CAT scan and to prepare for ENT surgery to "open up the sinuses more". We were desperate for something that would help us that didn't involve antibiotics or surgery.

Background: This story started many years ago when we (husband, myself, 2 sons) moved into a house with an incorrectly installed central air conditioning system. We all developed mold allergies and repeated bouts of acute sinusitis, which then led to chronic sinusitis. Eventually we discovered the problem, ripped out and replaced the air conditioning system and all ductwork, but by then the damage was done. Even though antibiotics helped acute sinusitis symptoms which occurred after every cold and sore throat, we always felt like we had chronic sinusitis. Over the years we tried everything we could think of, including antibiotics, decongestants, allergy pills, nasal sprays, daily sinus rinsing with salt water, vitamins, steam inhalation, etc. Both sons even had balloon sinuplasties, which had helped for a short while, but no longer. We had avoided sinus surgeries because we didn't know of anyone who had been "cured" going that route, even with repeat surgeries.

The research:  But then last winter I read with great interest all the latest research about bacteria and how all of us have hundreds of species of microorganisms (our microbiome), and how they may play a role in our health.  In fact we are more microbes than cells!

Especially exciting was a small study published in September 2012 which looked at 20 patients about to undergo nasal surgery - 10 healthy patients (the controls) and 10 chronic rhinosinusitis (sinusitis) patients. The researchers found that the chronic rhinosinusitis sufferers had reduced bacterial diversity in their sinuses, especially depletion of lactic acid bacteria (including Lactobacillus sakei) and an increase in Corynebacterium tuberculostearicum (which is normally considered a harmless skin bacteria). They then did a second study in mice which found that Lactobacillus sakei  bacteria protected against sinusitis, even in the presence of Corynebacterium tuberculostearicum. The researchers were going forward with more research in this area with the hope, that if all goes well, of developing a nasal spray with the beneficial bacteria, but that was a few years away. (Source: Nicole A. Abreu et al - Sinus Microbiome Diversity Depletion and Corynebacteriumt uberculostearicum Enrichment Mediates Rhinosinusitis. Science Translational Medicine, September 12, 2012. http://www.ncbi.nlm.nih.gov/pubmed/22972842 )

But we were desperate now and didn't want to wait. What to do? 

The Experiment: I thought that the answer lay with Lactobacillus sakei (or L.sakei) and I read everything I could find on it. I tried to find a natural and safe source for it, and eventually decided on kimchi. Kimchi is a Korean fermented vegetable product which can be made with varying ingredients, usually with cabbage. According to studies done in Korea, many (but not all) brands of traditionally made kimchi contain L. sakei  (as well as many other species of bacteria) after fermentation. It seemed to me that my best bet was to try an all natural kimchi made with cabbage, without any additives, preservatives, and no fish or seafood in it (this last was personal preference). The kimchi brands I bought had to be refrigerated before and after opening. They could not be pasteurized because it was bacteria that I wanted, lots of bacteria. Kimchi fermentation is carried out by the various microorganisms in the kimchi ingredients, and among the bacteria formed are the lactic acid bacteria, one of which can be L. sakei.

In February of 2013 I was off all antibiotics, but feeling sicker (with sinusitis) each day, when I decided to go ahead with the Sinusitis Experiment and purchased several brands of cabbage kimchi (all natural, vegan). Over the next  2 weeks I tried two brands, one after another. Not only did I eat a little bit every day , but I also smeared a little bit of the kimchi juice in my nose, going up about 1/2" in each nostril - as if I were an extremely messy eater. I did this once or twice a day initially. And yes, I was nervous about what I was doing for this was absolutely NOT medically approved. Obviously I did not discuss this with any doctor.

What if harmful bacteria got up in my sinuses and overwhelmed my system?  What if the microbes in the kimchi did harm, even permanent harm?  What really was in the kimchi? Even if the kimchi contained L. sakei, it also contained many other species of bacteria. The studies said that the bacteria in kimchi varied depending on kimchi ingredients (and each brand was different), length of fermentation, and temperature of fermentation.  L.sakei is found in meat (and used in preserving meat), seafood, and some vegetables, but I was nervous about other microbes found in sea food. This was a major reason I avoided any kimchi with seafood in it. After all, the labels on the kimchi I purchased said it was a "live product" (fermentation). When I opened the jars sometimes the liquid inside was bubbling and sometimes even overflowed down the sides of the jar. It takes a leap of faith to put a bubbling strong smelling liquid in the nose!

Results of the Sinusitis Experiment: By the end of the week I found that the one brand worked and it truly felt like a miracle!  Within 24 hours of first applying it I was feeling better, and day by day my sinusitis improved. All the problematic sinusitis symptoms (yellow mucus, constant sore throat from postnasal drip, aching teeth, etc.) slowly went away and within about 2 to 3 weeks I felt great - the sinusitis was gone. After a few weeks the rest of the family followed, one by one, in the Sinusitis Experiment. All improved to the point of feeling great (healthy) and have been off all antibiotics since then. All four of us feel we no longer have chronic sinusitis. We are very, very pleased with the results.

To continue reading the story...

Last year a small study by Abreu et al raised the exciting possibility that the sinus microbiome (the microbial community in our sinuses) being seriously out of whack could be behind chronic sinusitis. Which some day could result in sinusitis treatment being the restoration of beneficial microorganisms that should be there, perhaps with a nasal spray. From Science Daily, September 12, 2012:

Sinusitis Linked to Microbial Diversity

A common bacteria ever-present on the human skin and previously considered harmless, may, in fact, be the culprit behind chronic sinusitis, a painful, recurring swelling of the sinuses that strikes more than one in ten Americans each year, according to a study by scientists at the University of California, San Francisco.

The team reports this week in the journal Science Translational Medicine that sinusitis may be linked to the loss of normal microbial diversity within the sinuses following an infection and the subsequent colonization of the sinuses by the culprit bacterium, which is called Corynebacterium tuberculostearicum.

In their study, the researchers compared the microbial communities in samples from the sinuses of 10 patients with sinusitis and from 10 healthy people, and showed that the sinusitis patients lacked a slew of bacteria that were present in the healthy individuals. The patients also had large increases in the amount of Corynebacterium tuberculostearicum in their sinuses, which are located in the forehead, cheeks and eyes.

The team also identified a common bacterium found within the sinuses of healthy people called Lactobacillus sakei that seems to help the body naturally ward off sinusitis. In laboratory experiments, inoculating mice with this one bacterium defended them against the condition. 

"Presumably these are sinus-protective species," said Susan Lynch, PhD, an associate professor of medicine and director of the Colitis and Crohn's Disease Microbiome Research Core at UCSF. What it all suggests, she added, is that the sinuses are home to a diverse "microbiome" that includes protective bacteria. These "microbial shields" are lost during chronic sinusitis, she said, and restoring the natural microbial ecology may be a way of mitigating this common condition.

Though the sinuses' underlying purpose is still unclear, they are all too familiar to American doctors and their patients because of what happens when the thin tissues lining them become inflamed, as occurs in chronic sinusitis -- one of the most common reasons why people go to the doctor in the United States. There are about 30 million cases each year, and the cost to the healthcare system is an estimated $2.4 billion dollars annually.

The pain of sinusitis can last for months. Doctors typically prescribe bacteria-killing antibiotics and, in more severe and long-lasting cases, conduct sinus surgeries. However, said Andrew Goldberg, MSCE, MD, the director of rhinology and sinus surgery at UCSF and a co-author on the paper, "the premise for our understanding of chronic sinusitis and therapeutic treatment appears to be wrong, and a different therapeutic strategy seems appropriate."

There is a new procedure in which microbiota (the microbes) from a healthy individual are introduced into the gastrointestinal system of a diseased individual via a fecal transplant.  The purpose of the fecal transplant is to replace good bacteria which has been suppressed or killed (usually by antibiotics) , and which has caused bad bacteria, such as Clostridium difficile, to overpopulate the gut. This is having amazing success rates.  It has been used the most for Clostridium difficile (C. difficile) infections, which sickens about half a million Americans annually. This infection can be so debilitating and so resistant to all antibiotics that about 14,000 Americans die each year from it. Even though not that many have been done, fecal transplants are gaining in popularity (some even being done by do-it-yourselfers using fecal enemas at home) because fecal transplants can have a 95 to 98% success rate.                      

New research is starting to see if the fecal transplant can be made even easier (via a "poop pill"), and also if fecal transplants will work for Inflammatory Bowel Diseases (IBD). This would mean the future treatment possibility of transplanting microbiota from healthy individuals to individuals sick with IBD. From the October 4, 2013 Science Daily:  

 Fecal Transplant Pill Knocks out Recurrent C. Diff Infection

C. diff infection can occur after people take antibiotics, wiping out the good bacteria in the gastrointestinal (GI) system, allowing C. diff to flourish and leading to severe diarrhea. In some patients, infection continues to recur despite standard treatment with antibiotics. For patients trapped in that cycle, doctors have transplanted feces from healthy donors into their GI system to rebalance the bacteria and stop infections from recurring.

University of Calgary researchers reported a 100 percent success rate -- none of the 27 patients who took the tablet-sized pills had a recurrence of C. diff, even though all of them previously had had at least four bouts of the infection. Patients ingested between 24 and 34 capsules containing fecal bacteria, often donated by family members.

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There is even the site The Power of Poop  which calls itself a "patient information resource dedicated to promoting safe accessible Fecal Microbiota Transplant (FMT) and to raising awareness of the role of the human microbiome in digestive illness."    http://thepowerofpoop.com