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Category: human microbiome

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Two related studies showing the importance of the intestinal bacterial community for health and preventing diseases. Both also discuss how antibiotics disrupt the gut microbial community. From Science Daily:

Microbes help to battle infection: Gut microbes help develop immune cells, study finds

The human relationship with microbial life is complicated. Although there are types of bacteria that can make us sick, Caltech professor of biology and biological engineering Sarkis Mazmanian and his team are most interested in the thousands of other bacteria -- many already living inside our bodies -- that actually keep us healthy. Now, he and his team have found that these good bugs might also prepare the immune cells in our blood to fight infections from harmful bacteria.

In the recent study, published on March 12 in the journal Cell Host & Microbe, the researchers found that beneficial gut bacteria were necessary for the development of innate immune cells -- specialized types of white blood cells that serve as the body's first line of defense against invading pathogens.

In addition to circulating in the blood, reserve stores of immune cells are also kept in the spleen and in the bone marrow. When the researchers looked at the immune cell populations in these areas in so-called germ-free mice, born without gut bacteria, and in healthy mice with a normal population of microbes in the gut, they found that germ-free mice had fewer immune cells -- specifically macrophages, monocytes, and neutrophils -- than healthy mice. Germ-free mice also had fewer granulocyte and monocyte progenitor cells, stemlike cells that can eventually differentiate into a few types of mature immune cells. 

Khosravi and his colleagues next wanted to see if the reduction in immune cells in the blood would make the germ-free mice less able to fight off an infection by the harmful bacterium Listeria monocytogenes -- a well-studied human pathogen often used to study immune responses in mice. While the healthy mice were able to bounce back after being injected with Listeria, the infection was fatal to germ-free mice. When gut microbes that would normally be present were introduced into germ-free mice, the immune cell population increased and the mice were able to survive the Listeria infection.

The researchers also gave injections of Listeria to healthy mice after those mice were dosed with broad-spectrum antibiotics that killed off both harmful and beneficial bacteria. Interestingly, these mice also had trouble fighting the Listeria infection. "We didn't look at clinical data in this study, but we hypothesize that this might also happen in the clinic," says Mazmanian. "For example, when patients are put on antibiotics for something like hip surgery, are you damaging their gut microbe population and making them more susceptible to an infection that had nothing to do with their hip surgery?"

More importantly, the research also suggests that a healthy population of gut microbes can actually provide a preventative alternative to antibiotics, Khosravi says. 

From Science Daily:

Large study identifies exact gut bacteria involved in Crohn's disease

While the causes of Crohn's disease are not well understood, recent research indicates an important role for an abnormal immune response to the microbes that live in the gut. In the largest study of its kind, researchers have now identified specific bacteria that are abnormally increased or decreased when Crohn's disease develops. The findings, which appear in the March 12 issue of the Cell Press journal Cell Host & Microbe, suggest which microbial metabolites could be targeted to treat patients with this chronic and currently incurable inflammatory bowel disease.

Twenty-eight gastroenterology centers across North America have been working together to uncover how microbes contribute to the inflammatory cascade of Crohn's disease. Researchers took biopsies from 447 individuals with new-onset Crohn's disease and 221 nonaffected individuals at multiple locations along the gastrointestinal tract and then looked for differences between the two groups. They also validated their methods in additional individuals, resulting in a total of 1,742 samples from pediatric and adult patients with either new-onset or established disease.

The team found that microbial balance was disrupted in patients with Crohn's disease, with beneficial microbes missing and pathological ones flourishing. Having more of the disease-associated organisms correlated with increasing clinical disease activity. 

When the researchers analyzed the effects of antibiotics, which are sometimes used to treat Crohn's disease symptoms prior to diagnosis, they found that antibiotic usage in children with Crohn's disease could be counterproductive because it causes a loss of good microbes and an increase in pathological ones.

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From Science Daily:

Dropped your toast? Five-second food rule exists, new research suggests

Food picked up just a few seconds after being dropped is less likely to contain bacteria than if it is left for longer periods of time, according to the findings of research carried out at Aston University's School of Life and Health Sciences.

The findings suggest there may be some scientific basis to the '5 second rule' -- the urban myth about it being fine to eat food that has only had contact with the floor for five seconds or less. Although people have long followed the 5 second rule, until now it was unclear whether it actually helped.

The study, undertaken by final year Biology students and led by Anthony Hilton, Professor of Microbiology at Aston University, monitored the transfer of the common bacteria Escherichia coli (E. coli) and Staphylococcus aureus from a variety of indoor floor types (carpet, laminate and tiled surfaces) to toast, pasta, biscuit and a sticky sweet when contact was made from 3 to 30 seconds.

The results showed that:  - Time is a significant factor in the transfer of bacteria from a floor surface to a piece of food; and  - The type of flooring the food has been dropped on has an effect, with bacteria least likely to transfer from carpeted surfaces and most likely to transfer from laminate or tiled surfaces to moist foods making contact for more than 5 seconds.

Professor Hilton said: "Consuming food dropped on the floor still carries an infection risk as it very much depends on which bacteria are present on the floor at the time; however the findings of this study will bring some light relief to those who have been employing the five-second rule for years, despite a general consensus that it is purely a myth. We have found evidence that transfer from indoor flooring surfaces is incredibly poor with carpet actually posing the lowest risk of bacterial transfer onto dropped food.

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It is now over a year since I successfully started treating chronic sinusitis with kimchi, and almost a year for the other 3 family members. The kimchi treatment continues to be amazingly effective. We all continue to feel great and we have not taken any antibiotics in all this time. (See my December 6, 2013 post or the Sinusitis Treatment Summary page for details on how we do various easy Sinusitis Treatments.)

No more symptoms of acute or chronic sinusitis! We have made some recent changes though. We decided to stop doing frequent kimchi "booster" or "maintenance" treatments. Instead, we decided to only use kimchi when there is a definite need, for example after a cold or other virus when we have gone into acute sinusitis, or when our sinuses don't feel right for several days. Since adopting this policy we haven't done a kimchi treatment in over a month and continue to feel great. (Our new motto: If it ain't broke, don't fix it.)

We came to this decision because in December two of us noticed we were only getting a partial response to the brand of kimchi we had been using for almost a year, but when we switched to a new kind of kimchi (but again vegan) we once again felt fantastic. Why did this occur? I have two possible hypotheses: 1) Since kimchi contains so many types of bacteria, perhaps frequent "booster applications" also increased other bacteria in the sinuses that competed with the Lactobacillus sakei, and switching to a new kind of kimchi corrected this problem. OR 2) Perhaps the kimchi company changed their kimchi recipe or ingredients, and thus the Lactobacillus sakei numbers went way down.

We think that since we still get acute sinusitis after a cold or flu-type virus means that our sinus bacterial communities (sinus microbiome) are still not quite right, even thought they must be better than they've been in years (after all, we feel great and not ill, and have not taken antibiotics in over a year). Thus we are making every effort to eat fermented and pickled foods, fruits, vegetables, whole grains, yogurt, raw cheeses, and kefir to naturally increase our beneficial bacteria numbers. We are not taking probiotics because no brand of probiotics currently available contains Lactobacillus sakei. We are also planning to test other brands of kimchi to see what brands are effective. And, of course, I'm always looking for new sources of Lactobacillus sakei and other effective natural sinusitis treatments.

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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. 

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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.

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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.

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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’s 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.

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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.

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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. 

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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.

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