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Category: microbes

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Research is accumulating that the microbial exposure from a vaginal birth, breastfeeding, and pets in the first year of life are all good for a baby's developing immune system and the gut microbiome.

From Science Daily: Breastfeeding, other factors help shape immune system early in life

Researchers say that breastfeeding and other factors influence a baby's immune system development and susceptibility to allergies and asthma by what's in their gut. The striking findings from a series of studies further advance the so-called hygiene hypothesis theory that early childhood exposure to microorganisms affects the immune system's development and onset of allergies, says Christine Cole Johnson, Ph.D., MPH, chair of Henry Ford's Department of Public Health Sciences and principal research investigator.

The gut microbiome is the collection of microorganisms in the gastrointestional, or GI, tract, and the human body has billions of these microbes... The gut microbiome is known to play an important role in immune system development, and is thought to contribute to a host of diseases like obesity, autoimmune diseases, circulating disorders and pediatric allergies and infection.

"For years now, we've always thought that a sterile environment was not good for babies. Our research shows why. Exposure to these microorganisms, or bacteria, in the first few months after birth actually help stimulate the immune system," Dr. Johnson says."The immune system is designed to be exposed to bacteria on a grand scale. If you minimize those exposures, the immune system won't develop optimally."

In six separate studies, researchers sought to evaluate whether breastfeeding and maternal and birth factors had any effect on a baby's gut microbiome and allergic and asthma outcomes. Using data collected from the WHEALS birth cohort, researchers analyzed stool samples from infants taken at one month and six months after birth. They also looked at whether the gut microbiome impacted the development of regulatory T-cells, or Treg, which are known to regulate the immune system. Highlights:

• Breastfed babies at one month and six months had distinct microbiome compositions compared to non-breastfed babies. These distinct compositions may influence immune system development. • Breastfed babies at one month were at decreased risk of developing allergies to pets. • Asthmatic children who had nighttime coughing or flare-ups had a distinct microbiome composition during the first year of life. • For the first time, gut microbiome composition was shown to be associated with increasing Treg cells.

Researchers found that a baby's gut microbiome patterns vary by: • A mother's race/ethnicity. • A baby's gestational age at birth. • Prenatal and postnatal exposure to tobacco smoke. • Caesarean section versus vaginal delivery.• Presence of pets in the home.

Henry Ford's landmark 2002 study found exposure to dogs or cats in the first year of a baby's life reduced their risk for allergies.

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Gut bacteria in children varies among different Asian countries. A recent study found that microbiota of 303 subjects could be classified into two main clusters: driven by Prevotella (P-type) or by Bifidobacterium/Bacteroides (BB-type).

The majority of children in China, Japan and Taiwan harbored Bifidobacterium/Bacteroides (BB type), whereas those from Indonesia and Khon Kaen in Thailand mainly harbored Prevotella (P-type). It was interesting in that even eating different types of rice result in different gut bacteria.

From Asian Scientist: Diet, Location And Your Kid’s Gut Bacteria

An Asia-wide study of the gut microbiota of primary school children has identified differences linked to diet and geographical location.  ...continue reading "Gut Bacteria of School Children In Different Asian Countries"

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This research suggests that emulsifiers (which are added to most processed foods to aid texture and extend shelf life) can alter the gut microbiota (the community of microbes that live in our gut) in such a way as to cause intestinal inflammation. Even though the study was done on mice, it is thought it also applies to humans. From Medical Daily:

You Are What You Eat: Food Additive Emulsifier Inflames Mouse Gut And Causes Obesity

Processed foods have changed the way we eat. Food can sit longer on shelves, but what does that mean for the stomach? In a new study published in the journal Nature, researchers from Georgia State University investigated how the widely used processed food additive emulsifiers played a role in the gut.

Emulsifiers are added to most processed foods in order to extend shelf life and add texture to the foods. The research team decided to feed mice a couple of the most common emulsifiers on the market — polysorbate 80 and carboxymethylcellulose — at doses comparable to a human’s consumption of processed foods. They watched the emulsifier change the mice’s gut microbiota, which is an individual’s personal 100 trillion bacteria inside the intestinal tract. Not only did this increase their chance of developing obesity-related disorders, but also inflammatory bowel disease. It’s no coincidence both conditions have been increasing since the 1950s.

"The dramatic increase in these diseases has occurred despite consistent human genetics, suggesting a pivotal role for an environmental factor," the study’s coauthor Benoit Chassaing, a researcher from GSU’s Institute for Biomedical Sciences, said in a press release. "Food interacts intimately with the microbiota, so we considered what modern additions to the food supply might possibly make gut bacteria more pro-inflammatory."

The emulsifiers, which are groups of oil-and water-friendly molecules, help to hold food together. Mayonnaise without emulsifiers, for example, will separate from an oily top layer to a thicker white layer that rests on the bottom of the jar. Once the emulsifiers were digested by the mice, their blood-glucose levels went awry, inflamed their intestinal mucus layer, which left them with weight gain, specifically concentrated in the abdomen. The bacterial changed triggered chronic colitis from causing intestinal inflammation and metabolic syndrome, which includes obesity, hyperglycemia, and insulin resistance.

Ultimately, microbiologists say you are what you eat. If your diet is smeared with margarine, mayonnaise, creamy sauces, candy, ice cream, and most other packaged and processed baked goods, you and your gut may be at risk. "We do not disagree with the commonly held assumption that over-eating is a central cause of obesity and metabolic syndrome," the study’s coauthor Andrew T. Gewirtz, a researcher from GSU’s Institute for Biomedical Sciences, said in a press release. "Rather, our findings reinforce the concept suggested by earlier work that low-grade inflammation resulting from an altered microbiota can be an underlying cause of excess eating."

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Further reasons to be cautious of using antibiotics, and more support for finding beneficial bacteria and other microbes to outcompete the "bad" microbes. I especially liked the last paragraph that stressed for a healthy microbiota (microbial community):"Instead of trying to kill the "bad" bacteria causing an illness, a healthy and functioning microbiota may be able to outcompete the unwanted microbes and improve immune function." From Medical Xpress:

Unwanted impact of antibiotics broader, more complex than previously known

Researchers at Oregon State University have discovered that antibiotics have an impact on the microorganisms that live in an animal's gut that's more broad and complex than previously known. The findings help to better explain some of the damage these medications can do, and set the stage for new ways to study and offset those impacts.

Researchers have known for some time that antibiotics can have unwanted side effects, especially in disrupting the natural and beneficial microbiota of the gastrointestinal system. But the new study helps explain in much more detail why that is happening, and also suggests that powerful, long-term antibiotic use can have even more far-reaching effects. Scientists now suspect that antibiotic use, and especially overuse, can have unwanted effects on everything from the immune system to glucose metabolism, food absorption, obesity, stress and behavior.

The issues are rising in importance, since 40 percent of all adults and 70 percent of all children take one or more antibiotics every year, not to mention their use in billions of food animals. Although when used properly antibiotics can help treat life-threatening bacterial infections, more than 10 percent of people who receive the medications can suffer from adverse side effects.

This research used a "cocktail" of four antibiotics frequently given to laboratory animals, and studied the impacts."Prior to this most people thought antibiotics only depleted microbiota and diminished several important immune functions that take place in the gut," Morgun said. "Actually that's only about one-third of the picture. They also kill intestinal epithelium. Destruction of the intestinal epithelium is important because this is the site of nutrient absorption, part of our immune system and it has other biological functions that play a role in human health."

The research also found that antibiotics and antibiotic-resistant microbes caused significant changes in mitochondrial function, which in turn can lead to more epithelial cell death....Mitochondria plays a major role in cell signaling, growth and energy production, and for good health they need to function properly.

Morgun and Schulzhenko's research group also found that one of the genes affected by antibiotic treatment is critical to the communication between the host and microbe. "When the host microbe communication system gets out of balance it can lead to a chain of seemingly unrelated problems," Morgun said. Digestive dysfunction is near the top of the list, with antibiotic use linked to such issues as diarrhea and ulcerative colitis. But new research is also finding links to obesity, food absorption, depression, immune function, sepsis, allergies and asthma.

Healthy microbiota may also be another way to address growing problems with antibiotic resistance, Morgun said. Instead of trying to kill the "bad" bacteria causing an illness, a healthy and functioning microbiota may be able to outcompete the unwanted microbes and improve immune function.

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This is very interesting, and raises all sorts of possibilities for microbial transplants. While it's looking at only one person, this seems to be evidence that microbes are involved with our weight and manipulating them may result in weight gain or loss. From Science Daily:

Rapid and unexpected weight gain after fecal transplant

A woman successfully treated for a recurrent Clostridium difficile infection with stool from an overweight donor rapidly gained weight herself afterwards, becoming obese, according to a case report published in the new journal Open Forum Infectious Diseases.

Fecal microbiota transplant (FMT) is a promising treatment for relapsing C. difficile infections, a common cause of antibiotic-related diarrhea that in severe cases may be life-threatening. The case suggests that clinicians should avoid selecting stool donors who are overweight. The report also raises questions about the role of gut bacteria in metabolism and health.

At the time of the woman's fecal transplant in 2011, her weight was stable at 136 pounds, and her Body Mass Index (BMI) was 26. Then 32 years old, she had always been of normal weight. The transplant used donor stool from the woman's overweight but otherwise healthy teenage daughter, administered via colonoscopy, to restore a healthy balance of bacteria in the woman's gut, curing her C. difficile infection.

Sixteen months later, the woman weighed 170 pounds, and her BMI was 33, meeting medical criteria for obesity. The weight gain persisted despite a medically supervised liquid protein diet and exercise program. Continuing efforts to diet and exercise did not lower her weight: Three years after the transplant, she weighed 177 pounds with a BMI of 34.5, and she remains obese today.

"We're questioning whether there was something in the fecal transplant, whether some of those 'good' bacteria we transferred may have had an impact on her metabolism in a negative way," said Colleen R. Kelly, MD, of the Warren Alpert Medical School of Brown University, who wrote the case report with Neha Alang, MD, of Newport Hospital in Rhode Island. Such a link between bacteria in the gastrointestinal tract and weight is supported by previously published animal studies, where transfer of gut bacteria from obese to normal-weight mice can lead to a marked increase in fat. In light of the case and the animal data, the authors recommend selecting stool donors who are not overweight for fecal transplants.

Importantly, the FMT was not the only possible cause of the woman's weight gain. In addition to treatment for C. difficile, she had also been treated with several antibiotics for Helicobacter pylori infection. Other possible contributing factors in the woman's weight gain include the resolution of her C. difficile infection, genetic factors, aging, and stress related to illness. However, as noted above, she had never been overweight before.

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Now we are finally finding out about all the microbes we encounter when go through New York City's subway system: touching handrails, turnstiles, and just sitting on benches. This study looked at the microbial communities of NYC's subway system. From the Wall Street Journal:

Big Data and Bacteria: Mapping the New York Subway’s DNA

Aboard a No. 6 local train in Manhattan, Weill Cornell researcher Christopher Mason patiently rubbed a nylon swab back and forth along a metal handrail, collecting DNA in an effort to identify the bacteria in the New York City subway. In 18 months of scouring the entire system, he has found germs that can cause bubonic plague uptown, meningitis in midtown, stomach trouble in the financial district and antibiotic-resistant infections throughout the boroughs.

The big-data project, the first genetic profile of a metropolitan transit system, is in many ways “a mirror of the people themselves who ride the subway,” said Dr. Mason, a geneticist at the Weill Cornell Medical College... By documenting the miniature wildlife, microbiologists hope to discover new ways to track disease outbreaks—including contagious diseases like Ebola or measles—detect bioterrorism attacks and combat the growing antibiotic resistance among microbes, which causes about 1.7 million hospital infections every year.“We know next to nothing about the ecology of urban environments,” said evolutionary biologist Jonathan Eisen at the University of California at Davis. “How will we know if there is something abnormal if we don’t know what normal is?”

Dr. Mason and his research team gathered DNA from turnstiles, ticket kiosks, railings and benches in a transit system shared by 5.5 million riders every day. They sequenced the genetic material they found at the subway’s 466 open stations—more than 10 billion fragments of biochemical code—and sorted it by supercomputer. They compared the results to genetic databases of known bacteria, viruses and other life-forms to identify these all-but-invisible fellow travelers.

In the process, they uncovered how commuters seed the city subways every day with bacteria from the food they eat, the pets or plants they keep, and their shoes, trash, sneezes and unwashed hands. The team detected signs of 15,152 types of life-forms. Almost half of the DNA belonged to bacteria—most of them harmless; the scientists said the levels of bacteria they detected pose no public-health problem. Data from the PathoMap Project, as Dr. Mason calls it, was published online in the journal Cell Systems on Thursday.

As more and more scientists probe urban microbiology, they are also hoping to find ways to foster beneficial bacteria through building design and to learn how to eliminate construction practices that create living conditions for the germs that make people ill.

This emerging field reflects the growing awareness that the human body swarms with bacteria. Typically, every person is home to about a hundred trillion microbial cells bearing five million different genes, totaling about 5 pounds of micro-organisms per person. Indeed, microbes in and on the body outnumber human cells about 10 to one. The body’s collection of microbes, called the microbiome, influences health in ways that researchers are only beginning to understand. 

Broadly speaking, city living leaves its mark on people. That includes the sorts of microbes that collect inside them. A recent comparison of urban and rural residents in Russia found that city dwellers had different sets of stomach microbes than people in the countryside. Every person trails a distinctive collection of microbes, by shedding about 1.5 million microscopic skin cells every hour. Bacteria from a person’s body can colonize a hotel room in less than six hours, scientists at the U.S. Department of Energy’s Argonne National Laboratory in Illinois recently discovered.

Depending on the material involved, some surfaces can have thousands of different types of bacteria while others may have only a few hundred, researchers monitoring the new Chicago hospital found. Pathogens responsible for common infections, such as the strep germs that cause an estimated 700 million infections world-wide every year, can survive for months on a dry surface, researchers in Germany reported in September in the journal BMC Infectious Diseases.

The New York subway study quickly hit the current limits of science. Most microbes have never been isolated or studied. Only a few thousand creatures of any sort have ever had their entire set of genes analyzed, so identifications of DNA sequences through online computer comparisons can be inaccurate. All told, the biodiversity of the subway isn’t as rich as normal soil. The dirt in Central Park contains 167,000 types of micro-organisms—about 11 times the number of species in the transit system... But a deep breath of subway air contains about as many free-floating bacteria as fresh air at street level, researchers at the University of Colorado Boulder reported last year in the journal Applied and Environmental Microbiology.

No two subway stations were exactly the same, said Weill Cornell project leader Ebrahim Afshinnekoo, who helped analyze the data.The greatest subway biodiversity was found at the Myrtle-Willoughby Avenue stop for the G train in Bedford-Stuyvesant, Brooklyn, where 95 unique bacteria groups were detected....Among the DNA of higher organisms, the researchers found across the system that genetic material from beetles and flies was the most prevalent—the cockroach genome hasn’t been sequenced yet so that DNA wasn’t identified... Human DNA ranked fourth.

So far, scientists have identified 562 species of bacteria, most of them benign or low risk. At least 67 of those species can make people sick. Even these infectious bacteria were all detected at such low levels that they were unlikely to cause illness in a healthy person...Among the pathogenic and infectious bacteria, the Cornell researchers identified DNA related to strep infections at 66 stations and urinary tract infections at 192 stations. They found E. coli at 56 stations and other bacteria related to food poisoning at 215 stations.

 

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Published on 2 Comments on Two Years (and Counting) Without Sinusitis

It is now 104 weeks being free of chronic sinusitis and off all antibiotics! Two full years since I started my easy do-it-yourself sinusitis treatment! And my sinuses feel great! I would never ever have thought such a thing was possible several years ago. Thanks to the probiotic (beneficial bacteria) Lactobacillus sakei I got my life back. Yes, I know I'm gushing...

After reading the original ground-breaking research on sinusitis done by Abreu et al (2012), it led to finding and trying L. sakei as a sinusitis treatment. Of course, there is an entire community of microbes that live in healthy sinuses (the sinus microbiome), but L. sakei seems to be a key one for sinus health. As you may have guessed, the name of this web-site Lacto Bacto is in homage to the bacteria Lactobacillus sakei.

Thank you all who have written to me  - whether publicly or privately. Please keep writing because it is adding to the sinusitis treatment knowledge base. I will keep posting updates.

I will be trying to find more sources of L. sakei this year and also look for other microbes that help treat sinusitis. And the foods or products that they're in. As of today, my family (all 4 members) have successfully used live kimchi and even sausage starter culture (both containing L. sakei) to treat both acute and chronic sinusitis these past 2 years. Based on our experiences and those of others, finding live L. sakei in kimchi (not all brands have L. sakei in it) and other products can be tricky, but when the product has live L. sakei in it - the results are absolutely great! We have also learned that L.sakei products should be used sparingly - only as needed.

[NOTE: Since then I've posted a number of posts with sinusitis treatment information. The updated (November 2018) The Best Probiotic For Sinus Infections has products and sources of L. sakei. The Sinusitis Treatment Summary page has treatment methods. And news about a Lactobacillus sakei product which I really like - Lacto Sinus. One can also click on SINUSITIS under CATEGORIES to see more posts, such as "Which Kimchi is Best for Sinusitis Treatment: Vegan or Seafood?"]

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Another study that shows that differences in the gut microbiota appear early in life, and appear to be based on length of gestation (pregnancy) and type of delivery (vaginal vs C-section). From Science Daily:

Birth method, gestation duration may alter infants' gut microbiota

Environmental factors like mode of delivery and duration of gestation may affect how infants' gut bacteria mature, and that rate could help predict later body fat, international researchers have found.

Among a group of 75 infants, those who were vaginally delivered and had a longer gestation before birth tended to more quickly develop a more mature gut microbiota, and had typical body fat at 18 months. By contract, babies who were delivered via Caesarean section and had shorter gestations took longer to acquire a more mature gut microbiota and had lower body fat at 18 months.

"It seems like the early environment, for instance mode of delivery, mode of feeding, the duration of gestation and living environment may be influencing the rate at which babies acquire their gut microbiota," said senior study author Joanna Holbrook, a senior principal investigator at the Singapore Institute for Clinical Sciences, "and that in turn has an association with how babies grow and put on body fat."

At birth, human infants start accumulating intestinal microbiota until a relatively stable state is reached, Holbrook said. The rate at which babies acquire gut microbiota is believed to have a considerable impact on later health outcomes.

For the study, Holbrook and colleagues used a laboratory technique called 16s rRNA sequencing to analyze stool samples that had been collected from 75 infants participating in the GUSTO (Growing Up in Singapore Toward Healthy Outcomes) study, which includes members of the three main ethnic groups in Singapore: Chinese, Indian and Malay. The samples were taken when the infants were three days old, three weeks old, three months old and six months old. 

Their work found that the samples could be classified into three distinct clusters based on when infants' gut microbiota matured. Of 17 infants who had a more mature, six month-like microbiota profile high in the bacteria Bifidobacterium and Collinsella by day three, 16 were delivered vaginally. Other babies took up to six months to reach that stage.

Most infants acquired a similar microbiota by the age of six months. Infants that acquired a profile high in Bifidobacterium and Collinsella at an earlier age had typical body fat at age 18 months, while those that acquired this profile later had relatively low body fat.

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An amazing breakthrough for those suffering from peanut allergies. The bacteria Lactobacillus rhamnosus is added to some yogurts and kefir, but in smaller amounts.From The Telegraph:

Fatal peanut allergies could be cured by probiotic bacteria, say Australian doctors

A strain of probiotic bacteria could offer a cure for potentially fatal peanut allergies, according to scientists in Australia. The breakthrough followed a trial in which a group of children were given increasing amounts of peanut flour, along with a probiotic called Lactobacillus rhamnosus, over an 18-month period. About 80 per cent of the children who had peanut allergies were subsequently able to tolerate peanuts.

Mimi Tang, the lead researcher, said the families involved believed the treatment had "changed their lives". "These findings provide the vital first step towards developing a cure for peanut allergy and possibly for all food allergies," she told Melbourne's Herald Sun.

The randomised trial, involving a group of about 30 children, was conducted by Murdoch Childrens Research Institute in Melbourne. The children, aged one to ten, were given small amounts of peanut flour, gradually building up to two grams, or the equivalent of six or seven nuts.They were also given daily doses of Lactobacillus rhamnosus, which is found in yoghurt but was given in quantities equivalent to the amount found in 44 pounds of yoghurt.

Following the treatment, about 80 per cent of the children were able to tolerate four grams of peanut protein, equivalent to about 14 peanuts. Typically, about four per cent of children would have overcome their peanut allergy during this time.

Rates of peanut allergies have dramatically increased in the past two decades, particularly in developed countries. For most sufferers, the condition is lifelong.

A link to the press release from the Murdoch Childrens Research Institute (their researchers are doing the research), has more:

Oral Therapy Could Provide Treatment For Peanut Allergies

Over 60 peanut allergic children in the study were either given a dose of a probiotic, Lactobacillus rhamnosus, together with peanut protein in increasing amounts, or a placebo over 18 months to assess whether children would become tolerant to peanut.

The probiotic was a fixed daily dose, while the peanut oral immunotherapy was a daily dose of peanut protein starting at very low doses followed by a dose increase every two weeks until the maintenance dose (2 grams peanut protein) was reached. At the end of the treatment, the child's ability to tolerate peanut was assessed by a peanut challenge performed two to five weeks after stopping treatment.

23 of 28 (82.1%) probiotic treated children and one of 28 (3.6%) placebo-treated children were able to include peanut in their diet at the end of the trial. The likelihood of success was high - if nine children were given probiotic and peanut therapy, seven would benefit.

The need for a curative treatment is greatest for peanut allergy since this is usually lifelong, and is the most common cause of fatality due to food induced anaphylaxis. Further research is now required to confirm whether patients can still tolerate peanut years after the study has finished.

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This is very exciting research if it holds up. Basically a bacterial cause for urologic chronic pelvic pain syndrome (UCPPS), also known as non-bacterial chronic prostatitis, means that it is really a urinary tract infection. Bacteria were found that can only be found with state of the art genome sequencing, and NOT with ordinary cultures. From American Microbiome Institute:

Bacteria may be responsible for chronic prostatitis

Some people suffer from an enigmatic diagnosis known as ), also known as non-bacterial chronic prostatitis.  UCPPS’s symptoms are rather similar to urinary tract infections (UTI’s), with a conspicuous lack of a bacterial cause.  In order to diagnose UCPPS doctors must do a bacterial culture of the urine, and if no bacteria grow then the UCPPS diagnosis may be given. 

While many believe that this disease may be caused by stress or hormone imbalances, a team of researchers from across the U.S. and Canada investigated if there was a bacterial cause.  As we know, much of the microbiome is unculturable, and can only be identified through genome sequencing.  These researchers hypothesized that bacteria are the true cause of UCPPS, and that UCPPS is similar to UTI, only the bacteria are unculturable, and so basic hospital screens for the bacteria fail to identify them.  The scientists recently published the results of their study in The Journal of Urology.

The researchers did genome analyses on 110 urine samples from male patients suffering from UCPPS and 115 urine samples from normal males with no UCPPS diagnosis.  The results showed that both the groups had approximately 75 bacteria in their urine, all of which would unlikely have cultured in normal hospital assays.  When they compared the types of bacteria between the groups they noticed that Burkholderia cenocepacia was highly abundant in patients with UCPPS but not the control group.  Interestingly, this species had been previously identified as a possible urologic pathogen.

The study had a number of limitations, and the authors admit as much.  For example, it is unclear their sampling procedures would adequately identify any bacteria causing biofilms, and they limited the study to bacteria so fungi and viruses went untested.  Still, it is compelling evidence for a bacterial cause to a disease that had previously been thought to not have a bacterial origin.  These findings really speak to what prominent microbiome scientist, and member of the AMI’s scientific advisory board, Rob Knight recently said in an interview with NPR:  “When you consider the number of diseases where, just over the last five years, it went from being crazy to think the microbes were involved to now being crazy to think the microbes aren't involved, it's amazing how rapidly the evidence has been accumulating.”